Muir, C.D. and M.W. Hahn (in press) The limited contribution of reciprocal gene loss to increased speciation rates following whole genome duplication. The American Naturalist.

The Gibbon Genome Sequencing and Analysis Consortium (in press) The gibbon genome provides a novel perspective on the accelerated karyotype evolution of small apes. Nature.

The Marmoset Genome Sequencing and Analysis Consortium (in press) The common marmoset genome provides insight into primate biology and evolution. Nature Genetics.

Cruickshank, T.E. 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., S.V. Zhang, 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

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

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

*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

*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

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

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

*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

Cristianini, N. and M.W. Hahn (2007) Introduction to Computational Genomics. Cambridge University Press. Website

Hahn, M.W. (2007) Detecting natural selection on cis-regulatory DNA. Genetica. 129:7-18. PDF

*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

*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

*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

*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(9):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(6):901-906. PDF

Hahn, M.W. and G.A. Wray (2002) The G-value paradox. Evolution and Development 4(2):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

*Papers with media coverage or reviews