Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3 von Han, Mira V, Thomas, Gregg W C, Lugo-Martinez, Jose, Hahn, Matthew W

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Convergent evolution of the genomes of marine mammals von Foote, Andrew D, Liu, Yue, Thomas, Gregg W C, Vinař, Tomáš, Alföldi, Jessica, Deng, Jixin, Dugan, Shannon, van Elk, Cornelis E, Hunter, Margaret E, Joshi, Vandita, Khan, Ziad, Kovar, Christie, Lee, Sandra L, Lindblad-Toh, Kerstin, Mancia, Annalaura, Nielsen, Rasmus, Qin, Xiang, Qu, Jiaxin, Raney, Brian J, Vijay, Nagarjun, Wolf, Jochen B W, Hahn, Matthew W, Muzny, Donna M, Worley, Kim C, Gilbert, M Thomas P, Gibbs, Richard A

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PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance von Yan, Han, Hu, Zhirui, Thomas, Gregg W C, Edwards, Scott V, Sackton, Timothy B, Liu, Jun S

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Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques von Thomas, Gregg W C, Wang, Richard J, Nguyen, Jelena, Alan Harris, R, Raveendran, Muthuswamy, Rogers, Jeffrey, Hahn, Matthew W

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Evolution of salivary glue genes in Drosophila species von Da Lage, Jean-Luc, Thomas, Gregg W C, Bonneau, Magalie, Courtier-Orgogozo, Virginie

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Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals von Thomas, Gregg W C, Hahn, Matthew W

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Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability von Wang, Richard J, Thomas, Gregg W C, Raveendran, Muthuswamy, Harris, R Alan, Doddapaneni, Harshavardhan, Muzny, Donna M, Capitanio, John P, Radivojac, Predrag, Rogers, Jeffrey, Hahn, Matthew W

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Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host von Palesch, David, Bosinger, Steven E., Tharp, Gregory K., Vanderford, Thomas H., Paiardini, Mirko, Chahroudi, Ann, Johnson, Zachary P., Kirchhoff, Frank, Hahn, Beatrice H., Norgren, Robert B., Patel, Nirav B., Sodora, Donald L., Dawoud, Reem A., Stewart, Caro-Beth, Seepo, Sara M., Harris, R. Alan, Liu, Yue, Raveendran, Muthuswamy, Han, Yi, English, Adam, Thomas, Gregg W. C., Hahn, Matthew W., Pipes, Lenore, Mason, Christopher E., Muzny, Donna M., Gibbs, Richard A., Sauter, Daniel, Worley, Kim, Rogers, Jeffrey, Silvestri, Guido

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A fast, reproducible, high-throughput variant calling workflow for population genomics von Mirchandani, Cade D, Shultz, Allison J, Thomas, Gregg W C, Smith, Sara J, Baylis, Mara, Arnold, Brian, Corbett-Detig, Russ, Enbody, Erik, Sackton, Timothy B

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Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication von Montague, Michael J., Li, Gang, Gandolfi, Barbara, Khan, Razib, Aken, Bronwen L., Searle, Steven M. J., Minx, Patrick, Hillier, LaDeana W., Koboldt, Daniel C., Davis, Brian W., Driscoll, Carlos A., Barr, Christina S., Blackistone, Kevin, Quilez, Javier, Lorente-Galdos, Belen, Marques-Bonet, Tomas, Alkan, Can, Thomas, Gregg W. C., Hahn, Matthew W., Menotti-Raymond, Marilyn, O'Brien, Stephen J., Wilson, Richard K., Lyons, Leslie A., Murphy, William J., Warren, Wesley C.

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Reproductive Longevity Predicts Mutation Rates in Primates von Thomas, Gregg W.C., Wang, Richard J., Puri, Arthi, Harris, R. Alan, Raveendran, Muthuswamy, Hughes, Daniel S.T., Murali, Shwetha C., Williams, Lawrence E., Doddapaneni, Harsha, Muzny, Donna M., Gibbs, Richard A., Abee, Christian R., Galinski, Mary R., Worley, Kim C., Rogers, Jeffrey, Radivojac, Predrag, Hahn, Matthew W.

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Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits von Sun, Cheng, Huang, Jiaxing, Wang, Yun, Zhao, Xiaomeng, Su, Long, Thomas, Gregg W C, Zhao, Mengya, Zhang, Xingtan, Jungreis, Irwin, Kellis, Manolis, Vicario, Saverio, Sharakhov, Igor V, Bondarenko, Semen M, Hasselmann, Martin, Kim, Chang N, Paten, Benedict, Penso-Dolfin, Luca, Wang, Li, Chang, Yuxiao, Gao, Qiang, Ma, Ling, Ma, Lina, Zhang, Zhang, Zhang, Hongbo, Zhang, Huahao, Ruzzante, Livio, Robertson, Hugh M, Zhu, Yihui, Liu, Yanjie, Yang, Huipeng, Ding, Lele, Wang, Quangui, Ma, Dongna, Xu, Weilin, Liang, Cheng, Itgen, Michael W, Mee, Lauren, Cao, Gang, Zhang, Ze, Sadd, Ben M, Hahn, Matthew W, Schaack, Sarah, Barribeau, Seth M, Williams, Paul H, Waterhouse, Robert M, Mueller, Rachel Lockridge

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Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly von Bentz, Alexandra B., Thomas, Gregg W. C., Rusch, Douglas B., Rosvall, Kimberly A.

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Genomics and conservation: Guidance from training to analyses and applications von Schiebelhut, Lauren M., Guillaume, Annie S., Kuhn, Arianna, Schweizer, Rena M., Armstrong, Ellie E., Beaumont, Mark A., Byrne, Margaret, Cosart, Ted, Hand, Brian K., Howard, Leif, Mussmann, Steven M., Narum, Shawn R., Rasteiro, Rita, Rivera‐Colón, Angel G., Saarman, Norah, Sethuraman, Arun, Taylor, Helen R., Thomas, Gregg W. C., Wellenreuther, Maren, Luikart, Gordon

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Referee: Reference Assembly Quality Scores von Thomas, Gregg W C, Hahn, Matthew W

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The Effects of Increasing the Number of Taxa on Inferences of Molecular Convergence von Thomas, Gregg W. C., Hahn, Matthew W., Hahn, Yoonsoo

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The human mutation rate is increasing, even as it slows von Thomas, Gregg W C, Hahn, Matthew W

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The comparative genomics and complex population history of Papio baboons von Rogers, Jeffrey, Raveendran, Muthuswamy, Harris, R Alan, Mailund, Thomas, Leppälä, Kalle, Athanasiadis, Georgios, Schierup, Mikkel Heide, Cheng, Jade, Munch, Kasper, Walker, Jerilyn A, Konkel, Miriam K, Jordan, Vallmer, Steely, Cody J, Beckstrom, Thomas O, Bergey, Christina, Burrell, Andrew, Schrempf, Dominik, Noll, Angela, Kothe, Maximillian, Kopp, Gisela H, Liu, Yue, Murali, Shwetha, Billis, Konstantinos, Martin, Fergal J, Muffato, Matthieu, Cox, Laura, Else, James, Disotell, Todd, Muzny, Donna M, Phillips-Conroy, Jane, Aken, Bronwen, Eichler, Evan E, Marques-Bonet, Tomas, Kosiol, Carolin, Batzer, Mark A, Hahn, Matthew W, Tung, Jenny, Zinner, Dietmar, Roos, Christian, Jolly, Clifford J, Gibbs, Richard A, Worley, Kim C

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The Evolution of Widespread Recombination Suppression on the Dwarf Hamster (Phodopus) X Chromosome von Moore, Emily C., Thomas, Gregg W. C., Mortimer, Sebastian, Kopania, Emily E. K., Hunnicutt, Kelsie E., Clare-Salzler, Zachary J., Larson, Erica L., Good, Jeffrey M.

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Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise von Prost, Stefan, Armstrong, Ellie E, Nylander, Johan, Thomas, Gregg W C, Suh, Alexander, Petersen, Bent, Dalen, Love, Benz, Brett W, Blom, Mozes P K, Palkopoulou, Eleftheria, Ericson, Per G P, Irestedt, Martin

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