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  2020 (1)
Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network. Lima, L., F., O.; Weissman, M.; Reed, M.; Papudeshi, B.; Alker, A., T.; Morris, M., M.; Edwards, R., A.; de Putron, S., J.; Vaidya, N., K.; and Dinsdale, E., A. mBio, 11(2). 3 2020.
Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network [pdf]Paper   Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network [link]Website   bibtex   abstract
  2019 (1)
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. [pdf]Paper   Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. [link]Website   bibtex   abstract
  2018 (3)
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. Journal of Biological Chemistry. 2018.
Stilbenoid prenyltransferases define key steps in the diversification of peanut phytoalexins [pdf]Paper   bibtex   abstract
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, 115(20): E4642-E4650. 2018.
Escherichia coli cultures maintain stable subpopulation structure during long-term evolution [pdf]Paper   bibtex   abstract
Limited Mutation-Rate Variation within Paramecium aurelia species complex. Long, Hongan., Doak, G, Thomas., Lynch, M. G3:Gene, Genome, Genetics, 8(7): 2532-2526. 2018.
Limited Mutation-Rate Variation within Paramecium aurelia species complex [pdf]Paper   Limited Mutation-Rate Variation within Paramecium aurelia species complex [link]Website   bibtex   abstract
  2017 (8)
Diversity and universality of endosymbiotic Rickettsia in the fish parasite Ichthyophthirius multifiliis. Zaila, K., E.; Doak, T., G.; Ellerbrock, H.; Tung, C., H.; Martins, M., L.; Kolbin, D.; Yao, M., C.; Cassidy-Hanley, D., M.; Clark, T., G.; and Chang, W., J. Frontiers in Microbiology, 8: 189. 2017.
Diversity and universality of endosymbiotic Rickettsia in the fish parasite Ichthyophthirius multifiliis [pdf]Paper   bibtex   abstract
STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. Haas, B.; Dobin, A.; Stransky, N.; Li, B.; Yang, X.; Tickle, T.; Bankapur, A.; Ganote, C.; Doak, T.; Pochet, N.; Sun, J.; Wu, C.; Gingeras, T.; and Regev, A. bioRxiv. 3 2017.
STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq [link]Website   bibtex   abstract
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. 5 2017.
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.
bibtex
A voice for bioinformatics. Ganote, C.; Sanders, S.; Papudeshi, B.; Blood, P.; and Doak, T. In ACM International Conference Proceeding Series, volume Part F1287, 2017.
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. 2017.
Estimating Seven Coefficients of Pairwise Relatedness Using Population Genomic Data [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. 2017.
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes [pdf]Paper   bibtex   abstract
Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software. Sczyrba, A.; Hofmann, P.; Belmann, P.; Koslicki, D.; Janssen, S.; Droege, J.; Gregor, I.; Majda, S.; Fiedler, J.; Dahms, E.; Bremges, A.; Fritz, A.; Garrido-Oter, R.; Jorgensen, T., S.; Shapiro, N.; Blood, P., D.; Gurevich, A.; Bai, Y.; Turaev, D.; DeMaere, M., Z.; Chikhi, R.; Nagarajan, N.; Quince, C.; Hansen, L., H.; Sorensen, S., J.; Chia, B., K., H.; Denis, B.; Froula, J., L.; Wang, Z.; Egan, R.; Kang, D., D.; Cook, J., J.; Deltel, C.; Beckstette, M.; Lemaitre, C.; Peterlongo, P.; Rizk, G.; Lavenier, D.; Wu, Y.; Singer, S., W.; Jain, C.; Strous, M.; Klingenberg, H.; Meinicke, P.; Barton, M.; Lingner, T.; Lin, H.; Liao, Y.; Gueiros, G.; Cuevas, D., A.; Edwards, R., A.; Saha, S.; Piro, V., C.; Renard, B., Y.; Pop, M.; Klenk, H.; Goeker, M.; Kyrpides, N.; Woyke, T.; Vorholt, J., A.; Schulze-Lefert, P.; Rubin, E., M.; Darling, A., E.; Rattei, T.; and McHardy, A., C. bioRxiv,099127+. 1 2017.
Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software [link]Website   bibtex   abstract
  2016 (7)
The Advanced Cyberinfrastructure Research and Education Facilitators Virtual Residency: Toward a National Cyberinfrastructure Workforce. Neeman, H.; Bergstrom, A.; Brunson, D.; Ganote, C.; Gray, Z.; Guilfoos, B.; Kalescky, R.; Lemley, E.; Moore, B., G.; Ramadugu, S., K.; Romanella, A.; Rush, J.; Sherman, A., H.; Stengel, B.; and Voss, D. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, of XSEDE16, pages 57:1--57:8, 2016. ACM
The Advanced Cyberinfrastructure Research and Education Facilitators Virtual Residency: Toward a National Cyberinfrastructure Workforce [link]Website   bibtex
Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data. Ghaffari, N.; Abante, J.; Singh, R.; Blood, P., D.; and Johnson, C., D. In Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16, pages 1-4, 2016. ACM Press
Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data [pdf]Paper   Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data [link]Website   bibtex
TCGA Expedition: A Data Acquisition and Management System for TCGA Data. Chandran, U., R.; Medvedeva, O., P.; Barmada, M., M.; Blood, P., D.; Chakka, A.; Luthra, S.; Ferreira, A.; Wong, K., F.; Lee, A., V.; Zhang, Z.; Budden, R.; Scott, J., R.; Berndt, A.; Berg, J., M.; and Jacobson, R., S. PLOS ONE, 11(10): e0165395. 10 2016.
TCGA Expedition: A Data Acquisition and Management System for TCGA Data [pdf]Paper   TCGA Expedition: A Data Acquisition and Management System for TCGA Data [link]Website   bibtex
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 (Bethesda, Md.), 6(7): 2157-2163. 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
Integrated bottom-up and top-down proteomics of patient-derived breast tumor xenografts. Ntai, I.; LeDuc, R.; and Fellers, R. Molecular & Cellular. 2016.
Integrated bottom-up and top-down proteomics of patient-derived breast tumor xenografts [link]Website   bibtex
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: 852. 6 2016.
Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola. [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. 9 2016.
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli [pdf]Paper   Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli [link]Website   bibtex   abstract
  2015 (7)
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. Wang, M.; Doak, T., T., G.; and Ye, Y. Genome biology, 16. 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.; Doak, T.; and Barnett, W. In Proceedings of the XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, 2015.
Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome [link]Website   bibtex
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. Bao, G.; Wang, M.; Doak, T.; and Ye, Y. Frontiers in microbiology. 2015.
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota [link]Website   bibtex
Saccharide breakdown and fermentation by the honey bee gut microbiome. Lee, F.; Rusch, D.; and Stewart, F. Environmental. 2015.
Saccharide breakdown and fermentation by the honey bee gut microbiome [pdf]Paper   Saccharide breakdown and fermentation by the honey bee gut microbiome [link]Website   bibtex
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, of XSEDE '15, pages 4:1--4:5, 2015. ACM
NCBI-BLAST Programs Optimization on XSEDE Resources for Sustainable Aquaculture [pdf]Paper   NCBI-BLAST Programs Optimization on XSEDE Resources for Sustainable Aquaculture [link]Website   bibtex
Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Zhang, Y., Y.; Kong, W.; Gao, Y.; Liu, X.; Gao, K.; Xie, H.; Wu, Y.; Zhang, Y., Y.; Wang, J.; Gao, F.; Wu, X.; Jiang, Y.; Youssef, N., H.; Couger, M., B.; Struchtemeyer, C., G.; Liggenstoffer, A., S.; Prade, R., A.; Najar, F., Z.; Atiyeh, H., K.; Wilkins, M., R.; Elshahed, M., S.; Wu, Z.; Yang, L.; Ren, X.; He, G.; Zhang, J., J.; Yang, J.; Qian, Z.; Dong, J.; Sun, L.; Zhu, Y.; Du, J.; Yang, F.; Zhang, S.; Jin, Q.; Uy, K.; LeDuc, R.; Ganote, C.; Tarpy, D., R.; Mattila, H., R.; Newton, I., I., L., G.; Subramanian, S.; Chaparala, S.; Avali, V.; Ganapathiraju, M., K.; 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.; Yakub, M.; Sugawara, M.; Sadowsky, M., J.; Young, N., D.; Tiffin, P.; Sousounis, K.; Qi, F.; Yadav, M., C.; Millan, J., L.; Toyama, F.; Chiba, C.; Eguchi, Y.; Eguchi, G.; Tsonis, P., A.; Roncalli, V.; Cieslak, M., C., M.; Lenz, P., P., H.; Rokop, Z., P.; Horton, M., A.; Newton, I., I., L., G.; Raborn, R., T.; Spitze, K.; Brendel, V., P., V.; Lynch, M.; Qin, X.; Huang, S.; Liu, Y.; Bian, M.; Shi, W.; Zuo, Z.; Yang, Z.; Pipes, L.; Li, S.; Bozinoski, M.; Palermo, R., E.; Peng, X.; Blood, P., D., P.; Kelly, S.; Weiss, J., M.; Thierry-Mieg, J.; Thierry-Mieg, D.; Zumbo, P.; Chen, R.; Schroth, G., P.; Mason, C., E.; Katze, M., G.; Phuong, M., A.; Mahardika, G., N.; Peterson, M.; Malloy, J.; Buonaccorsi, V.; Marden, J.; Petersen, I., T.; Bates, J., E.; Dodge, K., A.; Lansford, J., E.; Pettit, G., S.; Peng, X.; Pipes, L.; Xiong, H.; Green, R., R.; Jones, D., C.; Ruzzo, W., L.; Schroth, G., P.; Mason, C., E.; Palermo, R., E.; Katze, M., G.; Orsini, L.; Gilbert, D.; Podicheti, R.; Jansen, M.; Brown, J., B.; Solari, O., S.; Spanier, K., I.; Colbourne, J., K.; Rush, D.; Decaestecker, E.; Asselman, J.; De Schamphelaere, K., A., C.; Ebert, D.; Haag, C., R.; Kvist, J.; Laforsch, C.; Petrusek, A.; Beckerman, A., P.; Little, T., J.; Chaturvedi, A.; Pfrender, M., E.; De Meester, L.; Frilander, M., J.; Newton, I., I., L., G.; Sheehan, K., K., B.; Motamayor, J., C.; Mockaitis, K.; Schmutz, J.; Haiminen, N.; III, D., L.; Cornejo, O.; Findley, S., D.; Zheng, P.; Utro, F.; Royaert, S.; Saski, C.; Jenkins, J.; Podicheti, R.; Zhao, M.; Scheffler, B., E.; Stack, J., C.; Feltus, F., A.; Mustiga, G., M.; Amores, F.; Phillips, W.; Marelli, J., P.; May, G., D.; Shapiro, H.; Ma, J.; Bustamante, C., D.; Schnell, R., J.; Main, D.; Gilbert, D.; Parida, L.; Kuhn, D., D., N.; McGrath, C., L., C.; Gout, J., J.; Johri, P.; Doak, T., G., T.; Yanagi, A.; Lynch, M.; Martínez, T.; Ropelewski, A., J.; González-Mendez, R.; Vázquez, G., J.; Robledo, I., E.; Martinez, T.; Aquino, E., E.; Robledo, I., E.; Martinez, I.; Vazquez, G., J.; Aquino, E., E.; Robledo, I., E.; Lipovich, L.; Hou, Z.; Jia, H.; Sinkler, C.; McGowen, M.; Sterner, K., N.; Weckle, A.; Sugalski, A., B.; Pipes, L.; Gatti, D., L.; Mason, C., E.; Sherwood, C., C.; Hof, P., R.; Kuzawa, C., W.; Grossman, L., I.; Goodman, M.; Wildman, D., E.; 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Lang, E., G.; Kennedy, R., C.; Kwon, H.; Perera, R.; Qi, Y.; Radolf, J., D.; Sakamoto, J., M.; Sanchez-Gracia, A.; Severo, M., S.; Silverman, N.; Simo, L.; Tojo, M.; Tornador, C.; Van Zee, J., P.; Vazquez, J.; Vieira, F., G.; Villar, M.; Wespiser, A., R.; Yang, Y.; Zhu, J.; Arensburger, P.; Pietrantonio, P., V.; Barker, S., C.; Shao, R.; Zdobnov, E., M.; Hauser, F.; Grimmelikhuijzen, C., J., P.; Park, Y.; Rozas, J.; Benton, R.; Pedra, J., H., F.; Nelson, D., R.; Unger, M., F.; Tubio, J., M., C.; Tu, Z.; Robertson, H., M.; Shumway, M.; Sutton, G.; Wortman, J., R.; Lawson, D.; Wikel, S., K.; Nene, V., M.; Fraser, C., M.; Collins, F., H.; Birren, B.; Nelson, K., E.; Caler, E.; Hill, C., A.; Ghaffari, N.; Sanchez-Flores, A.; Doan, R.; Garcia-Orozco, K., D.; Chen, P., L.; Ochoa-Leyva, A.; Lopez-Zavala, A., A.; Carrasco, J., S.; Hong, C.; Brieba, L., G.; Rudiño-Piñera, E.; Blood, P., D., P.; Sawyer, J., E.; Johnson, C., D.; Dindot, S., V.; Sotelo-Mundo, R., R.; Criscitiello, M., F.; Gao, K.; Tankovic, A.; Zhang, Y., Y.; Kusumoto, H.; Zhang, J., J.; Chen, W.; XiangWei, W.; Shaulsky, G., H.; Hu, C.; Traynelis, S., F.; Yuan, H.; Jiang, Y.; Fergus, D., J.; Feng, N., Y.; Bass, A., H.; Fergus, D., J.; Bass, A., H.; Duncan, R., P.; Feng, H.; Nguyen, D., M.; Wilson, A., C., C.; Darris, C., E.; Tyus, J., E.; Kelley, G.; Ropelewski, A., J.; Nicholas, H., B.; Wang, X.; Nahashon, S.; Nahashon, S.; Couger, M., B.; Pipes, L.; Squina, F.; Boyd, B., M.; Allen, J., M.; Nguyen, N.; Sweet, A., D.; Warnow, T.; Shapiro, M., D.; Villa, S., M.; Bush, S., E.; Clayton, D., H.; Johnson, K., P.; Blood, P., D., P.; Marcus, S.; Schatz, M., C.; Bahreini, A.; Levine, K.; Santana-Santos, L.; Benos, P., V.; Wang, P.; Andersen, C.; Oesterreich, S.; Lee, A., V.; Armstrong, E., J.; Stillman, J., H.; Arafat, A.; Jing, P.; Ma, Y.; Pu, M.; Nan, G.; Fang, H.; Chen, C.; Fei, Y.; Almada, A., A.; and Tarrant, A., M. BMC genomics, 16(1): 1032-1037. 2 2015.
Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors [pdf]Paper   Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors [link]Website   bibtex   abstract
Physiological effects of heat stress on Hawaiian picture-wing Drosophila: genome-wide expression patterns and stress-related traits. Uy, K.; LeDuc, R.; and Ganote, C. Conservation. 2015.
Physiological effects of heat stress on Hawaiian picture-wing Drosophila: genome-wide expression patterns and stress-related traits [link]Website   bibtex
  2014 (10)
Expanding the catalog of cas genes with metagenomes. Zhang, Q.; Doak, T., T., G.; and Ye, Y. Nucleic acids research, 42(4): 2448–2459. 2 2014.
Expanding the catalog of cas genes with metagenomes [pdf]Paper   Expanding the catalog of cas genes with metagenomes [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.; Martinez-Garcia, P., J.; Holt, C.; Yandell, M.; Zimin, A., V.; Yorke, J., A.; Crepeau, M., W.; Puiu, D.; Salzberg, S., L.; de Jong, P., J.; Mockaitis, K.; Main, D.; Langley, C., H.; and Neale, D., B. Genetics, 196(3): 891-909. 3 2014.
Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation [link]Website   bibtex   abstract
The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics. LeDuc, R.; Fellers, R.; Early, B.; and Greer, J. Journal of proteome. 2014.
The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics [link]Website   bibtex
Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. McGrath, C.; Gout, J.; Doak, T.; and Yanagi, A. Genetics. 2014.
Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence [link]Website   bibtex
Differential retention and divergent resolution of duplicate genes following whole-genome duplication. McGrath, C.; Gout, J.; Johri, P.; and Doak, T. Genome. 2014.
Differential retention and divergent resolution of duplicate genes following whole-genome duplication [link]Website   bibtex
Development of single nucleotide polymorphism (SNP) markers from the mango (Mangifera indica) transcriptome for mapping and estimation of genetic diversity. Kuhn, D.; Dillon, N.; Innes, D.; and Wu, L. Lives, Livelihoods and …. 2014.
Development of single nucleotide polymorphism (SNP) markers from the mango (Mangifera indica) transcriptome for mapping and estimation of genetic diversity [link]Website   bibtex
De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)–the dominant zooplankter of the North Atlantic Ocean. Lenz, P.; Roncalli, V.; Hassett, R.; Wu, L.; and Cieslak, M. PloS one. 2014.
De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)–the dominant zooplankter of the North Atlantic Ocean [link]Website   bibtex
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.; Carlson, J., W.; Cherbas, L.; Eads, B., D.; Miller, D.; Mockaitis, K.; Roberts, J.; Davis, C., A.; Frise, E.; Hammonds, A., S.; Olson, S.; Shenker, S.; Sturgill, D.; Samsonova, A., A.; Weiszmann, R.; Robinson, G.; Hernandez, J.; Andrews, J.; Bickel, P., J.; Carninci, P.; Cherbas, P.; Gingeras, T., R.; Hoskins, R., A.; Kaufman, T., C.; Lai, E., C.; Oliver, B.; Perrimon, N.; Graveley, B., R.; and Celniker, S., E. Nature, 512(7515): 393-399. 3 2014.
Diversity and dynamics of the Drosophila transcriptome [link]Website   bibtex   abstract
Leveraging the national cyberinfrastructure for biomedical research. LeDuc, R.; Vaughn, M.; and Fonner, J. Journal of the. 2014.
Leveraging the national cyberinfrastructure for biomedical research [link]Website   bibtex
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Chen, X.; Bracht, J.; Goldman, A.; and Dolzhenko, E. Cell. 2014.
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development [link]Website   bibtex
  2013 (5)
National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research. LeDuc, R., D., R., R., D.; Wu, L., L.; Ganote, C., L.; Doak, T.; Blood, P., D., P., P., D.; Vaughn, M.; Wu, L., L.; Blood, P., D., P., P., D.; Ganote, C., L.; and Vaughn, M. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, of XSEDE '13, pages 13:1--13:7, 2013. ACM
National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research [pdf]Paper   National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research [link]Website   bibtex   abstract
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): e1001473. 1 2013.
The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes [pdf]Paper   The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes [link]Website   bibtex
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, 110(46): 18590-18595. 11 2013.
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria [link]Website   bibtex   abstract
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Haas, B., J.; Papanicolaou, A.; Yassour, M.; Grabherr, M.; Blood, P., D.; Bowden, J.; Couger, M., B.; Eccles, D.; Li, B.; Lieber, M.; Matthew D MacManes, M., O.; Orvis, J.; Pochet, N.; Strozzi, F.; Weeks, N.; Westerman, R.; William, T.; Dewey, C., N.; Henschel, R.; LeDuc, R., D.; Friedman, N.; and Regev, A. Nat Protocols, 8. 2013.
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis [link]Website   bibtex
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.; Ganote, C., L.; Doak, T.; and Lenz, P., H. General and Comparative Endocrinology, 187: 117-135. 6 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   abstract
  2012 (2)
Diverse CRISPRs Evolving in Human Microbiomes. Rho, M.; Wu, Y.; Tang, H.; Doak, T., G.; and Ye, Y. PLoS Genetics, 8(6): e1002441. 6 2012.
Diverse CRISPRs Evolving in Human Microbiomes [pdf]Paper   Diverse CRISPRs Evolving in Human Microbiomes [link]Website   bibtex   abstract
Trinity RNA-Seq assembler performance optimization. Henschel, R.; Lieber, M.; Wu, L.; and Nista, P. Proceedings of the 1st. 2012.
Trinity RNA-Seq assembler performance optimization [link]Website   bibtex