Orkin, J.D., L.F.K. Kuderna, N. Hermosilla-Albala, C. Fontsere, M.L. Aylward, M. Janiak, N. Andriaholinirina, P. Balaresque, M.E. Blair, J.-L. Fausser, I.G. Gut, M. Gut, M.W. Hahn, R.A. Harris, J.E. Horvath, C. Keyser, A.C. Kitchener, M.D. Le, E. Lizano, S. Merker, T. Nadler, G.H. Perry, C.J. Rabarivola, M. Raveendran, C. Roos, D.D. Wu, A. Zaramody, G. Zhang, D. Zinner, L. Pozzi, J. Rogers, K.K.-H. Farh, T. Marques Bonet (in press) Genomic diversity and demographic history of the non-anthropoid primates. Nature Ecology & Evolution.

Smith, M.L. and M.W. Hahn (2024) Selection leads to false inferences of introgression using popular methods. Genetics 227:iyae089. PDF

Wong, T.K.F., C. Cherryh, A.G. Rodrigo, M.W. Hahn, B.Q. Minh, and R. Lanfear (2024) MAST: Phylogenetic inference with mixtures across sites and trees. Systematic Biology 73:375-391. PDF

Hibbins, M.S. and M.W. Hahn (2024) Distinguishing between histories of speciation and introgression using genomic data. Bulletin of the Society of Systematic Biologists. 3: https://doi.org/10.18061/bssb.v3i1.9227.  PDF

Hahn, M.W., Y. Peña-Garcia, and R.J. Wang (2023) The “faulty male” hypothesis for sex-biased mutation and disease. Current Biology 33:R1166-R1172. PDF

Smith. M.L. and M.W. Hahn (2023) Phylogenetic inference using generative adversarial networks. Bioinformatics 39:btad543. PDF

Yan, Q., R.F. Guerrero, R.R. Khan, A.A. Surujnarine, R.J. Wapner, M.W. Hahn, A. Raja, A. Salleb-Aouissi, W.A. Grobman, H. Simhan, N. Blue, R. Silver, J.H. Chung, U.M. Reddy, P. Radivojac, I. Pe’er, and D.M. Haas (2023) Searching and visualizing genetics associations of pregnancy traits by using GnuMoM2b. Genetics 225:iyad151. PDF

Wang, R.J., J. Rogers, and M.W. Hahn (2023) Robust inference of historical human generation times. bioRxiv 2023.07.20.549788. PDF [Permanent version]

Hibbins, M.S., L.C. Breithaupt, and M.W. Hahn (2023) Phylogenomic comparative methods: accurate evolutionary inferences in the presence of gene tree discordance. Proceedings of the National Academy of Sciences 120:e2220389120. PDF

Bertram, J. B. Fulton, J. Tourigny, Y. Peña-Garcia, L.C. Moyle, and M.W. Hahn (2023) CAGEE: computational analysis of gene expression evolution. Molecular Biology and Evolution 40:msad106. PDF

Wang, R.J., S.I. Al-Saffar, J. Rogers, and M.W. Hahn (2023) Human generation times across the past 250,000 years. Science Advances 9:eabm7047. PDF

Mo, Y.K., R. Lanfear, M.W. Hahn, and B.Q. Minh (2023) Updated site concordance factors minimize effects of homoplasy and taxon sampling. Bioinformatics 39:btac741. PDF

Wang, R.J., Y. Peña-Garcia, M.G. Bibby, M. Raveendran, R.A. Harris, H.T. Jansen, C.T. Robbins, J. Rogers, J.L. Kelley, and M.W. Hahn (2022b) Examining the effect of hibernation on germline mutation rates in grizzly bears. Genome Biology and Evolution 14:evac148. PDF

Rusch, D.B., J. Huang, C. Hemmerich, and M.W. Hahn (2022) High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS. ISME Communications 2:99. PDF

Pagel, K. A., H. Chu, R. Ramola, R.F. Guerrero, J.H. Chung, S. Parry, U.M. Reddy, R.M. Silver, J.G. Steller, L.M. Yee, R.J. Wapner, M.W. Hahn, S. Natarajan, D.M. Haas, and P. Radivojac (2022) Association of genetic predisposition and physical activity with risk of gestational diabetes in nulliparous women. JAMA Network Open 5:e2229158. PDF

Al-Saffar, S.I. and M.W. Hahn (2022) Evaluating methods for estimating the proportion of adaptive amino acid substitutions. bioRxiv 2022.08.15.504017. PDF [Permanent version]

Wang, R.J., M. Raveendran, R.A. Harris, W.J. Murphy, L.A. Lyons, J. Rogers, and M.W. Hahn (2022a) De novo mutations in domestic cat are consistent with an effect of reproductive longevity on both the rate and spectrum of mutations. Molecular Biology and Evolution 39:msac147. PDF

Smith, M.L. and M.W. Hahn (2022) The frequency and topology of pseudoorthologs. Systematic Biology 71:649-659. PDF

Smith, M.L., D. Vanderpool, and M.W. Hahn (2022) Using all gene families vastly expands data available for phylogenomic inference. Molecular Biology and Evolution 39:msac112. PDF

Hibbins, M.S. and M.W. Hahn (2022) Phylogenomic approaches to detecting and characterizing introgression. Genetics 220:iyab173. PDF

Bergeron, L. A., S. Besenbacher, T. N. Turner, C. J. Versoza, R. J. Wang, A. L. Price, E. Armstrong, M. Riera, J. Carlson, H.-y. Chen, M. W. Hahn, K. Harris, A. Snøfrid Kleppe, E. H. López-Nandam, P. Moorjani, S. P. Pfeifer, G. P. Tiley, A. D. Yoder, G. Zhang, and M. H. Schierup (2022) Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates. eLife 11:e73577. PDF

Yan, Z., M.L. Smith, P. Du, M.W. Hahn, and L. Nakhleh (2022) Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs. Systematic Biology 71:367-381. PDF

Hibbins, M.S. and M.W. Hahn (2021) The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes. PLoS Genetics 17:e1009892. PDF

Alcalay, Y., S. Fuchs, R. Galizi, F. Bernardini, R.E. Haghighat-Khah, D.B. Rusch, J.R. Adrion, M.W. Hahn, P. Tortosa, and P.A. Papathanos (2021) The potential for a released autosomal X-shredder becoming a driving-Y chromosome and invasively suppressing wild populations of malaria mosquitoes. Frontiers in Bioengineering and Biotechnology 9:752253. PDF

Albecker, M.A., L.G.E. Wilkins, S.A. Krueger-Hadfield, S.M. Bashevkin, M.W. Hahn, M.P. Hare, H.K. Kindsvater, M.A. Sewell, K.E. Lotterhos, and A.M. Reitzel (2021) Does a complex life cycle affect adaptation to environmental change? Genome-informed approaches for characterizing selection across life cycle stages. Proceedings of the Royal Society B 288:20212122. PDF

Wu, M., D.C. Haak, G.J. Anderson, M.W. Hahn, L.C. Moyle, and R.F. Guerrero (2021) Inferring the genetic basis of sex determination from the genome of a dioecious nightshade. Molecular Biology and Evolution 38:2946-2957. PDF

Broz, A., A. Simpson-Van Dam, A. Tovar-Méndez, M.W. Hahn, B.A. McClure, and P. Bedinger (2021) Spread of self-compatibility constrained by an intrapopulation crossing barrier. New Phytologist 231:878-891. PDF

Thomas, G.W.C., R.J. Wang, J. Nguyen, R.A. Harris, M. Raveendran, J. Rogers, and M.W. Hahn (2021) Origins and long-term patterns of copy-number variation in rhesus macaques. Molecular Biology and Evolution 38:1460-1471. PDF

Wang, R.J., P. Radivojac, and M.W. Hahn (2021) Distinct error rates for reference and non-reference genotypes estimated by pedigree analysis. Genetics 217:iyaa014. PDF

Sun, C., J. Huang, Y. Wang, X. Zhao, L. Su, G. W. C. Thomas, M. Zhao, X. Zhang, I. Jungreis, M. Kellis, S. Vicario, I. V. Sharakhov, S. M. Bondarenko, M. Hasselmann, C. N. Kim, B. Paten, L. Penso-Dolfin, L. Wang, Y. Chang, Q. Gao, L. Ma, L. Ma, Z. Zhang, H. Zhang, H. Zhang, L. Ruzzante, H. M. Robertson, Y. Zhu, Y. Liu, H. Yang, L. Ding, Q. Wang, W. Xu, C. Liang, M. W. Itgen, L. Mee, B. M. Sadd, G. Cao, Z. Zhang, M. W. Hahn, S. Schaack, S. M. Barribeau, P. H. Williams, R. M. Waterhouse, and R. L. Mueller (2021) Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution 38:486-501. PDF

Smith, M.L. and M.W. Hahn (2021) New approaches for inferring phylogenies in the presence of paralogs. Trends in Genetics 37:156-169. PDF

Mendes, F.K., D. Vanderpool, B. Fulton, and M.W. Hahn (2020) CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36:5516-5518. PDF

Hibbins, M.S., M.J.S. Gibson, and M.W. Hahn (2020) Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression. eLife 9:e63753. PDF

Vanderpool, D., B.Q. Minh, R. Lanfear, D. Hughes, S. Murali, R.A. Harris, M. Raveendran, D.M. Muzny, M.S. Hibbins, R.J. Williamson, R.A. Gibbs, K.C. Worley, J. Rogers, and M.W. Hahn (2020) Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. PLoS Biology 18: e3000954. PDF

Small, S.T., F. Labbé, N.F. Lobo, L.L. Koekemoer, C.H. Sikaala, D.E. Neafsey, M.W. Hahn, M.C. Fontaine, and N.J. Besansky (2020) Radiation with reticulation marks the origin of a major malaria vector. Proceedings of the National Academy of Sciences 117: 31583–31590. PDF

The Anopheles gambiae 1000 Genomes Consortium (2020) Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii. Genome Research 30:1533-1546. PDF

Wang, R.J., G.W.C. Thomas, M. Raveendran, R.A. Harris, H. Doddapaneni, D.M. Muzny, J.P. Capitanio, P. Radivojac, J. Rogers, and M.W. Hahn (2020) Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Research 30:826–834. PDF

Minh, B.Q., M.W. Hahn, and R. Lanfear (2020) New methods to calculate concordance factors for phylogenomic datasets. Molecular Biology and Evolution 37:2727-2733. PDF

Stamboulian, M., R.F. Guerrero, M.W. Hahn, and P. Radivojac (2020) The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. Bioinformatics (ISMB 2020) 36:i219–i226. PDF

Bryant, D. and M.W. Hahn (2020) The concatenation question. In: Phylogenetics in the Genomic Era. Pp. 3.4:1-3.4:23 C. Scornavacca, F. Delsuc, and N. Galtier, eds. No commercial publisher | Authors open access book. PDF

Thomas, G.W.C., E. Dohmen, D.S.T. Hughes, S.C. Murali, M. Poelchau, K. Glastad, C.A. Anstead, N.A. Ayoub, P. Batterham, M. Bellair, G.J. Binford, H. Chao, Y.H. Chen, C. Childers, H. Dinh, H. Doddapaneni, J.J. Duan, S. Dugan, L.A. Esposito, M. Friedrich, J. Garb, R.B.B. Gasser, M.A.D. Goodisman, D.E. Gundersen-Rindal, Y. Han, A.M. Handler, M. Hatakeyama, L. Hering, W.B. Hunter, P. Ioannidis, J.C. Jayaseelan, D. Kalra, A. Khila, P.K. Korhonen, C.E. Lee, S.L. Lee, Y. Li, A.R.I. Lindsey, G. Mayer, A.P. McGregor, D.D. McKenna, B. Misof, M. Munidasa, M. Munoz-Torres, D.M. Muzny, O. Niehuis, N. Osuji-Lacy, S.R. Palli, K.A. Panfilio, M. Pechmann, T. Perry, R.S. Peters, H.C. Poynton, N.-M. Prpic, J. Qu, D. Rotenberg, C. Schal, S.D. Schoville, E.D. Scully, E. Skinner, D.B. Sloan, R. Stouthamer, M.R. Strand, N.U. Szucsich, A. Wijeratne, N.D. Young, E.E. Zattara, J.B. Benoit, E.M. Zdobnov, M.E. Pfrender, K.J. Hackett, J.H. Werren, K.C. Worley, R.A. Gibbs, A.D. Chipman, R.M. Waterhouse, E. Bornberg-Bauer, M.W. Hahn, and S. Richards (2020) Gene content evolution in arthropods. Genome Biology 21:15. PDF

Waterhouse, R.M., S. Aganezov, Y. Anselmetti, J. Lee, L. Ruzzante, M.J. Reijnders, R. Feron, S. Bèrard, P. George, M.W. Hahn, P.I. Howell, M. Kamali, S. Koren, D. Lawson, G. Maslen, A. Peery, A.M. Phillippy, M.V. Sharakhova, E. Tannier, M.F. Unger, S.V. Zhang, M.A. Alekseyev, N.J. Besansky, C. Chauve, S.J. Emrich, and I.V. Sharakhov (2020) Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biology 18:1. PDF

M.W. Hahn and M.S. Hibbins (2019) A three-sample test for introgression. Molecular Biology and Evolution 12:2878-2882.PDF

Thomas, G.W.C. and M.W. Hahn (2019) Referee: reference assembly quality scores. Genome Biology and Evolution 11:1483-1486. PDF

Yang, R., Y. Jiang, S. Mathews, E.A. Housworth, M.W. Hahn, and P. Radivojac (2019) A new class of metrics for learning on real-valued and structured data. Data Mining and Knowledge Discovery 33:995-1016. PDF

Mendes, F.K., A.P. Livera, and M.W. Hahn (2019) The perils of intralocus recombination for inferences of molecular convergence. Philosophical Transactions of the Royal Society B 374:20180244. PDF

Adrion, J.R., D.J. Begun, and M.W. Hahn (2019) Patterns of transposable element variation and clinality in Drosophila. Molecular Ecology 28:1523-1536. PDF

Ayala, D., S. Zhang, M. Chateau, C. Fouet, I. Morlais, C. Costantini, M.W. Hahn, and N.J. Besansky (2019) Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae. Molecular Ecology 28:1333–1342. PDF

Rogers, J., R. Muthuswamy, R. A. Harris, T. Mailund, K. Leppälä, G. Athanasiadis, M.H. Schierup, J. Cheng, K. Munch, J.A. Walker, M. Konkel, V. Jordan, C. Steely, T. Beckstrom, C. Bergey, A. Burrell, D. Schrempf, A. Noll, M. Kothe, G.H. Kopp, Y. Liu, S. Murali, K. Billis, F. J. Martin, M. Muffato, L. Cox, J. Else, T. Disotell, D.M. Muzny, J. Phillips-Conroy, B. Aken, E.E. Eichler, T. Marques-Bonet, C. Kosiol, M.A. Batzer, M.W. Hahn, J. Tung, D. Zinner, C. Roos, C.J. Jolly, R.A. Gibbs, K.C. Worley and the Baboon Genome Analysis Consortium (2019) The comparative genomics and complex population history of Papio baboons. Science Advances 5:eaau6947. PDF

Hibbins, M.S. and M.W. Hahn (2019) The timing and direction of introgression under the multispecies network coalescent. Genetics 211:1059-1073. PDF

Guerrero, R.F. and M.W. Hahn (2018) Quantifying the risk of hemiplasy in phylogenetic inference. Proceedings of the National Academy of Sciences 115:12787-12792. PDF Appendix

Thomas, G.W.C., R. J. Wang, A. Puri, R.A. Harris, M. Raveendran, D. Hughes, S. Murali, L. Williams, H. Doddapaneni, D. Muzny, R.A. Gibbs, C. Abee, M. R. Galinski, K.C. Worley, J. Rogers, P. Radivojac, and M.W. Hahn (2018) Reproductive longevity predicts mutation rates in primates. Current Biology 28:3193-3197. PDF

Wang, R.J. and M.W. Hahn (2018) Speciation genes are more likely to have discordant gene trees. Evolution Letters 2:281-296. PDF

Cheng, C., J.C. Tan, M.W. Hahn, and N.J. Besansky (2018) A systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae. Proceedings of the National Academy of Sciences 115:E7005-E7014. PDF

Wu, M., J.L. Kostyun, M.W. Hahn, and L.C. Moyle (2018) Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance. Molecular Ecology 27:3301-3316. PDF

Mendes, F.K., J.A. Fuentes-González, J.G. Schraiber, and M.W. Hahn (2018) A multispecies coalescent model for quantitative traits. eLife 7:e36482. PDF

Venkat, A., M.W. Hahn, and J.W. Thornton (2018) Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nature Ecology & Evolution 2:1280-1288. PDF

Kern, A.D. and M.W. Hahn (2018) The neutral theory in light of natural selection. Molecular Biology and Evolution 35:1366-1371. PDF

House, G.L. and M.W. Hahn (2018) Evaluating methods to visualize patterns of genetic differentiation on a landscape. Molecular Ecology Resources 18:448-460. PDF

Ramalho, R.F., S. Li, P. Radivojac, and M.W. Hahn (2018) Proteomic evidence for in-frame and out-of-frame alternatively spliced isoforms in human and mouse. IEEE-ACM Transactions on Computational Biology and Bioinformatics 15:1284-1289 PDF

Warren, W.C., R. García-Pérez, S. Xu, K.P. Lampert, D. Chalopin, M. Stöck, L. Kuderna, P. Minx, M.J. Montague, C. Tomlinson, L.W. Hillier, D.N. Murphy, J. Wang, Z. Wang, T. Marques-Bonet, C.M. Garcia, G.W.C. Thomas, M.W. Hahn, J.-N. Volff, F. Farias, B. Aken, K.D. Pruitt, S. Kneitz, M. Lynch, and M. Schartl (2018) Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly. Nature Ecology & Evolution 2:669-679. PDF

Palesch, D., S. E. Bosinger, G. K. Tharp, T. H. Vanderford, M. Paiardini, A. M. Chahroudi, Z. P. Johnson, F. Kirchhoff, B. Hahn, R. B. Norgren Jr, H. RA, S. Murali, Y. Liu, M. Raveendran, G. W. C. Thomas, M. W. Hahn, L. Pipes, C. E. Mason, D. Muzny, R. A. Gibbs, K. C. Worley, J. Rogers, and G. Silvestri (2018) Sooty mangabey genome sequence reveals new insights into mechanisms of disease resistance in natural hosts of SIV. Nature 553:77-81.PDF

Mendes, F.K. and M.W. Hahn (2018) Why concatenation fails near the anomaly zone. Systematic Biology 67:158-169. PDF Appendix

Guerrero, R.F. and M.W. Hahn (2017) Speciation as a sieve for ancestral polymorphism. Molecular Ecology 26:5362-5368. PDF

The Anopheles gambiae 1000 Genomes Consortium (2017) Natural diversity of the malaria vector Anopheles gambiae. Nature 552:96-100. PDF

Thomas, G.W.C, S.H. Ather, and M.W. Hahn (2017) Gene-tree reconciliation with MUL-trees to resolve polyploidy events. Systematic Biology 66:1007-1018. PDF

Adrion, J.R., M. Song, D.R. Schrider, M.W. Hahn, and S. Schaack (2017) Genome-wide estimates of transposable element insertion and deletion rates in Drosophila melanogaster. Genome Biology and Evolution 9:1329-1340. PDF

Roda, F., F.K. Mendes, M.W. Hahn, and R. Hopkins (2017) Genomic evidence of gene flow during reinforcement in Texas Phlox. Molecular Ecology 26:2317-2330. PDF

Thomas, G.W.C, M.W. Hahn, and Y. Hahn (2017) The effects of increasing the number of taxa on inferences of molecular convergence. Genome Biology and Evolution 9:213-221. PDF

Broz, A.K., R.F. Guerrero, A.M. Randle, Y.S. Baek, M.W. Hahn, P.A. Bedinger (2017) Linking gene expression to unilateral pollen-pistil reproductive barriers. BMC Plant Biology 17:81. PDF

Bromberg, Y., M.W. Hahn, and P. Radivojac (2017) Computational approaches to understanding the evolution of molecular function. Pacific Symposium on Biocomputing 22:1-2. PDF

Mendes, F.K., Y. Hahn, and M.W. Hahn (2016) Gene tree discordance can generate patterns of diminishing convergence over time. Molecular Biology and Evolution 33:3299-3307. PDF

Zhang, S.V., L. Zhuo, and M.W. Hahn (2016) AGOUTI: improving genome assembly and annotation using transcriptome data. GigaScience 5:31. PDF

Mendes, F.K. and M.W. Hahn (2016) Gene tree discordance causes apparent substitution rate variation. Systematic Biology 65:711-721. PDF

Pease, J.B., R.F. Guerrero, N.A. Sherman, M.W. Hahn, and L.C. Moyle (2016) Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis. Molecular Ecology 25:2592-2608. PDF

Rosenzweig, B.K., J.B. Pease, N.J. Besansky, and M.W. Hahn (2016) Powerful methods for detecting introgressed regions from population genomic data. Molecular Ecology 25:2387-2397. PDF

Wen, D., Y. Yu, M.W. Hahn, and L. Nakhleh (2016) Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis. Molecular Ecology 25:2361-2372. PDF

Schrider, D.R., M.W. Hahn, and D.J. Begun (2016) Parallel evolution of copy-number variation across continents in Drosophila melanogaster. Molecular Biology and Evolution 33:1308-1316. PDF

Guerrero, R.F., A.L. Posto, L.C. Moyle, and M.W. Hahn (2016) Genome-wide patterns of regulatory divergence revealed by introgression lines. Evolution 70:696-706. PDF

Hall A.B., P.-A. Papathanos, A. Sharma, C. Cheng, O.S. Akbari, L.A. Assour, N.H. Bergman, A. Cagnetti, A. Crisanti, T. Dottorini, E. Fiorentini, R. Galizi, J. Hnath, X. Jiang, S. Koren, T. Nolan, D. Radune, M.V. Sharakhova, A. Steele, V.A. Timoshevskiy, N. Windbichler, S.V. Zhang, M.W. Hahn, A.M. Phillippy, S.J. Emrich, I.V. Sharakhov, Z. Tu, and N.J. Besansky (2016) Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proceedings of the National Academy of Sciences 113:E2114-E2123. PDF

Hahn, M.W. and L. Nakhleh (2016) Irrational exuberance for resolved species trees. Evolution 70:7-17. PDF

Mallet, J., N.J. Besansky, and M.W. Hahn (2016) How reticulated are species? BioEssays 38:140-149. PDF

Muir, C.D. and M.W. Hahn (2015) The limited contribution of reciprocal gene loss to increased speciation rates following whole genome duplication. The American Naturalist. 185:70-86. PDF

Warren W.C…G.W.C. Thomas, M.W. Hahn…et al. (2015) The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Research. 25:1921-1933. PDF

Cooper, B.S., C.R. Burrus, C. Ji, M.W. Hahn, and K.L. Montooth (2015) Similar efficacies of selection shape mitochondrial and nuclear genes in both Drosophila melanogaster and Homo sapiens. G3. 5:2165-2176. PDF

Pease, J.B. and M.W. Hahn (2015) Detection and polarization of introgression in a five-taxon phylogeny. Systematic Biology. 64:651-662. PDF

Adrion, J.R., M.W. Hahn, and B.S. Cooper (2015) Revisiting classic clines in Drosophila melanogaster in the age of genomics. Trends in Genetics. 31:434-444. PDF

Schrider, D.R., F.K. Mendes, M.W. Hahn, and A.D. Kern (2015) Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps. Genetics. 200:267-284. PDF

Thomas, G.W.C. and M.W. Hahn (2015) Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals. Molecular Biology and Evolution. 32:1232-1236. PDF

Aganezov, S., N. Sitdykova, The Anopheles Genomes Cluster Consortium, and M.A. Alekseyev (2015) Scaffold assembly based on genome rearrangement analysis. Computational Biology and Chemistry. 57:46-53. PDF

Foote, A.D., Y. Liu, G.W.C. Thomas, T. Vinar, J. Alföldi, J. Deng, S. Dugan, N. van Elk, V. Joshi, Z. Khan, C. Kovar, S.L. Lee, K. Lindblad-Toh, A. Mancia, R. Nielsen, X. Qin, J. Qu, B.J. Raney, N. Vijay, J.B.W. Wolf, M.W. Hahn, D.M. Muzny, K.C. Worley, M.T.P. Gilbert, R.A. Gibbs. (2015) Convergent evolution of the genomes of marine mammals. Nature Genetics. 47:272-275. PDF

Neafsey, D.E….G.W.C. Thomas, M.W. Hahn…et al. (2015) Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science. 347:1258522. PDF Supplementary Materials

Fontaine, M.C., J.B. Pease, A. Steele, R.M. Waterhouse, D.E. Neafsey, I.V. Sharakhov, X. Jiang, A.B. Hall, F. Catteruccia, E. Kakani, S.N. Mitchell, Y.-C. Wu, H.A. Smith, R.R. Love, M.K.N. Lawniczak, M.A. Slotman, S.J. Emrich, M.W. Hahn, N.J. Besansky (2015) Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science. 347:1258524. PDF Supplementary Materials

Montague, M.J., G. Li, B. Gandolfi, R. Khan, B.L. Aken, S.M.J. Searle, P. Minx, L. Hillier, D. Kolboldt, B.W. Davis, C.A. Driscoll, C. Barr, K. Blackistone, J. Quilez, B. Lorente-Galdos, T. Marques-Bonet, C. Alkan, G.W.C. Thomas, M.W. Hahn, M. Menotti-Raymond, S.J. O’Brien, R.K. Wilson, L.A. Lyons, W.J. Murphy, and W.C. Warren (2014) Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.  Proceedings of the National Academy of Sciences. 111:17230-17235. PDF

Abbott, A.G., M.E. Staton, J.M. Lohtka, L.E. DeWald, T. Zhebentyayeva, B. Kapoor, A.M. Thomas, D.A. Larson, D. Hadziabdic, S. DeBolt, C.D. Nelson, and J.E. Carlson (2024) Will “tall oaks from little acorns grow”? White oak (Quercus alba) biology in the anthropocene. Forests 15:269.

Wang, Z., Y. Zhou, Y. Zhang, Y.K. MO, and Y. Wang (2023) XMR: an explainable multimodal neural network for drug response prediction. Frontiers in Bioinformatics 3:1164482.

Fountain-Jones, N.M., M.L. SMITH, and F. Austerlitz (2021) Machine learning in molecular ecology. Molecular Ecology Resources 21:2589-2597.

Hamlin, J.A.P., M.S. HIBBINS, and L.C. Moyle (2020) Assessing biological factors affecting postspeciation introgression. Evolution Letters 4:137-154.

Jewell, C.P., S.V. ZHANG, M.J.S. Gibson, A. Tovar-Méndez, B. McClure B, and L.C. Moyle (2020) Intraspecific genetic variation underlying postmating reproductive barriers between species in the wild tomato clade (Solanum sect. Lycopersicon). Journal of Heredity 111:216-226.

GUERRERO, R.F., S.V. Scarpino, J.V. Rodrigues, D.L. Hartl, and C.B. Ogbunugafor (2019) Proteostasis environment shapes higher-order epistasis operating on antibiotic resistance. Genetics 212:565-575.

Prost, S., E.E. Armstrong, J. Nylander, G.W.C. THOMAS, A. Suh, B. Petersen, L. Dalen, B. Benz, M.P.K. Blom, E. Palkopoulou, P.G.P. Ericson, M. Irestedt (2019) Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise. GigaScience 8:giz003.

Da Lage, J.L., G.W.C. THOMAS, M. Bonneau, and V. Courtier-Orgogozo (2019) Evolution of salivary glue genes in Drosophila species. BMC Evolutionary Biology 19:36.

Berrio, A., R.F. GUERRERO, G.V. Aglyamova, M. Okhovat, M.V. Matz, S.M. Phelps (2018) Evidence of balancing selection, regulatory interactions and population differentiation in the prairie vole Avpr1a locus. Molecular Ecology 27:419-431.

Schoville, S.D., et al. (2018) A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Scientific Reports 8:1931. (G.W.C. THOMAS, co-author)

PEASE, J.B. and B.K. ROSENZWEIG (2018) Encoding data using biological principles: the Multisample Variant Format for phylogenomics and population genomics. IEEE-ACM Transactions on Computational Biology and Bioinformatics 15:1231-1238.

R.F. GUERRERO, C.D. Muir, S. Josway, and L.C. Moyle (2017) Pervasive antagonistic interactions among hybrid incompatibility loci. PLoS Genetics 13:e1006817.

Des Marais, D.L., R.F. GUERRERO, J.R. Lasky, and S.V. Scarpino (2017) Topological features of a gene co-expression network predict patterns of natural diversity in environmental response. Proceedings of the Royal Society B. 284:20170914.

ADRION, J.R., P.S. White, and K.L. Montooth (2016) The roles of compensatory evolution and constraint in aminoacyl tRNA synthetase evolution. Molecular Biology and Evolution. 33:152-161.

HOUSE, G.L., S. Ekanayake, Y. Ruan, U.M.E. Schütte, W. Kaonongbua, G. Fox, Y. Ye, and J.D. Bever (2016) Phylogenetically structured differences in rRNA gene sequence variation among species of arbuscular mycorrhizal fungi and their implications for sequence clustering. Applied and Environmental Microbiology. 82:4921-4930.

Muir, C.D., J.B. PEASE, and L.C. Moyle (2014) Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae). Genetics. 198:1629-1643.