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  2019 (2)
Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. Johri, P.; Marinov, G., K.; Doak, T., G.; and Lynch, M. Genome Biology and Evolution, 11(5): 1398-1416. 2019.
Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. [link]Website   bibtex   abstract  
  2018 (6)
Escherichia coli cultures maintain stable subpopulation structure during long-term evolution. Behringer, M., G.; Choi, B., I.; Miller, S., F.; Doak, T., G.; Karty, J., A.; Guo, W.; and Lynch, M. Proceedings of the National Academy of Sciences of the United States of America, 115(20): E4642-E4650. 2018.
Escherichia coli cultures maintain stable subpopulation structure during long-term evolution [link]Website   bibtex   abstract  
Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina. Zheng, W.; Wang, C.; Yan, Y.; Gao, F.; Doak, T., G.; and Song, W. Genome Biology and Evolution, 10(3): 883-894. 2018.
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Limited mutation-rate variation within the Paramecium aurelia species complex. Long, H.; Doak, T., G.; and Lynch, M. G3: Genes, Genomes, Genetics, 8(7): 2523-2526. 7 2018.
Limited mutation-rate variation within the Paramecium aurelia species complex [pdf]Paper   bibtex   abstract  
Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins. Yang, T.; Fang, L.; Sanders, S.; Jayanthi, S.; Rajan, G.; Podicheti, R.; Thallapuranam, S., K.; Mockaitis, K.; and Medina-Bolivar, F. The Journal of biological chemistry, 293(1): 28-46. 2018.
Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins. [pdf]Paper   Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins. [link]Website   bibtex   abstract  
ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report. Michaels, S., D.; Doak, T., G.; Stewart, C., A.; and Michaels, S., D., (. Technical Report 9 2018.
ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report [pdf]Paper   ABI Sustaining: The National Center for Genome Analysis Support 2018 Annual Report [link]Website   bibtex   abstract  
Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop. Sanders, S., A.; Ganote, C., L.; Papudeshi, B.; Stewart, C., A.; and Doak, T., G. Technical Report 6 2018.
Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop [pdf]Paper   Summary of the National Center for Genome Analysis Support (NCGAS) 2018 de Novo Transcriptome Workflow and Workshop [link]Website   bibtex  
  2017 (10)
Population Genomics of Paramecium Species. Johri, P.; Krenek, S.; Marinov, G., K.; Doak, T., G.; Berendonk, T., U.; and Lynch, M. Molecular Biology and Evolution, 34(5): 1194-1216. 2017.
Population Genomics of Paramecium Species [link]Website   bibtex   abstract  
ABI Sustaining: The National Center for Genome Analysis Support 2017 Annual Report. Doak, T., G.; Stewart, C., A.; and Michaels, S., D. Technical Report 2017.
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Summary of the 2017 NCGAS User Survey. Doak, T., G.; Stewart, C., A.; and Michaels, S., D. Technical Report 2017.
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A voice for bioinformatics. Ganote, C., L.; Sanders, S., A.; Papudeshi, B., N.; Blood, P., D.; and Doak, T., G. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (PEARC17), volume Part F1287, 2017. Association for Computing Machinery
A voice for bioinformatics [link]Website   bibtex   abstract  
Estimating seven coefficients of pairwise relatedness using population-genomic data. Ackerman, M., S.; Johri, P.; Spitze, K.; Xu, S.; Doak, T., G.; Young, K.; and Lynch, M. Genetics, 206(1): 105-118. 2017.
Estimating seven coefficients of pairwise relatedness using population-genomic data [link]Website   bibtex   abstract  
Diversity and universality of endosymbiotic Rickettsia in the fish parasite Ichthyophthirius multifiliis. Zaila, K., E.; Doak, T., G.; Ellerbrock, H.; Tung, C.; Martins, M., L.; Kolbin, D.; Yao, M.; Cassidy-Hanley, D., M.; Clark, T., G.; and Chang, W. Frontiers in Microbiology, 8(FEB): 189. 2017.
Diversity and universality of endosymbiotic Rickettsia in the fish parasite Ichthyophthirius multifiliis [link]Website   bibtex   abstract  
Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of Macaca fascicularis. Klegarth, A., R.; Sanders, S., A.; Gloss, A., D.; Lane‐deGraaf, K., E.; Jones‐Engel, L.; Fuentes, A.; and Hollocher, H. American Journal of Physical Anthropology. 2017.
Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of Macaca fascicularis [link]Website   bibtex  
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes. Papudeshi, B.; Haggerty, J., M.; Doane, M.; Morris, M., M.; Walsh, K.; Beattie, D., T.; Pande, D.; Zaeri, P.; Silva, G., G.; Thompson, F.; Edwards, R., A.; and Dinsdale, E., A. BMC Genomics, 18(1). 2017.
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes [link]Website   bibtex   abstract  
Summary of the Survey of Field/Marine Station Directors and Managers. Doak, Thomas G.; Stewart, Craig A.; Wernert, Julie; Hancock, David Y.; Miller, T. Technical Report 7 2017.
Summary of the Survey of Field/Marine Station Directors and Managers [link]Website   bibtex  
  2016 (5)
Genomic and metagenomic analysis of diversity-generating retroelements associated with Treponema denticola. Nimkulrat, S.; Lee, H.; Doak, T., G.; and Ye, Y. Frontiers in Microbiology, 7(JUN): pp 852. 2016.
Genomic and metagenomic analysis of diversity-generating retroelements associated with Treponema denticola [link]Website   bibtex   abstract  
Disentangling the taxonomy of Rickettsiales and description of two novel symbionts ("Candidatus Bealeia paramacronuclearis" and "Candidatus Fokinia cryptica") sharing the cytoplasm of the ciliate protist Paramecium biaurelia. Szokoli, F.; Castelli, M.; Sabaneyeva, E.; Schrallhammer, M.; Krenek, S.; Doak, T., G.; Berendonk, T., U.; and Petroni, G. Applied and Environmental Microbiology, 82(24): 7236-7247. 2016.
Disentangling the taxonomy of Rickettsiales and description of two novel symbionts ("Candidatus Bealeia paramacronuclearis" and "Candidatus Fokinia cryptica") sharing the cytoplasm of the ciliate protist Paramecium biaurelia [link]Website   bibtex   abstract  
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli. Lee, H.; Doak, T., G.; Popodi, E.; Foster, P., L.; and Tang, H. Nucleic Acids Research, 44(15): 7109-7119. 2016.
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli [link]Website   bibtex   abstract  
The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway. Kucukyildirim, S.; Long, H.; Sung, W.; Miller, S., F.; Doak, T., G.; and Lynch, M. G3: Genes, Genomes, Genetics, 6(7): 2157-63. 2016.
The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway. [link]Website   bibtex   abstract  
The advanced cyberinfrastructure research and education facilitators virtual residency: Toward a national cyberinfrastructure workforce. Neeman, H.; Ganote, C.; Kalescky, R.; Ramadugu, S., K.; Sherman, A., H.; Bergstrom, A.; Gray, Z.; Lemley, E.; Romanella, A.; Stengel, B.; Brunson, D.; Guilfoos, B.; Moore, B., G.; Rush, J.; and Voss, D. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (XSEDE16), volume 17-21-July-2016, 7 2016. Association for Computing Machinery
The advanced cyberinfrastructure research and education facilitators virtual residency: Toward a national cyberinfrastructure workforce [pdf]Paper   bibtex   abstract  
  2015 (12)
Draft genome sequence of Caedibacter varicaedens, a kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia. Suzuki, H.; Dapper, A., L.; Jackson, C., E.; Lee, H.; Pejaver, V.; Doak, T., G.; Lynch, M.; and Preer J.R., J. Genome Announcements, 3(6). 2015.
Draft genome sequence of Caedibacter varicaedens, a kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia [link]Website   bibtex   abstract  
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. Wang, M.; Doak, T., G.; and Ye, Y. Genome Biology, 16(1). 2015.
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes [link]Website   bibtex   abstract  
Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome. Wu, L.; Ganote, C., L.; Doak, T., G.; Barnett, W.; Mockaitis, K.; and Stewart, C., A. In Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15, volume 2015-July, pages 1-6, 7 2015. ACM Press
Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome [link]Website   bibtex   abstract  
Describing and predicting developmental profiles of externalizing problems from childhood to adulthood. Petersen, I., T.; Bates, J., E.; Dodge, K., A.; Lansford, J., E.; and Pettit, G., S. DEVELOPMENT AND PSYCHOPATHOLOGY. 2015.
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XCBC and XNIT - Tools for cluster implementation and management in research and training. Fischer, J.; Knepper, R.; Coulter, E.; Peck, C.; and Stewart, C. In Proceedings - IEEE International Conference on Cluster Computing, ICCC, volume 2015-Octob, 2015.
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Background mutational features of the radiation-resistant bacterium deinococcus radiodurans. Long, H.; Kucukyildirim, S.; Sung, W.; Williams, E.; Lee, H.; Ackerman, M., S.; Doak, T., G.; Tang, H.; and Lynch, M. Molecular Biology and Evolution, 32(9): 2383-2392. 2015.
Background mutational features of the radiation-resistant bacterium deinococcus radiodurans [link]Website   bibtex   abstract  
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. Bao, G.; Wang, M.; Doak, T., G.; and Ye, Y. Frontiers in Microbiology, 6(SEP). 2015.
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota [link]Website   bibtex   abstract  
The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Farlow, A.; Long, H.; Arnoux, S.; Sung, W.; Doak, T., G.; Nordborg, M.; and Lynch, M. Genetics, 201(2): 737-744. 2015.
The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe [link]Website   bibtex   abstract  
NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture. Seetharam, A.; Gomez, A.; Purcell, C., M.; Hyde, J., R.; Blood, P., D.; and Severin, A., J. In Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure (XSEDE '15), 2015.
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Mutation rate, spectrum, topology and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens Migula ATCC948. Long, H.; Sung, W.; Miller, S., F.; Ackerman, M., S.; Doak, T., G.; and Lynch, M. GENOME BIOLOGY AND EVOLUTION, 23: 262-271. 2015.
Mutation rate, spectrum, topology and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens Migula ATCC948 [link]Website   bibtex  
Saccharide breakdown and fermentation by the honey bee gut microbiome. Lee, F., J.; Rusch, D., B.; Stewart, F., J.; Mattila, H., R.; and Newton, I., L. Environmental Microbiology, 17(3): 796-815. 3 2015.
Saccharide breakdown and fermentation by the honey bee gut microbiome [pdf]Paper   bibtex   abstract  
Physiological effects of heat stress on Hawaiian picture-wing Drosophila: Genome-wide expression patterns and stress-related traits. Uy, K., L.; LeDuc, R.; Ganote, C.; and Price, D., K. Conservation Physiology, 3(1). 2015.
Physiological effects of heat stress on Hawaiian picture-wing Drosophila: Genome-wide expression patterns and stress-related traits [pdf]Paper   bibtex   abstract  
  2014 (19)
Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. Peng, X.; Pipes, L.; Xiong, H.; Green, R., R.; Jones, D., C.; Ruzzo, W., L.; Schroth, G., P.; Mason, C., E.; Palermo, R., E.; and Katze, M., G. JOURNAL OF MEDICAL PRIMATOLOGY. 2014.
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The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Chen, X.; Bracht, J., R.; Goldman, A., D.; Dolzhenko, E.; Clay, D., M.; Swart, E., C.; Perlman, D., H.; Doak, T., G.; Stuart, A.; Amemiya, C., T.; Sebra, R., P.; and Landweber, L., F. Cell, 158(5): 1187-1198. 2014.
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development [link]Website   bibtex   abstract  
Expanding the catalog of cas genes with metagenomes. Zhang, Q.; Doak, T., G.; and Ye, Y. Nucleic Acids Research, 42(4): 2448-2459. 2014.
Expanding the catalog of cas genes with metagenomes [link]Website   bibtex   abstract  
The Encrypted Germline Genome of the Ciliate Oxytricha: A Paragon of Genome Rearrangement. Chen, X., Bracht, J.R., Goldman, A.D., Dolzhenko, E., Swart, E.C., Clay, D.M., Perlman, D.H., Doak, T.G., Stuart, A., Amemiya, C.T, Landweber, L.; Chen, X.; Bracht, J., R.; Goldman, A., D.; Dolzhenko, E.; Swart, E., C.; Clay, D., M.; Perlman, D., H.; Doak, T., G.; Stuart, A.; Amemiya, C., T.; and Landweber, L., F. MIC. 2014.
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Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. Long, H.; Sung, W.; Miller, S., F.; Ackerman, M., S.; Doak, T., G.; and Lynch, M. Genome Biology and Evolution, 7(1): 262-271. 2014.
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948 [link]Website   bibtex   abstract  
Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation. Wegrzyn, J., L.; Liechty, J., D.; Stevens, K., A.; Wu, L.; Loopstra, C., A.; Vasquez-Gross, H., A.; Dougherty, W., M.; Lin, B., Y.; Zieve, J., J.; Mart\'\inez-Garc\'\ia, P., J.; Holt, C.; and Y Genetics, 196: 891-909. 2014.
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The mitochondrial genome of a Solanaceae cybrid plant is highly chimeric and retains a single form of most genes. Sanchez-Puerta, M., V.; Zubko, M.; and Palmer, J., D. GENOME RESEARCH. 2014.
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Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Neale, D.; Wegrzyn, J.; Stevens, K.; Zimin, A.; Puiu, D.; Crepeau, M.; Cardeno, C.; Koriabine, M.; Morris, A., H.; Liechty, J.; Garcia, P., M.; Gross, H., V.; Lin, B.; and Zieve, J. GENOME BIOLOGY, 15. 2014.
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The C-score: a bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics. LeDuc, R., D.; Fellers, R., T.; Early, B., P.; Greer, J., B.; Thomas, P., M.; and Kelleher, N., L. JOURNAL OF PROTEOME RESEARCH, 13: 3231-3324. 2014.
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National Center for Genome Analysis Program Year 2 Report - September 15, 2012 - September 14, 2013. Barnett, W., K.; LeDuc, R., D.; and Stewart, C., A. Technical Report NATIONAL CENTER FOR GENOME ANALYSIS, 2014.
National Center for Genome Analysis Program Year 2 Report - September 15, 2012 - September 14, 2013 [link]Website   bibtex  
Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. McGrath, C., L.; Gout, J.; Doak, T., G.; Yanagi, A.; and Lynch, M. Genetics, 197(4): 1417-1428. 2014.
Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence [link]Website   bibtex   abstract  
De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) -- The Dominant Zooplankter of the North Atlantic Ocean. Lenz, P., H.; Roncalli, V.; Hassett, R., P.; Wu, L.; Cieslak, M., C.; Hartline, D., K.; and Christie, A., E. PLOS ONE, 9. 2014.
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Differential retention and divergent resolution of duplicate genes following whole-genome duplication. McGrath, C., L.; Gout, J.; Johri, P.; Doak, T., G.; and Lynch, M. Genome Research, 24(10): 1665-1675. 2014.
Differential retention and divergent resolution of duplicate genes following whole-genome duplication [link]Website   bibtex   abstract  
Galaxy based BLAST submission to distributed national high throughput computing resources. Hayashi, S.; Gesing, S.; Quick, R.; Teige, S.; Ganote, C.; Wu, L.; and Prout, E. In Proceedings of Science, volume 23-28-Marc, 2014. Proceedings of Science (PoS)
Galaxy based BLAST submission to distributed national high throughput computing resources [link]Website   bibtex   abstract  
Diversity and dynamics of the Drosophila transcriptome. Brown, J., B.; Boley, N.; Eisman, R.; May, G., E.; Stoiber, M., H.; Duff, M., O.; Booth, B., W.; Wen, J.; Park, S.; Suzuki, A., M.; Wan, K., H.; Yu, C.; Zhang, D.; and Carlson, J., W. of NATURE 2014.
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Development of Single Nucleotide Polymorphism (SNP) Markers from the Mango (Mangifera indica ) Transcriptome for Mapping and Estimation of Genetic Diversity. Kuhn, D., N.; Dillon, N., L.; Innes, D., J.; Wu, L., S.; and Mockaitis, K. PLANT AND ANIMAL GENOME XXII CONFERENCE, 2014.
Development of Single Nucleotide Polymorphism (SNP) Markers from the Mango (Mangifera indica ) Transcriptome for Mapping and Estimation of Genetic Diversity [link]Website   bibtex  
Large-scale Sequencing and Assembly of Cereal Genomes Using Blacklight. Blood, P., D.; Marcus, S.; and Schatz, M., C. In XSEDE 14 CONFERENCE PROCEEDINGS, 2014.
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Leveraging the national cyberinfrastructure for biomedical research. LeDuc, R.; Vaughn, M.; Fonner, J., M.; Sullivan, M.; Williams, J., G.; Blood, P., D.; Taylor, J.; and Barnett, W. Journal of the American Medical Informatics Association, 21(2): 195-199. 2014.
Leveraging the national cyberinfrastructure for biomedical research [pdf]Paper   bibtex   abstract  
National Center for Genome Analysis Program Year 3 Report - September 15, 2013 - September 14, 2014. Barnett, W., K.; Doak, T., G.; and Stewart, C., A. Technical Report 2014.
National Center for Genome Analysis Program Year 3 Report - September 15, 2013 - September 14, 2014 [link]Website   bibtex   abstract  
  2013 (21)
National Center for Genome Analysis Program Year 1 Report - September 15, 2011 - September 14, 2012. Barnett, W.; Ganote, C.; Vaughn, M.; LeDuc, R., D.; and Stewart, C., A. Technical Report 2013.
National Center for Genome Analysis Program Year 1 Report - September 15, 2011 - September 14, 2012 [link]Website   bibtex   abstract  
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Haas, B., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P., Bowden, J., Couger, M., Eccles, D., Li, B., Lieber, M., MacManes, M., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C., Henschel, R., e., a.; Haas, B., J.; Papanicolaou, A.; Yassour, M.; Grabherr, M.; Blood, P., D.; Bowden, J.; Couger, M., B.; Eccles, D.; Li, B.; Lieber, M.; Macmanes, M., D.; Ott, M.; Orvis, J.; Pochet, N.; Strozzi, F.; Weeks, N.; Westerman, R.; William, T.; Dewey, C., N.; Henschel, R.; Leduc, R., D.; Friedman, N.; Regev, A.; and others Nature Protocols, 8(8): 1494-1512. 2013.
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis [link]Website   bibtex   abstract  
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Pipes, L.; Li, S.; Bozinoski, M.; Palermo, R.; Peng, X.; Blood, P.; Kelly, S.; Weiss, J., M.; Thierry-Mieg, J.; Thierry-Mieg, D.; Zumbo, P.; Chen, R.; Schroth, G., P.; Mason, C., E.; and Katze, M., G. NUCLEIC ACIDS RES, 41: D906-14. 2013.
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics [link]Website   bibtex  
Statistical Consideration for Identification and Quantification in Top-Down Proteomics. LeDuc, R. In American Society for Mass Spectrometry, Sanibel Conference 2013, 2013.
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Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. Christie, A.E., Roncalli, V., Wu, L.-S., Ganote, C.L., Doak, T.G., Lenz, P.; Christie, A., E.; Roncalli, V.; Wu, L.; Ganote, C., L.; Doak, T.; and Lenz, P., H. General and Comparative Endocrinology, 187: 117-135. 2013.
Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome [link]Website   bibtex  
Spliced DNA sequences in the Paramecium germline: Their properties and evolutionary potential. Catania, F.; McGrath, C., L.; Doak, T., G.; and Lynch, M. Genome Biology and Evolution, 5(6): 1200-1211. 2013.
Spliced DNA sequences in the Paramecium germline: Their properties and evolutionary potential [link]Website   bibtex   abstract  
Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate. Jin, M.; Bothfeld, W.; Austin, S.; Sato, T., K.; Alex, L., R.; Li, H.; Foston, M.; Gunawan, C.; LeDuc, R., D.; Quensen, J., F.; McGee, M.; Uppugundla, N.; Higbee, A.; and Ranatu BIORESOURCE TECHNOLOGY, 147: 212-220. 2013.
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The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Youssef, N., H.; Couger, M., B.; Struchtemeyer, C., G.; Liggenstoffer, A., S.; Prade, R., A.; Najar, F., Z.; Atiyeh, H., K.; Wilkins, M., R.; and Elshahed, M., S. APPL ENVIRON MICROBIOL, 79: 4620-4634. 2013.
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Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula. Stanton-Geddes, J.; Paape, T.; Epstein, B.; Briskine, R.; Yoder, J.; Mudge, J.; Bharti, A., K.; Farmer, A., D.; Zhou, P.; Denny, R.; May, G., D.; Erlandson, S.; and Yakub, M. PLOS ONE, 8. 2013.
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A genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria. Raymann, K.; Bobay, L.; Doak, T., G.; Lynch, M.; and Gribaldo, S. G3: Genes, Genomes, Genetics, 3(3): 505-516. 2013.
A genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria [link]Website   bibtex   abstract  
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. Zhang, Q.; Rho, M.; Tang, H.; Doak, T., G.; and Ye, Y. Genome Biology, 14(4). 2013.
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes [link]Website   bibtex   abstract  
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating traits: pod color as an example". Motamayor, J. C., Mockaitis, K., Schmutz, J., e., a., (., G., G.; Motamayor, J., C.; Mockaitis, K.; Schmutz, J.; Haiminen, N.; Donald; Cornejo, O.; Findley, S.; Zheng, P.; Utro, F.; Royaert, S.; Saski, C.; Jenkins, J.; Podicheti, R.; Zhao, M.; Motamayor, J. C., Mockaitis, K., Schmutz, J., e., a., (., G., G.; Motamayor, J., C.; Mockaitis, K.; Schmutz, J.; Haiminen, N.; Donald; Cornejo, O.; Findley, S.; Zheng, P.; Utro, F.; Royaert, S.; Saski, C.; Jenkins, J.; Podicheti, R.; Zhao, M.; and others Genome Biology, 14. 2013.
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The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. Swart, E., C.; Bracht, J., R.; Magrini, V.; Minx, P.; Chen, X.; Zhou, Y.; Khurana, J., S.; Goldman, A., D.; Nowacki, M.; Schotanus, K.; Jung, S.; Fulton, R., S.; Ly, A.; McGrath, S.; Haub, K.; Wiggins, J., L.; Storton, D.; Matese, J., C.; Parsons, L.; Chang, W.; Bowen, M., S.; Stover, N., A.; Jones, T., A.; Eddy, S., R.; Herrick, G., A.; Doak, T., G.; Wilson, R., K.; Mardis, E., R.; and Landweber, L., F. PLoS Biology, 11(1). 2013.
The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes [link]Website   bibtex   abstract  
The gain and loss of chromosomal integron systems in the Treponema species. Wu, Y.; Doak, T., G.; and Ye, Y. BMC Evolutionary Biology, 13(1). 2013.
The gain and loss of chromosomal integron systems in the Treponema species [link]Website   bibtex   abstract  
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Boscaro, V.; Felletti, M.; Vannini, C.; Ackerman, M., S.; Chain, P., S., G.; Malfatti, S.; Vergez, L., M.; Shin, M.; Doak, T., G.; Lynch, M.; and Petroni, G. Proceedings of the National Academy of Sciences of the United States of America, 110(46): 18590-18595. 2013.
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria [link]Website   bibtex   abstract  
Expanding the Catalog of Cas Proteins by Metagenomes. Zhang, Q., Doak, T.G., Rho, M., Ye, Y. PLoS CB. 2013.
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National center for genome analysis support leverages XSEDE to support life science research. Leduc, R., D.; Wu, L.; Ganote, C., L.; Doak, T.; Blood, P., D.; Vaughn, M.; and LeDuc, R., Wu, L.-S., Ganote, C., Doak, T., Blood, P., Vaughn, M., and Williams, B. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), 2013.
National center for genome analysis support leverages XSEDE to support life science research [link]Website   bibtex   abstract  
Reply to massey: Drift does influence mutation-rate evolution. Sung, W.; Ackerman, M., S.; Miller, S., F.; Doak, T., G.; and Lynch, M. Proceedings of the National Academy of Sciences of the United States of America, 110(10): E860. 2013.
Reply to massey: Drift does influence mutation-rate evolution [link]Website   bibtex  
Towards Virtual Computational Facilities for Genomics Research: How 100 Gbps Networking Will Change Bioinformatics. Barnett, W., Michael, S., Wu, L.-S., LeDuc, R., Doak, T. In eScience 2013, 2013.
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Making campus bridging work for researchers: A case study with mlRho. Thota, A.; Michael, S.; Xu, S.; Haubold, B.; Doak, T.; and Henschel, R. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13), pages 8, 2013.
Making campus bridging work for researchers: A case study with mlRho [link]Website   bibtex   abstract  
  2012 (5)
Trinity RNA-Seq assembler performance optimization. Henschel, R.; Nista, P., M.; Lieber, M.; Haas, B., J.; Wu, L.; Leduc, R., D.; and Henschel, R., Lieber, M., Wu, L-S, Nista, P. M., Haas, B.J., and LeDuc, R. In ACM International Conference Proceeding Series, 2012.
Trinity RNA-Seq assembler performance optimization [link]Website   bibtex   abstract  
2012 Annual Report on Training, Education, and Outreach Activities of the Indiana University Pervasive Technology Institute and affiliated organizations. Miller, T.; Ping, R., J.; Plale, B.; and Stewart, C., A. Technical Report 2012 ANNUAL REPORT ON TRAINING, EDUCATION, AND OUTREACH ACTIVITIES OF THE INDIANA UNIVERSITY PERVASIVE TECHNOLOGY INSTITUTE AND AFFILIATED ORGANIZATIONS, v p.., 2012.
bibtex  
Genomics, Transcriptomics, and Proteomics: Engaging Biologists (Workshop). LeDuc, R., D. In eScience 2012, 2012.
bibtex  
2012 Annual Report - Advanced Biomedical Information Technology Core. Barnett, W., K.; Shankar, G.; Hancock, D., Y.; Allen, M.; Seiffert, K.; Boyles, M.; Rogers, J., L.; Wernert, E.; Link, M., R.; Stewart, C., A.; Barnett, W., K.; Shankar, G.; Hancock, D., Y.; Allen, M.; Seiffert, K.; Boyles, M.; Rogers, J., L.; Wernert, E.; Link, M., R.; and Stewart, C., A. Technical Report 2012.
2012 Annual Report - Advanced Biomedical Information Technology Core [link]Website   bibtex