The Hahn Lab



  • 2024
  • Hibbins, M.S. and M.W. Hahn (in press) Distinguishing between histories of speciation and introgression using genomic data. Bulletin of the Society of Systematic Biologists.

  • 2023
  • 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

  • 2022
  • 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

  • 2021
  • 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

  • 2020
  • 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

  • 2019
  • 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

  • 2018
  • 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

  • 2017
  • 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

  • 2016
  • 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

  • Pease, J.B., D.C. Haak, M.W. Hahn, and L.C. Moyle (2016) Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLoS Biology 14:e1002379. PDF
  • 2015
  • 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

  • 2014
  • Denton, J.F., J. Lugo Martinez, A.E. Tucker, D.R. Schrider, W.C. Warren, and M.W. Hahn (2014) Extensive error in the number of genes inferred from draft genome assemblies. PLoS Computational Biology. 10:e1003998. PDF
  • 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

  • Carbone, L....G.W.C. Thomas, M.W. al. (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature. 513:195-201. PDF
  • The Marmoset Genome Sequencing and Analysis Consortium (2014) The common marmoset genome provides insight into primate biology and evolution. Nature Genetics. 46:850-857. PDF
  • Cruickshank, T.C. and M.W. Hahn (2014) Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology. 23:3133-3157. PDF
  • Bachtrog, D., J.E. Mank, C.L. Peichel, M. Kirkpatrick, S.P. Otto, T.-L. Ashman, M.W. Hahn, J. Kitano, I. Mayrose, R. Ming, N. Perrin, L. Ross, N. Valenzuela, and J.C. Vamosi. (2014) Sex determination: Why so many ways of doing it? PLoS Biology.12:e1001899. PDF
  • The Tree of Sex Consortium (2014) Tree of Sex: A database of sexual systems. Scientific Data. 1:140015. PDF
  • Cassone, B.J., C. Kamdem, C. Cheng, J.C. Tan, M.W. Hahn, C. Costantini, and N.J. Besansky (2014) Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaounde Cameroon. Molecular Ecology. 23:2242-2259. PDF
  • Hahn, M.W., Zhang, S.V., and L.C. Moyle. (2014) Sequencing, assembling, and correcting draft genomes using recombinant populations. G3 4:669-679. PDF
  • Thomas, G.W.C. and M.W. Hahn (2014) The human mutation rate is increasing, even as it slows. Molecular Biology and Evolution. 31:253-257. PDF
  • 2013
  • Han, M.V., G.W.C. Thomas, J. Lugo-Martinez, and M.W. Hahn (2013) Estimating gene gain and loss rates in the presence of genome assembly and annotation error using CAFE 3. Molecular Biology and Evolution. 30:1987-1997. PDF
  • Schrider, D.R., D. Houle, M. Lynch, and M.W. Hahn (2013) Rates and genomic consequences of spontaneous mutational events in Drosophila melanogaster. Genetics. 194:937-954. PDF
  • Neafsey, D.E., G.K. Christophides, F.H. Collins, S.J. Emrich, M.C. Fontaine, W. Gelbart, M.W. Hahn, P.I. Howell, F.C. Kafatos, D. Lawson, M.A.T. Muskavitch, R.M. Waterhouse, L.J. Williams, and N.J. Besansky (2013) The evolution of the Anopheles 16 genomes project. G3. 3:1191-1194. PDF
  • Pease, J.B. and M.W. Hahn (2013) More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting. Evolution. 67:2376-2384. PDF
  • Schrider, D.R., F.C.P. Navarro, P.A.F. Galante, R.B. Parmigiani, A.A. Camargo, M.W. Hahn, and S.J. de Souza (2013) Gene copy-number polymorphism caused by retrotransposition in humans. PLoS Genetics. 9:e1003242. PDF
  • Schrider, D.R., D.J. Begun, and M.W. Hahn (2013) Detecting highly differentiated copy-number variants from pooled population sequencing. Pacific Symposium on Biocomputing. 18:344-355. PDF
  • 2012
  • Casola, C., G.C. Conant, and M.W. Hahn (2012) Very low rate of gene conversion in the yeast genome. Molecular Biology and Evolution. 29:3817-3826. PDF
  • Langley, C.H., K.S. Stevens, C. Cardeno, Y.C.G. Lee, D.R. Schrider, J.E. Pool, S.A. Langley, C. Suarez, R. Detig-Corbett, B. Kolaczkowski, S. Fang, P.M. Nista, A.K. Holloway, A.D. Kern, C.N. Dewey, Y.S. Song, M.W. Hahn, and D.J. Begun (2012) Genomic variation in natural populations of Drosophila melanogaster. Genetics. 192:533-598. PDF
  • Pease, J.B. and M.W. Hahn (2012) Sex chromosomes evolved from independent ancestral linkage groups in winged insects. Molecular Biology and Evolution. 29:1645-1653. PDF
  • Cheng, C., B.J. White, C. Camdem, K. Mockaitis, C. Costantini, M.W. Hahn, and N.J. Besansky (2012) Ecological genomics of Anopheles gambiae along a latitudinal cline in Cameroon: a population resequencing approach. Genetics. 190:1417-1432. PDF
  • Casola, C., U. Zekonyte, A.D. Phillips, D.N. Cooper, and M.W. Hahn (2012) Interlocus gene conversion events introduce deleterious mutations in at least 1% of human genes associated with inherited disease. Genome Research. 22:429-435. PDF
  • Han, M.V. and M.W. Hahn (2012) Inferring the history of interchromosomal gene transposition in Drosophila using n-dimensional parsimony. Genetics. 190:813-825. PDF
  • Hahn, M.W., B.J. White, C.D. Muir, and N.J. Besansky (2012) No evidence for biased co-transmission of speciation islands in Anopheles gambiae. Philosophical Transactions of the Royal Society B: Biological Sciences. 367:374-384. PDF
  • 2011
  • Schrider, D.R., K.A. Stevens, C.M. Cardeno, C.H. Langley, and M.W. Hahn (2011) Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. Genome Research. 21:2087-2095. PDF
  • Toups, M.A., J.B. Pease, and M.W. Hahn (2011) No excess gene movement is detected off the avian or lepidopteran Z chromosome. Genome Biology and Evolution. 3:1381-1390. PDF
  • Schrider, D.R., J.-F. Gout, and M.W. Hahn (2011) Very few RNA and DNA sequence differences in the human transcriptome. PLoS ONE. 6:e25842. PDF
  • Nehrt, N.L., W.T. Clark, P. Radivojac, and M.W. Hahn (2011) Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS Computational Biology. 7:e1002073. PDF
  • Schrider, D.R., J.N. Hourmozdi, and M.W. Hahn (2011) Pervasive multinucleotide mutational events in eukaryotes. Current Biology. 21:1051-1054. PDF (includes Supplementary Materials)
  • Cassone, B.J., M.J. Molloy, C. Cheng, J.C. Tan, M.W. Hahn, and N.J.Besansky (2011) Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La. Molecular Ecology. 20:2567-2580. PDF
  • Bentley, R.A. and M.W. Hahn (2011) Is there a "Neutral Theory of Anthropology"? Current Anthropology. 52:117-118. PDF
  • Locke, D.P....C. Casola, D.R. Schrider, M.W. al. (2011) Comparative and demographic analysis of orang-utan genomes. Nature. 469:529-533. PDF
  • 2010
  • Toups, M.A. and M.W. Hahn (2010) Retrogenes reveal the direction of sex-chromosome evolution in mosquitoes. Genetics. 186:763-766. PDF
  • Schrider, D.R. and M.W. Hahn (2010) Gene copy-number polymorphism in nature. Proceedings of the Royal Society B: Biological Sciences. 277:3213-3221. PDF
  • Kostka, D., M.W. Hahn, and K.S. Pollard (2010) Non-coding sequences near duplicated genes evolve rapidly. Genome Biology and Evolution. 2:518-533 PDF
  • Moyle, L.C., C.D. Muir, M.V. Han, and M.W. Hahn (2010) The contribution of gene movement to the "Two Rules of Speciation". Evolution. 64:1541-1557. PDF
  • Casola, C., C.L. Ganote, and M.W. Hahn (2010) Nonallelic gene conversion in the genus Drosophila. Genetics. 185:95-103. PDF
  • Turner, T.L. and M.W. Hahn (2010) Genomic islands of speciation or genomic islands and speciation? Molecular Ecology. 19:848-850. PDF
  • Nuzhdin, S.V., A. Rachkova, and M.W. Hahn (2010) The strength of transcription-factor binding modulates co-variation in transcriptional networks. Trends in Genetics. 26:51-53. PDF
  • Schrider, D.R. and M.W. Hahn (2010) Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications. Molecular Biology and Evolution. 27:103-111. PDF
  • 2009
  • Schrider, D.R., J.C. Costello, and M.W. Hahn (2009) All human-specific gene losses are present in the genome as pseudogenes. Journal of Computational Biology. 16:1419-1427. PDF
  • Hahn, M.W. (2009) Distinguishing among evolutionary models for the maintenance of gene duplicates. Journal of Heredity. 100:605-617. PDF Correction
  • Meisel, R.P., M.V. Han, and M.W. Hahn (2009) A complex suite of forces drives gene traffic from Drosophila X chromosomes. Genome Biology and Evolution. 1:176-188. PDF
  • McGrath, C.L., C. Casola, and M.W. Hahn (2009) Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics. 182:615-622. PDF (includes Supplementary Materials)
  • Casola, C. and M.W. Hahn (2009) Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods. Journal of Molecular Evolution. 68:679-687. PDF
  • Han, M.V., J.P. Demuth, C.L. McGrath, C. Casola, and M.W. Hahn (2009) Adaptive evolution of young gene duplicates in mammals. Genome Research. 19:859-867. PDF
  • Demuth, J.P. and M.W. Hahn (2009) The life and death of gene families. BioEssays. 31:29-39. PDF
  • Han, M.V. and M.W. Hahn (2009) Identifying parent-daughter relationships among duplicated genes. Pacific Symposium on Biocomputing. 14:114-125. PDF
  • 2008
  • Li, Y., J.C. Costello, A.K. Holloway, and M.W. Hahn (2008) "Reverse ecology" and the power of population genomics. Evolution. 62:2984-2994. PDF
  • Nuzhdin, S.V., D.M. Tufts, and M.W. Hahn (2008) Abundant genetic variation in transcript level during early Drosophila development. Evolution & Development. 10:683-689. PDF
  • Costello, J.C., M.V. Han, and M.W. Hahn (2008) Limitations of pseudogenes in identifying gene losses. Sixth Annual RECOMB Satellite Workshop on Comparative Genomics. pp. 14-25. PDF
  • Radivojac, P., P.H. Baenziger, M.G. Kann, M. Mort, M.W. Hahn, and S.D. Mooney (2008) Gain and loss of phosphorylation sites in human cancer. Bioinformatics. 24:i241-i247. PDF
  • Cassone, B.J., K. Mouline, M.W. Hahn, B.J. White, M. Pombi, F. Simard, C. Costantini, and N.J. Besansky (2008) Differential gene expression in incipient species of Anopheles gambiae. Molecular Ecology. 17:2491-2504. PDF
  • Hahn, M.W. (2008) Toward a selection theory of molecular evolution. Evolution. 62:255-265. PDF
  • 2007
  • White, B.J., M.W. Hahn, M. Pombi, B.J. Cassone, N.F. Lobo, F. Simard, and N.J. Besansky (2007) Localization of candidate regions maintaining a common polymorphic inversion (2La) in Anopheles gambiae. PLoS Genetics. 3:e197. PDF
  • Hahn, M.W., J.P. Demuth, and S.-G. Han (2007) Accelerated rate of gene gain and loss in primates. Genetics. 177:1941-1949. PDF
  • Hahn, M.W., M.V. Han, and S.-G. Han (2007) Gene family evolution across 12 Drosophila genomes. PLoS Genetics. 3:e197. PDF
  • Begun, D.J., A.K. Holloway, K. Stephens, L.W. Hillier, Y.-P. Poh, M.W. Hahn, P.M. Nista, C.D. Jones, A.D. Kern, C. Dewey, L. Pachter, E. Myers, and C.H. Langley (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology. 5:e310. PDF
  • Drosophila Comparative Genome Sequencing and Analysis Consortium (2007) Evolution of genes and genomes in the context of the Drosophila phylogeny. Nature. 450:203-218. PDF
  • Stark, A., M.F. Lin, P. Kheradpour, J.S. Pedersen, L. Parts, J.W. Carlson, M.A. Crosby, M.D. Rasmussen, S. Roy, A.N. Deoras, J.G. Ruby, J. Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, E. Hodges, A.S. Hinrichs, A. Caspi, B. Paten, S.-W. Park, M.V. Han, M.L. Maeder, B.J. Polansky, B.E. Robson, S. Aerts, J. van Helden, B. Hassan, D.G. Gilbert, D.A. Eastman, M. Rice, M. Weir, M.W. Hahn, Y. Park, C.N. Dewey, L. Pachter, W.J. Kent, D. Haussler, E.C. Lai, D.P. Bartel, G.J. Hannon, T.C. Kaufman, M.B. Eisen, A.G. Clark, D. Smith, S.E. Celniker, W.M. Gelbart, and M. Kellis (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450:219-232. PDF
  • Turner, T.L. and M.W. Hahn (2007) Locus- and population-specific selection and differentiation between incipient species of Anopheles gambiae. Molecular Biology and Evolution. 24:2132-2138. PDF
  • Hahn, M.W. (2007) Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology. 8:R141 PDF
  • Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and biomedical insights from the Rhesus Macaque genome sequence. Science. 316:222-234. PDF Supplementary Materials
  • Bentley, R.A., C.P. Lipo, H.A. Herzog, and M.W. Hahn (2007) Regular rates of popular culture change reflect random copying. Evolution and Human Behavior. 28:151-158. PDF
  • Hahn, M.W. (2007) Detecting natural selection on cis-regulatory DNA. Genetica. 129:7-18. PDF
  • 2006
  • Demuth, J.P., T. De Bie, J.E. Stajich, N. Cristianini, and M.W. Hahn (2006) The evolution of mammalian gene families. PLoS ONE. 1:e85. PDF PLoS ONE
  • Hahn, M.W. (2006) Accurate inference and estimation in population genomics. Molecular Biology and Evolution. 23:911-918. PDF
  • De Bie, T., N. Cristianini, J.P. Demuth, and M.W. Hahn (2006) CAFE: a computational tool for the study of gene family evolution. Bioinformatics. 22:1269-1271. PDF
  • 2005
  • Rockman, M.V., M.W. Hahn, N. Soranzo, F. Zimprich, D.B. Goldstein, and G.A. Wray (2005) Ancient and recent positive selection transformed opioid cis-regulation in humans. PLoS Biology. 3:e387. PDF Supplementary Materials
  • Hahn, M.W., T. De Bie, J.E. Stajich, C. Nguyen, and N. Cristianini (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Research. 15:1153-1160. PDF Supplementary Materials
  • Turner, T.L., M.W. Hahn, and S.V. Nuzhdin (2005) Genomic islands of speciation in Anopheles gambiae. PLoS Biology. 3:e285. PDF Supplementary Materials
  • Hahn, M.W. and G.C. Lanzaro (2005) Female-biased gene expression in the malaria mosquito Anopheles gambiae. Current Biology. 15:192-193. PDF (includes Supplementary data)
  • Hahn, M.W. and A.D. Kern (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Molecular Biology and Evolution. 22:803-806. PDF Supplementary Materials
  • Hahn, M.W., J.G. Mezey, D.J. Begun, J.H. Gillespie, A.D. Kern, C.H. Langley, and L.C. Moyle (2005) Codon bias and selection on single genomes. Nature. 433:E5-E6. PDF
  • Stajich, J.E. and M.W. Hahn (2005) Disentangling the effects of demography and selection in human history. Molecular Biology and Evolution. 22:63-73. PDF
  • 2004
  • Rockman, M.V., M.W. Hahn, D. Loisel, N. Soranzo, D.B. Goldstein, and G.A. Wray (2004) Positive selection on MMP3 regulation has shaped heart disease risk. Current Biology. 14:1531-1539. PDF
  • Hahn, M.W., M.V. Rockman, N. Soranzo, D.B. Goldstein, and G.A. Wray (2004) Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the Factor VII locus in humans. Genetics. 167:867-877. PDF
  • Bentley, R.A., M.W. Hahn, and S.J. Shennan (2004) Random drift and culture change. Proceedings of the Royal Society London B. 271:1443-1450. PDF
  • Hahn, M.W. and S.V. Nuzhdin (2004) The fixation of malaria refractoriness in mosquitoes. Current Biology. 14:264-265. PDF (includes Supplementary data)
  • Herzog, H.A., R.A. Bentley, and M.W. Hahn (2004) Random drift and large shifts in the popularity of dog breeds. Proceedings of the Royal Society London B, Biology Letters. 271:S353-S356. PDF
  • Hahn, M.W., G. Conant, and A. Wagner (2004) Molecular evolution in large genetic networks: Does connectivity equal constraint? Journal of Molecular Evolution. 58:203-211. PDF
  • 2003
  • Rockman, M.V., M.W. Hahn, N. Soranzo, D.B. Goldstein, and G.A. Wray (2003) Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Current Biology 13:2118-2123. PDF
  • Hahn, M.W. and R.A. Bentley (2003) Drift as a mechanism for cultural change: An example from baby names. Proceedings of the Royal Society London B, Biology Letters, 270:S120-S123. PDF
  • Wray, G. A., M.W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. Romano (2003). The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution. 20:1377-1419. PDF
  • Hahn, M.W., J.E. Stajich, and G.A. Wray (2003) The effects of selection against spurious transcription factor binding sites. Molecular Biology and Evolution. 20:901-906. PDF
  • 2002
  • Hahn, M.W. and G.A. Wray (2002) The G-value paradox. Evolution and Development. 4:73-75. PDF
  • Tiffin, P. and M.W. Hahn (2002) Coding sequence divergence between two closely related plant species: Arabidopsis thaliana and Brassica rapa ssp. pekinensis. Journal of Molecular Evolution. 54:746-753. PDF
  • Hahn, M.W., M.D. Rausher, and C.W. Cunningham (2002) Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7. Genetics. 161:11-20. PDF


Post-doc and Student Publications

  • 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.

  • Emera, D., C. CASOLA, V.J. Lynch, D.E. Wildman, D. Agnew, and G.P. Wagner (2012) Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements. Molecular Biology and Evolution. 29:239-247.
  • Snell-Rood, E.C., A. Cash, M.V. HAN, T. Kijimoto, J. Andrews and A.P. Moczek (2011) Developmental decoupling of alternative phenotypes: Insights from the transcriptomes of horn-polyphenic beetles. Evolution. 65:231-245.
  • Colbourne, J., et al. (2011) The ecoresponsive genome of Daphnia pulex. Science. 331:555-561. (C. CASOLA, co-author)
  • Cruickshank, T. and P. NISTA (2011) Selection and constraint on regulatory elements in Drosophila simulans. Journal of Molecular Evolution. 73:94-100.
  • Kraemer, S.A., M.A. TOUPS, and G. J. Velicer (2010) Natural variation in developmental life-history traits of the bacterium Myxococcus xanthus. FEMS Microbiology Ecology. 73:226-233.
  • Arensburger, P., et al. (2010) Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science. 330:86-88. (C. CASOLA, co-author)
  • Costello, J.C., D. SCHRIDER, J. Gehlhausen, and M. Dalkilic (2009) Data-driven ontologies. Pacific Symposium on Biocomputing. 14:15-26.
  • HAN, M.V. and C.M. Zmasek (2009) phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics. 10:356.
  • Tribolium Genome Sequencing Consortium (2007) The genome of the model beetle and pest Tribolium castaneum. Nature. 452:949-955. (J.P. DEMUTH, co-author)



  • Cristianini, N. and M.W. Hahn (2007) Introduction to Computational Genomics. Cambridge University Press. Website
  • Hahn, M.W. (2018) Molecular Population Genetics. Sinauer Associates/Oxford University Press. EndNote library Bibtex library