@article{mitchell_physical_2016,
	title = {Physical {Activity} {Benefits} the {Skeleton} of {Children} {Genetically} {Predisposed} to {Lower} {Bone} {Density} in {Adulthood}},
	volume = {31},
	issn = {1523-4681},
	doi = {10.1002/jbmr.2872},
	abstract = {Both genetics and physical activity (PA) contribute to bone mineral density (BMD), but it is unknown if the benefits of physical activity on childhood bone accretion depend on genetic risk. We, therefore, aimed to determine if PA influenced the effect of bone fragility genetic variants on BMD in childhood. Our sample comprised US children of European ancestry enrolled in the Bone Mineral Density in Childhood Study (N = 918, aged 5 to 19 years, and 52.4\% female). We used a questionnaire to estimate hours per day spent in total, high-, and low-impact PA. We calculated a BMD genetic score (\% BMD lowering alleles) using adult genome-wide association study (GWAS)-implicated BMD variants. We used dual-energy X-ray absorptiometry to estimate femoral neck, total hip, and spine areal-BMD and total body less head (TBLH) bone mineral content (BMC) Z-scores. The BMD genetic score was negatively associated with each bone Z-score (eg, TBLH-BMC: estimate = -0.03, p = 1.3 × 10(-6) ). Total PA was positively associated with bone Z-scores; these associations were driven by time spent in high-impact PA (eg, TBLH-BMC: estimate = 0.05, p = 4.0 × 10(-10) ) and were observed even for children with lower than average bone Z-scores. We found no evidence of PA-adult genetic score interactions (p interaction {\textgreater} 0.05) at any skeletal site, and there was no evidence of PA-genetic score-Tanner stage interactions at any skeletal site (p interaction {\textgreater} 0.05). However, exploratory analyses at the individual variant level revealed that PA statistically interacted with rs2887571 (ERC1/WNT5B) to influence TBLH-BMC in males (p interaction = 7.1 × 10(-5) ), where PA was associated with higher TBLH-BMC Z-score among the BMD-lowering allele carriers (rs2887571 AA homozygotes: estimate = 0.08 [95\% CI 0.06, 0.11], p = 2.7 × 10(-9) ). In conclusion, the beneficial effect of PA on bone, especially high-impact PA, applies to the average child and those genetically predisposed to lower adult BMD (based on GWAS-implicated BMD variants). Independent replication of our exploratory individual variant findings is warranted. © 2016 American Society for Bone and Mineral Research.},
	language = {eng},
	number = {8},
	journal = {Journal of Bone and Mineral Research: The Official Journal of the American Society for Bone and Mineral Research},
	author = {Mitchell, Jonathan A. and Chesi, Alessandra and Elci, Okan and McCormack, Shana E. and Roy, Sani M. and Kalkwarf, Heidi J. and Lappe, Joan M. and Gilsanz, Vicente and Oberfield, Sharon E. and Shepherd, John A. and Kelly, Andrea and Grant, Struan Fa and Zemel, Babette S.},
	year = {2016},
	pmid = {27172274},
	pmcid = {PMC4970901},
	keywords = {Adolescent, Adult, BONE MINERAL DENSITY, Bone Density, Bone and Bones, CHILDREN, Child, Cohort Studies, EXERCISE, Exercise, Female, GENETIC, Genetic Loci, Genetic Predisposition to Disease, Humans, Male, PHYSICAL ACTIVITY, Polymorphism, Single Nucleotide, Risk Factors},
	pages = {1504--1512}
}

@article{brandl_planmine--mineable_2016,
	title = {{PlanMine}--a mineable resource of planarian biology and biodiversity},
	volume = {44},
	issn = {1362-4962},
	doi = {10.1093/nar/gkv1148},
	abstract = {Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history traits. PlanMine (http://planmine.mpi-cbg.de/) aims to accomplish two primary missions: First, to provide an easily accessible platform for sharing, comparing and value-added mining of planarian sequence data. Second, to catalyze the comparative analysis of the phenotypic diversity amongst planarian species. Currently, PlanMine houses transcriptomes independently assembled by our lab and community contributors. Detailed assembly/annotation statistics, a custom-developed BLAST viewer and easy export options enable comparisons at the contig and assembly level. Consistent annotation of all transcriptomes by an automated pipeline, the integration of published gene expression information and inter-relational query tools provide opportunities for mining planarian gene sequences and functions. For inter-species comparisons, we include transcriptomes of, so far, six planarian species, along with images, expert-curated information on their biology and pre-calculated cross-species sequence homologies. PlanMine is based on the popular InterMine system in order to make the rich biology of planarians accessible to the general life sciences research community.},
	language = {eng},
	number = {D1},
	journal = {Nucleic Acids Research},
	author = {Brandl, Holger and Moon, HongKee and Vila-Farré, Miquel and Liu, Shang-Yun and Henry, Ian and Rink, Jochen C.},
	month = jan,
	year = {2016},
	pmid = {26578570},
	pmcid = {PMC4702831},
	keywords = {Animals, Data Mining, Databases, Genetic, Gene Expression Profiling, Genes, Helminth, Phenotype, Planarians, Sequence Analysis},
	pages = {D764--773}
}

Website  abstract   bibtex   

@article{
 title = {Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics},
 type = {article},
 year = {2016},
 identifiers = {[object Object]},
 keywords = {Biological,Epigenesis,Exoribonucleases,Exoribonucleases: genetics,Exoribonucleases: metabolism,Genetic,Messenger,Messenger: genetics,Messenger: metabolism,Models,Physiological,Plant,Plant Physiological Phenomena,Plant Physiological Phenomena: genetics,Plant: genetics,Plant: metabolism,RNA,RNA Stability,Stress},
 pages = {e1501340-e1501340},
 volume = {2},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4788475&tool=pmcentrez&rendertype=abstract,http://advances.sciencemag.org/content/2/2/e1501340.abstract},
 id = {eefc4160-5d09-3c3b-94c8-46ad466c7330},
 created = {2017-10-14T10:53:37.429Z},
 file_attached = {false},
 profile_id = {57cbaa4c-3609-3597-b91c-bd12e56638fb},
 group_id = {b97159aa-8fdc-3227-aa16-9de80bf090dd},
 last_modified = {2017-10-14T10:53:37.429Z},
 read = {true},
 starred = {true},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Crisp2016},
 private_publication = {false},
 abstract = {Plants grow in dynamic environments where they can be exposed to a multitude of stressful factors, all of which affect their development, yield, and, ultimately, reproductive success. Plants are adept at rapidly acclimating to stressful conditions and are able to further fortify their defenses by retaining memories of stress to enable stronger or more rapid responses should an environmental perturbation recur. Indeed, one mechanism that is often evoked regarding environmental memories is epigenetics. Yet, there are relatively few examples of such memories; neither is there a clear understanding of their duration, considering the plethora of stresses in nature. We propose that this field would benefit from investigations into the processes and mechanisms enabling recovery from stress. An understanding of stress recovery could provide fresh insights into when, how, and why environmental memories are created and regulated. Stress memories may be maladaptive, hindering recovery and affecting development and potential yield. In some circumstances, it may be advantageous for plants to learn to forget. Accordingly, the recovery process entails a balancing act between resetting and memory formation. During recovery, RNA metabolism, posttranscriptional gene silencing, and RNA-directed DNA methylation have the potential to play key roles in resetting the epigenome and transcriptome and in altering memory. Exploration of this emerging area of research is becoming ever more tractable with advances in genomics, phenomics, and high-throughput sequencing methodology that will enable unprecedented profiling of high-resolution stress recovery time series experiments and sampling of large natural populations.},
 bibtype = {article},
 author = {Crisp, P. A. and Ganguly, D. and Eichten, S. R. and Borevitz, J. O. and Pogson, B. J.},
 journal = {Science Advances},
 number = {2}
}

Website  bibtex   

@article{
 title = {Unexpectedly high bacteriochlorophyll α concentrations in Neotropical tank bromeliads},
 type = {article},
 year = {2016},
 identifiers = {[object Object]},
 keywords = {accepted for publication and,ammonia oxidation,but has not been,diversity,genetic,horizontal gene transfer,marine group i archaea,nitrification,pagination and proofreading process,thaumarchaeota,this article has been,through the copyediting,typesetting,undergone full peer review,which may lead to},
 pages = {in press},
 volume = {2},
 websites = {http://doi.wiley.com/10.1111/1758-2229.12426},
 month = {6},
 id = {2eca8395-d200-3b06-a4da-de967e81a40c},
 created = {2016-07-26T12:36:41.000Z},
 file_attached = {false},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 group_id = {98cf6291-ef58-3f8a-a4b6-c8754044662f},
 last_modified = {2016-07-26T12:36:41.000Z},
 tags = {2016,sbr_phyto_mapp},
 read = {true},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 bibtype = {article},
 author = {Lehours, Anne-Catherine and Le Jeune, Anne-Hélène and Aguer, Jean-Pierre and Céréghino, Régis and Corbara, Bruno and Kéraval, Benoit and Leroy, Céline and Perrière, Fanny and Jeanthon, Christian and Carrias, Jean-François},
 journal = {Environmental Microbiology Reports}
}

@article{motenko_mousemine:_2015,
	title = {{MouseMine}: a new data warehouse for {MGI}},
	volume = {26},
	issn = {1432-1777},
	shorttitle = {{MouseMine}},
	doi = {10.1007/s00335-015-9573-z},
	abstract = {MouseMine (www.mousemine.org) is a new data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Based on the InterMine software framework, MouseMine supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. Through MouseMine, users can access a significant portion of MGI data in new and useful ways. Importantly, MouseMine is also a member of a growing community of online data resources based on InterMine, including those established by other model organism databases. Adopting common interfaces and collaborating on data representation standards are critical to fostering cross-species data analysis. This paper presents a general introduction to MouseMine, presents examples of its use, and discusses the potential for further integration into the MGI interface.},
	language = {eng},
	number = {7-8},
	journal = {Mammalian Genome: Official Journal of the International Mammalian Genome Society},
	author = {Motenko, H. and Neuhauser, S. B. and O'Keefe, M. and Richardson, J. E.},
	month = aug,
	year = {2015},
	pmid = {26092688},
	pmcid = {PMC4534495},
	keywords = {Animals, Data Mining, Databases, Genetic, Genomics, Internet, Mice, Software},
	pages = {325--330}
}

@article{lyne_cross-organism_2015,
	title = {Cross-organism analysis using {InterMine}},
	volume = {53},
	issn = {1526-968X},
	doi = {10.1002/dvg.22869},
	abstract = {InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community.},
	language = {eng},
	number = {8},
	journal = {Genesis (New York, N.Y.: 2000)},
	author = {Lyne, Rachel and Sullivan, Julie and Butano, Daniela and Contrino, Sergio and Heimbach, Joshua and Hu, Fengyuan and Kalderimis, Alex and Lyne, Mike and Smith, Richard N. and Štěpán, Radek and Balakrishnan, Rama and Binkley, Gail and Harris, Todd and Karra, Kalpana and Moxon, Sierra A. T. and Motenko, Howie and Neuhauser, Steven and Ruzicka, Leyla and Cherry, Mike and Richardson, Joel and Stein, Lincoln and Westerfield, Monte and Worthey, Elizabeth and Micklem, Gos},
	month = aug,
	year = {2015},
	pmid = {26097192},
	pmcid = {PMC4545681},
	keywords = {Animals, Computational Biology, Databases, Factual, Databases, Genetic, Genomics, Humans, Internet, Software, Systems Integration, User-Computer Interface, comparative analysis, cross-organism analysis, data analysis, data integration, genomics, integrative analysis, proteomics},
	pages = {547--560}
}

@article{libbrecht_machine_2015,
	title = {Machine learning applications in genetics and genomics},
	volume = {16},
	issn = {1471-0064},
	doi = {10.1038/nrg3920},
	abstract = {The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets. Here, we provide an overview of machine learning applications for the analysis of genome sequencing data sets, including the annotation of sequence elements and epigenetic, proteomic or metabolomic data. We present considerations and recurrent challenges in the application of supervised, semi-supervised and unsupervised machine learning methods, as well as of generative and discriminative modelling approaches. We provide general guidelines to assist in the selection of these machine learning methods and their practical application for the analysis of genetic and genomic data sets.},
	language = {eng},
	number = {6},
	journal = {Nature Reviews. Genetics},
	author = {Libbrecht, Maxwell W. and Noble, William Stafford},
	month = jun,
	year = {2015},
	pmid = {25948244},
	pmcid = {PMC5204302},
	keywords = {Amino Acid Sequence, Animals, Artificial Intelligence, Base Sequence, Computer Simulation, Discriminant Analysis, Genetics, Medical, Genomics, Humans, Models, Genetic, Molecular Sequence Annotation},
	pages = {321--332}
}

Paper  doi  abstract   bibtex   

@article{cieslak_life-history_2014,
	title = {Life-history specialization was not an evolutionary dead-end in {Pyrenean} cave beetles},
	volume = {281},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84980450217&doi=10.1098%2frspb.2013.2978&partnerID=40&md5=f217a42a541f99e686969f00b9d4d4ad},
	doi = {10.1098/rspb.2013.2978},
	abstract = {Research on subterranean organisms has focused on the colonization process and some of the associated phenotypic changes, but little is known on the long-term evolutionary dynamics of subterranean lineages and the origin of some highly specialized complex characters. One of the most extreme modifications is the reduction of the number of larval instars in some Leptodirini beetles from the ancestral 3 to 2 and ultimately a single instar. This reduction is usually assumed to have occurred independently multiple times within the same lineage and geographical area, but its evolution has never been studied in a phylogenetic framework. Using a comprehensive molecular phylogeny, we found a low number of independent origins of the reduction in the number of instars, with a single transition, dated to the Oligocene-Miocene, from 3 to 2 and then 1 instar in the Pyrenees, the best-studied area. In the Pyrenees, the 1-instar lineage had a diversification rate (0.22 diversification events per lineage per million years) significantly higher than that of 3- or 2-instar lineages (0.10), and similar to that seen in other Coleopteran radiations. Far from being evolutionary dead-ends, ancient lineages fully adapted to subterranean life seem able to persist and diversify over long evolutionary periods. © 2014 The Author(s) Published by the Royal Society. All rights reserved.},
	number = {1781},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Cieslak, A. and Fresneda, J. and Ribera, I.},
	year = {2014},
	keywords = {ADAPTATION, Adaptation, Biological, Animals, Article, Base Sequence, Bayes theorem, Beetles, Biological Evolution, Caves, Diversification, EVOLUTION, France, Larval development, Life Cycle Stages, Life cycle, Likelihood Functions, Models, Genetic, Molecular Sequence Data, Phylogeny, Pyrenees, Spain, Speciation, Subterranean environment, animal, beetle, biological model, cave, colonization, genetic analysis, geographical region, life cycle stage, life history, molecular genetics, nucleotide sequence, phylogenetics, physiology, sequence alignment, specialization, speciation (biology), species differentiation, statistical model}
}

Paper  Website  bibtex   

@article{
 title = {Genetics. Genealogy databases enable naming of anonymous DNA donors.},
 type = {article},
 year = {2013},
 identifiers = {[object Object]},
 keywords = {Anonymous Testing,Anonymous Testing: methods,DNA,DNA: genetics,Databases, Genetic,Genetic Markers,Genetic Privacy,Humans,Male,Names,Pedigree},
 pages = {262},
 volume = {339},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/23329025},
 month = {1},
 day = {18},
 id = {53f05a06-b98e-34c1-a2bc-7fec85b8fb59},
 created = {2017-06-19T13:39:20.325Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:39:20.470Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 bibtype = {article},
 author = {Bohannon, John},
 journal = {Science (New York, N.Y.)},
 number = {6117}
}

@article{curtis_scaffolding_2012,
	title = {The scaffolding and signalling functions of a localization factor impact polar development},
	volume = {84},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2012.08055.x},
	abstract = {In the differentiating alphaproteobacterium Caulobacter crescentus, organelle synthesis at cell poles is critical to forming different progeny after cell division. Co-ordination of polar organelle synthesis, including pili and holdfast, and flagellum ejection, is mediated in part by the scaffolding protein PodJ. At the time of cell division, PodJ undergoes regulated processing to a short form that persists at the flagellar pole of swarmer cells. This study analyses how PodJ's role in structural and signalling protein localization impacts organelle synthesis. A PodJ mutant with an internal deletion exhibits reduced sensitivity to pili-tropic phage ΦCbK, resulting from reduced pilA gene expression, which can be linked to altered signalling protein localization. The phage sensitivity defect of a ΔpodJ mutant can be partially suppressed by ectopic pilA expression. Induction of PodJ processing, by manipulation of podJ itself or controlled perP expression, resulted in decreased pilus biogenesis and, when coupled with a podJ mutation that reduced pilA expression, led to complete loss of phage sensitivity. As a whole, the results show that PodJ's scaffolding role for structural and signalling proteins both contribute to flagellar pole organelle development.},
	number = {4},
	journal = {Molecular microbiology},
	author = {Curtis, Patrick D and Quardokus, Ellen M and Lawler, Melanie L and Guo, Xiaoyun and Klein, David and Chen, Joseph C and Arnold, Randy J and Brun, Yves V},
	month = may,
	year = {2012},
	pmid = {22512778},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Bacteriophages, Caulobacter crescentus, Cell Division, Fimbriae, Bacterial, Gene expression, Membrane Proteins, Models, Biological, Molecular Sequence Data, Sequence Deletion, Suppression, Genetic},
	pages = {712--735}
}

@article{oconnor_combinatorial_2012,
	title = {Combinatorial pharmacogenetic interactions of bucindolol and β1, α2C adrenergic receptor polymorphisms},
	volume = {7},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0044324},
	abstract = {BACKGROUND: Pharmacogenetics involves complex interactions of gene products affecting pharmacodynamics and pharmacokinetics, but there is little information on the interaction of multiple genetic modifiers of drug response. Bucindolol is a β-blocker/sympatholytic agent whose efficacy is modulated by polymorphisms in the primary target (β(1) adrenergic receptor [AR] Arg389 Gly on cardiac myocytes) and a secondary target modifier (α(2C) AR Ins [wild-type (Wt)] 322-325 deletion [Del] on cardiac adrenergic neurons). The major allele homozygotes and minor allele carriers of each polymorphism are respectively associated with efficacy enhancement and loss, creating the possibility for genotype combination interactions that can be measured by clinical trial methodology.
METHODOLOGY: In a 1,040 patient substudy of a bucindolol vs. placebo heart failure clinical trial, we tested the hypothesis that combinations of β(1)389 and α(2C)322-325 polymorphisms are additive for both efficacy enhancement and loss. Additionally, norepinephrine (NE) affinity for β(1)389 AR variants was measured in human explanted left ventricles.
PRINCIPAL FINDINGS: The combination of β(1)389 Arg+α(2C)322-325 Wt major allele homozygotes (47\% of the trial population) was non-additive for efficacy enhancement across six clinical endpoints, with an average efficacy increase of 1.70-fold vs. 2.32-fold in β(1)389 Arg homozygotes+α(2C)322-325 Del minor allele carriers. In contrast, the minor allele carrier combination (13\% subset) exhibited additive efficacy loss. These disparate effects are likely due to the higher proportion (42\% vs. 8.7\%, P = 0.009) of high-affinity NE binding sites in β(1)389 Arg vs. Gly ARs, which converts α(2C)Del minor allele-associated NE lowering from a therapeutic liability to a benefit.
CONCLUSIONS: On combination, the two sets of AR polymorphisms 1) influenced bucindolol efficacy seemingly unpredictably but consistent with their pharmacologic interactions, and 2) identified subpopulations with enhanced (β(1)389 Arg homozygotes), intermediate (β(1)389 Gly carriers+α(2C)322-325 Wt homozygotes), and no (β(1)389 Gly carriers+α(2C)322-325 Del carriers) efficacy.},
	language = {eng},
	number = {10},
	journal = {PloS One},
	author = {O'Connor, Christopher M. and Fiuzat, Mona and Carson, Peter E. and Anand, Inder S. and Plehn, Jonathan F. and Gottlieb, Stephen S. and Silver, Marc A. and Lindenfeld, JoAnn and Miller, Alan B. and White, Michel and Walsh, Ryan and Nelson, Penny and Medway, Allen and Davis, Gordon and Robertson, Alastair D. and Port, J. David and Carr, James and Murphy, Guinevere A. and Lazzeroni, Laura C. and Abraham, William T. and Liggett, Stephen B. and Bristow, Michael R.},
	year = {2012},
	pmid = {23071495},
	pmcid = {PMC3468617},
	keywords = {Adrenergic beta-Antagonists, Adult, Aged, Female, Heart Failure, Heart Ventricles, Humans, Male, Middle Aged, Norepinephrine, Pharmacogenetics, Polymorphism, Genetic, Propanolamines, Receptors, Adrenergic, alpha-2, Receptors, Adrenergic, beta-1},
	pages = {e44324}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Human evolutionary genomics: ethical and interpretive issues.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Animals,Bioethics,Evolution, Molecular,Genome, Human,Genomics,Humans,Selection, Genetic},
 pages = {137-45},
 volume = {28},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/22265990},
 month = {3},
 publisher = {Elsevier Ltd},
 id = {89ec61e9-bb0e-313a-9fc8-3981b070543d},
 created = {2017-06-19T13:41:03.874Z},
 accessed = {2012-11-06},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:04.018Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Genome-wide computational studies can now identify targets of natural selection. The unique information about humans these studies reveal, and the media attention they attract, indicate the need for caution and precision in communicating results. This need is exacerbated by ways in which evolutionary and genetic considerations have been misapplied to support discriminatory policies, by persistent misconceptions of these fields and by the social sensitivity surrounding discussions of racial ancestry. We discuss the foundations, accomplishments and future directions of human evolutionary genomics, attending to ways in which the interpretation of good science can go awry, and offer suggestions for researchers to prevent misapplication of their work.},
 bibtype = {article},
 author = {Vitti, Joseph J and Cho, Mildred K and Tishkoff, Sarah a and Sabeti, Pardis C},
 journal = {Trends in genetics : TIG},
 number = {3}
}

@article{boni_no_2012,
	title = {No evidence for intra-segment recombination of 2009 {H1N1} influenza virus in swine.},
	volume = {494},
	copyright = {Copyright (c) 2011 Elsevier B.V. All rights reserved.},
	issn = {1879-0038 0378-1119},
	doi = {10.1016/j.gene.2011.10.041},
	abstract = {Hao (2011) reported that the PB2 genes of three swine influenza A viruses were likely generated through homologous recombination between two closely related parental strains. However, we show that Hao's observation is an artifact of incorrect taxon sampling arising through the lack of an appropriate evolutionary  context. Through rigorous phylogenetic analyses we explain the evolutionary origins of these stains and confirm the lack of any statistical support for intra-segmental recombination.},
	language = {eng},
	number = {2},
	journal = {Gene},
	author = {Boni, Maciej F. and Smith, Gavin J. D. and Holmes, Edward C. and Vijaykrishna, Dhanasekaran},
	month = feb,
	year = {2012},
	pmid = {22226809},
	pmcid = {PMC3427013},
	keywords = {*Evolution, Molecular, *Recombination, Genetic, Influenza A virus/*genetics},
	pages = {242--245},
}

@article{le_roex_novel_2012,
	title = {Novel {SNP} {Discovery} in {African} {Buffalo}, {Syncerus} caffer, using high-throughput {Sequencing}},
	volume = {7},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0048792},
	abstract = {The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43-54\% of the Bowtie SNPs and 57-58\% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.},
	language = {eng},
	number = {11},
	journal = {PloS One},
	author = {le Roex, Nikki and Noyes, Harry and Brass, Andrew and Bradley, Daniel G. and Kemp, Steven J. and Kay, Suzanne and van Helden, Paul D. and Hoal, Eileen G.},
	year = {2012},
	pmid = {23144973},
	pmcid = {PMC3492240},
	note = {00008 },
	keywords = {Animals, Buffaloes, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Selection, Genetic, Sequence Analysis, DNA},
	pages = {e48792},
}

Paper  doi  abstract   bibtex   

@article{Pinheiro2012,
	title = {Synthetic genetic polymers capable of heredity and evolution.},
	volume = {336},
	issn = {1095-9203},
	url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1217622 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3362463&tool=pmcentrez&rendertype=abstract},
	doi = {10.1126/science.1217622},
	abstract = {Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.},
	number = {6079},
	journal = {Science (New York, N.Y.)},
	author = {Pinheiro, Vitor B. and Taylor, Alexander I. and Cozens, Christopher and Abramov, Mikhail and Renders, Marleen and Zhang, Su and Chaput, John C. and Wengel, Jesper and Peak-Chew, S.-Y. Sew-Yeu S.-Y. and McLaughlin, Stephen H. and Herdewijn, Piet and Holliger, Philipp},
	month = apr,
	year = {2012},
	pmid = {22517858},
	note = {tex.ids= pinheiroSyntheticGeneticPolymers2012, pinheiroSyntheticGeneticPolymers2012a},
	keywords = {Aptamers, DNA, DNA-Directed DNA Polymerase, DNA-Directed DNA Polymerase: chemistry, DNA-Directed DNA Polymerase: genetics, DNA-Directed DNA Polymerase: metabolism, DNA: chemistry, DNA: genetics, Directed Molecular Evolution, Evolution, Genetic, Molecular, Molecular Mimicry, Nucleic Acids, Nucleic Acids: chemistry, Nucleic Acids: genetics, Nucleic Acids: metabolism, Nucleotide, Nucleotide: chemistry, Nucleotide: genetics, Nucleotide: metabolism, Polymers, Polymers: chemistry, Polymers: metabolism, RNA, RNA-Directed DNA Polymerase, RNA-Directed DNA Polymerase: chemistry, RNA-Directed DNA Polymerase: metabolism, RNA: chemistry, RNA: genetics, Reverse Transcription, Templates, Transcription},
	pages = {341--4},
}

Website  abstract   bibtex   

@article{
 title = {Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Animals,Arabidopsis,Arabidopsis: genetics,Arabidopsis: growth & development,DNA Methylation,DNA Transposable Elements,Epigenesis,Genetic,Mammals,Mammals: genetics,Plant,Plant: genetics,Plant: metabolism,Pollen,Pollen: genetics,RNA,Seeds,Seeds: genetics,Seeds: metabolism,Small Interfering,Small Interfering: genetics,Small Interfering: metabolism},
 pages = {194-205},
 volume = {151},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3697483&tool=pmcentrez&rendertype=abstract,http://www.sciencedirect.com/science/article/pii/S0092867412010665},
 month = {9},
 day = {28},
 id = {97acca20-e1ee-31fa-a14a-d4c196926799},
 created = {2017-10-14T10:53:33.037Z},
 accessed = {2015-11-12},
 file_attached = {false},
 profile_id = {57cbaa4c-3609-3597-b91c-bd12e56638fb},
 group_id = {b97159aa-8fdc-3227-aa16-9de80bf090dd},
 last_modified = {2017-10-14T10:53:33.037Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Calarco2012},
 source_type = {article},
 private_publication = {false},
 abstract = {Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information by germline reprogramming. We sequenced the methylome of three haploid cell types from developing pollen: the sperm cell, the vegetative cell, and their precursor, the postmeiotic microspore, and found that unlike in mammals the plant germline retains CG and CHG DNA methylation. However, CHH methylation is lost from retrotransposons in microspores and sperm cells and restored by de novo DNA methyltransferase guided by 24 nt small interfering RNA, both in the vegetative nucleus and in the embryo after fertilization. In the vegetative nucleus, CG methylation is lost from targets of DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), and their homologs, which include imprinted loci and recurrent epialleles that accumulate corresponding small RNA and are premethylated in sperm. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA. © 2012 Elsevier Inc.},
 bibtype = {article},
 author = {Calarco, Joseph P. and Borges, Filipe and Donoghue, Mark T A and Van Ex, Frédéric and Jullien, Pauline E. and Lopes, Telma and Gardner, Rui and Berger, Frédéric and Feijó, José A. and Becker, Jörg D. and Martienssen, Robert A.},
 journal = {Cell},
 number = {1}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Impact of fertility transmission and other sociodemographic factors on reproductive success and coalescent trees},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Child,Computer Simulation,DNA,Demography,Female,Fertility,Fertility: genetics,Genetic,Humans,Male,Mitochondrial,Mitochondrial: genetics,Models,Pedigree,Reproduction,Reproduction: genetics,Selection,Socioeconomic Factors},
 pages = {121-131},
 volume = {94},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/22647505},
 month = {6},
 id = {a18e731f-a7b9-387b-855e-2c00bc595d5d},
 created = {2017-06-19T13:39:53.156Z},
 accessed = {2013-05-22},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:39:53.295Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 notes = {<m:note>        <m:bold>From Duplicate 2 ( </m:bold>                <m:bold>          </m:bold><m:bold><m:italic>Impact of fertility transmission and other sociodemographic factors on reproductive success and coalescent trees.</m:italic></m:bold><m:bold>        </m:bold>                <m:bold> - Brandenburg, Jean-Tristan; Austerlitz, Frédéric; Toupance, Bruno )<m:linebreak/>        </m:bold>        <m:linebreak/>        <m:linebreak/>        <m:linebreak/>      </m:note>},
 abstract = {Fertility transmission (FT) is a phenomenon with a cultural and/or genetic basis, whereby a positive correlation exists between the number of offspring of an individual and that of his/her parents. Theoretical studies using a haploid individual-based model have shown that FT increases the variance and intergenerational correlation in reproductive success and results in an imbalance in the coalescent tree of sampled genes. This phenomenon has been documented in several demographic studies conducted on the correlation in fertility between generations, or through the reconstruction of the genealogical trees of mitochondrial DNA sequences. However, as mtDNA is a single locus, potentially subject to other forces (e.g. natural selection), it is of interest to extend the theory of FT to nuclear loci.We show that because random mating between individuals leads to a mixing of their fertility profiles, FT in these cases will have less influence on the variance and intergenerational correlation of reproductive success. This, in turn, results in less impact on the shape of the coalescent trees. Nevertheless, in the presence of FT, high heterogeneity in reproductive success and homogamy for family size will increase the imbalance in the coalescent tree. Thus, FT should be easier to detect when occurring in conjunction with these other factors.We also show the utility of analysing different kinds of loci (X-linked, Y-linked, mitochondrial and autosomal) to assess whether FT is matrilineal, patrilineal or biparental. Finally, we demonstrate that the shape of the coalescent tree depends upon population size, in contrast to the classical Kingman’s model.},
 bibtype = {article},
 author = {Brandenburg, Jean-Tristan and Austerlitz, Frédéric and Toupance, Bruno},
 journal = {Genetics research},
 number = {3}
}

Website  abstract   bibtex   

@article{
 title = {Rocking cell metabolism: revised functions of the key glycolytic regulator PKM2 in cancer.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Carrier Proteins,Carrier Proteins: genetics,Carrier Proteins: metabolism,Cell Nucleus,Cell Nucleus: genetics,Cell Nucleus: metabolism,Cell Proliferation,Enzyme Activation,Gene Expression Regulation, Neoplastic,Glycolysis,Humans,Isoenzymes,Isoenzymes: genetics,Isoenzymes: metabolism,Membrane Proteins,Membrane Proteins: genetics,Membrane Proteins: metabolism,Neoplasm Proteins,Neoplasm Proteins: genetics,Neoplasm Proteins: metabolism,Neoplasms,Neoplasms: enzymology,Neoplasms: metabolism,Phosphorylation,Reactive Oxygen Species,Reactive Oxygen Species: metabolism,Thyroid Hormones,Thyroid Hormones: genetics,Thyroid Hormones: metabolism,Transcription Factors,Transcription Factors: genetics,Transcription Factors: metabolism,Transcription, Genetic},
 pages = {309-16},
 volume = {37},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/22626471},
 month = {8},
 id = {60a497e7-eda1-35bf-a4b1-b655b6b18065},
 created = {2016-04-27T01:22:17.000Z},
 accessed = {2016-04-27},
 file_attached = {false},
 profile_id = {95ad1c8a-ddc5-3572-ab20-1b5660ace0c4},
 group_id = {409b6953-b59c-338c-b6e7-a89d45a37162},
 last_modified = {2016-04-27T01:22:17.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Cancer cell metabolism is exemplified by high glucose consumption and lactate production. Pyruvate kinase (PK), which catalyzes the final step of glycolysis, has emerged as a potential regulator of this metabolic phenotype. The M2 isoform of PK (PKM2) is highly expressed in cancer cells. However, the mechanisms by which PKM2 coordinates high energy requirements with high anabolic activities to support cancer cell proliferation are still not completely understood. Current research has elucidated novel regulatory mechanisms for PKM2, contributing to its important role in cancer. This review summarizes the current understanding and explores future directions in the field, highlighting controversies regarding the activity and specificity of PKM2 in cancer. In light of this knowledge, the potential therapeutic implications and strategies are critically discussed.},
 bibtype = {article},
 author = {Chaneton, Barbara and Gottlieb, Eyal},
 journal = {Trends in biochemical sciences},
 number = {8}
}

Paper  doi  abstract   bibtex   

@article{mitschke_experimentally_2011,
	title = {An experimentally anchored map of transcriptional start sites in the model cyanobacterium {Synechocystis} sp. {PCC6803}},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/108/5/2124},
	doi = {10.1073/pnas.1015154108},
	abstract = {There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64\% of all TSS give rise to antisense or ncRNAs in a genome that is to 87\% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5′ annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.},
	language = {en},
	number = {5},
	urldate = {2014-02-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Mitschke, Jan and Georg, Jens and Scholz, Ingeborg and Sharma, Cynthia M. and Dienst, Dennis and Bantscheff, Jens and Voß, Björn and Steglich, Claudia and Wilde, Annegret and Vogel, Jörg and Hess, Wolfgang R.},
	month = feb,
	year = {2011},
	pmid = {21245330},
	keywords = {Bacterial, Base Sequence, Genes, Genes, Bacterial, Genetic, Molecular Sequence Data, Nucleic Acid, Oligonucleotide Array Sequence Analysis, Open Reading Frames, RNA, RNA polymerase, RNA, Untranslated, Sequence Homology, Sequence Homology, Nucleic Acid, Synechocystis, Transcription, Transcription, Genetic, Untranslated, gene expression regulation, photosynthesis, promoter prediction},
	pages = {2124--2129},
}

@article{wang_coancestry:_2011,
	title = {{COANCESTRY}: a program for simulating, estimating and analysing relatedness and inbreeding coefficients},
	volume = {11},
	issn = {1755-0998},
	shorttitle = {{COANCESTRY}},
	doi = {10.1111/j.1755-0998.2010.02885.x},
	abstract = {The software package COANCESTRY implements seven relatedness estimators and three inbreeding estimators to estimate relatedness and inbreeding coefficients from multilocus genotype data. Two likelihood estimators that allow for inbred individuals and account for genotyping errors are for the first time included in this user-friendly program for PCs running Windows operating system. A simulation module is built in the program to simulate multilocus genotype data of individuals with a predefined relationship, and to compare the estimators and the simulated relatedness values to facilitate the selection of the best estimator in a particular situation. Bootstrapping and permutations are used to obtain the 95\% confidence intervals of each relatedness or inbreeding estimate, and to test the difference in averages between groups.},
	language = {eng},
	number = {1},
	journal = {Molecular Ecology Resources},
	author = {Wang, Jinliang},
	month = jan,
	year = {2011},
	pmid = {21429111},
	keywords = {Computer Simulation, Genetics, Population, Humans, Inbreeding, Models, Genetic, Pedigree, Software},
	pages = {141--145}
}

Paper  Website  abstract   bibtex   

@article{
 title = {The relation between reproductive value and genetic contribution.},
 type = {article},
 year = {2011},
 identifiers = {[object Object]},
 keywords = {Algorithms,Alleles,Animals,Gene Dosage,Genetic Fitness,Genetic Loci,Genetic Variation,Genetics, Population,Genome,Humans,Models, Genetic,Pedigree,Probability,Reproduction,Reproduction: genetics,Selection, Genetic},
 pages = {953-73},
 volume = {188},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3176105&tool=pmcentrez&rendertype=abstract},
 month = {8},
 id = {b19093a1-a13f-387f-8b47-4b28bfe03874},
 created = {2017-06-19T13:41:11.867Z},
 accessed = {2012-11-06},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:11.990Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a "pedigree" of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction (analogous to the Wright-Fisher model), an individual's reproductive value is determined within ∼10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it and that, conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of the ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value.},
 bibtype = {article},
 author = {Barton, Nicholas H and Etheridge, Alison M},
 journal = {Genetics},
 number = {4}
}

Paper  doi  abstract   bibtex   

@article{ Escoffre2010,
  abstract = {Among the nonviral methods for gene delivery in vitro, electroporation is simple, inexpensive and safe. To upregulate the expression level of transfected gene, we investigated the applicability of electrosonoporation. This approach consists of a combination of electric pulses and ultrasound assisted with gas microbubbles. Cells were first electroporated with plasmid DNA encoding-enhanced green fluorescent protein and then sonoporated in presence of contrast microbubbles. Twenty-four hours later, cells that received electrosonoporation demonstrated a four-fold increase in transfection level and a six-fold increase in transfection efficiency compared with cells having undergone electroporation alone. Although electroporation induced the formation of DNA aggregates into the cell membrane, sonoporation induced its direct propulsion into the cytoplasm. Sonoporation can improve the transfer of electro-induced DNA aggregates by allowing its free and rapid entrance into the cells. These results demonstrated that in vitro gene transfer by electrosonoporation could provide a new potent method for gene transfer.},
  author = {Escoffre, Jean-Michel and Kaddur, K and Rols, M P and Bouakaz, Ayache},
  doi = {10.1016/j.ultrasmedbio.2010.06.019},
  file = {:C$\backslash$:/Users/emnicolas/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Escoffre et al. - 2010 - In vitro gene transfer by electrosonoporation.pdf:pdf},
  issn = {1879-291X},
  journal = {Ultrasound in medicine \& biology},
  keywords = {Cells, Cultured,Contrast Media,Contrast Media: administration \& dosage,Electroporation,Electroporation: methods,Flow Cytometry,Flow Cytometry: methods,Genes, Reporter,Genes, Reporter: genetics,Green Fluorescent Proteins,Green Fluorescent Proteins: genetics,Microbubbles,Plasmids,Plasmids: genetics,Sonication,Sonication: methods,Transduction, Genetic,Transduction, Genetic: methods,Ultrasonics,Ultrasonics: methods},
  month = {October},
  number = {10},
  pages = {1746--55},
  pmid = {20850028},
  title = {{In vitro gene transfer by electrosonoporation.}},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/20850028},
  volume = {36},
  year = {2010}
}

@article{moller_analysis_2010,
	title = {Analysis of eight genes modulating interferon gamma and human genetic susceptibility to tuberculosis: a case-control association study},
	volume = {10},
	issn = {1471-2334},
	shorttitle = {Analysis of eight genes modulating interferon gamma and human genetic susceptibility to tuberculosis},
	doi = {10.1186/1471-2334-10-154},
	abstract = {BACKGROUND: Interferon gamma is a major macrophage-activating cytokine during infection with Mycobacterium tuberculosis, the causative pathogen of tuberculosis, and its role has been well established in animal models and in humans. This cytokine is produced by activated T helper 1 cells, which can best deal with intracellular pathogens such as M. tuberculosis. Based on the hypothesis that genes which regulate interferon gamma may influence tuberculosis susceptibility, we investigated polymorphisms in eight candidate genes.
METHODS: Fifty-four polymorphisms in eight candidate genes were genotyped in over 800 tuberculosis cases and healthy controls in a population-based case-control association study in a South African population. Genotyping methods used included the SNPlex Genotyping System, capillary electrophoresis of fluorescently labelled PCR products, TaqMan SNP genotyping assays or the amplification mutation refraction system. Single polymorphisms as well as haplotypes of the variants were tested for association with TB using statistical analyses.
RESULTS: A haplotype in interleukin 12B was nominally associated with tuberculosis (p = 0.02), but after permutation testing, done to assess the significance for the entire analysis, this was not globally significant. In addition a novel allele was found for the interleukin 12B D5S2941 microsatellite.
CONCLUSIONS: This study highlights the importance of using larger sample sizes when attempting validation of previously reported genetic associations. Initial studies may be false positives or may propose a stronger genetic effect than subsequently found to be the case.},
	language = {eng},
	journal = {BMC infectious diseases},
	author = {Möller, Marlo and Nebel, Almut and van Helden, Paul D. and Schreiber, Stefan and Hoal, Eileen G.},
	year = {2010},
	pmid = {20525402},
	pmcid = {PMC2891757},
	note = {00022 },
	keywords = {Adolescent, Adult, Female, Genetic Predisposition to Disease, Genotype, Humans, Interferon-gamma, Male, Molecular Sequence Data, Mycobacterium tuberculosis, Polymorphism, Genetic, South Africa, Tuberculosis, Young Adult},
	pages = {154},
}

Paper  Website  abstract   bibtex   

@article{
 title = {The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation.},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Adaptation, Biological,Adaptation, Biological: genetics,Genetics, Population,Humans,Multifactorial Inheritance,Multifactorial Inheritance: genetics,Selection, Genetic},
 pages = {R208-15},
 volume = {20},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2994553&tool=pmcentrez&rendertype=abstract},
 month = {2},
 publisher = {Elsevier Ltd},
 day = {23},
 id = {38488833-3f38-3b4f-a6b6-cec04bae2412},
 created = {2017-06-19T13:46:17.183Z},
 accessed = {2012-10-24},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:17.389Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative morphology and physiology, as well as population genetic studies of candidate loci and genome-wide data. However, the data also suggest that it is unusual for strong selection to drive new mutations rapidly to fixation in particular populations (the 'hard sweep' model). We argue, instead, for alternatives to the hard sweep model: in particular, polygenic adaptation could allow rapid adaptation while not producing classical signatures of selective sweeps. We close by discussing some of the likely opportunities for progress in the field.},
 bibtype = {article},
 author = {Pritchard, Jonathan K and Pickrell, Joseph K and Coop, Graham},
 journal = {Current biology : CB},
 number = {4}
}

Website  abstract   bibtex   

@article{
 title = {Establishing , maintaining and modifying DNA methylation patterns in plants and animals},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Animals,CpG Islands,DNA,DNA Methylation,DNA Methylation/ genetics/physiology,DNA Methylation: genetics,DNA Methylation: physiology,Epigenesis,Gametogenesis,Gametogenesis/genetics,Gametogenesis: genetics,Genetic,Histones,Histones/genetics/metabolism,Histones: genetics,Histones: metabolism,Models,Plant,Plant/genetics/metabolism,Plant: genetics,Plant: metabolism,Plants,Plants/genetics/metabolism,Plants: genetics,Plants: metabolism,RNA,Small Interfering,Small Interfering/genetics/metabolism,Small Interfering: genetics,Small Interfering: metabolism},
 pages = {204-220},
 volume = {11},
 websites = {http://dx.doi.org/10.1038/nrg2719},
 month = {3},
 publisher = {Nature Publishing Group},
 id = {e38badcf-b208-3875-995a-512806f6a978},
 created = {2017-10-14T10:53:30.488Z},
 file_attached = {false},
 profile_id = {57cbaa4c-3609-3597-b91c-bd12e56638fb},
 group_id = {b97159aa-8fdc-3227-aa16-9de80bf090dd},
 last_modified = {2017-10-14T10:53:30.488Z},
 read = {false},
 starred = {true},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Law2010a},
 source_type = {article},
 short_title = {Nat Rev Genet},
 private_publication = {false},
 abstract = {Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.},
 bibtype = {article},
 author = {Law, Julie A and Jacobsen, Steven E.},
 journal = {Nature Rev. Genet.},
 number = {MARCH}
}

@Article{Vapnik_2009_15070,
  author = {Vapnik, V. and Vashist, A.},
 journal = {Neural Networks},
 number = {5-6},
 pages = {544--57},
 publisher = {Elsevier Ltd},
 title = {A new learning paradigm: learning using privileged information.},
 volume = {22},
 year = {2009},
 issn = {1879-2782},
 keywords = {Algorithms,Artificial Intelligence,Bayes Theorem,Databases, Genetic,Forecasting,Forecasting: methods,Information Dissemination,Language,Learning,Mathematical Concepts,Protein Conformation,Proteins,Proteins: classification,Sequence Analysis, Protein,Sequence Analysis, Protein: methods,Time Factors},
 doi = {10.1016/j.neunet.2009.06.042},
 pmid = {19632812},
 title_with_no_special_chars = {A new learning paradigm learning using privileged information}
}

Paper  Website  abstract   bibtex   

@article{
 title = {A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles.},
 type = {article},
 year = {2009},
 identifiers = {[object Object]},
 keywords = {4-beta Xylanases,4-beta Xylanases: genetics,4-beta Xylanases: metabolism,Bacterial,Cloning,Endo-1,Escherichia coli,Escherichia coli: enzymology,Escherichia coli: genetics,Genetic,Genetic Vectors,Genomic Library,Genomics,Genomics: methods,Hot Temperature,Molecular,Molecular: methods,Recombination,Spirochaeta,Spirochaeta: enzymology,Spirochaeta: genetics,Thermus thermophilus,Thermus thermophilus: enzymology,Thermus thermophilus: genetics,Transformation},
 pages = {177-85},
 volume = {32},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/19285378},
 month = {5},
 id = {7bffd205-c6dc-3265-91ed-86c637dc7509},
 created = {2013-08-12T21:38:39.000Z},
 accessed = {2013-08-08},
 file_attached = {true},
 profile_id = {5224208a-a292-315a-8304-ffd095bfd482},
 last_modified = {2017-03-15T14:05:40.435Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Angelov2009},
 private_publication = {false},
 abstract = {A new cloning system is described, which allows the construction of large-insert fosmid libraries in Escherichia coli and the transfer of the recombinant libraries to the extreme thermophile Thermus thermophilus via natural transformation. Libraries are established in the thermophilic host by site-specific chromosomal insertion of the recombinant fosmids via single crossover or double crossover recombination at the T. thermophilus pyr locus. Comparative screening of a fosmid library constructed from genomic DNA from the thermophilic spirochaete, Spirochaeta thermophila, for clones expressing thermoactive xylanase activity revealed that 50% of the fosmids that conferred xylanase activity upon the corresponding T. thermophilus transformants did not give rise to xylanase-positive E. coli clones, indicating that significantly more S. thermophila genes are functionally expressed in T. thermophilus than in E. coli. The novel T. thermophilus host/vector system may be of value for the construction and functional screening of recombinant DNA libraries from individual thermophilic or extremely thermophilic organisms as well as from complex metagenomes isolated from thermophilic microbial communities.},
 bibtype = {article},
 author = {Angelov, Angel and Mientus, Markus and Liebl, Susanne and Liebl, Wolfgang},
 journal = {Systematic and applied microbiology},
 number = {3}
}

@article{cooke_mapping_2008,
	title = {Mapping of a novel susceptibility locus suggests a role for {MC3R} and {CTSZ} in human tuberculosis},
	volume = {178},
	issn = {1535-4970},
	doi = {10.1164/rccm.200710-1554OC},
	abstract = {RATIONALE: Tuberculosis remains a major cause of morbidity and mortality in the developing world. A better understanding of the mechanisms of disease protection could allow novel strategies to disease management and control.
OBJECTIVES: To identify human genomic loci with evidence of linkage to tuberculosis susceptibility and, within these loci, to identify individual genes influencing tuberculosis susceptibility.
METHODS: Affected sibling pair analysis in South African and Malawian populations. Independent case-control study in West Africa.
MEASUREMENTS AND MAIN RESULTS: Two novel putative loci for tuberculosis susceptibility are identified: chromosome 6p21-q23 and chromosome 20q13.31-33--the latter with the strongest evidence for any locus reported to date in human tuberculosis (single point LOD score of 3.1, P = 10(-4), with a maximum likelihood score [MLS] of 2.8). An independent, multistage genetic association study in West African populations mapped this latter region in detail, finding evidence that variation in the melanocortin 3 receptor (MC3R) and cathepsin Z (CTSZ) genes play a role in the pathogenesis of tuberculosis.
CONCLUSIONS: These results demonstrate how a genomewide approach to the complex phenotype of human tuberculosis can identify novel targets for further research.},
	language = {eng},
	number = {2},
	journal = {American Journal of Respiratory and Critical Care Medicine},
	author = {Cooke, Graham S. and Campbell, Sarah J. and Bennett, Steve and Lienhardt, Christian and McAdam, Keith P. W. J. and Sirugo, Giorgio and Sow, Oumou and Gustafson, Per and Mwangulu, Frank and van Helden, Paul and Fine, Paul and Hoal, Eileen G. and Hill, Adrian V. S.},
	month = jul,
	year = {2008},
	pmid = {18420963},
	pmcid = {PMC2643210},
	note = {00050 },
	keywords = {Africa, Western, African Continental Ancestry Group, Case-Control Studies, Cathepsin K, Cathepsin Z, Cathepsins, Genetic Linkage, Genetic Predisposition to Disease, Humans, Likelihood Functions, Malawi, Microsatellite Repeats, Pedigree, Polymorphism, Genetic, Receptor, Melanocortin, Type 3, Regression Analysis, Siblings, South Africa, Tuberculosis, Pulmonary},
	pages = {203--207},
}

@article{callahan_phenotypic_2008,
	title = {Phenotypic plasticity, costs of phenotypes, and costs of plasticity: toward an integrative view},
	volume = {1133},
	issn = {0077-8923},
	shorttitle = {Phenotypic plasticity, costs of phenotypes, and costs of plasticity},
	doi = {10.1196/annals.1438.008},
	abstract = {Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic basis of plasticity. In this vein, microbial work is especially illuminating and has three additional strengths. First, information about the machinery underlying plasticity--such as structural and regulatory genes, sensory proteins, and biochemical pathways--helps link population-level studies with underlying physiological and genetic mechanisms. Second, microbial studies involve many generations, large populations, and replication. Finally, empirical estimation of key parameters (e.g., mutation rates) is tractable. Together, these allow for rigorous investigation of gene interactions, drift, mutation, and selection--all potential factors influencing the maintenance or loss of inducible traits along with phenotypic and plasticity costs. Messages emerging from microbial work can guide future efforts to understand the evolution of plastic traits in diverse organisms.},
	language = {eng},
	journal = {Annals of the New York Academy of Sciences},
	author = {Callahan, Hilary S and Maughan, Heather and Steiner, Ulrich K},
	year = {2008},
	pmid = {18559815},
	keywords = {Adaptation, Physiological, Animals, Directed Molecular Evolution, Food Chain, Genetic Variation, Genome, Models, Biological, Models, Genetic, Phenotype, Predatory Behavior, Selection, Genetic},
	pages = {44--66}
}

@article{lochner_cluster_2008,
	title = {Cluster analysis of obsessive-compulsive symptomatology: identifying obsessive-compulsive disorder subtypes},
	volume = {45},
	issn = {0333-7308},
	shorttitle = {Cluster analysis of obsessive-compulsive symptomatology},
	abstract = {BACKGROUND: There is increasing evidence that obsessive-compulsive disorder (OCD) is a heterogeneous disorder. Different clinical subtypes may be characterized by differing pathophysiological mechanisms and treatment outcomes.
METHODS: A cluster analysis was performed on 45 items of the Yale-Brown Obsessive-Compulsive Symptoms Checklist (YBOCS-CL) for 261 patients with OCD. Cluster solutions emerging at different linkage distance levels, and the associations of identified clusters with demographic, clinical and relevant genetic variables, were investigated.
RESULTS: A 6-cluster solution emerged at a linkage distance level of 1.5, and a 3-cluster solution emerged at a linkage distance level of 2.1. The 3 clusters in the latter solution were labeled I) Contamination / washing, II) Hoarding / symmetry / ordering, and III) Obsessional / checking. Increased Cluster III scores were associated with earlier age of OCD onset and the Met/Met (L/L) genotype of the COMT Val158Met polymorphism.
CONCLUSION: The data here are consistent with previous work delineating the different symptom subtypes of OCD, also with previous work suggesting that the Met/Met (L/L) genotype of the COMT Val158Met polymorphism may be associated with anxiety symptoms, as well as with previous work suggesting that dopaminergic genes may be particularly important in early-onset OCD.},
	language = {eng},
	number = {3},
	journal = {The Israel Journal of Psychiatry and Related Sciences},
	author = {Lochner, Christine and Hemmings, Sian M. J. and Kinnear, Craig J. and Nel, Daan and Hemmings, Sian M. J. and Seedat, Soraya and Moolman-Smook, Johanna C. and Stein, Dan J.},
	year = {2008},
	pmid = {19398820},
	note = {00025 },
	keywords = {Adolescent, Adult, Aged, Analysis of Variance, Catechol O-Methyltransferase, Cluster Analysis, Female, Genotype, Humans, Male, Middle Aged, Obsessive-Compulsive Disorder, Polymerase Chain Reaction, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Young Adult},
	pages = {164--176},
}

@article{becquemont_evidence_2008,
	title = {Evidence for a pharmacogenetic adapted dose of oral anticoagulant in routine medical practice},
	volume = {64},
	issn = {1432-1041},
	doi = {10.1007/s00228-008-0542-2},
	abstract = {Oral anticoagulants (OA) are a leading cause of fatal haemorrhagic adverse events in relation with an important interindividual variability of response to these drugs. Besides several clinical factors, this interindividual variability of response to OA has a pharmacogenetic basis. Carriers of cytochrome P450 2C9 (CYP2C9)-deficient alleles have a reduced clearance of warfarin and are exposed to dramatic overdoses in the first weeks of treatment. Genetic polymorphisms of vitamin K epoxide reductase (VKORC1), the target of OA, identify patients with a high sensitivity to OA who are at risk of early overdose. Most pharmacogenetic evidence is presently restricted to warfarin. Several warfarin dosing algorithms have been constructed, adapted on CYP2C9 and VKORC1 genotypes and clinical factors, to predict the best dose for each patient. Carriers of one of allelic variant need a 20-30\% reduction of warfarin dose. However, definite evidence concerning the usefulness of these algorithms in terms of reducing the frequency of major bleeding episodes is still lacking. Ongoing prospective randomised trials will ascertain definitive answer over the coming years.},
	language = {eng},
	number = {10},
	journal = {European Journal of Clinical Pharmacology},
	author = {Becquemont, Laurent},
	month = oct,
	year = {2008},
	pmid = {18758764},
	keywords = {ANTICOAGULANTS (Medicine), Acenocoumarol, Administration, Oral, Algorithms, Anticoagulants, Aryl Hydrocarbon Hydroxylases, CYTOCHROMES, Cytochrome P-450 CYP2C9, Cytochrome P450 2C9, DRUGS -- Side effects, Dose-Response Relationship, Drug, Dosing algorithm, Dosing algorithm .Warfarin, Fluindione, GENETIC polymorphisms, Humans, International Normalized Ratio, Mixed Function Oxygenases, Oral anticoagulants, PHARMACOGENOMICS, Pharmacogenetics, Phenprocoumon, Polymorphism, Genetic, Randomized Controlled Trials as Topic, VKORC1, Vitamin K Epoxide Reductases, Vitamin K antagonists, Warfarin},
	pages = {953--960}
}

@article{ sibille_large-scale_2008,
  title = {Large-scale estimates of cellular origins of {mRNAs}: enhancing the yield of transcriptome analyses},
  volume = {167},
  issn = {0165-0270},
  shorttitle = {Large-scale estimates of cellular origins of {mRNAs}},
  doi = {10.1016/j.jneumeth.2007.08.009},
  abstract = {Gene expression profiling holds great promise for identifying molecular pathologies of central nervous system disorders. However, the analysis of brain tissue poses unique analytical challenges, as typical microarray signals represent averaged transcript levels across neuronal and glial cell populations. Here we have generated ratios of gene transcript levels between gray and adjacent white matter samples to estimate the relative cellular origins of expression. We show that incorporating these ratios into transcriptome analysis (i) provides new analytical perspectives, (ii) increases the potential for biological insight obtained from postmortem transcriptome studies, (iii) expands knowledge about glial and neuronal cellular programs and (iv) facilitates the generation of cell-type specific hypotheses. This approach represents a robust and cost-effective "add-on" to transcriptome analyses of the mammalian brain. As this approach can be applied post hoc, we provide tables of ratios for analysis of existing mouse and human brain datasets.},
  language = {eng},
  number = {2},
  journal = {Journal of Neuroscience Methods},
  author = {Sibille, Etienne and Arango, Victoria and Joeyen-Waldorf, Jennifer and Wang, Yingjie and Leman, Samuel and Surget, Alexandre and Belzung, Catherine and Mann, J. John and Lewis, David A.},
  month = {January},
  year = {2008},
  pmid = {17889939},
  pmcid = {PMC2262176},
  keywords = {Animals, Brain, Cluster Analysis, Cohort Studies, Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Humans, Mice, Microarray Analysis, Nerve Tissue Proteins, Neuroglia, Neurons, Postmortem Changes, {RNA}, Messenger, Transcription, Genetic},
  pages = {198--206}
}

Paper  doi  abstract   bibtex   

@article{foissac_astalavista:_2007,
	title = {{ASTALAVISTA}: dynamic and flexible analysis of alternative splicing events in custom gene datasets.},
	volume = {35},
	issn = {1362-4962},
	url = {http://nar.oxfordjournals.org/content/35/suppl_2/W297.abstract},
	doi = {10.1093/nar/gkm311},
	abstract = {In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon-intron structure between transcript variants and the need for computational tools to address 'complex' AS events. ASTALAVISTA (alternative splicing transcriptional landscape visualization tool) employs an intuitive and complete notation system to univocally identify such events. The method extracts AS events dynamically from custom gene annotations, classifies them into groups of common types and visualizes a comprehensive picture of the resulting AS landscape. Thus, ASTALAVISTA can characterize AS for whole transcriptome data from reference annotations (GENCODE, REFSEQ, ENSEMBL) as well as for genes selected by the user according to common functional/structural attributes of interest: http://genome.imim.es/astalavista.},
	number = {Web Server issue},
	journal = {Nucleic acids research},
	author = {Foissac, Sylvain and Sammeth, Michael},
	month = jul,
	year = {2007},
	pmid = {17485470},
	keywords = {Alternative Splicing, Alternative Splicing: genetics, Chromosome Mapping, Chromosome Mapping: methods, Computational Biology, Computational Biology: methods, DNA, DNA Probes, DNA Probes: genetics, DNA: methods, Databases, Genetic, Genome, Humans, Internet, Messenger, Messenger: metabolism, Oligonucleotide Array Sequence Analysis, Oligonucleotide Array Sequence Analysis: instrumen, Oligonucleotide Array Sequence Analysis: methods, RNA, RNA Splice Sites, RNA Splice Sites: genetics, Sequence Analysis, Software},
	pages = {297}
}

Paper  doi  abstract   bibtex   

@article{haddow_tackling_2007,
	title = {Tackling community concerns about commercialisation and genetic research: a modest interdisciplinary proposal},
	volume = {64},
	issn = {0277-9536},
	shorttitle = {Tackling community concerns about commercialisation and genetic research},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17050056},
	doi = {10.1016/j.socscimed.2006.08.028},
	abstract = {In recent years, there has been a rise in the creation of DNA databases promising a range of health benefits to individuals and populations. This development has been accompanied by an interest in, and concern for the ethical, legal and social aspects of such collections. In terms of policy solutions, much of the focus of these debates has been on issues of consent, confidentiality and research governance. However, there are broader concerns, such as those associated with commercialisation, which cannot be adequately addressed by these foci. In this article, we focus on the health-wealth benefits that DNA databases promise by considering the views of 10 focus groups on Generation Scotland, Scotland's first national genetic database. As in previous studies, our qualitative research on public/s and stakeholders' views of DNA databases show the prospect of utilising donated samples and information derived for wealth-related ends (i.e. for private profit), irrespective of whether there is an associated health-related benefit, arouses considerable reaction. While health-wealth benefits are not mutually exclusive ideals, the tendency has been to cast 'public' benefits as exclusively health-related, while 'private' commercial benefits for funders and/or researchers are held out as a necessary pay-off. We argue for a less polarised approach that reconsiders what is meant by 'public benefits' and questions the exclusivity of commercial interests. We believe accommodation can be achieved via the mobilisation of a grass roots solution known as 'benefit-sharing' or a 'profit pay-off'. We propose a sociologically informed model that has a pragmatic, legal framework, which responds seriously to public concerns.},
	number = {2},
	urldate = {2010-11-27},
	journal = {Social Science \& Medicine (1982)},
	author = {Haddow, Gillian and Laurie, Graeme and Cunningham-Burley, Sarah and Hunter, Kathryn G},
	month = jan,
	year = {2007},
	pmid = {17050056},
	keywords = {Commerce, Databases, Genetic, Drug Industry, Focus Groups, Genetic Research, Humans, Referral and Consultation, Scotland},
	pages = {272--282}
}

@article{watters_highly_2007,
	title = {The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection},
	volume = {128},
	issn = {0092-8674},
	doi = {10.1016/j.cell.2006.12.042},
	abstract = {To illuminate the evolutionary pressure acting on the folding free energy landscapes of naturally occurring proteins, we have systematically characterized the folding free energy landscape of Top7, a computationally designed protein lacking an evolutionary history. Stopped-flow kinetics, circular dichroism, and NMR experiments reveal that there are at least three distinct phases in the folding of Top7, that a nonnative conformation is stable at equilibrium, and that multiple fragments of Top7 are stable in isolation. These results indicate that the folding of Top7 is significantly less cooperative than the folding of similarly sized naturally occurring proteins, suggesting that the cooperative folding and smooth free energy landscapes observed for small naturally occurring proteins are not general properties of polypeptide chains that fold to unique stable structures but are instead a product of natural selection.},
	language = {eng},
	number = {3},
	journal = {Cell},
	author = {Watters, Alexander L and Deka, Pritilekha and Corrent, Colin and Callender, David and Varani, Gabriele and Sosnick, Tobin and Baker, David},
	month = feb,
	year = {2007},
	pmid = {17289578},
	keywords = {Circular Dichroism, Kinetics, Models, Chemical, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Point Mutation, Protein Folding, Protein Structure, Secondary, Proteins, Selection, Genetic, Thermodynamics},
	pages = {613--624}
}

@article{keightley_joint_2007,
	title = {Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies},
	volume = {177},
	issn = {0016-6731},
	doi = {10.1534/genetics.107.080663},
	abstract = {The distribution of fitness effects of new mutations (DFE) is important for addressing several questions in genetics, including the nature of quantitative variation and the evolutionary fate of small populations. Properties of the DFE can be inferred by comparing the distributions of the frequencies of segregating nucleotide polymorphisms at selected and neutral sites in a population sample, but demographic changes alter the spectrum of allele frequencies at both neutral and selected sites, so can bias estimates of the DFE if not accounted for. We have developed a maximum-likelihood approach, based on the expected allele-frequency distribution generated by transition matrix methods, to estimate parameters of the DFE while simultaneously estimating parameters of a demographic model that allows a population size change at some time in the past. We tested the method using simulations and found that it accurately recovers simulated parameter values, even if the simulated demography differs substantially from that assumed in our analysis. We use our method to estimate parameters of the DFE for amino acid-changing mutations in humans and Drosophila melanogaster. For a model of unconditionally deleterious mutations, with effects sampled from a gamma distribution, the mean estimate for the distribution shape parameter is approximately 0.2 for human populations, which implies that the DFE is strongly leptokurtic. For Drosophila populations, we estimate that the shape parameter is approximately 0.35. Differences in the shape of the distribution and the mean selection coefficient between humans and Drosophila result in significantly more strongly deleterious mutations in Drosophila than in humans, and, conversely, nearly neutral mutations are significantly less frequent.},
	language = {eng},
	number = {4},
	journal = {Genetics},
	author = {Keightley, Peter D. and Eyre-Walker, Adam},
	month = dec,
	year = {2007},
	pmid = {18073430},
	pmcid = {PMC2219502},
	keywords = {Amino Acid Substitution, Animals, Demography, Drosophila, Gene Frequency, Genetic, Humans, Likelihood Functions, Missense, Mutation, Polymorphism, Selection},
	pages = {2251--2261},
}

Paper  Website  abstract   bibtex   

@article{
 title = {Natural selection on female life-history traits in relation to socio-economic class in pre-industrial human populations.},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {Developing Countries,Developing Countries: economics,Developing Countries: history,Family,Family Characteristics,Female,Fertility,Finland,History, 19th Century,History, 20th Century,Humans,Life Expectancy,Longevity,Male,Reproduction,Reproduction: genetics,Reproduction: physiology,Selection, Genetic,Selection, Genetic: genetics,Social Class,Social Class: history},
 pages = {e606},
 volume = {2},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1904257&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {eaeb93b3-d15c-39b3-937f-629295484a44},
 created = {2017-06-19T13:39:31.040Z},
 accessed = {2013-05-22},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:39:31.139Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Life-history theory predicts that resource scarcity constrains individual optimal reproductive strategies and shapes the evolution of life-history traits. In species where the inherited structure of social class may lead to consistent resource differences among family lines, between-class variation in resource availability should select for divergence in optimal reproductive strategies. Evaluating this prediction requires information on the phenotypic selection and quantitative genetics of life-history trait variation in relation to individual lifetime access to resources. Here, we show using path analysis how resource availability, measured as the wealth class of the family, affected the opportunity and intensity of phenotypic selection on the key life-history traits of women living in pre-industrial Finland during the 1800s and 1900s. We found the highest opportunity for total selection and the strongest selection on earlier age at first reproduction in women of the poorest wealth class, whereas selection favoured older age at reproductive cessation in mothers of the wealthier classes. We also found clear differences in female life-history traits across wealth classes: the poorest women had the lowest age-specific survival throughout their lives, they started reproduction later, delivered fewer offspring during their lifetime, ceased reproduction younger, had poorer offspring survival to adulthood and, hence, had lower fitness compared to the wealthier women. Our results show that the amount of wealth affected the selection pressure on female life-history in a pre-industrial human population.},
 bibtype = {article},
 author = {Pettay, Jenni E and Helle, Samuli and Jokela, Jukka and Lummaa, Virpi},
 journal = {PloS one},
 number = {7}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Functional genomics and proteomics of the cellular osmotic stress response in 'non-model' organisms.},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {Adaptation, Physiological,Adaptation, Physiological: genetics,Animals,Computational Biology,Computational Biology: methods,Databases, Genetic,Electrophoresis, Gel, Two-Dimensional,Electrophoresis, Gel, Two-Dimensional: methods,Gene Regulatory Networks,Gene Regulatory Networks: genetics,Genomics,Genomics: methods,Models, Biological,Nucleic Acid Hybridization,Nucleic Acid Hybridization: methods,Polymerase Chain Reaction,Polymerase Chain Reaction: methods,Protein Interaction Mapping,Protein Interaction Mapping: methods,Proteomics,Proteomics: methods,Species Specificity,Water-Electrolyte Balance,Water-Electrolyte Balance: genetics},
 pages = {1593-601},
 volume = {210},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/17449824},
 month = {5},
 id = {b6d25d99-c033-3a18-9605-0f4802f65569},
 created = {2012-12-06T09:12:59.000Z},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kultz2007},
 abstract = {All organisms are adapted to well-defined extracellular salinity ranges. Osmoregulatory mechanisms spanning all levels of biological organization, from molecules to behavior, are central to salinity adaptation. Functional genomics and proteomics approaches represent powerful tools for gaining insight into the molecular basis of salinity adaptation and euryhalinity in animals. In this review, we discuss our experience in applying such tools to so-called 'non-model' species, including euryhaline animals that are well-suited for studies of salinity adaptation. Suppression subtractive hybridization, RACE-PCR and mass spectrometry-driven proteomics can be used to identify genes and proteins involved in salinity adaptation or other environmental stress responses in tilapia, sharks and sponges. For protein identification in non-model species, algorithms based on sequence homology searches such as MSBLASTP2 are most powerful. Subsequent gene ontology and pathway analysis can then utilize sets of identified genes and proteins for modeling molecular mechanisms of environmental adaptation. Current limitations for proteomics in non-model species can be overcome by improving sequence coverage, N- and C-terminal sequencing and analysis of intact proteins. Dependence on information about biochemical pathways and gene ontology databases for model species represents a more severe barrier for work with non-model species. To minimize such dependence, focusing on a single biological process (rather than attempting to describe the system as a whole) is key when applying 'omics' approaches to non-model organisms.},
 bibtype = {article},
 author = {Kültz, Dietmar and Fiol, Diego and Valkova, Nelly and Gomez-Jimenez, Silvia and Chan, Stephanie Y and Lee, Jinoo},
 journal = {The Journal of experimental biology},
 number = {Pt 9}
}

@article{hanekom_evidence_2007,
	title = {Evidence that the spread of {Mycobacterium} tuberculosis strains with the {Beijing} genotype is human population dependent},
	volume = {45},
	issn = {0095-1137},
	doi = {10.1128/JCM.02354-06},
	abstract = {This study describes a comparative analysis of the Beijing mycobacterial interspersed repetitive unit types of Mycobacterium tuberculosis isolates from Cape Town, South Africa, and East Asia. The results show a significant association between the frequency of occurrence of strains from defined Beijing sublineages and the human population from whom they were cultured (P {\textless} 0.0001).},
	language = {eng},
	number = {7},
	journal = {Journal of Clinical Microbiology},
	author = {Hanekom, M. and van der Spuy, G. D. and Gey van Pittius, N. C. and McEvoy, C. R. E. and Ndabambi, S. L. and Victor, T. C. and Hoal, E. G. and van Helden, P. D. and Warren, R. M.},
	month = jul,
	year = {2007},
	pmid = {17475755},
	pmcid = {PMC1933015},
	note = {00057 },
	keywords = {China, Far East, Genotype, Humans, Mycobacterium tuberculosis, Polymorphism, Genetic, Population Dynamics, South Africa, Tuberculosis, Pulmonary},
	pages = {2263--2266},
}

@article{noviello_maintenance_2007,
	title = {Maintenance of {Nef}-mediated modulation of major histocompatibility complex class {I} and {CD4} after sexual transmission of human immunodeficiency virus type 1},
	volume = {81},
	issn = {0022-538X},
	doi = {10.1128/JVI.01793-06},
	abstract = {Viruses encounter changing selective pressures during transmission between hosts, including host-specific immune responses and potentially varying functional demands on specific proteins. The human immunodeficiency virus type 1 Nef protein performs several functions potentially important for successful infection, including immune escape via down-regulation of class I major histocompatibility complex (MHC-I) and direct enhancement of viral infectivity and replication. Nef is also a major target of the host cytotoxic T-lymphocyte (CTL) response. To examine the impact of changing selective pressures on Nef functions following sexual transmission, we analyzed genetic and functional changes in nef clones from six transmission events. Phylogenetic analyses indicated that the diversity of nef was similar in both sources and acutely infected recipients, the patterns of selection across transmission were variable, and regions of Nef associated with distinct functions evolved similarly in sources and recipients. These results weighed against the selection of specific Nef functions by transmission or during acute infection. Measurement of Nef function provided no evidence that the down-regulation of either CD4 or MHC-I was optimized by transmission or during acute infection, although rare nef clones from sources that were impaired in these activities were not detected in recipients. Nef-specific CTL activity was detected as early as 3 weeks after infection and appeared to be an evolutionary force driving the diversification of nef. Despite the change in selective pressure between the source and recipient immune systems and concomitant genetic diversity, the majority of Nef proteins maintained robust abilities to down-regulate MHC-I and CD4. These data suggest that both functions are important for the successful establishment of infection in a new host.},
	language = {eng},
	number = {9},
	journal = {Journal of Virology},
	author = {Noviello, C. M. and Pond, S. L. Kosakovsky and Lewis, M. J. and Richman, D. D. and Pillai, S. K. and Yang, O. O. and Little, S. J. and Smith, D. M. and Guatelli, J. C.},
	month = may,
	year = {2007},
	pmid = {17329339},
	pmcid = {PMC1900175},
	keywords = {Amino Acid Sequence, Base Sequence, Blotting, Western, CD4 Antigens, Evolution, Molecular, Flow Cytometry, Gene Expression Regulation, Viral, Gene Products, nef, Genes, MHC Class I, Genetic Variation, HIV Infections, HIV-1, Humans, Likelihood Functions, Models, Genetic, Molecular Sequence Data, Phylogeny, Selection, Genetic, Sequence Alignment, Sequence Analysis, DNA, T-Lymphocytes, Cytotoxic, nef Gene Products, Human Immunodeficiency Virus},
	pages = {4776--4786},
}

Paper  doi  abstract   bibtex   

@article{hillson_caulobacter_2007,
	title = {Caulobacter crescentus as a whole-cell uranium biosensor},
	volume = {73},
	issn = {1098-5336},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17905881},
	doi = {10.1128/AEM.01566-07},
	abstract = {We engineered a strain of the bacterium Caulobacter crescentus to fluoresce in the presence of micromolar levels of uranium at ambient temperatures when it is exposed to a hand-held UV lamp. Previous microarray experiments revealed that several Caulobacter genes are significantly upregulated in response to uranium but not in response to other heavy metals. We designated one of these genes urcA (for uranium response in caulobacter). We constructed a reporter that utilizes the urcA promoter to produce a UV-excitable green fluorescent protein in the presence of the uranyl cation, a soluble form of uranium. This reporter is specific for uranium and has little cross specificity for nitrate ({\textless}400 microM), lead ({\textless}150 microM), cadmium ({\textless}48 microM), or chromium ({\textless}41.6 microM). The uranium reporter construct was effective for discriminating contaminated groundwater samples (4.2 microM uranium) from uncontaminated groundwater samples ({\textless}0.1 microM uranium) collected at the Oak Ridge Field Research Center. In contrast to other uranium detection methodologies, the Caulobacter reporter strain can provide on-demand usability in the field; it requires minimal sample processing and no equipment other than a hand-held UV lamp, and it may be sprayed directly on soil, groundwater, or industrial surfaces.},
	number = {23},
	urldate = {2009-09-30TZ},
	journal = {Applied and Environmental Microbiology},
	author = {Hillson, Nathan J and Hu, Ping and Andersen, Gary L and Shapiro, Lucy},
	month = dec,
	year = {2007},
	pmid = {17905881},
	keywords = {Biosensing Techniques, Cadmium, Caulobacter crescentus, Chromium, Gene Expression Regulation, Bacterial, Genes, Bacterial, Green Fluorescent Proteins, Lead, Nitrates, Promoter Regions, Genetic, Recombinant Fusion Proteins, Ultraviolet Rays, Uranium, Water Pollutants, Radioactive},
	pages = {7615--7621}
}

@article{yang_paml_2007,
	title = {{PAML} 4: phylogenetic analysis by maximum likelihood},
	volume = {24},
	issn = {0737-4038},
	shorttitle = {{PAML} 4},
	doi = {10.1093/molbev/msm088},
	abstract = {PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at – (http://abacus.gene.ucl.ac.uk/software/paml.html).},
	language = {eng},
	number = {8},
	journal = {Molecular Biology and Evolution},
	author = {Yang, Ziheng},
	month = aug,
	year = {2007},
	pmid = {17483113},
	keywords = {Animals, Computer Simulation, Genetic, Genetic Variation, Likelihood Functions, Models, Phylogeny, Selection, Software, Species Specificity},
	pages = {1586--1591},
}

@article{lyne_flymine:_2007,
	title = {{FlyMine}: an integrated database for {Drosophila} and {Anopheles} genomics},
	volume = {8},
	issn = {1474-760X},
	shorttitle = {{FlyMine}},
	doi = {10.1186/gb-2007-8-7-r129},
	abstract = {FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists.},
	language = {eng},
	number = {7},
	journal = {Genome Biology},
	author = {Lyne, Rachel and Smith, Richard and Rutherford, Kim and Wakeling, Matthew and Varley, Andrew and Guillier, Francois and Janssens, Hilde and Ji, Wenyan and Mclaren, Peter and North, Philip and Rana, Debashis and Riley, Tom and Sullivan, Julie and Watkins, Xavier and Woodbridge, Mark and Lilley, Kathryn and Russell, Steve and Ashburner, Michael and Mizuguchi, Kenji and Micklem, Gos},
	year = {2007},
	pmid = {17615057},
	pmcid = {PMC2323218},
	keywords = {Animals, Anopheles, Databases, Genetic, Drosophila, Genomics, Software},
	pages = {R129}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus.},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Codon,Consensus Sequence,DNA Primers,DNA Primers: genetics,DNA, Algal,DNA, Algal: genetics,Databases, Nucleic Acid,Expressed Sequence Tags,Genetic Markers,Microsatellite Repeats,Microsatellite Repeats: genetics,Open Reading Frames,Phylogeny,Phytophthora,Phytophthora: genetics,Species Specificity,Transcription, Genetic},
 pages = {245},
 volume = {7},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1594578&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {f0612254-194c-38b3-865d-113bae82d407},
 created = {2015-09-09T02:21:59.000Z},
 accessed = {2015-09-09},
 file_attached = {true},
 profile_id = {f95ef69b-8f96-32da-8de9-769c2acf0685},
 last_modified = {2015-09-09T02:22:11.000Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 abstract = {BACKGROUND: Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes.

RESULTS: The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database.

CONCLUSION: In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.},
 bibtype = {article},
 author = {Garnica, Diana P and Pinzón, Andrés M and Quesada-Ocampo, Lina M and Bernal, Adriana J and Barreto, Emiliano and Grünwald, Niklaus J and Restrepo, Silvia},
 journal = {BMC genomics}
}

Paper  Website  abstract   bibtex   

@article{
 title = {All-trans retinoic acid down-regulates human albumin gene expression through the induction of C/EBPbeta-LIP.},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Albumins,Albumins: biosynthesis,Albumins: genetics,Binding Sites,CCAAT-Enhancer-Binding Protein-beta,CCAAT-Enhancer-Binding Protein-beta: metabolism,Carcinoma, Hepatocellular,Carcinoma, Hepatocellular: genetics,Cell Line, Tumor,Down-Regulation,Gene Expression Regulation,Humans,Promoter Regions, Genetic,Protein Binding,Transcriptional Activation,Tretinoin,Tretinoin: physiology},
 pages = {345-53},
 volume = {397},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1513275&tool=pmcentrez&rendertype=abstract},
 month = {7},
 day = {15},
 id = {4dc1bbb0-4eb7-35b1-8e2c-c83e3f97a680},
 created = {2016-04-08T12:19:26.000Z},
 accessed = {2015-03-24},
 file_attached = {true},
 profile_id = {994bc413-6766-31df-917a-32165aa30f6c},
 group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
 last_modified = {2017-03-14T10:42:46.538Z},
 read = {true},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Masaki2006},
 folder_uuids = {37786225-e8d4-483b-be04-dfc97f200748},
 private_publication = {false},
 abstract = {ATRA (all-trans retinoic acid), which is a major bioactive metabolite of vitamin A and a potent regulator of development and differentiation, mediates down-regulation of the human albumin gene. However, the mechanism of ATRA-mediated down-regulation is not well understood. In the present study, deletion analysis and luciferase assays demonstrate that ATRA causes a marked decrease in the activity of the albumin promoter, the region between nt -367 and -167 from the transcription start site, where C/EBP (CCAAT/enhancer-binding protein)-binding sites are tightly packed, is indispensable for ATRA-mediated down-regulation. ChIP (chromatin immunoprecipitation) assays revealed that in vivo binding of C/EBPalpha to the region markedly decreases upon incubation with ATRA, whereas ATRA treatment marginally increases the recruitment of C/EBPbeta. We found that ATRA has the ability to differentially and directly induce expression of a truncated isoform of C/EBPbeta, which is an LIP (liver-enriched transcriptional inhibitory protein) that lacks a transactivation domain, and to increase the binding activity of C/EBPbeta-LIP to its response element. Overexpression of C/EBPbeta-LIP negatively regulates the endogenous expression of albumin, as well as the activity of the albumin promoter induced by C/EBP transactivators such as C/EBPalpha and full-length C/EBPbeta. In conclusion, we propose a novel model for down-regulation of the albumin gene, in which ATRA triggers an increase in the translation of C/EBPbeta-LIP that antagonizes C/EBP transactivators by interacting with their binding sites in the albumin promoter.},
 bibtype = {article},
 author = {Masaki, Takahiro and Matsuura, Tomokazu and Ohkawa, Kiyoshi and Miyamura, Tatsuo and Okazaki, Isao and Watanabe, Tetsu and Suzuki, Tetsuro},
 journal = {The Biochemical journal},
 number = {2}
}

@article{barreiro_promoter_2006,
	title = {Promoter variation in the {DC}-{SIGN}-encoding gene {CD209} is associated with tuberculosis},
	volume = {3},
	issn = {1549-1676},
	doi = {10.1371/journal.pmed.0030020},
	abstract = {BACKGROUND: Tuberculosis, which is caused by Mycobacterium tuberculosis, remains one of the leading causes of mortality worldwide. The C-type lectin DC-SIGN is known to be the major M. tuberculosis receptor on human dendritic cells. We reasoned that if DC-SIGN interacts with M. tuberculosis, as well as with other pathogens, variation in this gene might have a broad range of influence in the pathogenesis of a number of infectious diseases, including tuberculosis.
METHODS AND FINDINGS: We tested whether polymorphisms in CD209, the gene encoding DC-SIGN, are associated with susceptibility to tuberculosis through sequencing and genotyping analyses in a South African cohort. After exclusion of significant population stratification in our cohort, we observed an association between two CD209 promoter variants (-871G and -336A) and decreased risk of developing tuberculosis. By looking at the geographical distribution of these variants, we observed that their allelic combination is mainly confined to Eurasian populations.
CONCLUSIONS: Our observations suggest that the two -871G and -336A variants confer protection against tuberculosis. In addition, the geographic distribution of these two alleles, together with their phylogenetic status, suggest that they may have increased in frequency in non-African populations as a result of host genetic adaptation to a longer history of exposure to tuberculosis. Further characterization of the biological consequences of DC-SIGN variation in tuberculosis will be crucial to better appreciate the role of this lectin in interactions between the host immune system and the tubercle bacillus as well as other pathogens.},
	language = {eng},
	number = {2},
	journal = {PLoS medicine},
	author = {Barreiro, Luis B. and Neyrolles, Olivier and Babb, Chantal L. and Tailleux, Ludovic and Quach, Hélène and McElreavey, Ken and Helden, Paul D. van and Hoal, Eileen G. and Gicquel, Brigitte and Quintana-Murci, Lluis},
	month = feb,
	year = {2006},
	pmid = {16379498},
	pmcid = {PMC1324949},
	note = {00192 },
	keywords = {Adult, African Continental Ancestry Group, Case-Control Studies, Cell Adhesion Molecules, Dendritic Cells, Female, Genetic Predisposition to Disease, Humans, Lectins, C-Type, Male, Middle Aged, Mycobacterium tuberculosis, Phylogeny, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, Receptors, Cell Surface, Risk Factors, South Africa, Tuberculosis, Pulmonary},
	pages = {e20},
}

Paper  Website  abstract   bibtex   

@article{
 title = {A simple rule for the evolution of cooperation on graphs and social networks.},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Altruism,Animals,Biological Evolution,Cooperative Behavior,Costs and Cost Analysis,Game Theory,Humans,Models, Biological,Selection, Genetic,Social Support},
 pages = {502-5},
 volume = {441},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2430087&tool=pmcentrez&rendertype=abstract},
 month = {5},
 day = {25},
 id = {394b9e2a-eb7d-3260-be1b-97b4b67534dc},
 created = {2014-11-13T17:56:03.000Z},
 accessed = {2014-05-30},
 file_attached = {true},
 profile_id = {5a758209-74fb-3a9c-b322-2ae7f22f7b6c},
 group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
 last_modified = {2014-11-18T21:16:27.000Z},
 read = {false},
 starred = {true},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {A fundamental aspect of all biological systems is cooperation. Cooperative interactions are required for many levels of biological organization ranging from single cells to groups of animals. Human society is based to a large extent on mechanisms that promote cooperation. It is well known that in unstructured populations, natural selection favours defectors over cooperators. There is much current interest, however, in studying evolutionary games in structured populations and on graphs. These efforts recognize the fact that who-meets-whom is not random, but determined by spatial relationships or social networks. Here we describe a surprisingly simple rule that is a good approximation for all graphs that we have analysed, including cycles, spatial lattices, random regular graphs, random graphs and scale-free networks: natural selection favours cooperation, if the benefit of the altruistic act, b, divided by the cost, c, exceeds the average number of neighbours, k, which means b/c > k. In this case, cooperation can evolve as a consequence of 'social viscosity' even in the absence of reputation effects or strategic complexity.},
 bibtype = {article},
 author = {Ohtsuki, Hisashi and Hauert, Christoph and Lieberman, Erez and Nowak, Martin a},
 journal = {Nature},
 number = {7092}
}

Website  abstract   bibtex   

@article{
 title = {Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Arabidopsis,Arabidopsis: genetics,Arabidopsis: metabolism,Chromosome Mapping,Chromosome Mapping: methods,DNA Methylation,DNA Modification Methylases,DNA Modification Methylases: genetics,DNA Modification Methylases: metabolism,DNA, Plant,DNA, Plant: genetics,DNA, Plant: metabolism,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Regulation, Plant,Gene Expression Regulation, Plant: genetics,Gene Silencing,Gene Silencing: physiology,Genes, Plant,Genes, Plant: genetics,Genome, Plant,Genome, Plant: genetics,Molecular Sequence Data,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Promoter Regions, Genetic,Promoter Regions, Genetic: genetics,RNA, Small Interfering,RNA, Small Interfering: genetics,Transcription, Genetic,Transcription, Genetic: genetics},
 pages = {1189-1201},
 volume = {126},
 websites = {http://www.sciencedirect.com/science/article/pii/S009286740601018X},
 month = {9},
 day = {22},
 id = {a586b1f4-e03b-3e35-9aab-938a0666a153},
 created = {2017-10-14T10:53:33.674Z},
 accessed = {2015-09-07},
 file_attached = {false},
 profile_id = {57cbaa4c-3609-3597-b91c-bd12e56638fb},
 group_id = {b97159aa-8fdc-3227-aa16-9de80bf090dd},
 last_modified = {2017-10-14T10:53:33.674Z},
 read = {false},
 starred = {true},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zhang2006},
 private_publication = {false},
 abstract = {Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only ???5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation. ?? 2006 Elsevier Inc. All rights reserved.},
 bibtype = {article},
 author = {Zhang, Xiaoyu and Yazaki, Junshi and Sundaresan, Ambika and Cokus, Shawn and Chan, Simon W L and Chen, Huaming and Henderson, Ian R. and Shinn, Paul and Pellegrini, Matteo and Jacobsen, Steve E. and Ecker, Joseph R},
 journal = {Cell},
 number = {6}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Biological evidence for inheritance of exceptional longevity},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {Age Factors,Aged,Aged, 80 and over,Aging/*ethnology/*genetics,Alleles,Carrier Proteins/genetics,Case-Control Studies,Genotype,Glycoproteins/genetics,Homozygote,Humans,Lipids/metabolism,Lipoproteins, HDL/genetics/metabolism,Lipoproteins, LDL/genetics/metabolism,Longevity/*genetics,Phenotype,Polymorphism, Genetic,Valine/genetics},
 pages = {341-345},
 volume = {126},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15621216},
 id = {ac53ce7e-fc6c-35da-8438-be74b645fce9},
 created = {2017-06-19T13:45:30.857Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:31.024Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0047-6374<m:linebreak/>Journal Article</m:note>},
 abstract = {Subjects with exceptional longevity have a lower incidence and/or significant delay in the onset of age-related disease, and their family members may inherit biological factors that modulate aging processes and disease susceptibility. In a case control study, we aim to determine phenotype and genotype of exceptional longevity in a genetically homogenous population (Ashkenazi Jews), and their offspring, while an age-matched control group of Ashkenazi Jews was used as control groups. We demonstrated that exceptional longevity and healthy aging in humans is an inherited phenotype across three generations. Moreover, we demonstrated that subjects with exceptional longevity and their offspring have significantly larger high-density lipoprotein (HDL) levels and particle sizes and low-density lipoprotein (LDL) levels that reflect on their health and cognitive function performance. This phenotype have led us to study candidate genes involved in lipoprotein metabolism, and to the implication of homozygosity for the 405 valine (V) allele of cholesteryl ester transfer protein (CETP). A markedly higher frequency of a functional CETP variant that led to increased particle sizes of HDL and LDL and thus a better health performance is the first example of a phenotype and an associated genotype in humans with exceptional longevity. Hopefully, this line of research will lead us to establish which genotype is necessary (although not necessary sufficient) for a prolonged disease-free aging.},
 bibtype = {article},
 author = {Atzmon, G and Rincon, M and Rabizadeh, P and Barzilai, N},
 journal = {Mech Ageing Dev},
 number = {2}
}

@article{poplawski_polymorphisms_2005,
	title = {Polymorphisms of the {DNA} mismatch repair gene {HMSH2} in breast cancer occurence and progression},
	volume = {94},
	issn = {0167-6806},
	doi = {10.1007/s10549-005-4793-7},
	abstract = {The response of the cell to DNA damage and its ability to maintain genomic stability by DNA repair are crucial in preventing cancer initiation and progression. Therefore, polymorphism of DNA repair genes may affect the process of carcinogenesis. The importance of genetic variability of the components of mismatch repair (MMR) genes is well documented in colorectal cancer, but little is known about its role in breast cancer. hMSH2 is one of the crucial proteins of MMR. We performed a case-control study to test the association between two polymorphisms in the hMSH2 gene: an A --{\textgreater} G transition at 127 position producing an Asn --{\textgreater} Ser substitution at codon 127 (the Asn127Ser polymorphism) and a G --{\textgreater} A transition at 1032 position resulting in a Gly --{\textgreater} Asp change at codon 322 (the Gly322Asp polymorphism) and breast cancer risk and cancer progression. Genotypes were determined in DNA from peripheral blood lymphocytes of 150 breast cancer patients and 150 age-matched women (controls) by restriction fragment length polymorphism and allele-specific PCR. We did not observe any correlation between studied polymorphisms and breast cancer progression evaluated by node-metastasis, tumor size and Bloom-Richardson grading. A strong association between breast cancer occurrence and the Gly/Gly phenotype of the Gly322Asp polymorphism (odds ratio 8.39; 95\% confidence interval 1.44-48.8) was found. Therefore, MMR may play a role in the breast carcinogenesis and the Gly322Asp polymorphism of the hMSH2 gene may be considered as a potential marker in breast cancer.},
	language = {eng},
	number = {3},
	journal = {Breast Cancer Research and Treatment},
	author = {Poplawski, Tomasz and Zadrozny, Marek and Kolacinska, Agnieszka and Rykala, Jan and Morawiec, Zbigniew and Blasiak, Janusz},
	month = dec,
	year = {2005},
	pmid = {16252083},
	keywords = {Biomarkers, Tumor, Breast Neoplasms, Case-Control Studies, Cell Transformation, Neoplastic, DNA Damage, DNA Repair, Female, Genotype, Humans, Lymphocytes, Middle Aged, MutS Homolog 2 Protein, Phenotype, Point Mutation, Polymorphism, Genetic, Risk Factors, Tumor Markers, Biological},
	pages = {199--204},
}

Paper  Website  abstract   bibtex   

@article{
 title = {A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {*Genetics, Population,*Linkage Disequilibrium,African Americans/genetics,African Continental Ancestry Group/genetics,Asian Continental Ancestry Group/genetics,Chromosome Mapping,Chromosomes, Human, Pair 20,Comparative Study,European Continental Ancestry Group/genetics,Great Britain,Haplotypes,Humans,Recombination, Genetic,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.,United States},
 pages = {681-687},
 volume = {76},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15719321},
 id = {df641bec-fc57-358d-9cb4-13c6665f5e26},
 created = {2017-06-19T13:42:11.904Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:12.017Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0002-9297 (Print)<m:linebreak/>Journal Article</m:note>},
 abstract = {Large-scale studies of linkage disequilibrium (LD) have shown considerable variation in the extent and distribution of pairwise LD within and between populations. Taken at face value, these results suggest that genomewide LD maps for one population may not be generalizable to other populations. However, at least part of this diversity is due to some undesirable features of pairwise LD measures, which are well documented for the D' and r2 measures. In this report, we compare patterns of LD derived from pairwise measures with statistical estimates of population recombination rates ( rho ) along a 10-Mb stretch of chromosome 20 in four population samples, comprising East Asians, African Americans, and U.K. and U.S. individuals of western European descent. The results reveal the expected variability of D' within and between populations but show better concordance in estimates of r2 for the same markers across the population samples. Estimates of rho correlate well across populations, but there is still evidence of population-specific spikes and troughs in rho values. We conclude that it is unlikely that a single haplotype map will provide a definitive guide for association studies of many populations; rather, multiple maps will need to be constructed to provide the best-possible guides for gene mapping.},
 bibtype = {article},
 author = {Evans, D M and Cardon, L R},
 journal = {Am J Hum Genet},
 number = {4}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Mitochondrial DNA and human evolution},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {*Evolution, Molecular,DNA, Mitochondrial/*genetics,Female,Gene Dosage,Genetics, Population,Genome, Human,Humans,Male,Mutation,Recombination, Genetic,Variation (Genetics)},
 pages = {165-183},
 volume = {6},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16124858},
 edition = {2005/08/30},
 id = {78b8c248-c7aa-3681-8264-3afe319ea038},
 created = {2017-06-19T13:45:30.752Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:30.877Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Pakendorf, Brigitte<m:linebreak/>Stoneking, Mark<m:linebreak/>Review<m:linebreak/>United States<m:linebreak/>Annual review of genomics and human genetics<m:linebreak/>Annu Rev Genomics Hum Genet. 2005;6:165-83.</m:note>},
 abstract = {Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.},
 bibtype = {article},
 author = {Pakendorf, B and Stoneking, M},
 journal = {Annu Rev Genomics Hum Genet}
}

Paper  Website  abstract   bibtex   

@article{
 title = {On the meaning and existence of an effective population size.},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {Computer Simulation,Demography,Genetics, Population,Markov Chains,Models, Genetic,Models, Theoretical,Population Density,Population Dynamics,Stochastic Processes,Time Factors},
 pages = {1061-70},
 volume = {169},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1449138&tool=pmcentrez&rendertype=abstract},
 month = {2},
 id = {d902cc1f-59c2-3e7d-9a22-255af38fad85},
 created = {2017-06-19T13:41:23.890Z},
 accessed = {2012-10-24},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:24.045Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {We investigate conditions under which a model with stochastic demography or population structure converges to the coalescent with a linear change in timescale. We argue that this is a necessary condition for the existence of a meaningful effective population size. We find that such a linear timescale change is obtained when demographic fluctuations and coalescence events occur on different timescales. Simple models of population structure and randomly fluctuating population size are used to exemplify the ideas and provide an intuitive feel for the meaning of the conditions.},
 bibtype = {article},
 author = {Sjödin, P and Kaj, I and Krone, S and Lascoux, M and Nordborg, M},
 journal = {Genetics},
 number = {2}
}

@article{ holmes_early_2005,
  title = {Early life genetic, epigenetic and environmental factors shaping emotionality in rodents},
  volume = {29},
  issn = {0149-7634},
  doi = {10.1016/j.neubiorev.2005.04.012},
  abstract = {Childhood trauma is known to increase risk for emotional disorders and addiction. However, little is currently understood about the neurodevelopmental basis of these effects, or how genetic and epigenetic factors interact with the environment to shape the systems subserving emotionality. In this review, we discuss the use of rodent models of early life emotional experience to study these issues in the laboratory and present some of our pertinent findings. In rats, postnatal maternal separation can produce lasting increases in emotional behavior and stressor-reactivity, together with alterations in various brain neurotransmitter systems implicated in emotionality, including corticotropin-releasing factor, serotonin, norepinephrine, and glutamate. Genetic differences between inbred mouse strains have been exploited to further study how maternal behavior affects emotional development using techniques such as cross-fostering and generation of inter-strain hybrids. Together with our own recent data, the findings of these studies demonstrate the pervasive influence of maternal and social environments during sensitive developmental periods and reveal how genetic factors determine how these early life experiences can shape brain and behavior throughout life.},
  language = {eng},
  number = {8},
  journal = {Neuroscience and Biobehavioral Reviews},
  author = {Holmes, Andrew and le Guisquet, Anne Marie and Vogel, Elise and Millstein, Rachel A. and Leman, Samuel and Belzung, Catherine},
  year = {2005},
  pmid = {16095695},
  keywords = {Animals, Behavior, Animal, Behavioral Symptoms, Disease Models, Animal, Emotions, Environment, Epigenesis, Genetic, Rodentia},
  pages = {1335--1346}
}

Paper  doi  abstract   bibtex   

@article{muir_regulation_2004,
	title = {Regulation of {FlbD} activity by flagellum assembly is accomplished through direct interaction with the trans-acting factor, {FliX}},
	volume = {54},
	issn = {0950-382X},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15491362},
	doi = {10.1111/j.1365-2958.2004.04298.x},
	abstract = {The temporal and spatial transcription of late flagellar genes in Caulobacter crescentus is regulated by the sigma54 transcriptional activator, FlbD. One requirement for FlbD activity is the assembly of a structure encoded by early, class II flagellar genes. In this report, we show that the trans-acting factor FliX predominantly functions as a negative regulator of FlbD activity in the absence of the class II-encoded flagellar structure. In contrast, a mutant FliX that bypasses the transcriptional requirement for early flagellar assembly is incapable of repressing FlbD in a class II flagellar mutant. Expression of this mutant allele, fliX1, does not alter the temporal pattern of FlbD-dependent transcription. Remarkably, this mutation confers the correct cell cycle timing of hook operon transcription in a strain that cannot assemble the flagellum, indicating that the progression of flagellar assembly is a minor influence on temporal gene expression. Using a two-hybrid assay, we present evidence that FliX regulates FlbD through a direct interaction, a novel mechanism for this class of sigma54 transcriptional activator. Furthermore, increasing the cellular levels of FliX results in an increase in the concentration of FlbD, and a corresponding increase in FlbD-activated transcription, suggesting that FliX and FlbD form a stable complex in Caulobacter. FliX and FlbD homologues are present in several polar-flagellated bacteria, indicating that these proteins constitute an evolutionarily conserved regulatory pair in organisms where flagellar biogenesis is likely to be under control of the cell division cycle.},
	number = {3},
	urldate = {2009-10-03TZ},
	journal = {Molecular Microbiology},
	author = {Muir, Rachel E and Gober, James W},
	month = nov,
	year = {2004},
	pmid = {15491362},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Caulobacter crescentus, DNA-Binding Proteins, Dimerization, Flagella, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genes, Reporter, Membrane Proteins, Molecular Sequence Data, Mutation, Operon, Promoter Regions, Genetic, Sequence Alignment, Transcription, Genetic, Two-Hybrid System Techniques},
	pages = {715--730}
}

Paper  doi  abstract   bibtex   

@article{chen_over_2004,
	title = {Over 20\% of human transcripts might form sense-antisense pairs.},
	volume = {32},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=519112&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkh818},
	abstract = {The major challenge to identifying natural sense- antisense (SA) transcripts from public databases is how to determine the correct orientation for an expressed sequence, especially an expressed sequence tag sequence. In this study, we established a set of very stringent criteria to identify the correct orientation of each human transcript. We used these orientation-reliable transcripts to create 26 741 transcription clusters in the human genome. Our analysis shows that 22\% (5880) of the human transcription clusters form SA pairs, higher than any previous estimates. Our orientation-specific RT-PCR results along with the comparison of experimental data from previous studies confirm that our SA data set is reliable. This study not only demonstrates that our criteria for the prediction of SA transcripts are efficient, but also provides additional convincing data to support the view that antisense transcription is quite pervasive in the human genome. In-depth analyses show that SA transcripts have some significant differences compared with other types of transcripts, with regard to chromosomal distribution and Gene Ontology-annotated categories of physiological roles, functions and spatial localizations of gene products.},
	number = {16},
	journal = {Nucleic acids research},
	author = {Chen, Jianjun and Sun, Miao and Kent, W James and Huang, Xiaoqiu and Xie, Hanqing and Wang, Wenquan and Zhou, Guolin and Shi, Run Zhang and Rowley, Janet D},
	month = jan,
	year = {2004},
	pmid = {15356298},
	keywords = {Antisense, Antisense: analysis, Antisense: chemistry, Antisense: genetics, Base Pairing, Chromosomes, Genetic, Genome, Human, Humans, Messenger, Messenger: chemistry, RNA, Reverse Transcriptase Polymerase Chain Reaction, Transcription},
	pages = {4812--20}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Understanding human DNA sequence variation},
 type = {article},
 year = {2004},
 identifiers = {[object Object]},
 keywords = {*Base Sequence,*Genetic Variation,*Genetics, Population,*Models, Biological,Demography,Gene Frequency,Genetics/history/*trends,Geography,Haplotypes/genetics,Heterozygote Detection,History, 20th Century,History, 21st Century,Humans,Polymorphism, Genetic},
 pages = {406-420},
 volume = {95},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15388768},
 edition = {2004/09/25},
 id = {7dff6a8d-4751-36dd-847d-0b01133760d1},
 created = {2017-06-19T13:42:58.571Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:58.728Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Kidd, K K<m:linebreak/>Pakstis, A J<m:linebreak/>Speed, W C<m:linebreak/>Kidd, J R<m:linebreak/>AA09379/AA/NIAAA NIH HHS/United States<m:linebreak/>GM57672/GM/NIGMS NIH HHS/United States<m:linebreak/>MH62495/MH/NIMH NIH HHS/United States<m:linebreak/>Historical Article<m:linebreak/>Research Support, Non-U.S. Gov't<m:linebreak/>Research Support, U.S. Gov't, Non-P.H.S.<m:linebreak/>Research Support, U.S. Gov't, P.H.S.<m:linebreak/>Review<m:linebreak/>United States<m:linebreak/>The Journal of heredity<m:linebreak/>95/5/406<m:linebreak/>J Hered. 2004 Sep-Oct;95(5):406-20.</m:note>},
 abstract = {Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different populations and the species as a whole, among other studies. With the advent of DNA-based markers in the last quarter century, these studies have accelerated. One of the challenges for the next century is to understand that variation. One component of that understanding will be population genetics. We present here examples of many of the ways these new data can be analyzed from a population perspective using results from our laboratory on multiple individual DNA-based polymorphisms, many clustered in haplotypes, studied in multiple populations representing all major geographic regions of the world. These data support an "out of Africa" hypothesis for human dispersal around the world and begin to refine the understanding of population structures and genetic relationships. We are also developing baseline information against which we can compare findings at different loci to aid in the identification of loci subject, now and in the past, to selection (directional or balancing). We do not yet have a comprehensive understanding of the extensive variation in the human genome, but some of that understanding is coming from population genetics.},
 bibtype = {article},
 author = {Kidd, K K and Pakstis, A J and Speed, W C and Kidd, J R},
 journal = {J Hered},
 number = {5}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Transmission-ratio distortion and allele sharing in affected sib pairs: a new linkage statistic with reduced bias, with application to chromosome 6q25.3.},
 type = {article},
 year = {2004},
 identifiers = {[object Object]},
 keywords = {Algorithms,Alleles,Asthma,Asthma: genetics,Chromosome Mapping,Chromosome Mapping: methods,Chromosomes, Human, Pair 6,Chromosomes, Human, Pair 6: genetics,Genetic Linkage,Genetic Testing,Genetic Testing: methods,Humans,Inheritance Patterns,Inheritance Patterns: genetics,Models, Genetic,Pedigree,Research Design,Siblings},
 pages = {571-86},
 volume = {75},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1182045&tool=pmcentrez&rendertype=abstract},
 month = {10},
 id = {1db8b300-5a3e-3674-a29e-86a5aef444a2},
 created = {2017-06-19T13:46:39.022Z},
 accessed = {2011-06-01},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:39.257Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {We studied the effect of transmission-ratio distortion (TRD) on tests of linkage based on allele sharing in affected sib pairs. We developed and implemented a discrete-trait allele-sharing test statistic, Sad, analogous to the Spairs test statistic of Whittemore and Halpern, that evaluates an excess sharing of alleles at autosomal loci in pairs of affected siblings, as well as a lack of sharing in phenotypically discordant relative pairs, where available. Under the null hypothesis of no linkage, nuclear families with at least two affected siblings and one unaffected sibling have a contribution to Sad that is unbiased, with respect to the effects of TRD independent of the disease under study. If more distantly related unaffected individuals are studied, the bias of Sad is generally reduced compared with that of Spairs, but not completely. Moreover, Sad has higher power, in some circumstances, because of the availability of unaffected relatives, who are ignored in affected-only analyses. We discuss situations in which it may be an efficient use of resources to genotype unaffected relatives, which would give insights for promising study designs. The method is applied to a sample of pedigrees ascertained for asthma in a chromosomal region in which TRD has been reported. Results are consistent with the presence of transmission distortion in that region.},
 bibtype = {article},
 author = {Lemire, Mathieu and Roslin, Nicole M and Laprise, Catherine and Hudson, Thomas J and Morgan, Kenneth},
 journal = {American journal of human genetics},
 number = {4}
}

Website  abstract   bibtex   

@article{
 title = {Genetic factors in longevity},
 type = {article},
 year = {2003},
 identifiers = {[object Object]},
 keywords = {*Polymorphism,Aged,Apolipoproteins E/genetics,English Abstract,Environment,Genetic,Genetic Markers,Humans,Longevity/*genetics,Middle Aged,Twin Studies},
 pages = {365-369},
 volume = {32},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12712685},
 id = {362160a5-7ac7-38b4-a59b-5cbf995c24d1},
 created = {2017-06-19T13:43:48.429Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:43:48.541Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0755-4982<m:linebreak/>Journal Article</m:note>},
 abstract = {TO IDENTIFY THE GENETIC FACTORS: Family and twin studies showed that longevity results from the interaction of genetic and environmental factors. Despite progress the performed made in the study of animal models highlighting some interesting metabolic pathways, characterization of genetic factors remains difficult in human beings. Two genetic approaches are currently available: association studies and sib-pair analyses. ASSOCIATION STUDIES: The first method is based on the comparison of polymorphism repartitions on candidate genes in two matched populations of old people and young controls. SIB-PAIR ANALYSES: The second requires genotyping of brothers and/or sisters on a set of highly polymorphic markers, in order to identify new candidate regions on the genome. APOE: Until now, the only gene that remains clearly associated with longevity is the Apolipoprotein E gene.},
 bibtype = {article},
 author = {Blanche, H},
 journal = {Presse Med},
 number = {8}
}

Paper  abstract   bibtex   

@article{
 title = {Identification of multiple loci for Alzheimer disease in a consanguineous Israeli-Arab community},
 type = {article},
 year = {2003},
 identifiers = {[object Object]},
 keywords = {Aged,Aged, 80 and over,Alleles,Alzheimer Disease/*genetics,Arabs,Chromosome Mapping,Chromosomes, Human, Pair 10,Chromosomes, Human, Pair 12,Chromosomes, Human, Pair 2,Chromosomes, Human, Pair 9,Consanguinity,Dementia, Vascular/*genetics,Female,Gene Frequency,Genetic Markers,Genome, Human,Genotype,Heterozygote,Homozygote,Human,Israel,Linkage (Genetics),Lod Score,Male,Models, Genetic,Sequence Analysis, DNA,Support, Non-U.S. Gov't,Support, U.S. Gov't, P.H.S.},
 pages = {415-422},
 volume = {12},
 id = {cf9eab61-8a7f-38db-bc5f-f874a28d4f14},
 created = {2017-06-19T13:42:46.336Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:46.466Z},
 tags = {04/01/19},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article</m:note>},
 abstract = {We have observed an unusually high prevalence of dementia of the Alzheimer type (DAT) in Wadi Ara, an inbred Arab community in northern Israel comprising approximately 850 persons over the age of 60 years. Family studies revealed that more than one-third of the DAT cases are members of one hamula (tribal group) within Wadi Ara. To map chromosomal loci contributing to DAT susceptibility, we conducted a 10 cM scan in a series of five cases and five controls selected from this hamula. Markers from 18 chromosomal regions showed significant allelic association with DAT (P<0.05). Locations on chromosomes 2, 9 and 10 remained significant after testing additional affected and non-demented individuals. Significant associations were also observed for markers on chromosome 12 which overlap with a locus implicated in previous genome scans. Analysis of allele frequency distributions for 12 markers spanning 20 cM on chromosome 9 narrowed the possible location of an DAT susceptibility gene to a 13 cM interval between D9S157 and D9S259 (most significant result: P = 2.3 x 10(-7)). Analysis of 14 markers spanning 24 cM on chromosome 12 narrowed the possible location to a 14 cM interval distal to the LRP1 locus (most significant result: P = 1.3 x 10(-6)). Evidence for linkage on chromosome 9 stemmed primarily from excess homozygosity of marker alleles in cases compared with controls, suggesting that the gene at this location behaves in either a recessive or additive fashion. The unique characteristics of this community together with the emergent human genome data should allow for the rapid identification of DAT genes in these candidate regions.},
 bibtype = {article},
 author = {Farrer, L A and Bowirrat, A and Friedland, R P and Waraska, K and Korczyn, A D and Baldwin, C T},
 journal = {Hum Mol Genet},
 number = {4}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity.},
 type = {article},
 year = {2003},
 identifiers = {[object Object]},
 keywords = {Africa,Africa: ethnology,Alleles,Base Sequence,Chromosomes, Human,Chromosomes, Human: genetics,Dystrophin,Dystrophin: genetics,Evolution, Molecular,Genetic Variation,Genetic Variation: genetics,Geography,Haplotypes,Haplotypes: genetics,Humans,Microsatellite Repeats,Microsatellite Repeats: genetics,Molecular Sequence Data,Mosaicism,Mosaicism: genetics,Phylogeny,Polymorphism, Genetic,Polymorphism, Genetic: genetics,Recombination, Genetic,Recombination, Genetic: genetics},
 pages = {994-1015},
 volume = {73},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1180505&tool=pmcentrez&rendertype=abstract},
 month = {11},
 id = {9852212f-264c-3ef8-bd90-603a7eca798e},
 created = {2017-06-19T13:41:12.157Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:12.279Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Although Africa has played a central role in human evolutionary history, certain studies have suggested that not all contemporary human genetic diversity is of recent African origin. We investigated 35 simple polymorphic sites and one T(n) microsatellite in an 8-kb segment of the dystrophin gene. We found 86 haplotypes in 1,343 chromosomes from around the world. Although a classical out-of-Africa topology was observed in trees based on the variant frequencies, the tree of haplotype sequences reveals three lineages accounting for present-day diversity. The proportion of new recombinants and the diversity of the T(n) microsatellite were used to estimate the age of haplotype lineages and the time of colonization events. The lineage that underwent the great expansion originated in Africa prior to the Upper Paleolithic (27,000-56,000 years ago). A second group, of structurally distinct haplotypes that occupy a central position on the tree, has never left Africa. The third lineage is represented by the haplotype that lies closest to the root, is virtually absent in Africa, and appears older than the recent out-of-Africa expansion. We propose that this lineage could have left Africa before the expansion (as early as 160,000 years ago) and admixed, outside of Africa, with the expanding lineage. Contemporary human diversity, although dominated by the recently expanded African lineage, thus represents a mosaic of different contributions.},
 bibtype = {article},
 author = {Zietkiewicz, Ewa and Yotova, Vania and Gehl, Dominik and Wambach, Tina and Arrieta, Isabel and Batzer, Mark and Cole, David E C and Hechtman, Peter and Kaplan, Feige and Modiano, David and Moisan, Jean-Paul and Michalski, Roman and Labuda, Damian},
 journal = {American journal of human genetics},
 number = {5}
}

Paper  abstract   bibtex   

@article{
 title = {Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Pedigree,Algorithms,Alleles,Bayes Theorem,Bias (Epidemiology),Case-Control Studies,Chromosome Mapping/*methods/statistics & numerical,Computer Simulation,Cystic Fibrosis Transmembrane Conductance Regulato,Cystic Fibrosis/*genetics,Female,Genetic Heterogeneity,Genetic Markers/genetics,Haplotypes/genetics,Human,Linkage Disequilibrium/genetics,Male,Markov Chains,Models, Genetic,Monte Carlo Method,Mutation/genetics,Phylogeny,Probability,Recombination, Genetic/genetics,Sequence Deletion,Support, Non-U.S. Gov't},
 pages = {686-707.},
 volume = {70},
 id = {b7168238-9085-3a82-81a6-a75268e0c428},
 created = {2017-06-19T13:42:46.478Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:46.621Z},
 tags = {02/04/26},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {We present a Bayesian, Markov-chain Monte Carlo method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. The method explicitly models the genealogy underlying a sample of case chromosomes in the vicinity of a putative disease locus, in contrast with the assumption of a star-shaped tree made by many existing multipoint methods. Within this modeling framework, we can allow for missing marker information and for uncertainty about the true underlying genealogy and the makeup of ancestral marker haplotypes. A crucial advantage of our method is the incorporation of the shattered coalescent model for genealogies, allowing for multiple founding mutations at the disease locus and for sporadic cases of disease. Output from the method includes approximate posterior distributions of the location of the disease locus and population-marker haplotype proportions. In addition, output from the algorithm is used to construct a cladogram to represent genetic heterogeneity at the disease locus, highlighting clusters of case chromosomes sharing the same mutation. We present detailed simulations to provide evidence of improvements over existing methodology. Furthermore, inferences about the location of the disease locus are shown to remain robust to modeling assumptions.},
 bibtype = {article},
 author = {Morris, A P and Whittaker, J C and Balding, D J},
 journal = {Am J Hum Genet},
 number = {3}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {Arabs,Arabs: genetics,Chromosomes,Egypt,Emigration and Immigration,Emigration and Immigration: statistics & numerical,Gene Frequency,Gene Frequency: genetics,Genetic,Genetic Variation,Genetic Variation: genetics,Genetic: genetics,Genetics,Geography,Haplotypes,Haplotypes: genetics,Human,Humans,Morocco,Multivariate Analysis,Polymorphism,Population,Transients and Migrants,Transients and Migrants: statistics & numerical da,Y,Y: genetics},
 pages = {645-658},
 volume = {74},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/12495079},
 month = {10},
 id = {685d43bb-d61c-37f1-bdce-b022d0e2e246},
 created = {2017-06-19T13:42:00.980Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:01.135Z},
 tags = {03/05/15},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>        <m:bold>From Duplicate 1 ( </m:bold>        <m:bold>          </m:bold><m:bold><m:italic>Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa</m:italic></m:bold><m:bold>        </m:bold>        <m:bold> - Manni, F; Leonardi, P; Barakat, A; Rouba, H; Heyer, E; Klintschar, M; McElreavey, K; Quintana-Murci, L )<m:linebreak/>        </m:bold>        <m:linebreak/>Journal Article<m:linebreak/>        <m:linebreak/>      </m:note>},
 abstract = {The geographic location of Egypt, at the interface between North Africa, the Middle East, and southern Europe, prompted us to investigate the genetic diversity of this population and its relationship with neighboring populations. To assess the extent to which the modern Egyptian population reflects this intermediate geographic position, ten Unique Event Polymorphisms (UEPs), mapping to the nonrecombining portion of the Y chromosome, have been typed in 164 Y chromosomes from three North African populations. The analysis of these binary markers, which define 11 Y-chromosome lineages, were used to determine the haplogroup frequencies in Egyptians, Moroccan Arabs, and Moroccan Berbers and thereby define the Y-chromosome background in these regions. Pairwise comparisons with a set of 15 different populations from neighboring European, North African, and Middle Eastern populations and geographic analysis showed the absence of any significant genetic barrier in the eastern part of the Mediterranean area, suggesting that genetic variation and gene flow in this area follow the "isolation-by-distance" model. These results are in sharp contrast with the observation of a strong north-south genetic barrier in the western Mediterranean basin, defined by the Gibraltar Strait. Thus, the Y-chromosome gene pool in the modern Egyptian population reflects a mixture of European, Middle Eastern, and African characteristics, highlighting the importance of ancient and recent migration waves, followed by gene flow, in the region.},
 bibtype = {article},
 author = {Manni, Franz and Leonardi, Pascal and Barakat, Abdelhamid and Rouba, Hassan and Heyer, Evelyne and Klintschar, Michael and McElreavey, Ken and Quintana-Murci, Lluís},
 journal = {Human biology},
 number = {5}
}

@article{breitbart_genomic_2002,
	title = {Genomic analysis of uncultured marine viral communities},
	volume = {99},
	issn = {0027-8424},
	doi = {10.1073/pnas.202488399},
	abstract = {Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65\% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3\% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.},
	language = {eng},
	number = {22},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Breitbart, Mya and Salamon, Peter and Andresen, Bjarne and Mahaffy, Joseph M. and Segall, Anca M. and Mead, David and Azam, Farooq and Rohwer, Forest},
	month = oct,
	year = {2002},
	pmid = {12384570},
	pmcid = {PMC137870},
	keywords = {Bacteriophages, Base Sequence, DNA Viruses, DNA, Viral, Genetic Variation, Models, Genetic, Molecular Sequence Data, Phycodnaviridae, Seawater},
	pages = {14250--14255}
}

Paper  bibtex   

@article{
 title = {Human mutation--blame (mostly) men},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Mutation,Animal,Comparative Study,DNA/genetics,Evolution,Female,Genetic,Human,Male,Models,Molecular,Polymorphism (Genetics),Primates/genetics,RNA-Binding Proteins/genetics,X Chromosome/*genetics,Y Chromosome/*genetics},
 pages = {9-10.},
 volume = {31},
 id = {61983c7d-2056-316b-bd71-9cf44d9c9a9e},
 created = {2017-06-19T13:42:10.378Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:10.525Z},
 tags = {02/06/17},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>News</m:note>},
 bibtype = {article},
 author = {Ellegren, H},
 journal = {Nat Genet},
 number = {1}
}

Paper  abstract   bibtex   

@article{
 title = {Intrinsic and extrinsic contributions to stochasticity in gene expression.},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {Biophysical Phenomena,Biophysics,Escherichia coli,Escherichia coli: metabolism,Gene Expression Regulation,Genetic,Messenger,Messenger: metabolism,Models,Protein Biosynthesis,RNA,Theoretical,Time Factors,Transcription},
 pages = {12795-12800},
 volume = {99},
 id = {009fc879-22c6-3763-bc9b-659156a1c497},
 created = {2015-08-20T10:31:21.000Z},
 file_attached = {true},
 profile_id = {1593dc7b-4550-3536-a5a4-21ffd4cbffb8},
 group_id = {9cd45c01-6b67-3572-a936-df749337a5f1},
 last_modified = {2015-08-20T10:42:27.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Swain2002},
 abstract = {Gene expression is a stochastic, or "noisy," process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates "intrinsic" noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent "extrinsic" noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than approximately 2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable-a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.},
 bibtype = {article},
 author = {Swain, Peter S and Elowitz, Michael B and Siggia, Eric D},
 journal = {Proceedings of the National Academy of Sciences of the United States of America},
 number = {20}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Evolutionary and statistical properties of three genetic distances},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Evolution, Molecular,*Genetics, Population,Computer Simulation,Models, Genetic,Mutation},
 pages = {1263-1273},
 volume = {11},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12144649},
 edition = {2002/07/30},
 id = {45ffbee5-04e5-36be-85f2-5ddcbdfff387},
 created = {2017-06-19T13:42:46.622Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:46.787Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Kalinowski, Steven T<m:linebreak/>Review<m:linebreak/>England<m:linebreak/>Molecular ecology<m:linebreak/>1520<m:linebreak/>Mol Ecol. 2002 Aug;11(8):1263-73.</m:note>},
 abstract = {Many genetic distances have been developed to summarize allele frequency differences between populations. I review the evolutionary and statistical properties of three popular genetic distances: DS, DA, and theta;, using computer simulation of two simple evolutionary histories: an isolation model of population divergence and an equilibrium migration model. The effect of effective population size, mutation rate, and mutation mechanism upon the parametric value between pairs of populations in these models explored, and the unique properties of each distance are described. The effect of these evolutionary parameters on study design is also investigated and similar results are found for each genetic distance in each model of evolution: large sample sizes are warranted when populations are relatively genetically similar; and loci with more alleles produce better estimates of genetic distance.},
 bibtype = {article},
 author = {Kalinowski, S T},
 journal = {Mol Ecol},
 number = {8}
}

Website  abstract   bibtex   

@article{
 title = {A case-only approach for assessing gene by sex interaction in human longevity},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Epidemiologic Methods,*Models, Genetic,*Sex Characteristics,Aged,Cardiovascular Diseases/genetics,Female,Gene Frequency,HLA-DR7 Antigen/genetics,Humans,Longevity/*genetics,Male,Polymorphism, Genetic/physiology},
 pages = {B129-33},
 volume = {57},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11909876},
 id = {f70dbc19-9f0f-34a3-b7dc-8132561a739e},
 created = {2017-06-19T13:42:59.230Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:59.316Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>1079-5006<m:linebreak/>Journal Article</m:note>},
 abstract = {As one aspect of the complex feature of longevity, gene by sex interaction plays an important role in influencing human life span. With advances in molecular genetics, more studies aimed at assessing gene by sex interaction are expected. New and valid statistical methods are needed. In this article, we introduce a nontraditional approach, the case-only design, which was originally proposed for assessing gene and disease associations, to detect gene by sex interaction in human longevity. Applications of this method to data collected from centenarian studies show that it can produce consistent results as compared with results obtained from case-control and other approaches. The method cannot be used as a substitute for traditional case-control studies since it is limited to the detection of interactions only. However, the easily applicable case-only approach can be an important tool for screening many potential genes that contribute to human longevity.},
 bibtype = {article},
 author = {Tan, Q and Yashin, A I and Bladbjerg, E M and de Maat, M P and Andersen-Ranberg, K and Jeune, B and Christensen, K and Vaupel, J W},
 journal = {J Gerontol A Biol Sci Med Sci},
 number = {4}
}

@Article{Hood_2002_1342,
  author = {Hood, J. D. and Bednarski, M. and Frausto, R. and Guccione, S. and Reisfeld, R. A. and Xiang, R. and Cheresh, D. A.},
 journal = {Science},
 note = {Ca50286/ca/nci P41 rr09784/rr/ncrr T32 ca09696/ca/nci Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United States},
 number = {5577},
 pages = {2404-7},
 title = {Tumor regression by targeted gene delivery to the neovasculature},
 volume = {296},
 year = {2002},
 keywords = {Adenosine, Triphosphate/metabolism, Animals, Apoptosis, Cations, Endothelium, Vascular/cytology/metabolism/pathology, Gene, Targeting, Gene, Therapy/*methods, Gene, Transfer, Techniques, Genetic, Vectors, Humans, In, Situ, Nick-End, Labeling, Ligands, Lipids, Melanoma, Experimental/blood, supply/pathology/therapy, Mice, Mice, Inbred, BALB, C, Mutation, *Nanotechnology, Neoplasm, Metastasis, Neoplasm, Transplantation, Neoplasms, Experimental/blood, supply/pathology/*therapy, Neovascularization, Pathologic/pathology/*therapy, Proto-Oncogene, Proteins, c-raf/*genetics/metabolism, Random, Allocation, Receptors, Vitronectin/*metabolism, Tumor, Cells, Cultured},
 title_with_no_special_chars = {Tumor regression by targeted gene delivery to the neovasculature}
}

Paper  abstract   bibtex   

@article{
 title = {Detecting recombination in TT virus: a phylogenetic approach},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Phylogeny,*Recombination, Genetic,DNA, Viral/genetics,Evolution, Molecular,Support, Non-U.S. Gov't,Transfusion-Transmitted Virus/*genetics,Variation (Genetics),Viral Proteins/genetics},
 pages = {563-572},
 volume = {55},
 id = {07b0de60-3014-3ec3-b731-f0bdc6769cc5},
 created = {2017-06-19T13:44:32.858Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:33.014Z},
 tags = {03/05/15},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article</m:note>},
 abstract = {TT virus (TTV) has a remarkable genetic heterogeneity. To study TTV evolution, phylogenetic analyses were performed on 739 DNA sequences mapping in the N22 region of ORF1. Analysis of neighbor-joining consensus trees shows significant differences between DNA and protein phylogeny. Median joining networks phylogenetic clustering indicates that DNA sequence analysis is biased by homoplasy (i.e., genetic variability not originated by descent), indicative of either hypermutation or recombination. Statistical analysis shows that the significant excess of homoplasy is due to frequent recombination among closely related strains. Recombination events imply that the transmission of TTV is not clonal and provide the necessary basis to explain (i) the high degree of genetic divergence between TTV isolates, (ii) the lack of population structure on a world scale, and (iii) the number of highly divergent strains that seems typical of this virus. We show that recombination phenomena can be detected by phylogenetic analyses in very short sequences when a sufficiently large data set is available.},
 bibtype = {article},
 author = {Manni, F and Rotola, A and Caselli, E and Bertorelle, G and Di Luca, D},
 journal = {J Mol Evol},
 number = {5}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Genomewide scans of complex human diseases: true linkage is hard to find.},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {Asthma,Asthma: genetics,Chromosome Mapping,Databases, Genetic,Diabetes Mellitus, Type 2,Diabetes Mellitus, Type 2: genetics,Disease,Genetic Linkage,Genetic Linkage: genetics,Genome, Human,Humans,Multifactorial Inheritance,Multifactorial Inheritance: genetics,Regression Analysis},
 pages = {936-50},
 volume = {69},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1274370&tool=pmcentrez&rendertype=abstract},
 month = {11},
 id = {5d3be54c-8b02-31dc-a3b4-3edb22218ebf},
 created = {2017-06-19T13:41:50.038Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:50.188Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Many "complex" human diseases, which involve multiple genetic and environmental determinants, have increased in incidence during the past 2 decades. During the same time period, considerable effort and expense have been expended in whole-genome screens aimed at detection of genetic loci contributing to the susceptibility to complex human diseases. However, the success of positional cloning attempts based on whole-genome screens has been limited, and many of the fundamental questions relating to the genetic epidemiology of complex human disease remain unanswered. Both to review the success of the positional cloning paradigm as applied to complex human disease and to investigate the characteristics of the whole-genome scans undertaken to date, we created a database of 101 studies of complex human disease, which were found by a systematic Medline search (current as of December 2000). We compared these studies, concerning 31 different human complex diseases, with regard to design, methods, and results. The "significance" categorizations proposed by Lander and Kruglyak were used as criteria for the "success" of a study. Most (66.3% [n=67]) of the studies did not show "significant" linkage when the criteria of Lander and Kruglyak (1995) were used, and the results of studies of the same disease were often inconsistent. Our analyses suggest that no single study design consistently produces more-significant results. Multivariate analysis suggests that the only factors independently associated with increased study success are (a) an increase in the number of individuals studied and (b) study of a sample drawn from only one ethnic group. Positional cloning based on whole-genome screens in complex human disease has proved more difficult than originally had been envisioned; detection of linkage and positional cloning of specific disease-susceptibility loci remains elusive.},
 bibtype = {article},
 author = {Altmüller, J and Palmer, L J and Fischer, G and Scherb, H and Wjst, M},
 journal = {American journal of human genetics},
 number = {5}
}

Paper  abstract   bibtex   

@article{
 title = {After BRCA1 and BRCA2-what next? Multifactorial segregation analyses of three-generation, population-based Australian families affected by female breast cancer},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {Age Factors,Age of Onset,Australia,BRCA1 Protein/*genetics,BRCA2 Protein,Breast Neoplasms/*genetics,Cohort Studies,Family Health,Female,Heterozygote,Human,Male,Models, Genetic,Molecular Sequence Data,Mutation,Neoplasm Proteins/*genetics,Pedigree,Probability,Risk Factors,Statistics,Support, Non-U.S. Gov't,Support, U.S. Gov't, P.H.S.,Transcription Factors/*genetics},
 pages = {420-31.},
 volume = {68},
 id = {23f12ce0-3889-312a-be6e-926c320ad4f9},
 created = {2017-06-19T13:45:18.919Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:19.048Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {Mutations in BRCA1 and BRCA2 that cause a dominantly inherited high risk of female breast cancer seem to explain only a small proportion of the aggregation of the disease. To study the possible additional genetic components, we conducted single-locus and two-locus segregation analyses, with and without a polygenic background, using three-generation families ascertained through 858 women with breast cancer diagnosed at age <40 years, ascertained through population cancer registries in Melbourne and Sydney, Australia. Extensive testing for deleterious mutations in BRCA1 and BRCA2, to date, has identified 34 carriers. Our analysis suggested that, after other possible unmeasured familial factors are adjusted for and the known BRCA1 and BRCA2 mutation carriers are excluded, there appears to be a residual dominantly inherited risk of female breast cancer in addition to that derived from mutations in BRCA1 and BRCA2. This study also suggests that there is a substantial recessively inherited risk of early-onset breast cancer. According to the best-fitting model, after excluding known carriers of mutations in BRCA1 and BRCA2, about 1/250 (95% confidence interval [CI] 1/500 to 1/125) women have a recessive risk of 86% (95% CI 69%-100%) by age 50 years and of almost 100% by age 60 years. Possible reasons that our study has implicated a novel strong recessive effect include our inclusion of data on lineal aunts and grandmothers, study of families ascertained through women with early-onset breast cancer, allowance for multiple familial factors in the analysis, and removal of families for whom the cause (i.e., BRCA1 or BRCA2) is known. Our findings may have implications for attempts to identify new breast cancer-susceptibility genes.},
 bibtype = {article},
 author = {Cui, J and Antoniou, A C and Dite, G S and Southey, M C and Venter, D J and Easton, D F and Giles, G G and McCredie, M R and Hopper, J L},
 journal = {Am J Hum Genet},
 number = {2}
}

Website  abstract   bibtex   

@article{
 title = {Replication studies in longevity: puzzling findings in Danish centenarians at the 3'APOB-VNTR locus},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {Adult,Aged,Aged, 80 and over,Alleles,Apolipoproteins B/*genetics,Comparative Study,DNA/analysis/genetics,Demography,Denmark,Female,Gene Frequency/genetics,Genotype,Humans,Italy,Longevity/*genetics,Male,Middle Aged,Minisatellite Repeats/*genetics,Models, Genetic,Polymerase Chain Reaction,Research Support, Non-U.S. Gov't,Risk,Sex Characteristics},
 pages = {371-376},
 volume = {65},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11592926},
 id = {30365bd9-8031-3f7e-8ef2-9d02c1ab8dba},
 created = {2017-06-19T13:45:42.031Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:42.142Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0003-4800<m:linebreak/>Journal Article</m:note>},
 abstract = {In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20-64-year-old subjects. However, when Danish and Italian data were compared, a significant difference (p = 0.0004) was found between the frequencies of Small alleles in youths, which disappeared in centenarians (p = 0.290). Furthermore, the demographic-genetic approach revealed in Danes a significant gene-sex interaction relevant to Long alleles (more than 37 repeats). The different findings in Denmark and Italy suggest that gene/longevity associations are population-specific, and heavily affected by the population-specific genetic and environmental history.},
 bibtype = {article},
 author = {Varcasia, O and Garasto, S and Rizza, T and Andersen-Ranberg, K and Jeune, B and Bathum, L and Andreev, K and Tan, Q and Yashin, A I and Bonafe, M and Franceschi, C and De Benedictis, G},
 journal = {Ann Hum Genet},
 number = {Pt 4}
}

Paper  bibtex   

@article{
 title = {Protecting Against Bad Air},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {*Agriculture,*Glucosephosphate Dehydrogenase Deficiency/epidemi,*Variation (Genetics),Animal,Child,Erythrocytes/enzymology/parasitology,Evolution,Falciparum/*enzymology/epidemiology/*gene,Genetic,Glucosephosphate Dehydrogenase/blood/*genetics/met,Haplotypes,Human,Immunity,Malaria,Microsatellite Repeats,Models,Natural/genetics,Plasmodium falciparum/physiology,Polymorphism,Polymorphism (Genetics),Prevalence,Restriction Fragment Length,Selection (Genetics)},
 pages = {442-443},
 volume = {293},
 id = {e244ac6a-cafa-3de1-81ae-e83092bdc695},
 created = {2017-06-19T13:42:01.571Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:01.713Z},
 tags = {03/03/18},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>        <m:bold>From Duplicate 1 ( </m:bold>                <m:bold>          </m:bold><m:bold><m:italic>Malaria. Protecting against bad air</m:italic></m:bold><m:bold>        </m:bold>                <m:bold> - Luzzatto, L; Notaro, R )<m:linebreak/>        </m:bold>        <m:linebreak/>eng<m:linebreak/>Comment<m:linebreak/>Journal Article<m:linebreak/>        <m:linebreak/>      </m:note>},
 bibtype = {article},
 author = {Luzzatto, Lucio and Notaro, Rosario},
 journal = {Science},
 number = {July}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Increase of homozygosity in centenarians revealed by a new inter-Alu PCR technique},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {*Alu Elements,*Polymorphism, Genetic,Aged,Aged, 80 and over,Aging/*genetics,Heterozygote,Humans,Polymerase Chain Reaction/*methods,Research Support, Non-U.S. Gov't},
 pages = {1063-1073},
 volume = {36},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11404051},
 id = {3addbdbb-c5bc-347b-a722-ebeb1352f751},
 created = {2017-06-19T13:44:33.100Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:33.285Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0531-5565<m:linebreak/>Journal Article</m:note>},
 abstract = {In the present study a novel inter-Alu PCR technique that allows one to detect inter-individual differences in the genomic regions flanked by Alu repetitive sequences was developed. Two primers complementary to sequences present in different Alu repeats and marked with two different fluorochromes were used in the same PCR reaction, and the PCR products were separated and analyzed by capillary electrophoresis using an automatic sequencer. The method is highly reliable, and three patterns of peaks (QM376-400, QM780-790 and QM480) appeared to be representative for germ-line polymorphisms, as suggested by the results obtained in nine couples of monozygotic twins and four three-generation families. The frequency of these polymorphic peaks was studied in two different age groups (100 young subjects and 69 centenarians). In two out of the three regions (QM376-400 and QM480) a significant increase in homozygote genotypes frequency was observed in centenarians. These counterintuitive results suggest that increased homozygosity contributes to human longevity. This novel inter-Alu PCR approach could represent a valuable tool to identify longevity-associated DNA sequences interspersed throughout human genome, without making any a priori assumption about their nature and function.},
 bibtype = {article},
 author = {Bonafe, M and Cardelli, M and Marchegiani, F and Cavallone, L and Giovagnetti, S and Olivieri, F and Lisa, R and Pieri, C and Franceschi, C},
 journal = {Exp Gerontol},
 number = {7}
}

Paper  abstract   bibtex   

@article{
 title = {Detecting association in a case-control study while correcting for population stratification},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {*Case-Control Studies,*Selection Bias,Chromosome Mapping/*statistics & numerical data,Ethnic Groups/*statistics & numerical data,Gene Frequency,Human,Linkage Disequilibrium,Models, Genetic,Polymorphism, Single Nucleotide/*genetics,Support, Non-U.S. Gov't},
 pages = {4-16.},
 volume = {20},
 id = {530b08ff-e5bc-39f0-8050-9dce4c0ec9ca},
 created = {2017-06-19T13:45:09.287Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:09.471Z},
 tags = {02/11/15},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 abstract = {Case-control studies are subject to the problem of population stratification, which can occur in ethnically mixed populations and can lead to significant associations being detected at loci that have nothing to do with disease. Here, we describe a way to measure and correct for stratification by genotyping a moderate number of unlinked genetic markers in the same set of cases and controls in which a candidate association was found. The average of association statistics across the markers directly measures stratification. By dividing the candidate association statistic by this average, a P-value can be obtained that corrects for stratification.},
 bibtype = {article},
 author = {Reich, D E and Goldstein, D B},
 journal = {Genet Epidemiol},
 number = {1}
}

@article{
 title = {Gene-environment interaction and affected sib pair linkage analysis},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {*Genetic Techniques,*Statistics,Chromosome Mapping/methods,Chromosomes, Human,Computer Simulation,Environment,Family Characteristics,Human,Linkage (Genetics)/*genetics,Models, Genetic,Models, Statistical,Research Design,Sample Size,Software,Support, U.S. Gov't, P.H.S.},
 pages = {34-46.},
 volume = {52},
 id = {f5da3546-996f-3a85-b422-945d0b2bd58d},
 created = {2017-06-19T13:42:47.084Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:47.168Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {OBJECTIVES: Gene-environment (GxE) interaction influences risk for many complex disease traits. However, genome screens using affected sib pair linkage techniques are typically conducted without regard for GxE interaction. We propose a simple extension of the commonly used mean test and evaluate its power for several forms of GxE interaction. METHODS: We compute expected IBD sharing by sibling exposure profile, that is by whether two sibs are exposed (EE), unexposed (UU), or are discordant for exposure (EU). We describe a simple extension of the mean test, the "mean-interaction" test that utilizes heterogeneity in IBD sharing across EE, EU, and UU sib pairs in a test for linkage. RESULTS: The mean-interaction test provides greater power than the mean test for detecting linkage in the presence of moderate or strong GxE interaction, typically when the interaction relative risk (R(ge)) exceeds 3 or is less than 1/3. In the presence of strong interaction (R(ge) = 10), the required number of affected sib pairs to achieve 80% power for detecting linkage is approximately 30% higher when the environmental factor is ignored in the mean test, than when it is utilized in the mean-interaction test. CONCLUSION: Linkage methods that incorporate environmental data and allow for interaction can lead to increased power for localizing a disease gene involved in a GxE interaction.},
 bibtype = {article},
 author = {Gauderman, W J and Siegmund, K D},
 journal = {Hum Hered},
 number = {1}
}

@article{nierman_complete_2001,
	title = {Complete genome sequence of {Caulobacter} crescentus},
	volume = {98},
	issn = {0027-8424},
	doi = {10.1073/pnas.061029298},
	abstract = {The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.},
	number = {7},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Nierman, W C and Feldblyum, T V and Laub, M T and Paulsen, I T and Nelson, K E and Eisen, J A and Heidelberg, J F and Alley, M R and Ohta, N and Maddock, J R and Potocka, I and Nelson, W C and Newton, A and Stephens, C and Phadke, N D and Ely, B and DeBoy, R T and Dodson, R J and Durkin, A S and Gwinn, M L and Haft, D H and Kolonay, J F and Smit, J and Craven, M B and Khouri, H and Shetty, J and Berry, K and Utterback, T and Tran, K and Wolf, A and Vamathevan, J and Ermolaeva, M and White, O and Salzberg, S L and Venter, J C and Shapiro, L and Fraser, C M and Eisen, J},
	month = mar,
	year = {2001},
	pmid = {11259647},
	keywords = {Adaptation, Biological, Caulobacter crescentus, Cell Cycle, DNA Methylation, Dinucleotide Repeats, Genome, Bacterial, Molecular Sequence Data, Peptide Hydrolases, Phylogeny, Signal Transduction, Transcription, Genetic},
	pages = {4136--4141}
}

Website  abstract   bibtex   

@article{
 title = {Multivariate frailty model with a major gene: application to genealogical data},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {*Genetic Predisposition to Disease,*Models, Genetic,Adolescent,Adult,Alleles,Child,Child, Preschool,Female,Genotype,Humans,Infant,Infant, Newborn,Longevity/*genetics,Male,Mathematical Computing,Multivariate Analysis,Quebec,Risk,Software,Survival Analysis},
 pages = {412-416},
 volume = {77},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11187585},
 id = {23588418-0e3c-33dd-b0e4-fed475556b34},
 created = {2017-06-19T13:44:21.917Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:22.080Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0926-9630<m:linebreak/>Journal Article</m:note>},
 abstract = {Multivariate survival models are shown to be appropriate for the analysis of the genetic and the environmental nature of a human life-span. Models which involve continuously distributed individual frailty, play an important role in the genetic analysis of an individual's susceptibility to disease and death. These models, however, are not appropriate for the detection of the effects of separate genes on survival. For this purpose we developed a 'major gene' frailty model of multivariate survival and applied it to simulated and real pedigree data. The analysis shows that this model can be used for the detection of the presence of major genes in the population and for the evaluation of the effects of such genes on survival.},
 bibtype = {article},
 author = {Begun, A and Desjardins, B and Iachine, I and Yashin, A},
 journal = {Stud Health Technol Inform}
}

Paper  abstract   bibtex   

@article{
 title = {Why are the majority of hereditary cases of early-onset breast cancer sporadic? A simulation study},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Adult,Age Distribution,Age of Onset,Aged,Australia/epidemiology,Breast Neoplasms/*epidemiology/ethnology/*genetics,Computer Simulation,Family Health,Female,Gene Frequency,Genes, BRCA1,Great Britain/epidemiology,Human,Jews/statistics & numerical data,Middle Age,Models, Genetic,Mutation,Pedigree,Prevalence,Singapore/epidemiology,Support, Non-U.S. Gov't,Support, U.S. Gov't, P.H.S.,Washington/epidemiology},
 pages = {805-12.},
 volume = {9},
 id = {373ef46c-3714-3339-8c8d-5b9047cf28e7},
 created = {2017-06-19T13:44:21.419Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:21.571Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {Population-based studies, including those of Ashkenazi Jews, have observed that at least 50% of women with early-onset breast cancer who carry a germ line mutation in BRCA1 or BRCA2 do not report a family history of the disease. That is, the majority of "hereditary" cases are "sporadic." Furthermore, the great majority of "familial breast cancers" are not hereditary. We conducted a simulation study to evaluate the probability that a woman with early-onset breast cancer is a mutation carrier, given the number of affected relatives, for a range of plausible values of allele frequency (0.001-0.01), and increased risk in mutation carriers (5-20, equivalent to cumulative risks to age 70 of 25-70%, respectively, for Australian women). Families consisted of a case proband and her mother, sisters, and maternal and paternal grandmothers, and aunts. The numbers of sisters and aunts were generated according to Poisson distributions, and ages were assigned according to a Weibull distribution. The simulated distributions of family history and of the prevalence of mutation carriers among case probands were in general similar to those observed in population-based studies, although there was a suggestion of heterogeneity of breast cancer risk in mutation carriers. As is being observed empirically in population-based samples, a family history of breast cancer was not a strong predictor of mutation status; each affected female relative increased the risk of being a mutation carrier by only 2- to 3-fold. The probability of being a mutation carrier was generally low, except in families with extreme histories of breast cancer.},
 bibtype = {article},
 author = {Cui, J and Hopper, J L},
 journal = {Cancer Epidemiol Biomarkers Prev},
 number = {8}
}

Paper  abstract   bibtex   

@article{
 title = {Gene Mapping in the 20th and 21st Centuries : Statistical Methods , Data Analysis, and Experimental Design},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {*Data Interpretation,*Models,Algorithms,Chromosome Mapping/*methods/*trends,Environment,Forecasting,Genetic,Genetic Markers/genetics,Genetics,Genotype,Human,Likelihood Functions,Linkage Disequilibrium/genetics,Medical/*methods/*trends,Non-U.S. Gov't,P.H.S.,Pedigree,Phenotype,Quality of Life,Reproducibility of Results,Research Design/*trends,Statistical,Support,U.S. Gov't},
 pages = {63-132},
 volume = {72},
 id = {f667a7c8-144c-33b1-b2eb-5b9aac6d2875},
 created = {2017-06-19T13:42:01.817Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:02.064Z},
 tags = {02/11/15},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>        <m:bold>From Duplicate 2 ( </m:bold>        <m:bold>          </m:bold><m:bold><m:italic>Gene mapping in the 20th and 21st centuries: statistical methods, data analysis, and experimental design</m:italic></m:bold><m:bold>        </m:bold>        <m:bold> - Terwilliger, J D; Goring, H H )<m:linebreak/>        </m:bold>        <m:linebreak/>eng<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Academic<m:linebreak/>        <m:linebreak/>      </m:note>},
 abstract = {In the 20th century geneticists began to unravel some of the simpler aspects of the etiology of inherited diseases in humans. The theory of linkage analysis was developed and applied long before the advent of molecular biology, but only the technological advances of the second half of the 20th century made large-scale gene mapping with a dense genome-spanning set of markers a reality. More recently, the primary topic of interest has shifted from simple Mendelian diseases, for which genotypes of some gene are the cause of disease, to more complex diseases, for which genotypes of some set of genes together with environmental factors merely alter the probability that an individual gets the disease, although individual factors are typically insufficient to cause the disease outright. To this end, a great deal of dogma has evolved about the best way to skin this cat, although to date success has been minimal with any approach. We postulate that the main reason for this is a lack of attention to experimental design. Once the data have been ascertained, the most powerful statistical methods will not be able to salvage an inappropriately designed study (Andersen 1990). Each phenotype and/or population mandates its own individually tailored study design to maximize the chances of successful gene mapping. We suggest that careful consideration of the available data from real genotype-phenotype correlation studies (as opposed to oversimplified theoretically tractable models), and the practical feasibility of different ascertainment schemes dictate how one should proceed. In this review we review the theory and practice of gene mapping at the close of the 20th century, showing that most methods of linkage and linkage disequilibrium analysis are similar in a fundamental sense, with the differences being related more to study design and ascertainment than to technical details of the underlying statistical analysis. To this end, we propose a new focus in the field of statistical genetics that more explicitly highlights the primacy of study design as the means to increase power for gene mapping.},
 bibtype = {article},
 author = {Terwilliger, Joseph D and Goring, Harald H H},
 journal = {Human Biology},
 number = {1}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Natural selection and sex differences in morbidity and mortality in early life.},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Bacterial Infections,Bacterial Infections: mortality,Environment,Female,Humans,Infant Mortality,Infant, Newborn,Infant, Premature,Male,Morbidity,Nutrition Disorders,Nutrition Disorders: mortality,Selection, Genetic,Sex Ratio},
 pages = {65-76},
 volume = {202},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/10623500},
 month = {1},
 day = {7},
 id = {c7ae321d-1047-3c50-9895-f4dc5921672f},
 created = {2017-06-19T13:41:03.475Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:03.689Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Both morbidity and mortality are consistently reported to be higher in males than in females in early life, but no explanation for these findings has been offered. This paper argues that the sex difference in early vulnerability can be attributed to the natural selection of optimal maternal strategies for maximizing lifetime reproductive success, as modelled previously by Trivers and Willard. These authors theorized that males and females offer different returns on parental investment depending on the state of the environment. Natural selection has therefore favoured maternal ability to manipulate offspring sex in response to environmental conditions in early life, as shown in variation in the sex ratio at birth. This argument can be extended to the whole period of parental investment until weaning. Male vulnerability in response to environmental stress in early life is predicted to have been favoured by natural selection. This vulnerability is most evident in the harsh conditions resulting from pre-term birth, but can also be seen in term infants, and manifests as greater morbidity and mortality persisting into early childhood. Malnutrition, interacting with infection after birth, is suggested as the fundamental trigger mechanism. The model suggests that whatever improvements are made in medical care, any environmental stress will always affect males more severely than females in early life.},
 bibtype = {article},
 author = {Wells, J C},
 journal = {Journal of theoretical biology},
 number = {1}
}

@article{
 title = {Data mining applied to linkage disequilibrium mapping},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Adolescence,Adult,Aged,Aged, 80 and over,Algorithms,Alleles,Child,Child, Preschool,Chromosome Mapping/*methods/statistics & numerical,Computer Simulation,Diabetes Mellitus, Insulin-Dependent/genetics,Female,Founder Effect,Genes, Dominant/genetics,Genetic Predisposition to Disease/genetics,Great Britain,HLA Antigens/genetics,Haplotypes/*genetics,Human,Infant,Linkage Disequilibrium/*genetics,Male,Microsatellite Repeats/genetics,Middle Age,Models, Genetic,Mutation/genetics,Phenotype,Polymorphism, Single Nucleotide/genetics,Statistics, Nonparametric,Support, Non-U.S. Gov't},
 pages = {133-45.},
 volume = {67},
 id = {f0c72e95-0269-3a20-8f92-79ced23957fb},
 created = {2017-06-19T13:43:38.237Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:43:38.346Z},
 tags = {01/11/30},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {We introduce a new method for linkage disequilibrium mapping: haplotype pattern mining (HPM). The method, inspired by data mining methods, is based on discovery of recurrent patterns. We define a class of useful haplotype patterns in genetic case-control data and use the algorithm for finding disease-associated haplotypes. The haplotypes are ordered by their strength of association with the phenotype, and all haplotypes exceeding a given threshold level are used for prediction of disease susceptibility-gene location. The method is model-free, in the sense that it does not require (and is unable to utilize) any assumptions about the inheritance model of the disease. The statistical model is nonparametric. The haplotypes are allowed to contain gaps, which improves the method's robustness to mutations and to missing and erroneous data. Experimental studies with simulated microsatellite and SNP data show that the method has good localization power in data sets with large degrees of phenocopies and with lots of missing and erroneous data. The power of HPM is roughly identical for marker maps at a density of 3 single-nucleotide polymorphisms/cM or 1 microsatellite/cM. The capacity to handle high proportions of phenocopies makes the method promising for complex disease mapping. An example of correct disease susceptibility-gene localization with HPM is given with real marker data from families from the United Kingdom affected by type 1 diabetes. The method is extendable to include environmental covariates or phenotype measurements or to find several genes simultaneously.},
 bibtype = {article},
 author = {Toivonen, H T and Onkamo, P and Vasko, K and Ollikainen, V and Sevon, P and Mannila, H and Herr, M and Kere, J},
 journal = {Am J Hum Genet},
 number = {1}
}

Paper  abstract   bibtex   

@article{
 title = {Association mapping in structured populations},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {*Genetics, Population,Alleles,Case-Control Studies,Chromosome Mapping/*methods/statistics & numerical,Computer Simulation,Female,Genetic Diseases, Inborn/genetics,Genetic Markers/genetics,Human,Linkage Disequilibrium/genetics,Male,Models, Genetic,Nuclear Family,Pedigree,Phenotype,Polymorphism, Single Nucleotide/genetics,Reproducibility of Results,Sensitivity and Specificity,Statistical Distributions,Support, Non-U.S. Gov't,Support, U.S. Gov't, Non-P.H.S.},
 pages = {170-81.},
 volume = {67},
 id = {52b6a822-9e4a-36b5-8089-ea2febd3914d},
 created = {2017-06-19T13:46:04.983Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:05.122Z},
 tags = {02/12/06},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {The use, in association studies, of the forthcoming dense genomewide collection of single-nucleotide polymorphisms (SNPs) has been heralded as a potential breakthrough in the study of the genetic basis of common complex disorders. A serious problem with association mapping is that population structure can lead to spurious associations between a candidate marker and a phenotype. One common solution has been to abandon case-control studies in favor of family-based tests of association, such as the transmission/disequilibrium test (TDT), but this comes at a considerable cost in the need to collect DNA from close relatives of affected individuals. In this article we describe a novel, statistically valid, method for case-control association studies in structured populations. Our method uses a set of unlinked genetic markers to infer details of population structure, and to estimate the ancestry of sampled individuals, before using this information to test for associations within subpopulations. It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations.},
 bibtype = {article},
 author = {Pritchard, J K and Stephens, M and Rosenberg, N A and Donnelly, P},
 journal = {Am J Hum Genet},
 number = {1}
}

@article{
 title = {Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {*Alleles,*Quantitative Trait,Case-Control Studies,Chromosome Mapping/*methods/statistics & numerical,Computer Simulation,Gene Frequency/genetics,Genes, Dominant,Genes, Recessive,Genetic Markers/genetics,Haplotypes/genetics,Human,Linkage Disequilibrium/*genetics,Models, Genetic,Sample Size,Software,Support, U.S. Gov't, P.H.S.},
 pages = {1208-18.},
 volume = {67},
 id = {f12cf84e-6a1e-304d-80e6-7a9c46486cd8},
 created = {2017-06-19T13:44:43.573Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:43.706Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {Linkage disequilibrium (LD) mapping has been applied to many simple, monogenic, overtly Mendelian human traits, with great success. However, extensions and applications of LD mapping approaches to more complex human quantitative traits have not been straightforward. In this article, we consider the analysis of biallelic DNA marker loci and human quantitative trait loci in settings that involve sampling individuals from opposite ends of the trait distribution. The purpose of this sampling strategy is to enrich samples for individuals likely to possess (and not possess) trait-influencing alleles. Simple statistical models for detecting LD between a trait-influencing allele and neighboring marker alleles are derived that make use of this sampling scheme. The power of the proposed method is investigated analytically for some hypothetical gene-effect scenarios. Our studies indicate that LD mapping of loci influencing human quantitative trait variation should be possible in certain settings. Finally, we consider possible extensions of the proposed methods, as well as areas for further consideration and improvement.},
 bibtype = {article},
 author = {Schork, N J and Nath, S K and Fallin, D and Chakravarti, A},
 journal = {Am J Hum Genet},
 number = {5}
}

Paper  abstract   bibtex   

@article{
 title = {Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism?},
 type = {article},
 year = {1999},
 identifiers = {[object Object]},
 keywords = {*Evolution,*Selection (Genetics),Animal,DNA Replication,Human,Models, Genetic,Variation (Genetics)},
 pages = {11904-9.},
 volume = {96},
 id = {a48d23a0-771a-36b0-968c-60bbb311287c},
 created = {2017-06-19T13:45:32.688Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:32.806Z},
 tags = {02/12/04},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 abstract = {Two major clarifications have greatly abetted the understanding and fruitful expansion of the theory of natural selection in recent years: the acknowledgment that interactors, not replicators, constitute the causal unit of selection; and the recognition that interactors are Darwinian individuals, and that such individuals exist with potency at several levels of organization (genes, organisms, demes, and species in particular), thus engendering a rich hierarchical theory of selection in contrast with Darwin's own emphasis on the organismic level. But a piece of the argument has been missing, and individuals at levels distinct from organisms have been denied potency (although granted existence within the undeniable logic of the theory), because they do not achieve individuality with the same devices used by organisms and therefore seem weak by comparison. We show here that different features define Darwinian individuality across scales of size and time. In particular, species-individuals may develop few emergent features as direct adaptations. The interactor approach works with emergent fitnesses, not with emergent features; and species, as a consequence of their different mechanism for achieving individuality (reproductive exclusivity among subparts, that is, among organisms), express many effects from other levels. Organisms, by contrast, suppress upwardly cascading effects, because the organismic style of individuality (by functional integration of subparts) does not permit much competition or differential reproduction of parts from within. Species do not suppress the operation of lower levels; such effects therefore become available as exaptations conferring emergent fitness-a primary source of the different strength that species achieve as effective Darwinian individuals in evolution.},
 bibtype = {article},
 author = {Gould, S J and Lloyd, E A},
 journal = {Proc Natl Acad Sci U S A},
 number = {21}
}

Paper  doi  abstract   bibtex   

@article{waldo_rapid_1999,
	title = {Rapid protein-folding assay using green fluorescent protein},
	volume = {17},
	issn = {1087-0156},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10404163},
	doi = {10.1038/10904},
	abstract = {Formation of the chromophore of green fluorescent protein (GFP) depends on the correct folding of the protein. We constructed a "folding reporter" vector, in which a test protein is expressed as an N-terminal fusion with GFP. Using a test panel of 20 proteins, we demonstrated that the fluorescence of Escherichia coli cells expressing such GFP fusions is related to the productive folding of the upstream protein domains expressed alone. We used this fluorescent indicator of protein folding to evolve proteins that are normally prone to aggregation during expression in E. coli into closely related proteins that fold robustly and are fully soluble and functional. This approach to improving protein folding does not require functional assays for the protein of interest and provides a simple route to improving protein folding and expression by directed evolution.},
	number = {7},
	urldate = {2009-05-03TZ},
	journal = {Nature Biotechnology},
	author = {Waldo, G S and Standish, B M and Berendzen, J and Terwilliger, T C},
	month = jul,
	year = {1999},
	pmid = {10404163},
	keywords = {Archaeal Proteins, Directed Molecular Evolution, Escherichia coli, Ferritins, Fluorescence, Green Fluorescent Proteins, Inclusion Bodies, Luminescent Proteins, Point Mutation, Protein Biosynthesis, Protein Folding, Recombinant Fusion Proteins, Solubility, Temperature, Transcription, Genetic},
	pages = {691--695}
}

Paper  abstract   bibtex   

@article{
 title = {Use of unlinked genetic markers to detect population stratification in association studies},
 type = {article},
 year = {1999},
 identifiers = {[object Object]},
 keywords = {*Case-Control Studies,*Genetic Markers,*Linkage (Genetics),*Models, Genetic,Alleles,Genotype,Human,Research Design,Support, Non-U.S. Gov't,Support, U.S. Gov't, P.H.S.},
 pages = {220-8.},
 volume = {65},
 id = {b79d206a-a398-3b9a-8ad4-7f1e22c70cda},
 created = {2017-06-19T13:45:20.473Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:20.613Z},
 tags = {02/11/15},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {We examine the issue of population stratification in association-mapping studies. In case-control studies of association, population subdivision or recent admixture of populations can lead to spurious associations between a phenotype and unlinked candidate loci. Using a model of sampling from a structured population, we show that if population stratification exists, it can be detected by use of unlinked marker loci. We show that the case-control-study design, using unrelated control individuals, is a valid approach for association mapping, provided that marker loci unlinked to the candidate locus are included in the study, to test for stratification. We suggest guidelines as to the number of unlinked marker loci to use.},
 bibtype = {article},
 author = {Pritchard, J K and Rosenberg, N A},
 journal = {Am J Hum Genet},
 number = {1}
}

Website  abstract   bibtex   

@article{
 title = {Genetic factors in susceptibility to death: a comparative analysis of bivariate survival models},
 type = {article},
 year = {1999},
 identifiers = {[object Object]},
 keywords = {*Death,*Genetic Predisposition to Disease,*Models, Genetic,Cohort Studies,Denmark/epidemiology,Female,Humans,Male,Research Support, U.S. Gov't, P.H.S.,Statistics,Twins, Dizygotic/statistics & numerical data,Twins, Monozygotic/statistics & numerical data,Variation (Genetics)},
 pages = {53-60},
 volume = {4},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10613717},
 id = {949c19fe-b444-3008-8971-61b8e23d08fc},
 created = {2017-06-19T13:42:11.608Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:11.725Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>1359-5229<m:linebreak/>Journal Article<m:linebreak/>Twin Study</m:note>},
 abstract = {BACKGROUND: Molecular epidemiological studies of aging and longevity are focused on evaluating the effects of single genes on susceptibility to disease and death. The effects of all genetic factors on susceptibility can be evaluated from the analysis of survival data on related individuals. METHOD: The analyses of survival data on Danish monozygotic (MZ) and dizygotic (DZ) twins are performed using gamma, inverse Gaussian and three-parameter correlated frailty models. The semiparametric representations of the respective models are used to obtain maximum likelihood estimates of model parameters. The results are compared using the likelihood ratio test. RESULTS: The survival of Danish MZ and DZ twins can be characterised by the same marginal hazards and identical univariate frailty distributions for any of the three frailty models. In all three cases the genetic influence on frailty is statistically significant. CONCLUSION: All three models can be used to study genetic effects on susceptibility. The gamma and inverse Gaussian frailty models fit the Danish twin data equally well. Our analyses show that for the Danish twin data these two models are preferable to the three-parameter model.},
 bibtype = {article},
 author = {Yashin, A I and Begun, A Z and Iachine, I A},
 journal = {J Epidemiol Biostat},
 number = {1}
}

Website  abstract   bibtex   

@article{
 title = {How heritable is individual susceptibility to death? The results of an analysis of survival data on Danish, Swedish and Finnish twins},
 type = {article},
 year = {1998},
 identifiers = {[object Object]},
 keywords = {*Death,*Genetic Predisposition to Disease,Adult,Age Factors,Aged,Aged, 80 and over,Denmark,Disease Susceptibility,Environment,Epidemiology, Molecular,Female,Finland,Forecasting,Health,Humans,Life Tables,Likelihood Functions,Longevity/genetics,Male,Middle Aged,Models, Genetic,Research Support, Non-U.S. Gov't,Research Support, U.S. Gov't, P.H.S.,Sex Factors,Survival Analysis,Sweden,Twins/*genetics},
 pages = {196-205},
 volume = {1},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10100811},
 id = {161c25f0-f407-3983-ac34-656acbfb7169},
 created = {2017-06-19T13:42:57.913Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:58.237Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>1369-0523<m:linebreak/>Journal Article<m:linebreak/>Twin Study</m:note>},
 abstract = {Molecular epidemiological studies confirm a substantial contribution of individual genes to variability in susceptibility to disease and death for humans. To evaluate the contribution of all genes to susceptibility and to estimate individual survival characteristics, survival data on related individuals (eg twins or other relatives) are needed. Correlated gamma-frailty models of bivariate survival are used in a joint analysis of survival data on more than 31,000 pairs of Danish, Swedish and Finnish male and female twins using the maximum likelihood method. Additive decomposition of frailty into genetic and environmental components is used to estimate heritability in frailty. The estimate of the standard deviation of frailty from the pooled data is about 1.5. The hypothesis that variance in frailty and correlations of frailty for twins are similar in the data from all three countries is accepted. The estimate of narrow-sense heritability in frailty is about 0.5. The age trajectories of individual hazards are evaluated for all three populations of twins and both sexes. The results of our analysis confirm the presence of genetic influences on individual frailty and longevity. They also suggest that the mechanism of these genetic influences may be similar for the three Scandinavian countries. Furthermore, results indicate that the increase in individual hazard with age is more rapid than predicted by traditional demographic life tables.},
 bibtype = {article},
 author = {Iachine, I A and Holm, N V and Harris, J R and Begun, A Z and Iachina, M K and Laitinen, M and Kaprio, J and Yashin, A I},
 journal = {Twin Res},
 number = {4}
}

@article{riggs_cell-associated_1998,
	title = {Cell-associated viral {RNA} expression during acute infection with {HIV} type 1},
	volume = {14},
	issn = {0889-2229},
	doi = {10.1089/aid.1998.14.1141},
	abstract = {The mechanism of decline in viremia following acute infection with HIV is unknown. To characterize this process virologically, the expression of viral RNAs was analyzed in samples of peripheral blood mononuclear cells (PBMCs) from a patient who experienced a 100-fold decline in plasma viremia over a 13-day period prior to the initiation of antiretroviral therapy. Cell-associated viral RNA declined in association with the decline in plasma virus. During the initial 7 days of observation, plasma viremia declined more than 10-fold with no change in the ratio of unspliced to multiply spliced mRNAs. The efficiency of viral gene expression did not decline during the study period and varied from 380 to 2800 unspliced RNA copies per productively infected cell. Together, these data indicate no change in the relative proportion of cells in late- and early-stage gene expression during the initial decline and provide evidence against shortening of the viral replication cycle by immune surveillance. However, the prevalence of productively infected cells declined markedly during the 13 days of observation, from 1 in 250 to 1 in 25,000 PBMCs. These data are compatible with depletion of available target cells during the initial decline in viremia. As the level of plasma virus stabilized after 8 days of observation, the ratio of unspliced to multiply spliced mRNAs rose; this rise was due to a relatively greater decline in multiply spliced mRNA. These data suggest the possible onset of a blockade to new infection events (for example, by neutralizing antibody or chemokines), causing an increase in the relative proportion of cells in late-stage gene expression. They may also be explained, however, by the persistence of cell-associated virions together with the near disappearance of productively infected cells from the circulation.},
	language = {eng},
	number = {13},
	journal = {AIDS research and human retroviruses},
	author = {Riggs, N. L. and Little, S. J. and Richman, D. D. and Guatelli, J. C.},
	month = sep,
	year = {1998},
	pmid = {9737585},
	keywords = {Acute Disease, HIV Infections, HIV-1, Humans, Leukocytes, Mononuclear, RNA Splicing, RNA, Viral, Reverse Transcriptase Polymerase Chain Reaction, Time Factors, Transcription, Genetic, Viremia, Virus Replication},
	pages = {1141--1149},
}

Paper  abstract   bibtex   

@article{
 title = {Mapping genes through the use of linkage disequilibrium generated by genetic drift: 'drift mapping' in small populations with no demographic expansion},
 type = {article},
 year = {1998},
 identifiers = {[object Object]},
 keywords = {Chromosome Mapping/*methods,Gene Frequency/*genetics,Genetics, Population,Human,Linkage Disequilibrium/*genetics,Recombination, Genetic,Support, Non-U.S. Gov't},
 pages = {138-54.},
 volume = {48},
 id = {1be10902-2f34-3c10-a6a9-b703f644ef86},
 created = {2017-06-19T13:42:59.231Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:59.350Z},
 tags = {02/12/09},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 abstract = {Linkage disequilibrium has been a powerful tool in identifying rare disease alleles in human populations. To date, most research has been directed to isolated populations which have undergone a bottleneck followed by rapid exponential expansion. While this strategy works well for rare diseases in which all disease alleles in the population today are clonal copies of some common ancestral allele, for common disease genes with substantial allelic heterogeneity, this approach is not predicted to work. In this paper, we describe the dynamics of linkage disequilibrium in populations which have not undergone a demographic expansion. In these populations, it is shown that genetic drift creates disequilibrium over time, while in expanded populations, the disequilibrium decays with time. We propose that common disease alleles might be more efficiently identified by drift mapping - linkage disequilibrium mapping in small, old populations of constant size where the disequilibrium is the result of genetic drift, not founder effect. Theoretical models, empirical data, and simulated population models are presented as evidence for the utility of this approach.},
 bibtype = {article},
 author = {Terwilliger, J D and Zollner, S and Laan, M and Paabo, S},
 journal = {Hum Hered},
 number = {3}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Allelic disequilibrium and allele frequency distribution as a function of social and demographic history},
 type = {article},
 year = {1997},
 identifiers = {[object Object]},
 keywords = {*Alleles,*Gene Frequency,*Linkage Disequilibrium,Demography,Electrophoresis,Humans,Indians, North American/*genetics,Polymorphism, Genetic,Recombination, Genetic,Sociology,Statistics as Topic},
 pages = {197-204},
 volume = {60},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8981963},
 edition = {1997/01/01},
 id = {a646b09b-fc90-3866-8c54-cf33f27e14ae},
 created = {2017-06-19T13:44:32.781Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:32.925Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Thompson, E A<m:linebreak/>Neel, J V<m:linebreak/>GM-46255/GM/NIGMS NIH HHS/United States<m:linebreak/>Research Support, U.S. Gov't, Non-P.H.S.<m:linebreak/>Research Support, U.S. Gov't, P.H.S.<m:linebreak/>United states<m:linebreak/>American journal of human genetics<m:linebreak/>Am J Hum Genet. 1997 Jan;60(1):197-204.</m:note>},
 abstract = {Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis.},
 bibtype = {article},
 author = {Thompson, E A and Neel, J V},
 journal = {Am J Hum Genet},
 number = {1}
}

@article{
 title = {The genetical archaeology of the human genome},
 type = {article},
 year = {1996},
 identifiers = {[object Object]},
 keywords = {*Gene Pool,*Genome, Human,DNA, Mitochondrial/genetics,Evolution, Molecular,Female,Human,Male,Models, Genetic,Phylogeny,Support, Non-U.S. Gov't,Variation (Genetics)/*genetics},
 pages = {135-140},
 volume = {14},
 id = {da42c725-f648-32fa-a720-c48d07c5c47c},
 created = {2017-06-19T13:46:05.495Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:05.676Z},
 tags = {03/09/17},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 abstract = {Palaentology and archaeology are disciplines that traditionally deal with the reconstruction of human origins and history. Recently, however, molecular genetics has come to make increasing contributions to this area. In particular, several data sets indicate that variation of the human gene pool originated in Africa within the last 200,000 years. Furthermore, the study of DNA sequences allows the detection of expansions in population size. Here we briefly summarize and exemplify how DNA sequences can be used to reconstruct the history of populations.},
 bibtype = {article},
 author = {von Haeseler, A and Sajantila, A and Paabo, S},
 journal = {Nat Genet},
 number = {2}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Analysis of Hox gene expression in the chick limb bud.},
 type = {article},
 year = {1996},
 identifiers = {[object Object]},
 keywords = {Amino Acid Sequence,Animals,Base Sequence,Cell Movement,Chick Embryo,Extremities,Extremities: embryology,Gene Expression Regulation, Developmental,Gene Library,Genes, Homeobox,Hedgehog Proteins,Immunohistochemistry,In Situ Hybridization,Models, Genetic,Molecular Sequence Data,Morphogenesis,Muscles,Muscles: cytology,Muscles: embryology,Polymerase Chain Reaction,Proteins,Proteins: metabolism,Time Factors,Tissue Distribution,Trans-Activators,Transcription, Genetic},
 pages = {1449-66},
 volume = {122},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/8625833},
 month = {5},
 id = {9e81f849-717e-3abe-be53-e44f82a2f3f6},
 created = {2016-04-08T12:19:40.000Z},
 file_attached = {true},
 profile_id = {994bc413-6766-31df-917a-32165aa30f6c},
 group_id = {cec5aa9e-65e1-3c21-bc44-78fa6504020e},
 last_modified = {2017-03-14T10:42:46.538Z},
 read = {true},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Nelson1996},
 folder_uuids = {37786225-e8d4-483b-be04-dfc97f200748},
 private_publication = {false},
 abstract = {The vertebrate Hox genes have been shown to be important for patterning the primary and secondary axes of the developing vertebrate embryo. The function of these genes along the primary axis of the embryo has been generally interpreted in the context of positional specification and homeotic transformation of axial structures. The way in which these genes are expressed and function during the development of the secondary axes, particularly the limb, is less clear. In order to provide a reference for understanding the role of the Hox genes in limb patterning, we isolated clones of 23 Hox genes expressed during limb development, characterized their expression patterns and analyzed their regulation by the signalling centers which pattern the limb. The expression patterns of the Abd-B-related Hoxa and Hoxd genes have previously been partially characterized; however, our study reveals that these genes are expressed in patterns more dynamic and complex than generally appreciated, only transiently approximating simple, concentric, nested domains. Detailed analysis of these patterns suggests that the expression of each of the Hoxa and Hoxd genes is regulated in up to three independent phases. Each of these phases appears to be associated with the specification and patterning of one of the proximodistal segments of the limb (upper arm, lower arm and hand). Interestingly, in the last of these phases, the expression of the Hoxd genes violates the general rule of spatial and temporal colinearity of Hox gene expression with gene order along the chromosome. In contrast to the Abd-B-related Hoxa and Hoxd genes, which are expressed in both the fore and hind limbs, different sets of Hoxc genes are expressed in the two limbs. There is a correlation between the relative position of these genes along the chromosome and the axial level of the limb bud in which they are expressed. The more 3' genes are expressed in the fore limb bud while the 5' genes are expressed in the hind limb bud; intermediate genes are transcribed in both limbs. However, there is no clear correlation between the relative position of the genes along the chromosome and their expression domains within the limb. With the exception of Hoxc-11, which is transcribed in a posterior portion of the hind limb, Hoxc gene expression is restricted to the anterior/proximal portion of the limb bud. Importantly, comparison of the distributions of Hoxc-6 RNA and protein products reveals posttranscriptional regulation of this gene, suggesting that caution must be exercised in interpreting the functional significance of the RNA distribution of any of the vertebrate Hox genes. To understand the genesis of the complex patterns of Hox gene expression in the limb bud, we examined the propagation of Hox gene expression relative to cell proliferation. We find that shifts in Hox gene expression cannot be attributed to passive expansion due to cell proliferation. Rather, phase-specific Hox gene expression patterns appear to result from a context-dependent response of the limb mesoderm to Sonic hedgehog. Sonic hedgehog (the patterning signal from the Zone of Polarizing Activity) is known to be able to activate Hoxd gene expression in the limb. Although we find that Sonic hedgehog is capable of initiating and polarizing Hoxd gene expression during both of the latter two phases of Hox gene expression, the specific patterns induced are not determined by the signal, but depend upon the temporal context of the mesoderm receiving the signal. Misexpression of Sonic hedgehog also reveals that Hoxb-9, which is normally excluded from the posterior mesenchyme of the leg, is negatively regulated by Sonic hedgehog and that Hoxc-11, which is expressed in the posterior portion of the leg, is not affected by Sonic hedgehog and hence is not required to pattern the skeletal elements of the lower leg.},
 bibtype = {article},
 author = {Nelson, C E and Morgan, B a and Burke, a C and Laufer, E and DiMambro, E and Murtaugh, L C and Gonzales, E and Tessarollo, L and Parada, L F and Tabin, C},
 journal = {Development (Cambridge, England)},
 number = {5}
}

Paper  abstract   bibtex   

@article{greene_spo0a_1996,
	title = {The {Spo}0A protein of {Bacillus} subtilis inhibits transcription of the {abrB} gene without preventing binding of the polymerase to the promoter},
	volume = {271},
	issn = {0021-9258},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8626703},
	abstract = {Repression of transcription of the abrB gene is essential to expression of many of the postexponential genes in Bacillus. The repression is due to the activity of the response regulator protein Spo0A. We have used in vitro transcription and DNase I and hydroxyl radical footprinting to explore the mechanism of transcription inhibition. Spo0A binds to specific DNA sequences (0A boxes), and two such boxes are found downstream of the tandem promoters for the abrB gene. The data indicate that both RNA polymerase and Spo0A bind simultaneously to a DNA fragment containing the promoters and the 0A boxes. The Spo0A prevents the polymerase from inducing DNA strand denaturation at the promoter for the abrB gene.},
	number = {19},
	urldate = {2009-05-03TZ},
	journal = {The Journal of Biological Chemistry},
	author = {Greene, E A and Spiegelman, G B},
	month = may,
	year = {1996},
	pmid = {8626703},
	keywords = {Bacillus subtilis, Bacterial Proteins, Base Sequence, Binding Sites, DNA Footprinting, DNA, Bacterial, DNA-Binding Proteins, DNA-Directed RNA Polymerases, Deoxyribonuclease I, Escherichia coli, Gene Expression Regulation, Bacterial, Genes, Bacterial, Hydroxyl Radical, Kinetics, Molecular Sequence Data, Promoter Regions, Genetic, Transcription Factors, Transcription, Genetic},
	pages = {11455--11461}
}

@article{
 title = {Genetic epidemiology},
 type = {article},
 year = {1996},
 identifiers = {[object Object]},
 keywords = {Alcoholism/psychology,Disease Susceptibility,Epidemiologic Methods,Human,Linkage (Genetics),Mental Disorders/*epidemiology/*genetics,Models, Genetic,Substance-Related Disorders/genetics,Support, Non-U.S. Gov't},
 pages = {408-33.},
 volume = {52},
 id = {1651e57c-8e13-3a4c-a1cc-4e0fc67910bb},
 created = {2017-06-19T13:42:36.715Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:36.823Z},
 tags = {02/06/15},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Academic</m:note>},
 abstract = {Studies of families, twins, and adoptees have helped to quantify the genetic contributions to and overlaps between depression, anxiety, phobias and alcoholism, and to refine the boundaries of the schizophrenia spectrum. Analyses of covariance structures in twin data have confirmed genetic susceptibility and recent life stresses as the major determinants of depression. Genetic modelling of family data on schizophrenia and bipolar disorder indicates three or more common genes each having a small multiplicative effect on risk, although rare major genes may be present in some families. Linkage studies have localised genes for familial Alzheimer's disease on chromosomes 14 and 21; disease mutations on these chromosomes have since been isolated. Association studies have identified susceptibility (or protective) genes for Alzheimer's disease and alcoholism. Several tentative linkage and association findings in schizophrenia and bipolar disorder require further study.},
 bibtype = {article},
 author = {Sham, P},
 journal = {Br Med Bull},
 number = {3}
}

Paper  abstract   bibtex   

@article{
 title = {A model for the statistical fluctuations of protein numbers in a microbial population.},
 type = {article},
 year = {1978},
 identifiers = {[object Object]},
 keywords = {Bacterial Proteins,Bacterial Proteins: metabolism,Biological,Cell Count,Genes,Genetic,Mitosis,Models,Protein Biosynthesis,Regulator,Transcription,beta-Galactosidase,beta-Galactosidase: metabolism},
 pages = {587-603},
 volume = {71},
 id = {bf82197e-46c9-3ca5-ad78-f87104ef3f27},
 created = {2015-08-20T10:31:21.000Z},
 file_attached = {true},
 profile_id = {1593dc7b-4550-3536-a5a4-21ffd4cbffb8},
 group_id = {9cd45c01-6b67-3572-a936-df749337a5f1},
 last_modified = {2015-08-20T10:42:24.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Berg1978},
 abstract = {Abstract A model is presented for the distribution of protein molecules between the cells in a microbial population during steady-state growth. A general expression is derived under the sole assumption that each protein molecule has equal probability of joining either ... \n},
 bibtype = {article},
 author = {Berg, O G},
 journal = {Journal of theoretical biology},
 number = {4}
}

Paper  doi  bibtex   

@article{shapiro_differentiation_1976,
	title = {Differentiation in the {Caulobacter} cell cycle},
	volume = {30},
	issn = {0066-4227},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/185940},
	doi = {10.1146/annurev.mi.30.100176.002113},
	urldate = {2009-05-03TZ},
	journal = {Annual Review of Microbiology},
	author = {Shapiro, L},
	year = {1976},
	pmid = {185940},
	keywords = {Bacteria, Bacteriophages, Carbohydrate Metabolism, Cell Division, Cell Wall, Cyclic GMP, DNA, Bacterial, Enzyme Repression, Flagella, Morphogenesis, Mutation, Nucleotides, Cyclic, Protein Biosynthesis, Transcription, Genetic, Transduction, Genetic},
	pages = {377--407}
}

@article{lind_epihealth:_2013,
	title = {{EpiHealth}: a large population-based cohort study for investigation of gene-lifestyle interactions in the pathogenesis of common diseases.},
	volume = {28},
	issn = {1573-7284 0393-2990},
	doi = {10.1007/s10654-013-9787-x},
	abstract = {The most common diseases affecting middle-aged and elderly subjects in industrialized countries are multigenetic and lifestyle related. Several attempts have been made to study interactions between genes and lifestyle factors, but most such studies lack the power to examine interactions between several genes and several lifestyle components. The primary objective of the {EpiHealth} cohort study is to provide a resource to study interactions between several genotypes and lifestyle factors in a large cohort (the aim is 300,000 individuals) derived  from the Swedish population in the age range of 45-75 years regarding development of common degenerative disorders, such as cardiovascular diseases, cancer, dementia, joint pain, obstructive lung disease, depression, and osteoporotic fractures. The study consists of three parts. First, a collection of data on lifestyle factors by self-assessment using an internet-based questionnaire. Second, a visit to a test center where blood samples are collected and physiological parameters recorded. Third, the sample is followed for occurrence of outcomes using nationwide medical registers. This overview presents the study  design and some baseline characteristics from the first year of data collection in the {EpiHealth} study.},
	pages = {189--197},
	number = {2},
	journaltitle = {European journal of epidemiology},
	shortjournal = {Eur J Epidemiol},
	author = {Lind, Lars and Elmstahl, Solve and Bergman, Ebba and Englund, Martin and Lindberg, Eva and Michaelsson, Karl and Nilsson, Peter M. and Sundstrom, Johan},
	date = {2013-02},
	pmid = {23435790},
	keywords = {*Genotype, *Life Style, Aged, Aged, 80 and over, Biomarkers/*blood, Chronic Disease/epidemiology/prevention \& control, Databases, Genetic, Disease/ethnology/*genetics, Female, Genetic Predisposition to Disease/*epidemiology, Health Status, Humans, Longitudinal Studies, Male, Middle Aged, Molecular Epidemiology, Population Surveillance, Risk Factors, Self-Assessment, Surveys and Questionnaires, Sweden/epidemiology}
}