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1.

Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance.

Hibbins, Mark S; Breithaupt, Lara C; Hahn, Matthew W.

Proc Natl Acad Sci U S A; 120(22): e2220389120, 2023 05 30.

Artículo en Inglés | MEDLINE | ID: mdl-37216509

2.

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.

Wong, Thomas K F; Cherryh, Caitlin; Rodrigo, Allen G; Hahn, Matthew W; Minh, Bui Quang; Lanfear, Robert.

Syst Biol; 2024 Feb 29.

Artículo en Inglés | MEDLINE | ID: mdl-38421146

3.

CAGEE: Computational Analysis of Gene Expression Evolution.

Bertram, Jason; Fulton, Ben; Tourigny, Jason P; Peña-Garcia, Yadira; Moyle, Leonie C; Hahn, Matthew W.

Mol Biol Evol; 40(5)2023 05 02.

Artículo en Inglés | MEDLINE | ID: mdl-37158385

4.

New Approaches for Inferring Phylogenies in the Presence of Paralogs.

Smith, Megan L; Hahn, Matthew W.

Trends Genet; 37(2): 174-187, 2021 02.

Artículo en Inglés | MEDLINE | ID: mdl-32921510

5.

Phylogenetic inference using generative adversarial networks.

Smith, Megan L; Hahn, Matthew W.

Bioinformatics; 39(9)2023 09 02.

Artículo en Inglés | MEDLINE | ID: mdl-37669126

6.

Updated site concordance factors minimize effects of homoplasy and taxon sampling.

Mo, Yu K; Lanfear, Robert; Hahn, Matthew W; Minh, Bui Quang.

Bioinformatics; 39(1)2023 01 01.

Artículo en Inglés | MEDLINE | ID: mdl-36383168

7.

Applications of machine learning in phylogenetics.

Mo, Yu K; Hahn, Matthew W; Smith, Megan L.

Mol Phylogenet Evol; 196: 108066, 2024 Jul.

Artículo en Inglés | MEDLINE | ID: mdl-38565358

8.

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host.

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.

Nature; 553(7686): 77-81, 2018 01 03.

Artículo en Inglés | MEDLINE | ID: mdl-29300007

9.

The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes.

Hibbins, Mark S; Hahn, Matthew W.

PLoS Genet; 17(11): e1009892, 2021 11.

Artículo en Inglés | MEDLINE | ID: mdl-34748547

10.

Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference.

Smith, Megan L; Vanderpool, Dan; Hahn, Matthew W.

Mol Biol Evol; 39(6)2022 06 02.

Artículo en Inglés | MEDLINE | ID: mdl-35642314

11.

De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations.

Wang, Richard J; Raveendran, Muthuswamy; Harris, R Alan; Murphy, William J; Lyons, Leslie A; Rogers, Jeffrey; Hahn, Matthew W.

Mol Biol Evol; 39(7)2022 07 02.

Artículo en Inglés | MEDLINE | ID: mdl-35771663

12.

Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability.

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.

Genome Res; 30(6): 826-834, 2020 06.

Artículo en Inglés | MEDLINE | ID: mdl-32461224

13.

The Frequency and Topology of Pseudoorthologs.

Smith, Megan L; Hahn, Matthew W.

Syst Biol; 71(3): 649-659, 2022 04 19.

Artículo en Inglés | MEDLINE | ID: mdl-34951639

14.

Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.

Yan, Zhi; Smith, Megan L; Du, Peng; Hahn, Matthew W; Nakhleh, Luay.

Syst Biol; 71(2): 367-381, 2022 02 10.

Artículo en Inglés | MEDLINE | ID: mdl-34245291

15.

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.

Vanderpool, Dan; Minh, Bui Quang; Lanfear, Robert; Hughes, Daniel; Murali, Shwetha; Harris, R Alan; Raveendran, Muthuswamy; Muzny, Donna M; Hibbins, Mark S; Williamson, Robert J; Gibbs, Richard A; Worley, Kim C; Rogers, Jeffrey; Hahn, Matthew W.

PLoS Biol; 18(12): e3000954, 2020 12.

Artículo en Inglés | MEDLINE | ID: mdl-33270638

16.

Radiation with reticulation marks the origin of a major malaria vector.

Small, Scott T; Labbé, Frédéric; Lobo, Neil F; Koekemoer, Lizette L; Sikaala, Chadwick H; Neafsey, Daniel E; Hahn, Matthew W; Fontaine, Michael C; Besansky, Nora J.

Proc Natl Acad Sci U S A; 117(50): 31583-31590, 2020 12 15.

Artículo en Inglés | MEDLINE | ID: mdl-33262284

17.

Inferring the Genetic Basis of Sex Determination from the Genome of a Dioecious Nightshade.

Wu, Meng; Haak, David C; Anderson, Gregory J; Hahn, Matthew W; Moyle, Leonie C; Guerrero, Rafael F.

Mol Biol Evol; 38(7): 2946-2957, 2021 06 25.

Artículo en Inglés | MEDLINE | ID: mdl-33769517

18.

Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques.

Thomas, Gregg W C; Wang, Richard J; Nguyen, Jelena; Alan Harris, R; Raveendran, Muthuswamy; Rogers, Jeffrey; Hahn, Matthew W.

Mol Biol Evol; 38(4): 1460-1471, 2021 04 13.

Artículo en Inglés | MEDLINE | ID: mdl-33226085

19.

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.

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.

Mol Biol Evol; 38(2): 486-501, 2021 01 23.

Artículo en Inglés | MEDLINE | ID: mdl-32946576

20.

CAFE 5 models variation in evolutionary rates among gene families.

Mendes, Fábio K; Vanderpool, Dan; Fulton, Ben; Hahn, Matthew W.

Bioinformatics; 36(22-23): 5516-5518, 2021 Apr 01.

Artículo en Inglés | MEDLINE | ID: mdl-33325502

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Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance.

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.

CAGEE: Computational Analysis of Gene Expression Evolution.

New Approaches for Inferring Phylogenies in the Presence of Paralogs.

Phylogenetic inference using generative adversarial networks.

Updated site concordance factors minimize effects of homoplasy and taxon sampling.

Applications of machine learning in phylogenetics.

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host.

The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes.

Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference.

De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations.

Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability.

The Frequency and Topology of Pseudoorthologs.

Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.

Radiation with reticulation marks the origin of a major malaria vector.

Inferring the Genetic Basis of Sex Determination from the Genome of a Dioecious Nightshade.

Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques.

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.

CAFE 5 models variation in evolutionary rates among gene families.