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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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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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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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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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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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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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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Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events von Thomas, Gregg W. C., Ather, S. Hussain, Hahn, Matthew W.

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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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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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Rapid evolution of mitochondrion-related genes in haplodiploid arthropods von Li, Yiyuan, Thomas, Gregg W C, Richards, Stephen, Waterhouse, Robert M, Zhou, Xin, Pfrender, Michael E

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Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly von Warren, Wesley C., García-Pérez, Raquel, Xu, Sen, Lampert, Kathrin P., Chalopin, Domitille, Stöck, Matthias, Loewe, Laurence, Lu, Yuan, Kuderna, Lukas, Minx, Patrick, Montague, Michael J., Tomlinson, Chad, Hillier, LaDeana W., Murphy, Daniel N., Wang, John, Wang, Zhongwei, Garcia, Constantino Macias, Thomas, Gregg C. W., Volff, Jean-Nicolas, Farias, Fabiana, Aken, Bronwen, Walter, Ronald B., Pruitt, Kim D., Marques-Bonet, Tomas, Hahn, Matthew W., Kneitz, Susanne, Lynch, Michael, Schartl, Manfred

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

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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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