Nuzhdin, S.V., D.M. Tufts, and M.W. Hahn (in press) Abundant genetic variation in transcript level during early Drosophila development. Evolution & Development.
Li, Y., J.C. Costello, A.K. Holloway, and M.W. Hahn (in press) "Reverse ecology" and the power of population genomics. Evolution.
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
