@article{masaoka_alcohol_2020,
	title = {Alcohol {Drinking} and {Bladder} {Cancer} {Risk} {From} a {Pooled} {Analysis} of {Ten} {Cohort} {Studies} in {Japan}},
	volume = {30},
	issn = {1349-9092},
	doi = {10.2188/jea.JE20190014},
	abstract = {BACKGROUND: The association of alcohol drinking with bladder cancer risk remains unclear in East Asian populations. Aldehyde dehydrogenase 2 (ALDH2) enzyme oxidizes alcohol-metabolized carcinogenic acetaldehyde into acetate. It is well known that the inactive ALDH2 carriers, specific to East Asian populations, have an increased risk of several cancer types because of increased exposure to acetaldehyde after alcohol consumption. The aim of this study was to examine the association between alcohol drinking and bladder cancer risk using data from ten population-based prospective cohort studies in Japan, where approximately 40\% of the population has inactive ALDH2 enzyme.
METHODS: We analyzed 340,497 Japanese participants with average follow-up of 13.4 years. The association between alcohol drinking and bladder cancer risk was evaluated using Cox regression models within each study, and random-effects models were used to estimate pooled hazard ratios (HRs) with corresponding 95\% confidence intervals (CIs).
RESULTS: During 4,729,071 person-years, 936 men and 325 women were newly diagnosed with bladder cancer. Our results showed no evidence of significant association between alcohol drinking and bladder cancer risk even among men who consumed alcohol of ≥69 g/week, with HR of 1.02 (95\% CI, 0.79-1.33). The null result was observed consistently among women.
CONCLUSIONS: Our findings do not support an association between alcohol drinking and bladder cancer risk in the Japanese, at least without consideration of the polymorphisms of alcohol-metabolizing enzymes.},
	language = {eng},
	number = {7},
	journal = {Journal of Epidemiology},
	author = {Masaoka, Hiroyuki and Matsuo, Keitaro and Oze, Isao and Ito, Hidemi and Naito, Mariko and Wada, Keiko and Nagata, Chisato and Nakayama, Tomio and Kitamura, Yuri and Sadakane, Atsuko and Tamakoshi, Akiko and Tsuji, Ichiro and Sugawara, Yumi and Sawada, Norie and Mizoue, Tetsuya and Inoue, Manami and Tanaka, Keitaro and Tsugane, Shoichiro and Shimazu, Taichi},
	month = jul,
	year = {2020},
	pmid = {31204364},
	pmcid = {PMC7280052},
	keywords = {Adult, Alcohol Dehydrogenase, Alcohol Drinking, Aldehyde Dehydrogenase, Aldehyde Dehydrogenase, Mitochondrial, Asian Continental Ancestry Group, Female, Humans, Japan, Male, Middle Aged, Polymerase Chain Reaction, Polymorphism, Genetic, Prospective Studies, Urinary Bladder Neoplasms, alcohol drinking, bladder cancer, cohort study, pooled analysis},
	pages = {309--313},
}

@article{mandl_genomics_2020,
	title = {The {Genomics} {Research} and {Innovation} {Network}: creating an interoperable, federated, genomics learning system},
	volume = {22},
	issn = {1530-0366},
	shorttitle = {The {Genomics} {Research} and {Innovation} {Network}},
	doi = {10.1038/s41436-019-0646-3},
	abstract = {PURPOSE: Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care.
METHODS: Three of the nation's leading children's hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model.
RESULTS: Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype-phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications.
CONCLUSIONS: The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.},
	language = {eng},
	number = {2},
	journal = {Genetics in Medicine: Official Journal of the American College of Medical Genetics},
	author = {Mandl, Kenneth D. and Glauser, Tracy and Krantz, Ian D. and Avillach, Paul and Bartels, Anna and Beggs, Alan H. and Biswas, Sawona and Bourgeois, Florence T. and Corsmo, Jeremy and Dauber, Andrew and Devkota, Batsal and Fleisher, Gary R. and Heath, Allison P. and Helbig, Ingo and Hirschhorn, Joel N. and Kilbourn, Judson and Kong, Sek Won and Kornetsky, Susan and Majzoub, Joseph A. and Marsolo, Keith and Martin, Lisa J. and Nix, Jeremy and Schwarzhoff, Amy and Stedman, Jason and Strauss, Arnold and Sund, Kristen L. and Taylor, Deanne M. and White, Peter S. and Marsh, Eric and Grimberg, Adda and Hawkes, Colin and {Genomics Research and Innovation
Network}},
	month = feb,
	year = {2020},
	pmid = {31481752},
	pmcid = {PMC7000325},
	keywords = {Biological Specimen Banks, Biomedical Research, Data Management, Databases, Factual, Databases, Genetic, Electronic Data Processing, Ethics Committees, Research, Genomics, Humans, Information Dissemination, Information Storage and Retrieval, Research Personnel, biobanking, electronic health records, federated networks, genomic medicine, information technology},
	pages = {371--380},
}

@article{spinelli_identification_2019,
	title = {Identification of the novel {Ido1} imprinted locus and its potential epigenetic role in pregnancy loss},
	volume = {28},
	issn = {1460-2083},
	doi = {10.1093/hmg/ddy383},
	abstract = {Previous studies show that aberrant tryptophan catabolism reduces maternal immune tolerance and adversely impacts pregnancy outcomes. Tryptophan depletion in pregnancy is facilitated by increased activity of tryptophan-depleting enzymes [i.e. the indolamine-2,3 dioxygenase (IDO)1 and IDO2) in the placenta. In mice, inhibition of IDO1 activity during pregnancy results in fetal loss; however, despite its important role, regulation of Ido1 gene transcription is unknown. The current study shows that the Ido1 and Ido2 genes are imprinted and maternally expressed in mouse placentas. DNA methylation analysis demonstrates that nine CpG sites at the Ido1 promoter constitute a differentially methylated region that is highly methylated in sperm but unmethylated in oocytes. Bisulfite cloning sequencing analysis shows that the paternal allele is hypermethylated while the maternal allele shows low levels of methylation in E9.5 placenta. Further study in E9.5 placentas from the CBA/J X DBA/2 spontaneous abortion mouse model reveals that aberrant methylation of Ido1 is linked to pregnancy loss. DNA methylation analysis in humans shows that IDO1 is hypermethylated in human sperm but partially methylated in placentas, suggesting similar methylation patterns to mouse. Importantly, analysis in euploid placentas from first trimester pregnancy loss reveals that IDO1 methylation significantly differs between the two placenta cohorts, with most CpG sites showing increased percent of methylation in miscarriage placentas. Our study suggests that DNA methylation is linked to regulation of Ido1/IDO1 expression and altered Ido1/IDO1 DNA methylation can adversely influence pregnancy outcomes.},
	language = {eng},
	number = {4},
	journal = {Human Molecular Genetics},
	author = {Spinelli, Philip and Latchney, Sarah E. and Reed, Jasmine M. and Fields, Ashley and Baier, Brian S. and Lu, Xiang and McCall, Matthew N. and Murphy, Shawn P. and Mak, Winifred and Susiarjo, Martha},
	year = {2019},
	pmid = {30403776},
	pmcid = {PMC6360327},
	keywords = {Abortion, Spontaneous, Animals, CpG Islands, DNA Methylation, Epigenesis, Genetic, Female, Genomic Imprinting, Humans, Indoleamine-Pyrrole 2,3,-Dioxygenase, Male, Oocytes, Placenta, Pregnancy, Spermatozoa},
	pages = {662--674},
}

@article{nordstrom_unique_2019,
	title = {Unique and assay specific features of {NOMe}-, {ATAC}- and {DNase} {I}-seq data},
	volume = {47},
	issn = {1362-4962},
	doi = {10.1093/nar/gkz799},
	abstract = {Chromatin accessibility maps are important for the functional interpretation of the genome. Here, we systematically analysed assay specific differences between DNase I-seq, ATAC-seq and NOMe-seq in a side by side experimental and bioinformatic setup. We observe that most prominent nucleosome depleted regions (NDRs, e.g. in promoters) are roboustly called by all three or at least two assays. However, we also find a high proportion of assay specific NDRs that are often 'called' by only one of the assays. We show evidence that these assay specific NDRs are indeed genuine open chromatin sites and contribute important information for accurate gene expression prediction. While technically ATAC-seq and DNase I-seq provide a superb high NDR calling rate for relatively low sequencing costs in comparison to NOMe-seq, NOMe-seq singles out for its genome-wide coverage allowing to not only detect NDRs but also endogenous DNA methylation and as we show here genome wide segmentation into heterochromatic B domains and local phasing of nucleosomes outside of NDRs. In summary, our comparisons strongly suggest to consider assay specific differences for the experimental design and for generalized and comparative functional interpretations.},
	language = {eng},
	number = {20},
	journal = {Nucleic Acids Research},
	author = {Nordström, Karl J. V. and Schmidt, Florian and Gasparoni, Nina and Salhab, Abdulrahman and Gasparoni, Gilles and Kattler, Kathrin and Müller, Fabian and Ebert, Peter and Costa, Ivan G. and {DEEP consortium} and Pfeifer, Nico and Lengauer, Thomas and Schulz, Marcel H. and Walter, Jörn},
	month = nov,
	year = {2019},
	pmid = {31584093},
	pmcid = {PMC6847574},
	keywords = {Chromatin Immunoprecipitation Sequencing, Hep G2 Cells, Humans, Nucleosomes, Promoter Regions, Genetic},
	pages = {10580--10596},
	file = {Volltext:/Users/mschulz/Zotero/storage/CHJS57XE/Nordström et al. - 2019 - Unique and assay specific features of NOMe-, ATAC-.pdf:application/pdf},
}

Paper  doi  abstract   bibtex   

@article{ahlen_bergman_increased_2018,
	title = {Increased {CD}4(+) {T} cell lineage commitment determined by {CpG} methylation correlates with better prognosis in urinary bladder cancer patients},
	volume = {10},
	issn = {1868-7083},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/30075815},
	doi = {10.1186/s13148-018-0536-6},
	abstract = {BACKGROUND: Urinary bladder cancer is a common malignancy worldwide. Environmental factors and chronic inflammation are correlated with the disease risk. Diagnosis is performed by transurethral resection of the bladder, and patients with muscle invasive disease preferably proceed to radical cystectomy, with or without neoadjuvant chemotherapy. The anti-tumour immune responses, known to be initiated in the tumour and draining lymph nodes, may play a major role in future treatment strategies. Thus, increasing the knowledge of tumour-associated immunological processes is important. Activated CD4(+) T cells differentiate into four main separate lineages: Th1, Th2, Th17 and Treg, and they are recognized by their effector molecules IFN-γ, IL-13, IL-17A, and the transcription factor Foxp3, respectively. We have previously demonstrated signature CpG sites predictive for lineage commitment of these four major CD4(+) T cell lineages. Here, we investigate the lineage commitment specifically in tumour, lymph nodes and blood and relate them to the disease stage and response to neoadjuvant chemotherapy. RESULTS: Blood, tumour and regional lymph nodes were obtained from patients at time of transurethral resection of the bladder and at radical cystectomy. Tumour-infiltrating CD4(+) lymphocytes were significantly hypomethylated in all four investigated lineage loci compared to CD4(+) lymphocytes in lymph nodes and blood (lymph nodes vs tumour-infiltrating lymphocytes: IFNG -4229 bp p {\textless} 0.0001, IL13 -11 bp p {\textless} 0.05, IL17A -122 bp p {\textless} 0.01 and FOXP3 -77 bp p {\textgreater} 0.05). Examination of individual lymph nodes displayed different methylation signatures, suggesting possible correlation with future survival. More advanced post-cystectomy tumour stages correlated significantly with increased methylation at the IFNG -4229 bp locus. Patients with complete response to neoadjuvant chemotherapy displayed significant hypomethylation in CD4(+) T cells for all four investigated loci, most prominently in IFNG p {\textless} 0.0001. Neoadjuvant chemotherapy seemed to result in a relocation of Th1-committed CD4(+) T cells from blood, presumably to the tumour, indicated by shifts in the methylation patterns, whereas no such shifts were seen for lineages corresponding to IL13, IL17A and FOXP3. CONCLUSION: Increased lineage commitment in CD4(+) T cells, as determined by demethylation in predictive CpG sites, is associated with lower post-cystectomy tumour stage, complete response to neoadjuvant chemotherapy and overall better outcome, suggesting epigenetic profiling of CD4(+) T cell lineages as a useful readout for clinical staging.},
	language = {eng},
	number = {1},
	journal = {Clinical epigenetics},
	author = {Ahlén Bergman, Emma and Hartana, Ciputra Adijaya and Johansson, Markus and Linton, Ludvig B and Berglund, Sofia and Hyllienmark, Martin and Lundgren, Christian and Holmström, Benny and Palmqvist, Karin and Hansson, Johan and Alamdari, Farhood and Huge, Ylva and Aljabery, Firas and Riklund, Katrine and Winerdal, Malin E and Krantz, David and Zirakzadeh, A Ali and Marits, Per and Sjöholm, Louise K and Sherif, Amir and Winqvist, Ola},
	month = aug,
	year = {2018},
	keywords = {*CD4-positive T lymphocytes, *DNA Methylation, *DNA methylation, *Urinary bladder neoplasms, Aged, Aged, 80 and over, CD4-Positive T-Lymphocytes/*cytology/immunology, Cell Differentiation, Cell Lineage, Cells, Cultured, CpG Islands, Cystectomy, Drug Therapy, Epigenesis, Genetic, Female, Forkhead Transcription Factors/genetics, Humans, Interferon-gamma/genetics, Interleukin-13/genetics, Interleukin-17/genetics, Male, Middle Aged, Neoadjuvant Therapy, Neoplasm Staging, Prognosis, Sequence Analysis, DNA/*methods, Treatment Outcome, Urinary Bladder Neoplasms/genetics/immunology/*pathology/*surgery},
	pages = {102--102}
}

@Article{keseler17ecocyc,
  author                 = {Keseler, Ingrid M. and Mackie, Amanda and Santos-Zavaleta, Alberto and Billington, Richard and Bonavides-Mart{\'i}nez, C{\'e}sar and Caspi, Ron and Fulcher, Carol and Gama-Castro, Socorro and Kothari, Anamika and Krummenacker, Markus and Latendresse, Mario and Mu{\~n}iz-Rascado, Luis and Ong, Quang and Paley, Suzanne and Peralta-Gil, Martin and Subhraveti, Pallavi and Vel{\'a}zquez-Ram{\'i}rez, David A. and Weaver, Daniel and Collado-Vides, Julio and Paulsen, Ian and Karp, Peter D.},
  title                  = {The {EcoCyc} database: reflecting new knowledge about Escherichia coli K-12.},
  journal                = {Nucleic Acids Res},
  year                   = {2017},
  volume                 = {45},
  pages                  = {D543-D550},
  optmonth                  = jan,
  abstract               = {EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.},
  article-doi            = {10.1093/nar/gkw1003},
  article-pii            = {gkw1003},
  completed              = {20170615},
  electronic-issn        = {1362-4962},
  electronic-publication = {20161129},
  history                = {2016/12/01 06:00 [entrez]},
  number                 = {D1},
  keywords               = {Computational Biology/*methods, *Databases, Genetic, Energy Metabolism, Escherichia coli K12/*genetics/*metabolism, Escherichia coli Proteins/genetics/metabolism, Gene Expression Regulation, Bacterial, Metabolic Networks and Pathways, Signal Transduction, Software, Transcription Factors/metabolism, Web Browser},
  location-id            = {10.1093/nar/gkw1003 [doi]},
  nlm-unique-id          = {0411011},
  owner                  = {NLM},
  print-issn             = {0305-1048},
  publication-status     = {ppublish},
  registry-number        = {0 (Transcription Factors)},
  revised                = {20181113},
  source                 = {Nucleic Acids Res. 2017 Jan 4;45(D1):D543-D550. doi: 10.1093/nar/gkw1003. Epub 2016 Nov 29.},
  status                 = {MEDLINE},
  subset                 = {IM},
  title-abbreviation     = {Nucleic Acids Res},
}

@article{fischer_ascorbic_2017,
	title = {Ascorbic acid, but not dehydroascorbic acid increases intracellular vitamin {C} content to decrease {Hypoxia} {Inducible} {Factor} -1 alpha activity and reduce malignant potential in human melanoma},
	volume = {86},
	issn = {1950-6007},
	doi = {10.1016/j.biopha.2016.12.056},
	abstract = {INTRODUCTION: Accumulation of hypoxia inducible factor-1 alpha (HIF-1α) in malignant tissue is known to contribute to oncogenic progression and is inversely associated with patient survival. Ascorbic acid (AA) depletion in malignant tissue may contribute to aberrant normoxic activity of HIF-1α. While AA supplementation has been shown to attenuate HIF-1α function in malignant melanoma, the use of dehydroascorbic acid (DHA) as a therapeutic means to increase intracellular AA and modulate HIF-1α function is yet to be evaluated. Here we compared the ability of AA and DHA to increase intracellular vitamin C content and decrease the malignant potential of human melanoma by reducing the activity of HIF-1α.
METHODS: HIF-1α protein accumulation was evaluated by western blot and transcriptional activity was evaluated by reporter gene assay using a HIF-1 HRE-luciferase plasmid. Protein expressions and subcellular localizations of vitamin C transporters were evaluated by western blot and confocal imaging. Intracellular vitamin C content following AA, ascorbate 2-phosphate (A2P), or DHA supplementation was determined using a vitamin C assay. Malignant potential was accessed using a 3D spheroid Matrigel invasion assay. Data was analyzed by One or Two-way ANOVA with Tukey's multiple comparisons test as appropriate with p{\textless}0.05 considered significant.
RESULTS: Melanoma cells expressed both sodium dependent vitamin C (SVCT) and glucose (GLUT) transporters for AA and DHA transport respectively, however advanced melanomas responded favorably to AA, but not DHA. Physiological glucose conditions significantly impaired intracellular vitamin C accumulation following DHA treatment. Consequently, A2P and AA, but not DHA treated cells demonstrated lower HIF-1α protein expression and activity, and reduced malignant potential. The ability of AA to regulate HIF-1α was dependent on SVCT2 function and SVCT2 was not significantly inhibited at pH representative of the tumor microenvironment.
CONCLUSIONS: The use of ascorbic acid as an adjuvant cancer therapy remains under investigated. While AA and A2P were capable of modulating HIF-1α protein accumulation/activity, DHA supplementation resulted in minimal intracellular vitamin C activity with decreased ability to inhibit HIF-1α activity and malignant potential in advanced melanoma. Restoring AA dependent regulation of HIF-1α in malignant cells may prove beneficial in reducing chemotherapy resistance and improving treatment outcomes.},
	language = {eng},
	journal = {Biomedicine \& Pharmacotherapy = Biomedecine \& Pharmacotherapie},
	author = {Fischer, Adam P. and Miles, Sarah L.},
	month = feb,
	year = {2017},
	pmid = {28012930},
	keywords = {Ascorbic Acid, Ascorbic acid, Biological Transport, Cell Line, Cell Line, Tumor, Dehydroascorbic Acid, Dehydroascorbic acid, Glucose, Humans, Hypoxia inducible factor-1 alpha, Hypoxia-Inducible Factor 1, alpha Subunit, Melanoma, SVCT2, Sodium, Transcription, Genetic, Tumor Microenvironment},
	pages = {502--513},
}

@article{
 title = {Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.},
 type = {article},
 year = {2016},
 identifiers = {[object Object]},
 keywords = {Animals,Culicidae,Evolution, Molecular,Genome, Insect,Hybridization, Genetic,Models, Genetic,Phylogeny,genetics},
 pages = {2361-2372},
 volume = {25},
 month = {6},
 id = {4969f961-914c-3873-8586-ae1ca0c7c0e9},
 created = {2017-09-07T16:35:51.015Z},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {49665d18-5720-3154-b3f7-40652b55b7b9},
 last_modified = {2017-09-15T13:46:36.898Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wen2016},
 source_type = {Journal Article},
 language = {eng},
 country = {England},
 patent_owner = {NLM},
 folder_uuids = {213ba69b-866b-4785-8816-8fc333e9477c},
 private_publication = {false},
 abstract = {The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.},
 bibtype = {article},
 author = {Wen, Dingqiao and Yu, Yun and Hahn, Matthew W and Nakhleh, Luay},
 journal = {Molecular ecology},
 number = {11}
}

@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}
}

@article{tang_tools_2016,
	title = {Tools for {Predicting} the {Functional} {Impact} of {Nonsynonymous} {Genetic} {Variation}},
	volume = {203},
	issn = {1943-2631},
	doi = {10.1534/genetics.116.190033},
	abstract = {As personal genome sequencing becomes a reality, understanding the effects of genetic variants on phenotype-particularly the impact of germline variants on disease risk and the impact of somatic variants on cancer development and treatment-continues to increase in importance. Because of their clear potential for affecting phenotype, nonsynonymous genetic variants (variants that cause a change in the amino acid sequence of a protein encoded by a gene) have long been the target of efforts to predict the effects of genetic variation. Whole-genome sequencing is identifying large numbers of nonsynonymous variants in each genome, intensifying the need for computational methods that accurately predict which of these are likely to impact disease phenotypes. This review focuses on nonsynonymous variant prediction with two aims in mind: (1) to review the prioritization methods that have been developed to date and the principles on which they are based and (2) to discuss the challenges to further improving these methods.},
	language = {eng},
	number = {2},
	journal = {Genetics},
	author = {Tang, Haiming and Thomas, Paul D.},
	year = {2016},
	pmid = {27270698},
	pmcid = {PMC4896183},
	keywords = {Genome, Human, Genome-Wide Association Study, Genomics, Humans, Polymorphism, Genetic, genetic variation, human disease, phenotypic effects, protein mutation},
	pages = {635--647},
}

@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{tse_cruciferous_2014,
	title = {Cruciferous vegetables and risk of colorectal neoplasms: a systematic review and meta-analysis},
	volume = {66},
	issn = {1532-7914},
	shorttitle = {Cruciferous vegetables and risk of colorectal neoplasms},
	doi = {10.1080/01635581.2014.852686},
	abstract = {Evidence shows cruciferous vegetables exhibit chemoprotective properties, commonly attributed to their rich source of isothiocyanates. However, epidemiological data examining the association between cruciferous vegetable intake and colorectal neoplasms have been inconclusive. This meta-analysis examines the epidemiological evidence to characterize the association between cruciferous vegetable intake and risk of developing colorectal neoplasms. Thirty-three articles were included in the meta-analysis after a literature search of electronic databases. Subgroup analysis for individual cruciferae types (n = 8 studies) and GST polymorphism (n = 8 studies) were performed. Pooled adjusted odds ratios (ORs) comparing highest and lowest categories of dietary pattern scores were calculated. Results show a statistically significant inverse association between cruciferous vegetable intake and colon cancer [OR = 0.84; 95\% confidence interval (CI): 0.72-0.98; P value heterogeneity {\textless} 0.001]. Broccoli in particular exhibited protective benefits against colorectal (CRC) neoplasms (OR = 0.80; 95\% CI: 0.65-0.99; P value heterogeneity = 0.02). Stratification by GST genotype reveals that the GSTT1 null genotype confers a reduction in CRC risk (OR = 0.78; 95\% CI: 0.64-0.95; P value heterogeneity = 0.32). This study provides support to the hypothesis that cruciferous vegetable intake protects against cancer of the colon. This study also demonstrates the significance of gene-diet interactions and the importance of assessing individual cruciferous vegetables.},
	language = {eng},
	number = {1},
	journal = {Nutrition and Cancer},
	author = {Tse, Genevieve and Eslick, Guy D.},
	year = {2014},
	pmid = {24341734},
	keywords = {Animals, Brassica, Brassicaceae, Colorectal Neoplasms, Disease Models, Animal, Feeding Behavior, Gene-Environment Interaction, Genotype, Glutathione Transferase, Humans, Observational Studies as Topic, Polymorphism, Genetic, Risk Factors, Vegetables},
	pages = {128--139},
}

@article{chi_meiosis_2014,
	title = {Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway},
	volume = {31},
	issn = {1537-1719},
	doi = {10.1093/molbev/mst258},
	abstract = {To establish which meiosis genes are present in ciliates, and to look for clues as to which recombination pathways may be treaded by them, four genomes were inventoried for 11 meiosis-specific and 40 meiosis-related genes. We found that the set of meiosis genes shared by Tetrahymena thermophila, Paramecium tetraurelia, Ichthyophthirius multifiliis, and Oxytricha trifallax is consistent with the prevalence of a Mus81-dependent class II crossover pathway that is considered secondary in most model eukaryotes. There is little evidence for a canonical class I crossover pathway that requires the formation of a synaptonemal complex (SC). This gene inventory suggests that meiotic processes in ciliates largely depend on mitotic repair proteins for executing meiotic recombination. We propose that class I crossovers and SCs were reduced sometime during the evolution of ciliates. Consistent with this reduction, we provide microscopic evidence for the presence only of degenerate SCs in Stylonychia mytilus. In addition, lower nonsynonymous to synonymous mutation rates of some of the meiosis genes suggest that, in contrast to most other nuclear genes analyzed so far, meiosis genes in ciliates are largely evolving at a slower rate than those genes in fungi and animals.},
	language = {eng},
	number = {3},
	journal = {Molecular Biology and Evolution},
	author = {Chi, Jingyun and Mahé, Frédéric and Loidl, Josef and Logsdon, John and Dunthorn, Micah},
	month = mar,
	year = {2014},
	pmid = {24336924},
	keywords = {Phylogeny, meiosis, Meiosis, Synaptonemal Complex, Cell Nucleus, Ciliophora, Crossing Over, Genetic, crossover pathway, Genes, Protozoan, genome architecture, Ichthyophthirius, Likelihood Functions, Oxytricha, Paramecium, phylogeny, Tetrahymena},
	pages = {660--672},
	file = {Texte intégral:C\:\\Users\\qcarrade\\Zotero\\storage\\VJ2TJC9X\\Chi et al. - 2014 - Meiosis gene inventory of four ciliates reveals th.pdf:application/pdf},
}

Paper  doi  abstract   bibtex   

@article{kim_chronic_2014,
	title = {Chronic exposure to ethanol of male mice before mating produces attention deficit hyperactivity disorder-like phenotype along with epigenetic dysregulation of dopamine transporter expression in mouse offspring.},
	volume = {92},
	issn = {1097-4547},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24510599},
	doi = {10.1002/jnr.23275},
	abstract = {Preconception exposure to EtOH through the paternal route may affect neurobehavioral and developmental features of offspring. This study investigates the effects of paternal exposure to EtOH before conception on the hyperactivity, inattention, and impulsivity behavior of male offspring in mice. Sire mice were treated with EtOH in a concentration range approximating human binge drinking (0-4 g/kg/day EtOH) for 7 weeks and mated with untreated females mice to produce offspring. EtOH exposure to sire mice induced attention deficit hyperactivity disorder (ADHD)-like hyperactive, inattentive, and impulsive behaviors in offspring. As a mechanistic link, both protein and mRNA expression of dopamine transporter (DAT), a key determinant of ADHD-like phenotypes in experimental animals and humans, were significantly decreased by paternal EtOH exposure in cerebral cortex and striatum of offspring mice along with increased methylation of a CpG region of the DAT gene promoter. The increase in methylation of DAT gene promoter was also observed in the sperm of sire mice, suggesting germline changes in the epigenetic methylation signature of DAT gene by EtOH exposure. In addition, the expression of two key regulators of methylation-dependent epigenetic regulation of functional gene expression, namely, MeCP2 and DNMT1, was markedly decreased in offspring cortex and striatum sired by EtOH-exposed mice. These results suggest that preconceptional exposure to EtOH through the paternal route induces behavioral changes in offspring, possibly via epigenetic changes in gene expression, which is essential for the regulation of ADHD-like behaviors.},
	number = {5},
	urldate = {2015-05-16},
	journal = {Journal of neuroscience research},
	author = {Kim, Pitna and Choi, Chang Soon and Park, Jin Hee and Joo, So Hyun and Kim, Soo Young and Ko, Hyun Myung and Kim, Ki Chan and Jeon, Se Jin and Park, Seung Hwa and Han, Seol-Heui and Ryu, Jong Hoon and Cheong, Jae Hoon and Han, Jung Yeol and Ko, Ki Narm and Shin, Chan Young},
	month = may,
	year = {2014},
	pmid = {24510599},
	keywords = {Animals, Attention Deficit Disorder with Hyperactivity, Attention Deficit Disorder with Hyperactivity: che, Avoidance Learning, Avoidance Learning: physiology, Central Nervous System Depressants, Central Nervous System Depressants: toxicity, Disease Models, Animal, Dopamine Plasma Membrane Transport Proteins, Dopamine Plasma Membrane Transport Proteins: genet, Dopamine Plasma Membrane Transport Proteins: metab, Drinking Behavior, Epigenesis, Genetic, Epigenesis, Genetic: drug effects, Ethanol, Ethanol: toxicity, Exploratory Behavior, Exploratory Behavior: physiology, Female, Gene Expression Regulation, Gene Expression Regulation: drug effects, Male, Maze Learning, Maze Learning: physiology, Methyl-CpG-Binding Protein 2, Methyl-CpG-Binding Protein 2: genetics, Methyl-CpG-Binding Protein 2: metabolism, Mice, Mice, Inbred ICR, Phenotype, Pregnancy, Prenatal Exposure Delayed Effects, Prenatal Exposure Delayed Effects: chemically indu, Prenatal Exposure Delayed Effects: physiopathology},
	pages = {658--70},
}

Paper  doi  abstract   bibtex   

@article{Tarsounas2013,
	title = {Genomes and {G}-quadruplexes: {For} better or for worse},
	volume = {425},
	issn = {00222836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24076189 http://linkinghub.elsevier.com/retrieve/pii/S0022283613006104 http://dx.doi.org/10.1016/j.jmb.2013.09.026},
	doi = {10.1016/j.jmb.2013.09.026},
	abstract = {Genomic integrity is crucial for correct chromosome segregation and physiological rates of cell proliferation. Mutations, deletions and translocations, hallmarks of human tumors, drive the aberrant proliferation and metastatic behavior of cancer cells. These chromosomal rearrangements often occur at genomic sites susceptible to breakage during DNA replication, including regions with G-quadruplex (G4)-forming potential. G4s are stable secondary structures that guanine-rich single-stranded DNA can readily adopt in vitro. However, their formation in eukaryotic cells has remained elusive and thus a subject of debate ever since they were first described. Recent work has more convincingly implicated G4s in a variety of biological processes including telomere maintenance, gene expression, epigenetic regulation and DNA replication. However, the downside of employing thermodynamically very stable alternative DNA structures as regulatory entities lies in their potential to also interfere with normal DNA metabolic processes, such as transcription and replication, which require readability of each base to faithfully transmit genetic information. Indeed, it has become clear that G4 structures can pose prominent barriers to replication fork progression and that they are also intrinsically recombinogenic. Here, we discuss mechanisms that cells evolved to counteract these detrimental effects, thereby ensuring the faithful inheritance of G4-containing genomes.},
	number = {23},
	journal = {Journal of Molecular Biology},
	author = {Tarsounas, Madalena and Tijsterman, Marcel},
	month = sep,
	year = {2013},
	pmid = {24076189},
	note = {tex.ids= tarsounasGenomesGQuadruplexesBetter2013, tarsounasGenomesGQuadruplexesBetter2013a
ISBN: 00222836
publisher: Elsevier B.V.},
	keywords = {DNA, DNA Replication, DNA replication, DNA-Directed DNA Polymerase, DNA: chemistry, DNA: metabolism, Eukaryota, Eukaryota: genetics, Eukaryota: physiology, G-Quadruplexes, G-quadruplex, Genetic, Genomic Instability, Transcription, genomic instability},
	pages = {4782--9},
}

@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}
}

Paper  doi  abstract   bibtex   

@article{Millevoi2012,
	title = {G-quadruplexes in {RNA} biology.},
	volume = {3},
	issn = {1757-7012},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22488917},
	doi = {10.1002/wrna.1113},
	abstract = {G-quadruplexes are noncanonical structures formed by G-rich DNA and RNA sequences that fold into a four-stranded conformation. Experimental studies and computational predictions show that RNA G-quadruplexes are present in transcripts associated with telomeres, in noncoding sequences of primary transcripts and within mature transcripts. RNA G-quadruplexes at these specific locations play important roles in key cellular functions, including telomere homeostasis and gene expression. Indeed, RNA G-quadruplexes appear as important regulators of pre-mRNA processing (splicing and polyadenylation), RNA turnover, mRNA targeting and translation. The regulatory mechanisms controlled by RNA G-quadruplexes involve the binding of protein factors that modulate G-quadruplex conformation and/or serve as a bridge to recruit additional protein regulators. In this review, we summarize the current knowledge on the role of G-quadruplexes in RNA biology with particular emphasis on the molecular mechanisms underlying their specific function in RNA metabolism occurring in physiological or pathological conditions.},
	number = {4},
	journal = {Wiley interdisciplinary reviews. RNA},
	author = {Millevoi, Stefania and Moine, Hervé and Vagner, Stéphan},
	year = {2012},
	pmid = {22488917},
	keywords = {\#nosource, G-Quadruplexes, Genetic, Humans, Polyadenylation, RNA, RNA Splicing, RNA: chemistry, RNA: metabolism, Telomere, Telomere: metabolism, Transcription},
	pages = {495--507},
}

@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}
}

Paper  doi  abstract   bibtex   

@article{Collins2012,
	title = {Incorporating {RNA}-seq data into the zebrafish {Ensembl} genebuild.},
	volume = {22},
	issn = {1549-5469},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3460200&tool=pmcentrez&rendertype=abstract},
	doi = {10.1101/gr.137901.112},
	abstract = {Ensembl gene annotation provides a comprehensive catalog of transcripts aligned to the reference sequence. It relies on publicly available species-specific and orthologous transcripts plus their inferred protein sequence. The accuracy of gene models is improved by increasing the species-specific component that can be cost-effectively achieved using RNA-seq. Two zebrafish gene annotations are presented in Ensembl version 62 built on the Zv9 reference sequence. Firstly, RNA-seq data from five tissues and seven developmental stages were assembled into 25,748 gene models. A 3'-end capture and sequencing protocol was developed to predict the 3' ends of transcripts, and 46.1\% of the original models were subsequently refined. Secondly, a standard Ensembl genebuild, incorporating carefully filtered elements from the RNA-seq-only build, followed by a merge with the manually curated VEGA database, produced a comprehensive annotation of 26,152 genes represented by 51,569 transcripts. The RNA-seq-only and the Ensembl/VEGA genebuilds contribute contrasting elements to the final genebuild. The RNA-seq genebuild was used to adjust intron/exon boundaries of orthologous defined models, confirm their expression, and improve 3' untranslated regions. Importantly, the inferred protein alignments within the Ensembl genebuild conferred proof of model contiguity for the RNA-seq models. The zebrafish gene annotation has been enhanced by the incorporation of RNA-seq data and the pipeline will be used for other organisms. Organisms with little species-specific cDNA data will generally benefit the most.},
	number = {10},
	urldate = {2014-02-12},
	journal = {Genome research},
	author = {Collins, John E and White, Simon and Searle, Stephen M J and Stemple, Derek L},
	month = oct,
	year = {2012},
	pmid = {22798491},
	keywords = {3' Untranslated Regions, Animals, Computational Biology, Computational Biology: methods, DNA, Complementary, Databases, Nucleic Acid, Exons, Genomics, Genomics: methods, Introns, Male, Models, Genetic, Molecular Sequence Annotation, RNA, RNA: chemistry, RNA: genetics, Transcription, Genetic, Zebrafish, Zebrafish: genetics},
	pages = {2067--78},
}

@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},
}

Paper  doi  abstract   bibtex   

@ARTICLE{Musselman2012787,
author={Musselman, C.A. and Ramiŕez, J. and Sims, J.K. and Mansfield, R.E. and Oliver, S.S. and Denu, J.M. and Mackay, J.P. and Wade, P.A. and Hagman, J. and Kutateladze, T.G.},
title={Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression},
journal={Proceedings of the National Academy of Sciences of the United States of America},
year={2012},
volume={109},
number={3},
pages={787-792},
doi={10.1073/pnas.1113655109},
note={cited By 83},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856383786&doi=10.1073%2fpnas.1113655109&partnerID=40&md5=4d2a65c28bfef9051873d7efabd60bbd},
affiliation={Department of Pharmacology, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States; Integrated Department of Immunology, National Jewish Health, Denver, CO 80206, United States; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States; School of Molecular Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, United States},
abstract={CHD4 is a catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex essential in transcriptional regulation, chromatin assembly and DNA damage repair. CHD4 contains tandem plant homeodomain (PHD) fingers connected by a short linker, the biological function of which remains unclear. Here we explore the combinatorial action of the CHD4 PHD1/2 fingers and detail the molecular basis for their association with chromatin. We found that PHD1/2 targets nucleosomes in a multivalent manner, concomitantly engaging two histone H3 tails. This robust synergistic interaction displaces HP1γ from pericentric sites, inducing changes in chromatin structure and leading to the dispersion of the heterochromatic mark H3K9me3. We demonstrate that recognition of the histone H3 tails by the PHD fingers is required for repressive activity of the CHD4/NuRD complex. Together, our data elucidate the molecular mechanism of multivalent association of the PHD fingers with chromatin and reveal their critical role in the regulation of CHD4 functions.},
author_keywords={Epigenetics;  Gene repression;  Histone;  Posttranslational modifications},
keywords={adenosine triphosphatase;  chromodomain helicase DNA binding protein 4;  DNA binding protein;  heterochromatin protein 1;  histone deacetylase;  histone H3;  homeodomain protein;  unclassified drug, animal cell;  article;  chromatin;  controlled study;  dispersion;  molecular recognition;  nonhuman;  nucleosome;  priority journal, Amino Acid Sequence;  HEK293 Cells;  Heterochromatin;  Histones;  Homeodomain Proteins;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Models, Molecular;  Molecular Sequence Data;  Nucleosomes;  Protein Processing, Post-Translational;  Protein Structure, Tertiary;  Repressor Proteins;  Transcription, Genetic},
correspondence_address1={Kutateladze, T.G.; Department of Pharmacology, , Aurora, CO 80045, United States; email: Tatiana.Kutateladze@UCDenver.edu},
issn={00278424},
coden={PNASA},
pubmed_id={22215588},
language={English},
abbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},
document_type={Article},
source={Scopus},
}

Paper  doi  abstract   bibtex   

@article{dudley_epigenetic_2011,
	title = {Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders.},
	volume = {35},
	issn = {1873-7528},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21251925},
	doi = {10.1016/j.neubiorev.2010.12.016},
	abstract = {The impact that stressful encounters have upon long-lasting behavioural phenotypes is varied. Whereas a significant proportion of the population will develop "stress-related" conditions such as post-traumatic stress disorder or depression in later life, the majority are considered "resilient" and are able to cope with stress and avoid such psychopathologies. The reason for this heterogeneity is undoubtedly multi-factorial, involving a complex interplay between genetic and environmental factors. Both genes and environment are of critical importance when it comes to developmental processes, and it appears that subtle differences in either of these may be responsible for altering developmental trajectories that confer vulnerability or resilience. At the molecular level, developmental processes are regulated by epigenetic mechanisms, with recent clinical and pre-clinical data obtained by ourselves and others suggesting that epigenetic differences in various regions of the brain are associated with a range of psychiatric disorders, including many that are stress-related. Here we provide an overview of how these epigenetic differences, and hence susceptibility to psychiatric disorders, might arise through exposure to stress-related factors during critical periods of development.},
	number = {7},
	urldate = {2012-03-24},
	journal = {Neuroscience and biobehavioral reviews},
	author = {Dudley, Kevin J and Li, Xiang and Kobor, Michael S and Kippin, Tod E and Bredy, Timothy W},
	month = jun,
	year = {2011},
	pmid = {21251925},
	note = {Publisher: Elsevier Ltd},
	keywords = {Brain, Brain: growth \& development, Brain: physiology, Disease Susceptibility, Disease Susceptibility: psychology, Epigenesis, Genetic, Epigenesis, Genetic: genetics, Humans, Mental Disorders, Mental Disorders: complications, Mental Disorders: genetics, Mental Disorders: psychology, Models, Genetic, Resilience, Psychological, Stress, Psychological, Stress, Psychological: complications, Stress, Psychological: genetics, Stress, Psychological: psychology},
	pages = {1544--51},
}

@article{hollingworth_common_2011,
	title = {Common variants at {ABCA7}, {MS4A6A}/{MS4A4E}, {EPHA1}, {CD33} and {CD2AP} are associated with {Alzheimer}'s disease},
	volume = {43},
	issn = {1546-1718},
	doi = {10.1038/ng.803},
	abstract = {We sought to identify new susceptibility loci for Alzheimer's disease through a staged association study (GERAD+) and by testing suggestive loci reported by the Alzheimer's Disease Genetic Consortium (ADGC) in a companion paper. We undertook a combined analysis of four genome-wide association datasets (stage 1) and identified ten newly associated variants with P ≤ 1 × 10(-5). We tested these variants for association in an independent sample (stage 2). Three SNPs at two loci replicated and showed evidence for association in a further sample (stage 3). Meta-analyses of all data provided compelling evidence that ABCA7 (rs3764650, meta P = 4.5 × 10(-17); including ADGC data, meta P = 5.0 × 10(-21)) and the MS4A gene cluster (rs610932, meta P = 1.8 × 10(-14); including ADGC data, meta P = 1.2 × 10(-16)) are new Alzheimer's disease susceptibility loci. We also found independent evidence for association for three loci reported by the ADGC, which, when combined, showed genome-wide significance: CD2AP (GERAD+, P = 8.0 × 10(-4); including ADGC data, meta P = 8.6 × 10(-9)), CD33 (GERAD+, P = 2.2 × 10(-4); including ADGC data, meta P = 1.6 × 10(-9)) and EPHA1 (GERAD+, P = 3.4 × 10(-4); including ADGC data, meta P = 6.0 × 10(-10)).},
	language = {eng},
	number = {5},
	journal = {Nature Genetics},
	author = {Hollingworth, Paul and Harold, Denise and Sims, Rebecca and Gerrish, Amy and Lambert, Jean-Charles and Carrasquillo, Minerva M. and Abraham, Richard and Hamshere, Marian L. and Pahwa, Jaspreet Singh and Moskvina, Valentina and Dowzell, Kimberley and Jones, Nicola and Stretton, Alexandra and Thomas, Charlene and Richards, Alex and Ivanov, Dobril and Widdowson, Caroline and Chapman, Jade and Lovestone, Simon and Powell, John and Proitsi, Petroula and Lupton, Michelle K. and Brayne, Carol and Rubinsztein, David C. and Gill, Michael and Lawlor, Brian and Lynch, Aoibhinn and Brown, Kristelle S. and Passmore, Peter A. and Craig, David and McGuinness, Bernadette and Todd, Stephen and Holmes, Clive and Mann, David and Smith, A. David and Beaumont, Helen and Warden, Donald and Wilcock, Gordon and Love, Seth and Kehoe, Patrick G. and Hooper, Nigel M. and Vardy, Emma R. L. C. and Hardy, John and Mead, Simon and Fox, Nick C. and Rossor, Martin and Collinge, John and Maier, Wolfgang and Jessen, Frank and Rüther, Eckart and Schürmann, Britta and Heun, Reiner and Kölsch, Heike and van den Bussche, Hendrik and Heuser, Isabella and Kornhuber, Johannes and Wiltfang, Jens and Dichgans, Martin and Frölich, Lutz and Hampel, Harald and Gallacher, John and Hüll, Michael and Rujescu, Dan and Giegling, Ina and Goate, Alison M. and Kauwe, John S. K. and Cruchaga, Carlos and Nowotny, Petra and Morris, John C. and Mayo, Kevin and Sleegers, Kristel and Bettens, Karolien and Engelborghs, Sebastiaan and De Deyn, Peter P. and Van Broeckhoven, Christine and Livingston, Gill and Bass, Nicholas J. and Gurling, Hugh and McQuillin, Andrew and Gwilliam, Rhian and Deloukas, Panagiotis and Al-Chalabi, Ammar and Shaw, Christopher E. and Tsolaki, Magda and Singleton, Andrew B. and Guerreiro, Rita and Mühleisen, Thomas W. and Nöthen, Markus M. and Moebus, Susanne and Jöckel, Karl-Heinz and Klopp, Norman and Wichmann, H.-Erich and Pankratz, V. Shane and Sando, Sigrid B. and Aasly, Jan O. and Barcikowska, Maria and Wszolek, Zbigniew K. and Dickson, Dennis W. and Graff-Radford, Neill R. and Petersen, Ronald C. and {Alzheimer's Disease Neuroimaging Initiative} and van Duijn, Cornelia M. and Breteler, Monique M. B. and Ikram, M. Arfan and DeStefano, Anita L. and Fitzpatrick, Annette L. and Lopez, Oscar and Launer, Lenore J. and Seshadri, Sudha and {CHARGE consortium} and Berr, Claudine and Campion, Dominique and Epelbaum, Jacques and Dartigues, Jean-François and Tzourio, Christophe and Alpérovitch, Annick and Lathrop, Mark and {EADI1 consortium} and Feulner, Thomas M. and Friedrich, Patricia and Riehle, Caterina and Krawczak, Michael and Schreiber, Stefan and Mayhaus, Manuel and Nicolhaus, S. and Wagenpfeil, Stefan and Steinberg, Stacy and Stefansson, Hreinn and Stefansson, Kari and Snaedal, Jon and Björnsson, Sigurbjörn and Jonsson, Palmi V. and Chouraki, Vincent and Genier-Boley, Benjamin and Hiltunen, Mikko and Soininen, Hilkka and Combarros, Onofre and Zelenika, Diana and Delepine, Marc and Bullido, Maria J. and Pasquier, Florence and Mateo, Ignacio and Frank-Garcia, Ana and Porcellini, Elisa and Hanon, Olivier and Coto, Eliecer and Alvarez, Victoria and Bosco, Paolo and Siciliano, Gabriele and Mancuso, Michelangelo and Panza, Francesco and Solfrizzi, Vincenzo and Nacmias, Benedetta and Sorbi, Sandro and Bossù, Paola and Piccardi, Paola and Arosio, Beatrice and Annoni, Giorgio and Seripa, Davide and Pilotto, Alberto and Scarpini, Elio and Galimberti, Daniela and Brice, Alexis and Hannequin, Didier and Licastro, Federico and Jones, Lesley and Holmans, Peter A. and Jonsson, Thorlakur and Riemenschneider, Matthias and Morgan, Kevin and Younkin, Steven G. and Owen, Michael J. and O'Donovan, Michael and Amouyel, Philippe and Williams, Julie},
	month = may,
	year = {2011},
	pmid = {21460840},
	pmcid = {PMC3084173},
	keywords = {Aged, Alzheimer Disease, Humans, Female, Male, Aged, 80 and over, Genetic Predisposition to Disease, Case-Control Studies, Genome-Wide Association Study, Adaptor Proteins, Signal Transducing, Polymorphism, Single Nucleotide, Antigens, CD, Antigens, Differentiation, Myelomonocytic, ATP-Binding Cassette Transporters, Cytoskeletal Proteins, Databases, Genetic, Genetic Variation, Membrane Proteins, Multigene Family, Receptor, EphA1, Sialic Acid Binding Ig-like Lectin 3},
	pages = {429--435}
}

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{symington_double-strand_2011,
	title = {Double-strand break end resection and repair pathway choice},
	volume = {45},
	issn = {1545-2948},
	doi = {10.1146/annurev-genet-110410-132435},
	abstract = {DNA double-strand breaks (DSBs) are cytotoxic lesions that can result in mutagenic events or cell death if left unrepaired or repaired inappropriately. Cells use two major pathways for DSB repair: nonhomologous end joining (NHEJ) and homologous recombination (HR). The choice between these pathways depends on the phase of the cell cycle and the nature of the DSB ends. A critical determinant of repair pathway choice is the initiation of 5'-3' resection of DNA ends, which commits cells to homology-dependent repair, and prevents repair by classical NHEJ. Here, we review the components of the end resection machinery, the role of end structure, and the cell-cycle phase on resection and the interplay of end processing with NHEJ.},
	language = {eng},
	journal = {Annual Review of Genetics},
	author = {Symington, Lorraine S. and Gautier, Jean},
	year = {2011},
	keywords = {Animals, Cell cycle, DNA Breaks, Double-Stranded, DNA End-Joining Repair, DNA Helicases, Exodeoxyribonucleases, Fanconi Anemia, Gene Expression Regulation, Fungal, Genes, BRCA1, Genes, Fungal, Genes, cdc, Humans, Protein Conformation, Recombinational DNA Repair, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Translocation, Genetic},
	pages = {247--271},
}

@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}
}

@article{roepcke_tandem_2011,
	title = {A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins {NonO} and {SFPQ}},
	volume = {12},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-12-624},
	abstract = {BACKGROUND: Bioinformatic analyses of expression control sequences in promoters of co-expressed or functionally related genes enable the discovery of common regulatory sequence motifs that might be involved in co-ordinated gene expression. By studying promoter sequences of the human ribosomal protein genes we recently identified a novel highly specific Localized Tandem Sequence Motif (LTSM). In this work we sought to identify additional genes and LTSM-binding proteins to elucidate potential regulatory mechanisms.
RESULTS: Genome-wide analyses allowed finding a considerable number of additional LTSM-positive genes, the products of which are involved in translation, among them, translation initiation and elongation factors, and 5S rRNA. Electromobility shift assays then showed specific signals demonstrating the binding of protein complexes to LTSM in ribosomal protein gene promoters. Pull-down assays with LTSM-containing oligonucleotides and subsequent mass spectrometric analysis identified the related multifunctional nucleotide binding proteins NonO and SFPQ in the binding complex. Functional characterization then revealed that LTSM enhances the transcriptional activity of the promoters in dependency of the distance from the transcription start site.
CONCLUSIONS: Our data demonstrate the power of bioinformatic analyses for the identification of biologically relevant sequence motifs. LTSM and the here found LTSM-binding proteins NonO and SFPQ were discovered through a synergistic combination of bioinformatic and biochemical methods and are regulators of the expression of a set of genes of the translational apparatus in a distance-dependent manner.},
	language = {eng},
	journal = {BMC genomics},
	author = {Roepcke, Stefan and Stahlberg, Silke and Klein, Holger and Schulz, Marcel H. and Theobald, Lars and Gohlke, Sabrina and Vingron, Martin and Walther, Diego J.},
	month = dec,
	year = {2011},
	pmid = {22185324},
	pmcid = {PMC3262029},
	keywords = {DNA-Binding Proteins, Enhancer Elements, Genetic, Humans, Nuclear Matrix-Associated Proteins, Octamer Transcription Factors, Promoter Regions, Genetic, Protein Binding, Protein Biosynthesis, PTB-Associated Splicing Factor, RNA-Binding Proteins},
	pages = {624},
	file = {Volltext:/Users/mschulz/Zotero/storage/2IRGDRJH/Roepcke et al. - 2011 - A tandem sequence motif acts as a distance-depende.pdf:application/pdf},
}

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},
}

@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  doi  abstract   bibtex   

@article{Viglasky2009,
	title = {Platination of telomeric sequences and nuclease hypersensitive elements of human c-myc and {PDGF}-{A} promoters and their ability to form {G}-quadruplexes.},
	volume = {276},
	issn = {1742-4658},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19054066},
	doi = {10.1111/j.1742-4658.2008.06782.x},
	abstract = {Naturally occurring G-rich DNA sequences that are able to form G-quadruplex structures appear as potential targets for anti-cancer chemotherapy, and therefore play an important role in cellular processes, such as cell aging, death and carcinogenesis. The telomeric regions of DNA and nuclease hypersensitive elements of human c-myc and PDGF-A promoters represent a very appealing target for cisplatin and may interfere with normal DNA function. Platinum complexes bind covalently to nucleobases, and especially to the N7 atom of guanines, and the four guanines of a G-quartet have their N7 atoms involved in hydrogen bonding. Therefore, within a G-quadruplex structure, only the guanines out of the stack of G-quartets should react with electrophilic species such as platinum (II) complexes. Platinum complexes have significant influence on the formation of G-quadruplexes. Results obtained by CD spectroscopy and temperature gradient-gel electrophoresis clearly demonstrate that DNA platination significantly affects G-quadruplex folding for telomeric sequences; the abundance of un/misfolded DNAs compared to the G-quadruplex is proportional to the platinum concentration.},
	number = {2},
	journal = {The FEBS journal},
	author = {Viglasky, Viktor},
	month = jan,
	year = {2009},
	pmid = {19054066},
	keywords = {\#nosource, Chromosomal Instability, Circular Dichroism, Endonucleases, Endonucleases: metabolism, G-Quadruplexes, Genetic, Genetic: genetics, Humans, Models, Molecular, Platelet-Derived Growth Factor, Platelet-Derived Growth Factor: genetics, Platelet-Derived Growth Factor: metabolism, Platinum, Platinum: metabolism, Promoter Regions, Proto-Oncogene Proteins c-myc, Proto-Oncogene Proteins c-myc: genetics, Proto-Oncogene Proteins c-myc: metabolism, Substrate Specificity, Telomere, Telomere: genetics, Telomere: metabolism, Temperature, Transition Temperature},
	pages = {401--9},
}

Paper  doi  abstract   bibtex   

@article{Barros2009,
	title = {Effect of monovalent cations and {G}-quadruplex structures on the outcome of intramolecular homologous recombination.},
	volume = {276},
	issn = {1742-4658},
	url = {http://dx.doi.org/10.1111/j.1742-4658.2009.07013.x http://www.ncbi.nlm.nih.gov/pubmed/19490102},
	doi = {10.1111/j.1742-4658.2009.07013.x},
	abstract = {Homologous recombination is a very important cellular process, as it provides a major pathway for the repair of DNA double-strand breaks. This complex process is affected by many factors within cells. Here, we have studied the effect of monovalent cations (K+, Na+, and NH4+) on the outcome of recombination events, as their presence affects the biochemical activities of the proteins involved in recombination as well as the structure of DNA. For this purpose, we used an in vitro recombination system that includes a protein nuclear extract, as a source of recombination machinery, and two plasmids as substrates for intramolecular homologous recombination, each with two copies of different alleles of the human minisatellite MsH43. We found that the presence of monovalent cations induced a decrease in the recombination frequency, accompanied by an increase in the fidelity of the recombination. Moreover, there is an emerging consensus that secondary structures of DNA have the potential to induce genomic instability. Therefore, we analyzed the effect of the sequences capable of forming G-quadruplex on the production of recombinant molecules, taking advantage of the capacity of some MsH43 alleles to generate these kinds of structure in the presence of K+. We observed that the MsH43 recombinants containing duplications, generated in the presence of K+, did not include the repeats located towards the 5'-side of the G-quadruplex motif, suggesting that this structure may be involved in the recombination events leading to duplications. Our results provide new insights into the molecular mechanisms underlying the recombination of repetitive sequences.},
	number = {11},
	journal = {The FEBS journal},
	author = {Barros, Paula and Boán, Francisco and Blanco, Miguel G and Gómez-Márquez, Jaime},
	month = jun,
	year = {2009},
	pmid = {19490102},
	note = {tex.city: Departamento de Bioqumica e Bioloxa Molecular, Facultade de Bioloxa-CIBUS, Universidade de Santiago de Compostela, Spain},
	keywords = {\#nosource, Agar Gel, Ammonium Chloride, Ammonium Chloride: pharmacology, Cations, Electrophoresis, G-Quadruplexes, G-Quadruplexes: drug effects, Genetic, Genetic: drug effects, Humans, Microsatellite Repeats, Microsatellite Repeats: genetics, Models, Monovalent, Monovalent: pharmacology, Plasmids, Plasmids: genetics, Polymerase Chain Reaction, Potassium Chloride, Potassium Chloride: pharmacology, Recombination, Sodium Chloride, Sodium Chloride: pharmacology},
	pages = {2983--93},
}

Paper  doi  abstract   bibtex   

@article{Kumar2009,
	title = {Elevated polyamines induce c-{MYC} overexpression by perturbing quadruplex-{WC} duplex equilibrium.},
	volume = {37},
	issn = {1362-4962},
	url = {internal-pdf:/1081832707yc overexpression.pdf http://nar.oxfordjournals.org/cgi/content/abstract/37/10/3321 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2691834&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkp196},
	abstract = {The biological role of quadruplexes and polyamines has been independently associated with cancer. However, quadruplex-polyamine mediated transcriptional regulation remain unaddressed. Herein, using c-MYC quadruplex model, we have attempted to understand quadruplex-polyamine interaction and its role in transcriptional regulation. We initially employed biophysical approach involving CD, UV and FRET to understand the role of polyamines (spermidine and spermine) on conformation, stability, molecular recognition of quadruplex and to investigate the effect of polyamines on quadruplex-Watson Crick duplex transition. Our study demonstrates that polyamines affect the c-MYC quadruplex conformation, perturb its recognition properties and delays duplex formation. The relative free energy difference (DeltaDeltaG degrees) between the duplex and quadruplex structure indicate that polyamines stabilize and favor c-MYC quadruplex over duplex. Further, we investigated the influence of polyamine mediated perturbation of this equilibrium on c-MYC expression. Our results suggest that polyamines induce structural transition of c-MYC quadruplex to a transcriptionally active motif with distinctive molecular recognition property, which drives c-MYC expression. These findings may allow exploiting quadruplex-polyamines interaction for developing antiproliferative strategies to combat aberrant gene expression.},
	number = {10},
	journal = {Nucleic acids research},
	author = {Kumar, Niti and Basundra, Richa and Maiti, Souvik},
	month = jun,
	year = {2009},
	pmid = {19324889},
	keywords = {\#nosource, Circular Dichroism, Fluorescence Resonance Energy Transfer, G-Quadruplexes, G-Quadruplexes: drug effects, Genes, Genetic, HeLa Cells, Humans, Nucleic Acid Denaturation, Promoter Regions, Proto-Oncogene Proteins c-myc, Proto-Oncogene Proteins c-myc: genetics, Spermidine, Spermidine: pharmacology, Spermine, Spermine: pharmacology, Thermodynamics, myc},
	pages = {3321--31},
}

@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},
}

Paper  doi  abstract   bibtex   

@article{wood_high_2008,
	title = {High heritability for a composite index of children's activity level measures.},
	volume = {38},
	issn = {0001-8244},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2493057&tool=pmcentrez&rendertype=abstract},
	doi = {10.1007/s10519-008-9196-1},
	abstract = {Despite the high heritability of children's activity level, which forms part of the core symptom domain of hyperactivity-impulsivity within attention deficit hyperactivity disorder (ADHD), there has only been a limited success with identifying candidate genes involved in its etiology. This may reflect a lack of understanding about the different measures used to define activity level across studies. We aimed to study the genetic and environmental etiology across three measures of activity level: parent and teacher ratings of hyperactivity-impulsivity and actigraph measurements, within a population-based sample of 463 7-9 year old twin pairs. We further examined ways in which the three measures could be combined for future molecular studies. Phenotypic correlations across measures were modest, but a common underlying phenotypic factor was highly heritable (92\%); as was a simple aggregation of all three measurements (77\%). This suggests that distilling what is common to all three measures may be a good method for generating a quantitative trait suitable for molecular studies of activity level in children. The high heritabilities found are encouraging in this respect.},
	number = {3},
	urldate = {2015-05-12},
	journal = {Behavior genetics},
	author = {Wood, Alexis C and Rijsdijk, Frühling and Saudino, Kimberly J and Asherson, Philip and Kuntsi, Jonna},
	month = may,
	year = {2008},
	pmid = {18297388},
	keywords = {Attention Deficit and Disruptive Behavior Disorder, Child, Family Health, Female, Genetic Predisposition to Disease, Humans, Impulsive Behavior, Impulsive Behavior: genetics, Male, Models, Genetic, Models, Statistical, Motor Activity, Multivariate Analysis, Parents, Phenotype},
	pages = {266--76},
}

Website  abstract   bibtex   

@article{
 title = {Classifier subset selection for biomedical named entity recognition},
 type = {article},
 year = {2008},
 identifiers = {[object Object]},
 keywords = {algorithms,biomedical named entity recognition,classifier ensembles,classifier subset selection,genetic,natural language processing,weighted voting},
 pages = {267-282},
 volume = {31},
 websites = {http://www.springerlink.com/index/10.1007/s10489-008-0124-0},
 publisher = {Springer},
 id = {d9d0225b-5aa3-3e52-8638-0987c12ca320},
 created = {2012-12-24T15:02:36.000Z},
 file_attached = {false},
 profile_id = {5284e6aa-156c-3ce5-bc0e-b80cf09f3ef6},
 group_id = {066b42c8-f712-3fc3-abb2-225c158d2704},
 last_modified = {2017-03-14T14:36:19.698Z},
 tags = {named entity recognition},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Dimililer2008},
 private_publication = {false},
 abstract = {Classifier ensembling approach is considered for biomedical named entity recognition task. A vote-based classifier selection scheme having an intermediate level of search complexity between static classifier selection and real-valued and class-dependent weighting approaches is de- veloped. Assuming that the reliability of the predictions of each classifier differs among classes, the proposed approach is based on selection of the classifiers by taking into account their individual votes. A wide set of classifiers, each based on a different set of features and modeling parameter setting are generated for this purpose. A genetic algorithm is de- veloped so as to label the predictions of these classifiers as reliable or not. During testing, the votes that are labeled as being reliable are combined usingweighted majority voting. The classifier ensemble formed by the proposed scheme sur- passes the full object F-score of the best individual classifier by 2.75% and it is the highest score achieved on the data set considered.},
 bibtype = {article},
 author = {Dimililer, Nazife and Varoğlu, Ekrem and Altınçay, Hakan},
 journal = {Applied Intelligence},
 number = {3}
}

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  doi  abstract   bibtex   

@article{Scott2007,
	title = {Targeting neural circuitry in zebrafish using {GAL4} enhancer trapping.},
	volume = {4},
	issn = {1548-7091},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17369834},
	doi = {10.1038/nmeth1033},
	abstract = {We present a pilot enhancer trap screen using GAL4 to drive expression of upstream activator sequence (UAS)-linked transgenes in expression patterns dictated by endogenous enhancers in zebrafish. The patterns presented include expression in small subsets of neurons throughout the larval brain, which in some cases persist into adult. Through targeted photoconversion of UAS-driven Kaede and variegated expression of UAS-driven GFP in single cells, we begin to characterize the cellular components of labeled circuits.},
	number = {4},
	urldate = {2014-04-04},
	journal = {Nature methods},
	author = {Scott, Ethan K and Mason, Lindsay and Arrenberg, Aristides B and Ziv, Limor and Gosse, Nathan J and Xiao, Tong and Chi, Neil C and Asakawa, Kazuhide and Kawakami, Koichi and Baier, Herwig},
	month = apr,
	year = {2007},
	pmid = {17369834},
	keywords = {Animals, Animals, Genetically Modified, Brain, Brain: cytology, Brain: embryology, Brain: metabolism, DNA-Binding Proteins, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Humans, Neurons, Neurons: metabolism, Pilot Projects, Saccharomyces cerevisiae Proteins, Saccharomyces cerevisiae Proteins: biosynthesis, Saccharomyces cerevisiae Proteins: genetics, Transcription Factors, Transcription Factors: biosynthesis, Transcription Factors: genetics, Transgenes, Zebrafish, Zebrafish: embryology, Zebrafish: genetics, Zebrafish: metabolism, enhancer trap},
	pages = {323--6},
}

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},
}

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{RN6200,
   author = {Steidl, U. and Rosenbauer, F. and Verhaak, R. G. and Gu, X. and Ebralidze, A. and Otu, H. H. and Klippel, S. and Steidl, C. and Bruns, I. and Costa, D. B. and Wagner, K. and Aivado, M. and Kobbe, G. and Valk, P. J. and Passegué, E. and Libermann, T. A. and Delwel, R. and Tenen, D. G.},
   title = {Essential role of Jun family transcription factors in PU.1 knockdown-induced leukemic stem cells},
   journal = {Nat Genet},
   volume = {38},
   number = {11},
   pages = {1269-77},
   note = {Steidl, Ulrich
Rosenbauer, Frank
Verhaak, Roel G W
Gu, Xuesong
Ebralidze, Alexander
Otu, Hasan H
Klippel, Steffen
Steidl, Christian
Bruns, Ingmar
Costa, Daniel B
Wagner, Katharina
Aivado, Manuel
Kobbe, Guido
Valk, Peter J M
Passegué, Emmanuelle
Libermann, Towia A
Delwel, Ruud
Tenen, Daniel G
CA41456/CA/NCI NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
United States
2006/10/17
Nat Genet. 2006 Nov;38(11):1269-77. doi: 10.1038/ng1898. Epub 2006 Oct 15.},
   abstract = {Knockdown of the transcription factor PU.1 (encoded by Sfpi1) leads to acute myeloid leukemia (AML) in mice. We examined the transcriptome of preleukemic hematopoietic stem cells (HSCs) in which PU.1 was knocked down (referred to as 'PU.1-knockdown HSCs') to identify transcriptional changes preceding malignant transformation. Transcription factors c-Jun and JunB were among the top-downregulated targets. Restoration of c-Jun expression in preleukemic cells rescued the PU.1 knockdown-initiated myelomonocytic differentiation block. Lentiviral restoration of JunB at the leukemic stage led to loss of leukemic self-renewal capacity and prevented leukemia in NOD-SCID mice into which leukemic PU.1-knockdown cells were transplanted. Examination of human individuals with AML confirmed the correlation between PU.1 and JunB downregulation. These results delineate a transcriptional pattern that precedes leukemic transformation in PU.1-knockdown HSCs and demonstrate that decreased levels of c-Jun and JunB contribute to the development of PU.1 knockdown-induced AML by blocking differentiation and increasing self-renewal. Therefore, examination of disturbed gene expression in HSCs can identify genes whose dysregulation is essential for leukemic stem cell function and that are targets for therapeutic interventions.},
   keywords = {Animals
Cell Differentiation/genetics
Cell Transformation, Neoplastic/genetics
Down-Regulation
Granulocytes/cytology
Hematopoietic Stem Cell Transplantation
Hematopoietic Stem Cells/cytology/metabolism/*pathology
Humans
Leukemia, Myeloid, Acute/*genetics/metabolism/pathology
Mice
Mice, Inbred NOD
Mice, Knockout
Mice, SCID
Monocytes/cytology
Proto-Oncogene Proteins/*genetics/metabolism
Proto-Oncogene Proteins c-jun/genetics/metabolism/*physiology
Trans-Activators/*genetics/metabolism
Transcription, Genetic
Transduction, Genetic},
   ISSN = {1061-4036 (Print)
1061-4036},
   DOI = {10.1038/ng1898},
   year = {2006},
   type = {Journal Article}
}

@article{mulholland_genomic_2006,
	title = {Genomic profiling identifies discrete deletions associated with translocations in glioblastoma multiforme},
	volume = {5},
	issn = {1551-4005},
	doi = {10.4161/cc.5.7.2631},
	abstract = {Glioblastoma multiforme is the most common tumor arising in the central nervous system. Patients with these tumors have limited treatment options and their disease is invariably fatal. Molecularly targeted agents offer the potential to improve patient treatment, however the use of these will require a fuller understanding of the genetic changes in these complex tumors. In this study, we identify copy number changes in a series of glioblastoma multiforme tumors and cell lines by applying high-resolution microarray comparative genomic hybridization. Molecular cytogenetic characterization of the cell lines revealed that copy number changes define translocation breakpoints. We focused on chromosome 6 and further characterized three regions of copy number change associated with translocations including a discrete deletion involving IGF2R, PARK2, PACRG and QKI and an unbalanced translocation involving POLH, GTPBP2 and PTPRZ1.},
	language = {eng},
	number = {7},
	journal = {Cell Cycle (Georgetown, Tex.)},
	author = {Mulholland, Paul J. and Fiegler, Heike and Mazzanti, Chiara and Gorman, Patricia and Sasieni, Peter and Adams, Joanna and Jones, Tania A. and Babbage, Jane W. and Vatcheva, Radost and Ichimura, Koichi and East, Philip and Poullikas, Chrysanthos and Collins, V. Peter and Carter, Nigel P. and Tomlinson, Ian P. M. and Sheer, Denise},
	month = apr,
	year = {2006},
	pmid = {16582634},
	keywords = {Adult, Aged, Cell Line, Tumor, Chromosome Deletion, Chromosomes, Human, Pair 6, Chromosomes, Human, Pair 7, Cytogenetics, Female, Gene Dosage, Gene Expression, Gene Expression Profiling, Genome, Human, Genomics, Glioblastoma, Humans, In Situ Hybridization, Fluorescence, Male, Middle Aged, Nucleic Acid Hybridization, Translocation, Genetic},
	pages = {783--791},
}

@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 = {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  doi  abstract   bibtex   

@article{Yafe2005,
	title = {Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes.},
	volume = {33},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1133794&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gki606},
	abstract = {Clustered guanine residues in DNA readily generate hairpin or a variety of tetrahelical structures. The myogenic determination protein MyoD was reported to bind to a tetrahelical structure of guanine-rich enhancer sequence of muscle creatine kinase (MCK) more tightly than to its target E-box motif [K. Walsh and A. Gualberto (1992) J. Biol. Chem., 267, 13714-13718], suggesting that tetraplex structures of regulatory sequences of muscle-specific genes could contribute to transcriptional regulation. In the current study we show that promoter or enhancer sequences of various muscle-specific genes display a disproportionately high incidence of guanine clusters. The sequences derived from the guanine-rich promoter or enhancer regions of three muscle-specific genes, human sarcomeric mitochondrial creatine kinase (sMtCK), mouse MCK and alpha7 integrin formed diverse secondary structures. The sMtCK sequence folded into a hairpin structure; the alpha7 integrin oligonucleotide generated a unimolecular tetraplex; and sequences from all three genes associated to generate bimolecular tetraplexes. Furthermore, two neighboring non-contiguous guanine-rich tracts in the alpha7 integrin promoter region also paired to form a tetraplex structure. We also show that homodimeric MyoD bound bimolecular tetraplex structures of muscle-specific regulatory sequences more efficiently than its target E-box motif. These results are consistent with a role of tetrahelical structures of DNA in the regulation of muscle-specific gene expression.},
	number = {9},
	journal = {Nucleic acids research},
	author = {Yafe, Anat and Etzioni, Shulamit and Weisman-Shomer, Pnina and Fry, Michael},
	month = jan,
	year = {2005},
	pmid = {15908587},
	keywords = {\#nosource, Antigens, Base Sequence, CD, CD: genetics, Creatine Kinase, Creatine Kinase: genetics, DNA, DNA: chemistry, E-Box Elements, Enhancer Elements, G-Quadruplexes, Genetic, Guanine, Guanine: analysis, Integrin alpha Chains, Integrin alpha Chains: genetics, Isoenzymes, Isoenzymes: genetics, MM Form, Mitochondrial Form, Molecular Sequence Data, Muscles, Muscles: metabolism, MyoD Protein, MyoD Protein: metabolism, Nucleic Acid Conformation, Porphyrins, Porphyrins: chemistry, Promoter Regions, Temperature},
	pages = {2887--900},
}

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  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}
}

@Article{Backwell2004,
  author   = {Patricia R Y Backwell and Michael D Jennions},
  journal  = {Nature},
  title    = {Animal behaviour: {C}oalition among male fiddler crabs.},
  year     = {2004},
  number   = {6998},
  pages    = {417},
  volume   = {430},
  abstract = {Until now, no compelling evidence has emerged from studies of animal
	territoriality to indicate that a resident will strategically help
	a neighbour to defend its territory against an intruder. We show
	here that territory-owning Australian fiddler crabs will judiciously
	assist other crabs in defending their neighbouring territories. This
	cooperation supports the prediction that it is sometimes less costly
	to assist a familiar neighbour than to renegotiate boundaries with
	a new, and possibly stronger, neighbour.},
  doi      = {10.1038/430417a},
  keywords = {Animals, Attention, Brain, Decision Making, Face, Female, Haplorhini, Housing, Humans, Magnetic Resonance Imaging, Male, Models, Neurological, Pattern Recognition, Visual, Photic Stimulation, Prefrontal Cortex, Research Support, Non-U.S. Gov't, U.S. Gov't, P.H.S., Visual Perception, Choice Behavior, Cognition, Dopamine, Learning, Schizophrenia, Substance-Related Disorders, Generalization (Psychology), Motor Skills, Non-P.H.S., Nerve Net, Neuronal Plasticity, Perception, Cerebral Cortex, Memory, Neurons, Sound Localization, Synapses, Synaptic Transmission, Neural Pathways, Non-, Acoustic Stimulation, Adult, Age of Onset, Aging, Blindness, Child, Preschool, Infant, Newborn, Pitch Perception, Analysis of Variance, Animal Welfare, Laboratory, Behavior, Animal, Hybridization, Genetic, Maze Learning, Mice, Inbred C57BL, Inbred DBA, Phenotype, Reproducibility of Results, Darkness, Deafness, Finches, Sleep, Sound, Sunlight, Time Factors, Vocalization, Energy Metabolism, Evolution, Fossils, History, Ancient, Hominidae, Biological, Physical Endurance, Running, Skeleton, Walking, Acoustics, Auditory Perception, Cues, Discrimination Learning, Pair Bond, Social Behavior, Songbirds, Adolescent, England, Habituation (Psychophysiology), Korea, Language, Semantics, Vocabulary, Action Potentials, Hippocampus, Pyramidal Cells, Rats, Rotation, Australia, Brachyura, Cooperative Behavior, Logistic Models, Territoriality, 15269757},
}

Paper  abstract   bibtex   

@article{Shammas2004,
	title = {Telomerase inhibition and cell growth arrest after telomestatin treatment in multiple myeloma.},
	volume = {10},
	issn = {1078-0432},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/14760100},
	abstract = {The aim of this study was to test the efficacy of telomestatin, an intramolecular G-quadruplex intercalating drug with specificity for telomeric sequences, as a potential therapeutic agent for multiple myeloma.},
	number = {2},
	journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
	author = {Shammas, Masood a and Reis, Robert J Shmookler and Li, Cheng and Koley, Hemanta and Hurley, Laurence H and Anderson, Kenneth C and Munshi, Nikhil C},
	month = jan,
	year = {2004},
	pmid = {14760100},
	keywords = {\#nosource, Apoptosis, Cell Cycle, Cell Division, Cell Line, Cell Survival, DNA Repair, Dose-Response Relationship, Drug, Gene Expression Regulation, Genetic, Humans, Multiple Myeloma, Multiple Myeloma: drug therapy, Multiple Myeloma: enzymology, Multiple Myeloma: pathology, Neoplastic, Oligonucleotide Array Sequence Analysis, Oxazoles, Oxazoles: pharmacology, Recombination, Telomerase, Telomerase: antagonists \& inhibitors, Telomerase: metabolism, Telomere, Telomere: metabolism, Time Factors, Tumor},
	pages = {770--6},
}

@Article{Mellars2004,
  author   = {Paul Mellars},
  journal  = {Nature},
  title    = {Neanderthals and the modern human colonization of {E}urope.},
  year     = {2004},
  number   = {7016},
  pages    = {461-5},
  volume   = {432},
  abstract = {The fate of the Neanderthal populations of Europe and western Asia
	has gripped the popular and scientific imaginations for the past
	century. Following at least 200,000 years of successful adaptation
	to the glacial climates of northwestern Eurasia, they disappeared
	abruptly between 30,000 and 40,000 years ago, to be replaced by populations
	all but identical to modern humans. Recent research suggests that
	the roots of this dramatic population replacement can be traced far
	back to events on another continent, with the appearance of distinctively
	modern human remains and artefacts in eastern and southern Africa.},
  doi      = {10.1038/nature03103},
  keywords = {Animals, Attention, Brain, Decision Making, Face, Female, Haplorhini, Housing, Humans, Magnetic Resonance Imaging, Male, Models, Neurological, Pattern Recognition, Visual, Photic Stimulation, Prefrontal Cortex, Research Support, Non-U.S. Gov't, U.S. Gov't, P.H.S., Visual Perception, Choice Behavior, Cognition, Dopamine, Learning, Schizophrenia, Substance-Related Disorders, Generalization (Psychology), Motor Skills, Non-P.H.S., Nerve Net, Neuronal Plasticity, Perception, Cerebral Cortex, Memory, Neurons, Sound Localization, Synapses, Synaptic Transmission, Neural Pathways, Non-, Acoustic Stimulation, Adult, Age of Onset, Aging, Blindness, Child, Preschool, Infant, Newborn, Pitch Perception, Analysis of Variance, Animal Welfare, Laboratory, Behavior, Animal, Hybridization, Genetic, Maze Learning, Mice, Inbred C57BL, Inbred DBA, Phenotype, Reproducibility of Results, Darkness, Deafness, Finches, Sleep, Sound, Sunlight, Time Factors, Vocalization, Energy Metabolism, Evolution, Fossils, History, Ancient, Hominidae, Biological, Physical Endurance, Running, Skeleton, Walking, Acoustics, Auditory Perception, Cues, Discrimination Learning, Pair Bond, Social Behavior, Songbirds, Adolescent, England, Habituation (Psychophysiology), Korea, Language, Semantics, Vocabulary, Action Potentials, Hippocampus, Pyramidal Cells, Rats, Rotation, Australia, Brachyura, Cooperative Behavior, Logistic Models, Territoriality, Africa, Archaeology, Emigration and Immigration, Europe, Geography, Phylogeny, Population Dynamics, 15565144},
}

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  doi  abstract   bibtex   

@article{Risitano2003,
	title = {Stability of intramolecular {DNA} quadruplexes: comparison with {DNA} duplexes.},
	volume = {42},
	issn = {0006-2960},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12767234},
	doi = {10.1021/bi026997v},
	abstract = {We have determined the stability of intramolecular quadruplexes that are formed by a variety of G-rich sequences, using oligonucleotides containing appropriately placed fluorophores and quenchers. The stability of these quadruplexes is compared with that of the DNA duplexes that are formed on addition of complementary C-rich oligonucleotides. We find that the linkers joining the G-tracts are not essential for folding and can be replaced with nonnucleosidic moieties, though their sequence composition profoundly affects quadruplex stability. Although the human telomere repeat sequence d[G(3)(TTAG(3))(3)] folds into a quadruplex structure, this forms a duplex in the presence of the complementary C-rich strand at physiological conditions. The Tetrahymena sequence d[G(4)(T(2)G(4))(3)], the sequence d[G(3)(T(2)G(3))(3)], and sequences related to regions of the c-myc promoter d(G(4)AG(4)T)(2) and d(G(4)AG(3)T)(2) preferentially adopt the quadruplex form in potassium-containing buffers, even in the presence of a 50-fold excess of their complementary C-rich strands, though the duplex predominates in the presence of sodium. The HIV integrase inhibitor d[G(3)(TG(3))(3)] forms an extremely stable quadruplex which is not affected by addition of a 50-fold excess of the complementary C-rich strand in both potassium- and sodium-containing buffers. Replacing the TTA loops of the human telomeric repeat with AAA causes a large decrease in quadruplex stability, though a sequence with AAA in the first loop and TTT in the second and third loops is slightly more stable.},
	number = {21},
	journal = {Biochemistry},
	author = {Risitano, Antonina and Fox, Keith R},
	month = jul,
	year = {2003},
	pmid = {12767234},
	keywords = {\#nosource, Animals, DNA, DNA: chemistry, Fluorescence, Genetic, HIV Integrase Inhibitors, HIV Integrase Inhibitors: chemistry, Humans, Nucleic Acid Conformation, Oligonucleotides, Oligonucleotides: chemistry, Promoter Regions, Protein Conformation, Protein Denaturation, Spectrometry, Telomere, Telomere: chemistry, Temperature, Tetrahymena, Tetrahymena: metabolism, Thermodynamics, Time Factors},
	pages = {6507--13},
}

@article{durant_vanillins--novel_2003,
	title = {Vanillins--a novel family of {DNA}-{PK} inhibitors},
	volume = {31},
	issn = {1362-4962},
	abstract = {Non-homologous DNA end-joining (NHEJ) is a major pathway of double strand break (DSB) repair in human cells. Here we show that vanillin (3-methoxy-4-hydroxybenzaldehyde)--a naturally occurring food component and an acknowledged antimutagen, anticlastogen and anticarcinogen--is an inhibitor of NHEJ. Vanillin blocked DNA end-joining by human cell extracts by directly inhibiting the activity of DNA-PK, a crucial NHEJ component. Inhibition was selective and vanillin had no detectable effect on other steps of the NHEJ process, on an unrelated protein kinase or on DNA mismatch repair by cell extracts. Subtoxic concentrations of vanillin did not affect the ATM/ATR-dependent phosphorylation of Chk2 or the S-phase checkpoint response after ionising radiation. They significantly potentiated the cytotoxicity of cisplatin, but did not affect sensitivity to UVC. A limited screen of structurally related compounds identified two substituted vanillin derivatives that were 100- and 50-fold more potent than vanillin as DNA-PK inhibitors. These compounds also sensitised cells to cisplatin. The inhibition of NHEJ is consistent with the antimutagenic and other biological properties of vanillin, possibly altering the balance between DSB repair by NHEJ and homologous recombination.},
	language = {eng},
	number = {19},
	journal = {Nucleic Acids Research},
	author = {Durant, Stephen and Karran, Peter},
	month = oct,
	year = {2003},
	keywords = {Antimutagenic Agents, Antineoplastic Agents, Benzaldehydes, Cell Line, Cisplatin, DNA Repair, DNA-Activated Protein Kinase, DNA-Binding Proteins, Drug Synergism, Enzyme Inhibitors, Humans, Nuclear Proteins, Protein Kinases, Protein-Serine-Threonine Kinases, Rad51 Recombinase, Recombination, Genetic, Tumor Cells, Cultured},
	pages = {5501--5512},
}

Paper  abstract   bibtex   

@article{Celik2002,
	title = {Selective targeting of zebrafish olfactory receptor neurons by the endogenous {OMP} promoter.},
	volume = {15},
	issn = {0953-816X},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11906521},
	abstract = {The olfactory nervous system of fish, in particular zebrafish, has become a valid model for that of higher vertebrates. However, no genetic markers for olfactory specific cell types, e.g. the olfactory receptor neurons, have been established in this species. Olfactory marker protein (OMP) is a reliable marker for olfactory receptor neurons in several other vertebrates. We have cloned zOMP, the zebrafish homologue of olfactory marker protein. During development, zOMP is expressed exclusively in the olfactory placode, presumably in olfactory receptor neurons, as shown by in situ hybridization. In the adult nasal epithelium zOMP is found restricted to the sensory region. zOMP appears to be a single gene, without close family members. The 5'-flanking region lacks most of the expected regulatory sequence motifs, both general and cell type-specific ones. Nevertheless, it drives reporter gene expression strongly and specifically in olfactory receptor neurons during the whole developmental period examined. Thus the zOMP promoter constitutes a powerful tool which should be useful to selectively introduce a wide variety of genetic modifications into olfactory receptor neurons.},
	number = {5},
	urldate = {2015-12-09},
	journal = {The European journal of neuroscience},
	author = {Celik, Arzu and Fuss, Stefan H and Korsching, S I},
	month = mar,
	year = {2002},
	pmid = {11906521},
	keywords = {\#nosource, Animals, Bacterial Proteins, Bacterial Proteins: diagnostic use, Bacterial Proteins: genetics, Cell Differentiation, Cell Differentiation: genetics, Cell Division, Cell Division: physiology, Cloning, Molecular, DNA, Complementary, DNA, Complementary: genetics, DNA, Complementary: isolation \& purification, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Gene Expression Regulation, Developmental: genetic, Gene Targeting, Gene Targeting: methods, Genetic Vectors, Genetic Vectors: genetics, Larva, Luminescent Proteins, Luminescent Proteins: diagnostic use, Luminescent Proteins: genetics, Models, Biological, Molecular Sequence Data, Nerve Tissue Proteins, Nerve Tissue Proteins: genetics, Nerve Tissue Proteins: metabolism, Olfactory Marker Protein, Olfactory Receptor Neurons, Olfactory Receptor Neurons: embryology, Olfactory Receptor Neurons: growth \& development, Olfactory Receptor Neurons: metabolism, Phylogeny, Promoter Regions, Genetic, Promoter Regions, Genetic: genetics, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Stem Cells, Stem Cells: cytology, Stem Cells: metabolism, Transgenes, Transgenes: genetics, Zebrafish, Zebrafish Proteins, Zebrafish: embryology, Zebrafish: growth \& development, Zebrafish: metabolism, olfaction, zebrafish},
	pages = {798--806},
}

Paper  doi  abstract   bibtex   

@article{purcell_variance_2002,
	title = {Variance components models for gene-environment interaction in twin analysis.},
	volume = {5},
	issn = {1369-0523},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12573187},
	doi = {10.1375/136905202762342026},
	abstract = {Gene-environment interaction is likely to be a common and important source of variation for complex behavioral traits. Often conceptualized as the genetic control of sensitivity to the environment, it can be incorporated in variance components twin analyses by partitioning genetic effects into a mean part, which is independent of the environment, and a part that is a linear function of the environment. The model allows for one or more environmental moderator variables (that possibly interact with each other) that may i). be continuous or binary ii). differ between twins within a pair iii). interact with residual environmental as well as genetic effects iv) have nonlinear moderating properties v). show scalar (different magnitudes) or qualitative (different genes) interactions vi). be correlated with genetic effects acting upon the trait, to allow for a test of gene-environment interaction in the presence of gene-environment correlation. Aspects and applications of a class of models are explored by simulation, in the context of both individual differences twin analysis and, in a companion paper (Purcell \& Sham, 2002) sibpair quantitative trait locus linkage analysis. As well as elucidating environmental pathways, consideration of gene-environment interaction in quantitative and molecular studies will potentially direct and enhance gene-mapping efforts.},
	number = {6},
	urldate = {2015-05-16},
	journal = {Twin research : the official journal of the International Society for Twin Studies},
	author = {Purcell, Shaun},
	month = dec,
	year = {2002},
	pmid = {12573187},
	keywords = {Computer Simulation, Environment, Genetics, Behavioral, Humans, Models, Genetic, Twins, Twins: genetics},
	pages = {554--71},
}

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 = {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{Antony2001,
	title = {A molecular beacon strategy for the thermodynamic characterization of triplex {DNA}: triplex formation at the promoter region of cyclin {D1}.},
	volume = {40},
	issn = {0006-2960},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11478908},
	abstract = {We studied the formation of triplex DNA in the purine-pyrimidine-rich promoter site sequence of cyclin D1, located at -116 to -99 from the transcription initiation site, with a molecular beacon comprised of a G-rich 18-mer triplex forming oligodeoxyribonucleotide. Formation of triplex DNA was monitored by enhanced fluorescence of the beacon, due to the weakening of fluorescence energy transfer, upon its binding to the target duplex. Electrophoretic mobility shift assay confirmed triplex DNA formation by these oligonucleotides. In low salt buffer (10 mM Na(+)), triplex DNA formation was not observed in the absence of a ligand such as spermine. At room temperature (22 degrees C), the equilibrium association constant (K(a)) calculated in the presence of 1 microM spermine and 10 mM Na(+) was 3.2 x 10(8) M(-1). The K(a) value was 1.0 x 10(9) M(-1) in the presence of 150 mM Na(+), and it increased by 10-fold by the addition of 1 mM spermine. Delta H, Delta S, and Delta G of triplex DNA formation, calculated from the temperature dependence of K(a) in the range of 20–45 degrees C, were -35.9 kcal/mol, -77 cal/(mol.K), and -13 kcal/mol, respectively, in the presence of 150 mM NaCl. The corresponding values were -52.9 kcal/mol, -132.5 cal/(mol.K), and -13.4 kcal/mol in the presence of 150 mM NaCl and 1 mM spermine. Structurally related polyamines exerted different degrees of triplex DNA stabilization, as determined by binding constant measurements. Comparison of spermine versus hexamine showed a 17-fold increase in the equilibrium association constant, whereas bis(ethyl) derivatization lead to a 4-fold decrease of this value. In the absence of added duplex and polyamines, the molecular beacon dissociated with a melting temperature of 67 degrees C. Thermodynamic parameters of beacon melting were calculated from the melting curve, and the Delta H, Delta S, and Delta G values were 37.8 kcal/mol, 112 cal/(mol.K), and 4.4 kcal/mol, respectively. These results demonstrate that molecular beacons can be used for the direct determination of the equilibrium association constants and thermodynamic parameters of triplex DNA formation in the presence of ligands such as polyamines.},
	number = {31},
	journal = {Biochemistry},
	author = {Antony, T and Thomas, T and Sigal, L H and Shirahata, a and Thomas, T J},
	month = aug,
	year = {2001},
	pmid = {11478908},
	keywords = {\#nosource, Cyclin D1, Cyclin D1: genetics, Cyclin D1: metabolism, DNA, DNA Probes, DNA Probes: chemical synthesis, DNA Probes: metabolism, DNA: genetics, DNA: metabolism, Electrophoresis, Fluorescence, Fluorescent Dyes, Fluorescent Dyes: chemical synthesis, Fluorescent Dyes: metabolism, Genetic, Humans, Nucleic Acid Conformation, Oligonucleotide Probes, Oligonucleotide Probes: chemical synthesis, Oligonucleotide Probes: metabolism, Polyacrylamide Gel, Promoter Regions, Protein Denaturation, Sodium Chloride, Spectrometry, Spermine, Spermine: metabolism, Temperature, Thermodynamics},
	pages = {9387--95},
}

Paper  abstract   bibtex   

@article{Vaish2000,
	title = {Expanding the structural and functional diversity of {RNA}: analog uridine triphosphates as candidates for in vitro selection of nucleic acids.},
	volume = {28},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=110695&tool=pmcentrez&rendertype=abstract},
	abstract = {Two analog uridine triphosphates tethering additional functionality, one a primary amino group and the second a mercapto group, were prepared and tested for their compatibility with in vitro RNA selection procedures. 5-(3-Aminopropyl)uridine triphosphate (UNH(2)) as a uridine substitute was a more effective substrate for T7 RNA polymerase than 5-(2-mercaptoethyl)uridine triphosphate (USH). However, both functioned in transcription assays of 100 nt templates to generate RNA transcripts in quantities sufficient to initiate RNA selection procedures. Transcription of RNA pools with T7 RNA polymerase and UNH(2) or USH occurred with efficiencies of 43 and 29\%, respectively, of the values obtained for native UTP transcription. In addition, the transcribed RNA containing roughly 25\% UNH(2) residues exhibited better substrate properties for SuperScript(TM) II RNase H reverse transcriptase than did RNA transcripts containing approximately 25\% of the USH analog. With either analog, both transcription and reverse transcription proceeded with high fidelity for insertion of the analog residue.},
	number = {17},
	journal = {Nucleic acids research},
	author = {Vaish, N K and Fraley, a W and Szostak, J W and McLaughlin, L W},
	month = sep,
	year = {2000},
	pmid = {10954600},
	keywords = {\#nosource, Base Sequence, Chromatography, DNA-Directed RNA Polymerases, DNA-Directed RNA Polymerases: metabolism, Genetic, Genetic: genetics, High Pressure Liquid, Kinetics, Molecular Sequence Data, RNA, RNA-Directed DNA Polymerase, RNA-Directed DNA Polymerase: metabolism, RNA: biosynthesis, RNA: genetics, RNA: metabolism, Ribonuclease H, Ribonuclease H: metabolism, Substrate Specificity, Templates, Transcription, Uridine, Uridine Triphosphate, Uridine Triphosphate: analogs \& derivatives, Uridine Triphosphate: chemical synthesis, Uridine Triphosphate: chemistry, Uridine Triphosphate: metabolism, Uridine: analogs \& derivatives, Uridine: chemistry, Uridine: metabolism, Viral Proteins},
	pages = {3316--22},
}

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{young_genetic_2000,
	title = {Genetic and environmental influences on behavioral disinhibition.},
	volume = {96},
	issn = {0148-7299},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11054778},
	abstract = {Comorbidity among childhood disruptive behavioral disorders is commonly reported in both epidemiologic and clinical studies. These problems are also associated with early substance use and other markers of behavioral disinhibition. Previous twin research has suggested that much of the covariation between antisocial behavior and alcohol dependence is due to common genetic influences. Similar results have been reported for conduct problems and hyperactivity. For the present study, an adolescent sample consisting of 172 MZ and 162 DZ twin pairs, recruited through the Colorado Twin Registry and the Colorado Longitudinal Twin Study were assessed using standardized psychiatric interviews and personality assessments. DSM-IV symptom counts for conduct disorder and attention deficit hyperactivity disorder, along with a measure of substance experimentation and novelty seeking, were used as indices of a latent behavioral disinhibition trait. A confirmatory factor model fit to individual-level data showed a strong common factor accounting for 16-42\% of the observed variance in each measure. A common pathway model evaluating the genetic and environmental architecture of the latent phenotype suggested that behavioral disinhibition is highly heritable (a(2) = 0.84), and is not influenced significantly by shared environmental factors. A residual correlation between conduct disorder and substance experimentation was explained by shared environmental effects, and a residual correlation between attention deficit hyperactivity disorder and novelty seeking was accounted for by genetic dominance. These results suggest that a variety of adolescent problem behaviors may share a common underlying genetic risk.},
	number = {5},
	urldate = {2015-04-13},
	journal = {American journal of medical genetics},
	author = {Young, S E and Stallings, M C and Corley, R P and Krauter, K S and Hewitt, J K},
	month = oct,
	year = {2000},
	pmid = {11054778},
	keywords = {Adolescent, Adolescent Behavior, Adolescent Behavior: psychology, Attention Deficit Disorder with Hyperactivity, Attention Deficit Disorder with Hyperactivity: gen, Comorbidity, Conduct Disorder, Conduct Disorder: genetics, Data Interpretation, Statistical, Environment, Humans, Inhibition (Psychology), Models, Genetic, Personality Disorders, Personality Disorders: genetics, Phenotype, Psychiatric Status Rating Scales, Psychology, Adolescent, Substance-Related Disorders, Substance-Related Disorders: genetics, Twins, Dizygotic, Twins, Dizygotic: genetics, Twins, Dizygotic: psychology, Twins, Monozygotic, Twins, Monozygotic: genetics, Twins, Monozygotic: psychology},
	pages = {684--95},
}

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}
}

@article{goel_familial_1999,
	title = {Familial antiphospholipid antibody syndrome: criteria for disease and evidence for autosomal dominant inheritance.},
	volume = {42},
	doi = {10.1002/1529-0131(199902)42:2<318::AID-ANR15>3.0.CO;2-5},
	abstract = {OBJECTIVE: To develop diagnostic criteria for a familial form of antiphospholipid antibody syndrome (APS), identify families with {\textgreater}1 affected member, examine possible modes of inheritance, and determine linkage to potential candidate genes. METHODS: Family members of probands with primary APS were analyzed for clinical and laboratory abnormalities associated with APS. Families with {\textgreater} or =2 affected members were analyzed by segregation analysis and typed for candidate genetic markers. RESULTS: Seven families were identified. Thirty of 101 family members met diagnostic criteria for APS. Segregation studies rejected both environmental and autosomal recessive models, and the data were best fit by either a dominant or codominant model. Linkage analysis showed independent segregation of APS and several candidate genes. CONCLUSION: Clinical and laboratory criteria are essential to identify the spectrum of disease associated with APS. We believe a set of criteria was developed that can precisely define affected family members with APS. Modeling studies utilizing these criteria strongly support a genetic basis for disease in families with APS and suggest that a susceptibility gene is inherited in an autosomal dominant pattern. However, in these families, APS was not linked with HLA, Fas, or other candidate genes, including beta2-glycoprotein 1, HLA, T cell receptor beta chain, Ig heavy chain, antithrombin III, Fas ligand, factor V, complement factor H, IgK, and Fas.},
	language = {eng},
	number = {2},
	journal = {Arthritis Rheum},
	author = {Goel, N and Ortel, T L and Bali, D and Anderson, J P and Gourley, I S and Smith, H and Morris, C A and DeSimone, M and Branch, D W and Ford, P and Berdeaux, D and Roubey, R A and Kostyu, D D and Kingsmore, S F and Thiel, T and Amos, C and Seldin, M F},
	year = {1999},
	pmid = {10025927},
	note = {Place: UNITED STATES
ISBN: 0004-3591},
	keywords = {Adolescent, Adult, Aged, Antiphospholipid Syndrome, DNA Primers, Enzyme-Linked Immunosorbent Assay, Female, Genes, Dominant, HLA-D Antigens, Histocompatibility Testing, Humans, Linkage (Genetics), Male, Middle Aged, Models, Genetic, Pedigree, Polymerase Chain Reaction, research support, non-u.s. gov't, research support, u.s. gov't, p.h.s.},
	pages = {318--327},
}

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}
}

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}
}

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}
}

Paper  doi  abstract   bibtex   

@article{frank-kamenetskii_triplex_1995,
	title = {Triplex {DNA} structures.},
	volume = {64},
	issn = {0066-4154},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7574496},
	doi = {10.1146/annurev.bi.64.070195.000433},
	abstract = {A DNA triplex is formed when pyrimidine or purine bases occupy the major groove of the DNA double Helix forming Hoogsteen pairs with purines of the Watson-Crick basepairs. Intermolecular triplexes are formed between triplex forming oligonucleotides (TFO) and target sequences on duplex DNA. Intramolecular triplexes are the major elements of H-DNAs, unusual DNA structures, which are formed in homopurine-homopyrimidine regions of supercoiled DNAs. TFOs are promising gene-drugs, which can be used in an anti-gene strategy, that attempt to modulate gene activity in vivo. Numerous chemical modifications of TFO are known. In peptide nucleic acid (PNA), the sugar-phosphate backbone is replaced with a protein-like backbone. PNAs form P-loops while interacting with duplex DNA forming triplex with one of DNA strands leaving the other strand displaced. Very unusual recombination or parallel triplexes, or R-DNA, have been assumed to form under RecA protein in the course of homologous recombination.},
	journal = {Annual review of biochemistry},
	author = {Frank-Kamenetskii, M D and Mirkin, S M},
	month = jan,
	year = {1995},
	pmid = {7574496},
	note = {tex.ids= frank-kamenetskiiTriplexDNAStructure, frank-kamenetskiiTriplexDNAStructures, frank-kamenetskiiTriplexDNAStructuresa},
	keywords = {Animals, DNA, DNA: chemistry, DNA: genetics, Drug Stability, Genetic, Humans, Molecular Structure, Nucleic Acid Conformation, Nucleic Acids, Nucleic Acids: chemistry, Peptides, Peptides: chemistry, Recombination},
	pages = {65--95},
}

Paper  abstract   bibtex   

@article{plomin_variability_1994,
	title = {Variability and stability in cognitive abilities are largely genetic later in life.},
	volume = {24},
	issn = {0001-8244},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7945151},
	abstract = {The powerful quantitative genetic design of identical and fraternal twins reared apart (112 pairs) and matched twins reared together (111 pairs) was employed to assess the extent of genetic influence on individual differences in cognitive abilities during the last half of the life span. General cognitive ability yielded a heritability estimate of about .80 in two assessments 3 years apart as part of the Swedish Adoption/Twin Study of Aging. This is one of the highest heritabilities reported for a behavioral trait. Across the two ages, average heritabilities are about .60 for verbal tests, .50 for spatial and speed-of-processing tests, and .40 for memory tests. For general cognitive ability, the phenotypic stability across the 3 years is .92 and stable genetic factors account for nearly 90\% this stability. These findings suggest that general cognitive ability is a reasonable target for research that aims to identify specific genes for complex traits.},
	number = {3},
	urldate = {2013-09-30},
	journal = {Behavior genetics},
	author = {Plomin, R and Pedersen, N L and Lichtenstein, P and McClearn, G E},
	month = may,
	year = {1994},
	pmid = {7945151},
	keywords = {Aging, Aging: psychology, Aptitude, Female, Humans, Intelligence, Intelligence: genetics, Male, Middle Aged, Models, Genetic, Social Environment, Twins, Twins, Dizygotic, Twins, Dizygotic: genetics, Twins, Dizygotic: psychology, Twins, Monozygotic, Twins, Monozygotic: genetics, Twins, Monozygotic: psychology, Twins: genetics, Twins: psychology},
	pages = {207--15},
}

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}
}

Paper  bibtex   

@article{Lezius1967,
	title = {Enzymatic synthesis of {DNA} with 4-thio-thymidine triphosphate as substitute for {dTTP}.},
	volume = {3},
	issn = {0014-2956},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/4295053},
	number = {1},
	journal = {European journal of biochemistry / FEBS},
	author = {Lezius, a G and Scheit, K H},
	month = dec,
	year = {1967},
	pmid = {4295053},
	keywords = {\#nosource, Animals, Carbon Isotopes, Catalysis, Cattle, Cellulose, Centrifugation, Chromatography, DNA, DNA Nucleotidyltransferases, Density Gradient, Deoxyribonucleases, Escherichia coli, Escherichia coli: enzymology, Genetic, Glass, Nucleotides, Pancreas, Pancreas: enzymology, Paper, Phosphoric Monoester Hydrolases, Phosphorus Isotopes, Polymers, Snakes, Spectrophotometry, Sulfhydryl Compounds, Templates, Thymidine, Thymus Gland, Thymus Gland: enzymology, Tritium, Venoms},
	pages = {85--94},
}