Our Publications

Foley, N.M., Harris, A.J., Bredemeyer, K.R., Ruedi, M., Puechmaille, S.J., Teeling, E.C., Criscitiello, M.F., and J. Murphy. 2024. Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation. Cell Genomics [In press]

Yuan, J., Kitchener, A.C., Sun, T., Jiangzuo, Q., Tuohetahong, Y., Zhao, L., Yang, P., Wang, G., Wang, J., Hou, W., Liu, Y., Chen, W., Murphy, W.J., and Li. The genome of the black-footed cat: revealing a rich natural history and urgent conservation priorities for small felids. Proc. Natl Acad. Sci. USA [in press]

Lescroart, J., Bonilla-Sánchez, A., Napolitano, C., Torres, D.L.B., Ramírez-Chaves, H.E., Pulido-Santacruz, P., Murphy, W.J., Svardal, H., Eizirik, E. 2023. Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus. Biol. Evol. msad255

Howard-McCombe, J., Jamieson, A., Carmagnini, A., Russo, I.M., Ghazali, M., Campbell, R., Driscoll, C., Murphy, W.J., Nowak C., O’Connor, T., Tomsett, L., Lyons, L.A., Munoz-Fuentes, V., Bruford, M., Kitchener, A.C., Larson, G., Frantz, L., Senn, H., Lawson, D.J., and M. Beaumont. 2023. Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease. Current Biology 33: 4761-4769.

Jamieson, A., Carmagnini, A., Howard-McCombe, J., Doherty, S., Hirons, A.,  Dimopolous, E., Lin, A.T., Allen, R., Anderson-Whymark, H., Barnett, R., Batey, C., Beglane, F., Bowden, W., Bratten, J., Drew, E., Foley, M., Fowler, T., Fox, A., Geigl, E., Gotfredsen, A.B., Grange, T.,  Griffiths, D., Gro, D., Haruda, A., Hjermind, J., Knapp, Z., Lebrasseur, O., Librado, P., Mainland, I., McDonnell, C., Munoz-Fuentes, V., Nowak, C., O’Connor, T., Peters, J., Russo, I.M., Ryan, H., Sheridan, A., Sinding, M.H.S., Skoglund, P., Swali, P., Symmons, R., Thomas, G., Trolle Jensen, T.Z., Kitchener, A.C., Senn, H., Lawson, D., Driscoll, C., Murphy, W.J., Beaumont, M., Ottoni, C., Sykes, N., Larson, G., and L. Frantz. 2023. Limited historical admixture between European wildcats and domestic cats. Current Biology 33: 4751-4760.

Bredemeyer, K.R., Hillier, L., Harris, A.J., Hughes, G.M., Foley, N.M., Lawless, C., Carroll, R.A., Storer, J.M., Batzer, M.A., Rice, E.S., Davis, B.W., Raudsepp, T., O’Brien, S.J., Lyons, L.A., Warren, W.C., and W.J. Murphy. 2023. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nature Genetics  doi: 10.1038/s41588-023-01548-y.

Yuan, J., Wang, G., Zhao, L., Sun, T., Kitchener, A.C., Chen, W., Huang, C., Wang, C., Xu, X., Wang, J., Lu, H., Xu, L., Jiangzuo, Q., Murphy, W.J., Wu, D., and Li. 2023. How genomic insights into the evolutionary history of clouded leopards inform their conservation. Science Advances 9(40): eadh9143

Haghani, A., Li, C.Z., Lu, A.T., Robeck, T.R., Belov, K., Breeze, C.E., Brooke, R.T., Clarke, S., Faulkes, C.G., Fei, Z., Ferguson, S.H., Finno, C.J., Gladyshev, V.N., Gorbunova, V., Goya, R.G., Hogan, A.N., Hogg, C.J., Hore, T.A., Kiaris, H., Kordowitzki, P., Takahashi, J.S., Acosta Rodríguez, V.A., Niehrs, C., Wallingford, M.C., Poganik, J.R., Zhang, B., Shindyapina, A.V., Lee, S.G., Shafer, A.B.A., Cossette, M.L., Peters, K.J., Gerber, L., Krützen, M., Ablaeva, J., Adams, D.M., Almunia, J., Aloysius, A., Amor, N.M.S., Ardehali, R., Arneson, A., Baker, C.S., Banks, G., Black, P., Blumstein, D.T., Bors, E.K., Brown, J.L., Carter, G., Caulton, A., Cavin, J.M., Chakrabarti, L., Chatzistamou, I., Chen, H., Cheng, K., Chiavellini, P., Choi, O.W., Cooper, L.N., Day, J., DeYoung, J., Dirocco, S., Dold, C., Ehmke, E.E., Emmons, C.K., Emmrich, S., Erbay, E., Erlacher-Reid, C., Flower, J.E., Gaillard, J.M., Garde, E., Grant, M.J., Green, C.B., Hanson, M.B., Haulena, M., Herrick, K., Huang, T., Izpisua Belmonte, J.C., Jasinska, A.J., Jones, G., Jourdain, E., Kashpur, O., Katcher, H., Katsumata, E., Kaza, V., Kobor, M.S., Kwon, S.B., Larison, B., Lehmann, M., Lemaitre, J.F., Levine, A.J., Li, X., Li, C., Lim, A.R., Lin, D.T.S., Lindemann, D.M., Macoretta, N., Maddox, D., Matkin, C.O., Mattison, J.A., McClure, M., Mergl, J., Meudt, J.J, Montano, G.A., Murphy, W.J., Nagy, M., Narayan, P., Nathaniels, P.W., Nguyen, N.B., Nyamsuren, B., O’Tierney Ginn, P., Odom, D.T., Ophir, A.G., Osborn, S., Paul, K.C., Pedersen, A.B., Pellegrini, M., Petersen, J.L., Pietersen, D.W., Pinho, G.M., Prado, N.A., Reddy, P., Rey, B., Ritz, B.R., Rodriguez, M., Russell, J., Rydkina, E., Sailer, L.L., Salmon, A.B., Sanghavi, A., Schachtschneider, K.M., Schmitt, D., Schmitt, T., Schomacher, L., Schook, L.B., Simmons, M., Singh, K., Sinha, I., Slone, J., Snell, R.G., Soltanmohammadi, E., Spangler, M.L., Spriggs, M., Staggs, L., Stedman, N., Stewart, D.T., Sugrue, V.J., Takasugi, M., Teeling, E.C., Van Bonn, B., Vernes, S.C., Vinters, H.V., Vu, H., Williams, R.W., Yao, M., Zhang, Z., Zhao, Y., Zhao, P., Zhou, W., Alagaili, A.N., Hart, D.W., Bennett, N.C., Little, T.J., Seifert, A.W., Chavez, A.S., Dunnum, J.L., Cook, J.A., Liphardt, S.W., O’Brien, J.K., Munshi-South, J., Koski, W.R., Mozhui, K., Naderi, A., Ostrander, E.A., Parsons, K.M., Plassais, J., Robbins, J., Sears, K.E., Seluanov, A., Steinman, K.J., Szladovits, B., Thompson, M.J., Villar, D., Wang, N., Wilkinson, G.S., , Yan, Q., Young, B.G., Zhang, J., Zoller, J.A., Ernst, J., Yang, X.W., Raj, K., Horvath, S., Mammalian Methylation Consortium. DNA methylation networks underlying mammalian traits. Science 381: eabq5693.

Foley, N.M., Mason, V.C., Harris, A.J., Bredemeyer, K.R., Damas, J., Lewin, H.A., Eizirik, E., Gatesy, J., Karlsson E., Lindblad-Toh, K., Zoonomia Consortium, Springer, M.S., and W.J. Murphy. 2023. A genomic timescale for placental mammal evolution. Science 380: eabl8189.

Christmas, M.J., Kaplow, I.M., Genereux, D.P., Dong, M.X., Hughes, G.M., Li, X., Sullivan, P.F., Hindle, A.G., Andrews, G., Armstrong, J.C., Bianchi, M., Breit, A.M., Diekhans, M., Fanter, F., Foley, N.M., Goodman, L., Keoug, K.C., Kirilenko, B., Kowalczyk, A., Lawless, C., Lind, A., Meadows, J.R.S., Moreira, L., Ryan, L., Swofford, R., Valenzuela, A., Wagner, F., Wallerman, O., Damas, J., Fan, K., Grimshaw, J., Johnson, J., Kozyrev, S.V., Lawler, A.J., Marinescu, V.D., Osmanski, A., Paulat, N.S., Phan, B.A., Reilly, S.K., Schäffer, D.E., Steiner, C., Supple, M.A., Wilder, A.P., Wirthlin, M.E., Xue, J.R., Zoonomia Consortium, Birren, B.W., Gazal, S., Hubley, R.M., Koepfli, K.P., Marques-Bonet, T., Meyer, W., Nweeia, M., Shapiro, B., Smit, A.F., Springer, M., Teeling, E.C., Weng, Z., Hiller, M., Levesque, D.L., Lewin, H.A., Murphy, W.J., Navarro, A., Paten, B., Pollard, K.S., Ray, D.R., Ruf, R., Ryder, O.A., Pfenning, A.R., Lindblad-Toh, K., and E.K. Karlsson. 2023. Evolutionary constraint and innovation across hundreds of placental mammals. Science 380: eabl3943. 

Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Zoonomia Consortium*, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR.  Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 380(6643): eabm7993. *Consortium member

Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J, Zoonomia Consortium*, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K.Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 380(6643): eabn2937. *Consortium member 

Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Zoonomia Consortium*, Nowakowski T, Ahituv N, Pollen A, Pollard KS.Three-dimensional genome rewiring in loci with human accelerated regions. Science 380(6643): eabm1696. *Consortium member e

Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium*, Hiller M.Integrating gene annotation with orthology inference at scale. Science 380(6643): eabn3107. *Consortium member

Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Zoonomia Consortium*, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, Reilly SK.The functional and evolutionary impacts of human-specific deletions in conserved elements. Science 380(6643): eabn2253. *Consortium member

Moon KL, Huson HJ, Morrill K, Wang MS, Li X, Srikanth K, Zoonomia Consortium*, Lindblad-Toh K, Svenson GJ, Karlsson EK, Shapiro B. ​Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs. Science 380(6643): eabn5887. *Consortium member

Andrews G, Fan K, Pratt HE, Phalke N, Zoonomia Consortium*, Karlsson EK, Lindblad-Toh K, Gazal S, Moore JE, Weng Z. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science 380(6643): eabn7930. *Consortium member

Wilder AP, Supple MA, Subramanian A, Mudide A, Swofford R, Serres-Armero A, Steiner C, Koepfli KP, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK, Zoonomia Consortium*, Ryder OA, Shapiro B. The contribution of historical processes to contemporary extinction risk in placental mammals. Science 380(6643): eabn5856. *Consortium member

Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, Zoonomia Consortium*, Rosen J, Storer JM, Hubley R, Smit AFA, Dávalos LM, Karlsson EK, Lindblad-Toh K, Ray DA. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science 380(6643): eabn1430. *Consortium member

Dindot, S.V., Christian, S., Murphy W.J., Berent, A., Panagoulias, J., Shlafer, A., Ballard, J., Radeva, K., Robinson, R., Myers, L., Jepp, T., Shaheen, H., Hillman, P., Kongati, K., Hillhouse, A., Bredemeyer, K.R., Black, L., Douville, J., and the FIRE Consortium. 2023. An ASO therapy for Angelman syndrome that targets an evolutionarily conserved region at the start of the UBE3A-AS transcript. Science Translational Medicine 2023 Mar 22;15(688): eabf4077.

Myers, A.N., Lawhon, S.D., Diesel, A.B., Liu, W., Rodrigues Hoffmann, A., 99Lives Genome Consortium, and W.J. Murphy. 2022. An ancient haplotype containing antimicrobial peptide genes is associated with severe fungal skin disease in Persian cats. PLoS Genetics 18(2): e101006.

Dindot, S.V., Christian, S., Murphy W.J., Berent, A., Panagoulias, J., Shlafer, A., Ballard, J., Radeva, K., Robinson, R., Myers, L., Jepp, T., Shaheen, H., Hillman, P., Kongati, K., Hillhouse, A., Bredemeyer, K.R., Black, L., Douville, J., and the FIRE Consortium. Development of an ASO therapy for Angelman syndrome by targeting a conserved region at the start of the UBE3A-AS transcript. bioRxiv https://doi.org/10.1101/2021.07.27.453820

Lorenzana, G.P., Figueiró, H.V., Kaelin, C.B., Barsh, G.S., Johnson, J., Karlsson, E., Morato, R.G., Sana, D.A., Cullen, L., May, J.A., Moraes, E.A. Jr, E., Kantek, D.L.Z., Silveira, L., Murphy, W.J., Ryder, O.A., and E. Eizirik. 2022. Whole-genome sequences shed light onto demographic history and contemporaneous genetic erosion of free-ranging jaguar (Panthera onca) populations. Journal of Genetics and Genomics 49: 77-80.

vonHoldt, B. M., Brzeski, K., Aardema, M., Schell, C., Rutledge, L.Y., Fain, S., Shutt, A., Linderholm, A., and W.J. Murphy. 2021. Persistence and expansion of cryptic red wolf genomic ancestry along the American Gulf coast. Molecular Ecology 31: 1353-1365.

Bredemeyer, K.R., Seabury, C.M., Stickney, M.J., McCarrey, J.R., vonHoldt, B.M., and W.J. Murphy. 2021. Rapid macrosatellite evolution promotes X-linked hybrid male sterility in a feline interspecies cross. Molecular Biology and Evolution In press doi: 10.1093/molbev/msab274.

Burnett, S.D., Moumita, K., Murphy, W.J., Chiu, W.A., and I. Rusyn. 2021. A new approach method for characterizing inter-species toxicodynamic variability. Journal of Toxicology and Environmental Health, Part A: Current Issues Aug 24:1-20

Brashear, W.A., Bredemeyer, K.R., and W. J. Murphy. 2021. Genomic architecture constrained placental mammal X chromosome evolution. Genome Research 31: 1353-1365.

Trindade, F.J., Rodrigues, M.R., Figueiró, H.V., Li, G., Murphy, W.J., and E. Eizirik. 2021. Genome-wide SNP data help disentangle a complex felid radiation and support recognition of an additional species of wild cat. Molecular Biology and Evolution 38: 4987-4991.

Bredemeyer, Kevin R., Andrew J. Harris, Gang Li, Le Zhao, Nicole M. Foley, Melody Roelke-Parker, Stephen J. O’Brien, Leslie A. Lyons, Wesley C. Warren, and William J. Murphy. 2020. Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis). Journal of Heredity https://doi.org/10.1093/jhered/esaa057.

Hughes, Jennifer F., Helen Skaletsky, Tatyana Pyntikova, Natalia Koutseva, Terje Raudsepp, Laura G. Brown, Daniel W. Bellott et al. 2020. Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages. Genome Research 30, no. 12: 1716-1726.

Murphy, William J., Nicole M. Foley, Kevin R. Bredemeyer, John Gatesy, and Mark S. Springer. 2020. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annual Review of Animal Biosciences 9.

Curry, Caitlin J., Brian W. Davis, Laura D. Bertola, Paula A. White, William J. Murphy, and James N. Derr. 2020. Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation Across Africa. Molecular Biology and Evolution https://doi.org/10.1371/journal.pone.0143827.

Bugno‐Poniewierska, Monika, Barbara Kij, Wojciech Witarski, Magdalena Wojtaszek, Anna Radko, Angelika Podbielska, Izabela Szczerbal, and William J. Murphy. 2020. Fertile male tortoiseshell cat with true chimerism 38, XY/38, XY. Reproduction in Domestic Animals 55, 9:1139-1144.

Allen, Richard, Hannah Ryan, Brian W. Davis, Charlotte King, Laurent Frantz, Evan Irving-Pease, Ross Barnett et al. 2020. A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proceedings of the Royal Society B 287:1928.

Cogné, Benjamin, Xenia Latypova, Lokuliyanage Dona Samudita Senaratne, Ludovic Martin, Daniel C. Koboldt, Georgios Kellaris, Lorraine Fievet et al. 2020. Mutations in the Kinesin-2 Motor KIF3B Cause an Autosomal-Dominant Ciliopathy. The American Journal of Human Genetics. 106:893-904.

Genereux, Diane P., Aitor Serres, Joel Armstrong, Jeremy Johnson, Voichita Marinescu, Eva Murén, David Juan et al. 2020. A comparative genomics multitool for scientific discovery and conservation. Nature 587, no. 7833: 240-245.

Buckley, R.M., Davis, B.W., Brashear, W.A., Farias, F.H.G., Kuroki, K., Graves, T., Hillier, L.W., Kremitzki, M., Li, G., Middleton, R., Minx, P., Tomlison, C., Lyons, L.A., Murphy, W.J., Warren, W.C., 99 Lives Consortium. 2020. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLOS Genetics doi: 10.1371/journal.pgen.1008926.

Allen, R., Ryan, H., Davis, B.W., King, C., Frantz, L., Barnett, R., Linderholm, A., Loog, L., Haile, J., Lebrasseur, O., White, M., Kitchener, A., Murphy, W.J., and G. Larson. 2020. Using a genetic divergence proxy to predict the reproductive compatibility of mammalian hybrids. Proceedings of the Royal Society B, Biological Sciences 287: 20200690.

Springer, M.S., Foley, N.M., Brady, P., Gatesy, J., and W.J. Murphy. 2019. Evolutionary models for the diversification of placental mammals across the KPg boundary. Frontiers in Genetics 10: 1241.

Beichman, A.C., Koepfli, K.-P., Li G., Murphy, W., Dobrynin, P., Kilver, S., Tinker, T., Schenck, C., Schenck, E., Johnson, J., Karlsson, E., Estes, J., Lohmueller, K., and R.K. Wayne. 2019. Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter (Enhydra lutris) and giant otter (Pteronura brasiliensis). Molecular Biology and Evolution. doi: 10.1093/molbev/msz101.

Li, G., Figueiró, H.X., Eizirik, E., and W.J. Murphy. 2019. Recombination-aware phylogenomics reveals the structured genomic landscape of hybridizing cat species. Molecular Biology and Evolution. 36: 2111-2126.

Mason, V.C., Helgen, K.M., and W.J. Murphy. 2019. Comparative phylogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland. Journal of Heredity 110: 158-172. Cover article

Genova F, Longeri M, Lyons LA, Bagnato A, 99Lives Consortium*, Strillacci MG. 2018. First genome-wide CNV mapping in Felis catus using next generation sequencing data. BMC Genomics 19(1): 895. *Consortium member

Brashear, W.A., Raudsepp, T., and W.J. Murphy. 2018. Evolutionary conservation of Y chromosome ampliconic gene families despite extensive structural variation. Genome Research 28: 1841-1815.

Mason, V.C., Helgen, K.M., and W.J. Murphy. 2018. Comparative biogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland. Journal of Heredity Sep 21. doi: 10.1093/jhered/esy046.

Janečka, J.E., Davis, B.W., Ghosh, S., Paria, N., Das, P., Orlando, L., Schubert, M., Nielsen, M., Stout, T., Brashear, W.A., Li, G., Johnson, C., Metz, R., A., Al Zadjali, A. M., Love, C., Varner, D., Bellott, D., Murphy, W.J., Chowdhary, B.P., and T. Raudsepp. 2018. Horse Y chromosome assembly displays unique evolutionary features, putative stallion fertility genes. Nature Communications 9: 2945.

Janečka, J.E., Janecka, M.J., Helgen, K.M., and Murphy W.J. The validity of three snow leopard subspecies: response to Senn et al. Heredity 120: 586-590.

Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Dodman, N.H., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Pederson, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, G.D., Warren, W.C., and L.A. Lyons. 2018. Applications and efficiencies of the first cat 63K DNA array. Scientific Reports 8: 7024.

Hughes, G.M., Boston, E.M., Finarelli, J.A., Murphy, W.J., Higgins, D.G., and E.C. Teeling. 2018. The birth and death of olfactory receptor gene families in mammalian niche adaptation. Molecular Biology and Evolution 35: 1390-1406.

Bird, D.J., Murphy, W.J., Fox-Rosales, L., Hamid, I., and B. Van Valkenburg. 2018. Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia. Proc. Royal Soc. B. Mar 14;285(1874). pii: 20180100.

Springer, M.S., Murphy, W.J., and A.L. Roca. 2018. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Molecular Phylogenetics and Evolution 121:158-165.

Brandt, A.L., Grigorev, K., Afanador-Hernandez, Y.M., Paulino, L.A., Murphy, W.J., Nuñez, A., Komissarov, A., Brandt, J.R., Maria, R., O’Brien, S.J., Rodriguez, L.E., Martinez-Cruzado, J.C., Oleksyk, T.K., and A.L. Roca. 2017. Mitogenomic sequences support a north-south subdivision within Solenodon paradoxus. Mitochondrial DNA, A DNA Mapp. Seq Anal. 20: 1-9.

Figueiró, H.X, Li, G., Trindade, F.J., Assis, J., Pais, F., Fernandes, G., Santos, S.H.D., Hughes, G.M., Komissarov, A., Antunes, A., Trinca, C.S., Rodrigues, M.R., Linderoth, T., Bi, K., Silveira, L., Azevedo, F.C.C, Kantek, D., Ramalho, E., Brassaloti, R.A., Villela, P.M.S., Nunes, A.L.V., Teixeira, R.H.F., Morato, R.G., Loska, D., Saraguëta, P., Gabaldón, T., Teeling, E.C., O’Brien, S.J., Nielsen, R., Coutinho, R.L., Oliveira, G., Murphy, W.J., and E. Eizirik. 2017. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Science Advances, 3: e1700299.

Gatesy, J., Meredith, R.W., Janečka, J.E., Simmons, M.P., Murphy, W.J., and M.S. Springer. 2017. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia. Cladistics, 33: 295-332.

Janečka, J.E., Zhang, Y-Q., Li, D-Q., Munkhtsog, M., Munkhtsog, B., Galsandorj, N., Wangchuk, T.R., Karmacharya, D., McCarthy, T., Gaur, A., Kumar, S., Hussain, S., Muhammad, G., Jevit, M., Hacker, C., Burger, P., Wultsch, C., Janečka, M. J., Helgen, K.M., Murphy, W.J., and R. Jackson. 2017. Range-wide snow leopard phylogeography supports three subspecies. Journal of Heredity 108: 597-607.

A., Pearce, J.W., Gandolfi, B., Creighton, E.K., Suedmeyer, W.K., Selig, M., Bosiack, A.P., Castaner, L.J., Whiting, R.E., Belknap, E.B., and L.A. Lyons. 2017. 99 Lives Consortium. Early-onset progressive retinal atrophy associated with an IQCB1 variant in African black-footed cats (Felis nigripes). Scientific Reports 7: 43918.

Mauler, D.A., Gandolfi, B., Reinero, C.R., O’Brien, D.P., Spooner, J.L., Lyons, L.A., 99 Lives Consortium. 2017. Precision medicine in cats: novel Niemann-Pick Type C diagnosed by whole genome sequencing. Journal of Veterinary Internal Medicine 31: 539-544.

Springer M.S., Emerling, C.A., Meredith, R.W., Janečka, J.E., Eizirik, E., and W.J. Murphy. 2017. Waking the undead: implications of a soft explosive model for the timing of placental mammal diversification. Molecular Phylogenetics and Evolution, 106: 86-102.

Aberdein, D., Munday, J.S., Gandolfi, B., Dittmer, K.E., Malik, R., Garrick, D.J., Lyons, L.A., 99 Lives Consortium. 2017. A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats. Mammalian Genome, 28: 47-55.

Abascal, F., Alioto, T., Cruz, F., Corvelo, A., Villanueva-Cañas, J.L., Vlasova, A., Marcet-Houben, M., Martínez-Cruz, B., Prieto, P., Yu Cheng, J., Quesada, V., Lorente-Galdos, B., Li, G., García, F., Rodríguez, J.L., Frias, L., Ribeca, P., Câmara, F., Lowy, E., Cozzuto, L., Erb, I., Tress, M.L., Rubio-Camarillo, M., Capella-Gutiérrez, S., Rodriguez-Alés, J.L., Ruiz-Orera, J., Reverter, F., Casas-Marce, M., Soriano, L., Rodríguez-Arango, J., Puente, X.S., Derdak, S., Galán, B., Blanc, J., Gut, M., Quilez, J., Andrés-Nieto, M., Mailund, T., Murphy, W.J., Notredame, C., Roma, G., Gabaldón, T., Mar Albà, M., López-Otín, C., Ruiz-Herrera, A., Marques-Bonet, T., Valencia, A., Gut, I., García, J.L., Guigó, R., and J.A. Godoy. 2016. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology, 17: 251.

Mason, V.C., Li, G., Minx, P., Schmitz, J., Churakov, G., Doronina, L., Melin, A.D., Dominy, N.J., Lim, N. T-L., Springer, M.S., Wilson, R.K., Warren, W.C., Helgen, K.M., and W. J. Murphy. 2016. Genomic analysis reveals remarkable hidden biodiversity within colugos, the sister group to primates. Science Advances, 2: e1600633.

Li, G., Hillier, L.W., Grahn, R.A., Zimin, A., Makunin, A., David, V.A., Menotti-Raymond, M., Hannah, S., Hendrickson, S., O’Brien, S.J., Minx, P., Wilson, R.K., Lyons, L.A., Warren, W.C., and W.J. Murphy. 2016. A high-resolution SNP array-based linkage map anchors a new domestic cat draft genome assembly and provides detailed patterns of recombination. G3 (Bethesda), 6: 1-10.

Lacher, T.E., Murphy, W.J., Rogan, J., Smith, A.T., and N.S. Upham. 2016. “Evolution, phylogeny, ecology, and conservation of the clade Glires: Lagomorpha and Rodentia”. Pp. 15-26 In: Handbook of the Mammals of the World (D.E. Wilson, T.E. Lacher, and R.A. Mittermeier, eds.) Lynx Edicions, Barcelona.

Li, G., Davis, B.W., Eizirik, E., and W.J. Murphy. 2016. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Research 26: 1-11.

Halley, Y.A., Oldeshulte, D.L., Bhattarai, E.K., Hill, J., Metz, R.P., Johnson, C.D., Presley, S.M., Ruzicka, R.E., Rollins, D., Peterson, M.J., Murphy, W.J., and C.M. Seabury. 2015. Northern bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy. PLOS ONE 10: e0144913.

Springer, M.S., Signore, A.V., Paijmans, J.L.A., Vélez-Juarbe, J., Domning, D.P., Bauer, C.E., He, K., Crerar, L., Murphy, W.J., Meredith, R.W., Gatesy, J., Willerslev, E., MacPhee, R.D.E., Hofreiter, M., and K.L. Campbell. Interordinal gene capture, the phylogenetic position of Steller’s Sea Cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. 2015. Molecular Phylogenetics and Evolution 91: 178-193.

Davis, B.W., Seabury, C.S., Brashear, W., Li, G., Roelke Parker, M., and W.J. Murphy. 2015. Mechanisms underlying mammalian hybrid sterility in two feline interspecies models. Molecular Biology and Evolution 32: 2534-2546.

Montague, M., Li, G., Gandolfi, B., Khan, R., Aken, B.L., Searle, S.M.J., Minx, P., Hillier, L., Kolboldt, D.C., Davis, B.W., Driscoll, C.A., Barr, C., Blackstone, K., Quilez, J., Lorente-Galdos, B., Marques-Bonet, T., Alkan, C., Thomas G.W.C., Hahn, M.W., Menotti-Raymond, M., O’Brien, S.J., Wilson, R.K., Lyons, L.A., Murphy, W.J., 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 USA 111: 17230-17235.

Gershony, L.C., Cortes, A., Penedo, M.C.T., Davis, B.W., Murphy, W.J., Helps, C.R., and L.A. Lyons. 2014. Who’s behind that mask and cape? The Asian Leopard Cat’s Agouti (ASIP) allele affects coat colour phenotype in the Bengal cat breed. Animal Genetics 45: 893-897.

Soh, Y.Q., Alföldi, J., Pyntikova, T., Brown, L.G., Graves, T., Minx, P.J., Fulton, R.S., Kremitzki, C., Koutseva, N., Mueller, J.L., Rozen, S., Hughes, J.F., Owens, E., Womack, J.E., Murphy, W.J., Cao Q., de Jong, P., Warren, W.C., Wilson, R.K., Skaletsky, H., and D.C. Page. 2014. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 159: 800-813.

Janečka, J.E., Jackson, R., Munkhtsog, B., and W. J. Murphy. 2014. Characterization of 9 microsatellites and primers in snow leopards, and a species-specific PCR assay for identifying non-invasive samples. Conservation Genetics Resources 6: 369-373.

Hayden, S., Davalos, L.M., Bekaert, M., Goodbla, A., Murphy, W.J., and E.C. Teeling. 2014. A cluster of olfactory receptor genes linked to frugivory in bats. Molecular Biology and Evolution 31: 917-927.

Li, G., Davis, B.W., Raudsepp, T., Pearks Wilkerson, A.J., Mason, V.C., Ferguson-Smith, M.A., O’Brien, P., Waters, P., and W. J. Murphy.  2013. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Research 23: 1486-1495.

Springer M.S., Meredith, R.W., Teeling, E.C., and W. J. Murphy. 2013. Technical comment on “The placental mammal ancestor and the post-KPg radiation of placental mammals“. Science 341: 613.

Hughes, G., Li, G., Murphy, W. J., Higgins, D., and E.C. Teeling. 2013. Using Illumina next generation sequencing technologies to sequence multigene families in de novo species. Molecular Ecology Resources 13: 510-521.

Springer, M. S., Meredith, R. W., Gatesy, J., Emerling, C.A., Park, J., Rabosky, D.L., Stadler, T., Steiner, C., Ryder, O.A., Janecka, J.E., Fisher, C.A. and W. J. Murphy. 2012. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS ONE 7: e49521.

Janečka, J. E., Chowdhary, B., and W. Murphy. 2012. Exploring the correlations between sequence evolution rate and phenotypic divergence across the mammalian tree provides insight into adaptive evolution. Journal of Biosciences 37: 897-909.

Murphy, W. J., Janečka, J.E., Stadler, T., Eizirik, E., Ryder, O.A., Gatesy, J., Meredith, R.W., and M.S. Springer. 2012. Response to comment on “Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on mammal diversification.” Science 337: 34.

Janečka, J. E., Tewes, M.E., Laack, L.L., Caso, A., Grassman, L.I., Haines, A.M., Shindle, D.B., Davis, B.W., Murphy, W. J., and R.L. Honeycutt. 2011. Reduced genetic diversity and isolation of remnant ocelot populations occupying a severely fragmented landscape in southern Texas. Animal Conservation 14: 608-619.

Meredith, R. W., Janečka, J.E., Gatesy, J., Ryder, O. A., Fisher, C.A., Teeling, E.C., Goodbla, A., Eizirik, E., Simão, T. L. L., Stadler, T., Rabosky, D. L., Honeycutt, R. L., Flynn, J. J., Ingram, C. M., Steiner, C., Williams, T. L., Robinson, T. J., Burk-Herrick, A., Westerman, M., Ayoub, N. A., Springer, M. S., and W. J. Murphy. 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on mammal diversification. Science 334: 521-525.

Mason, V.C., Li, G., Helgen, K. M., and W. J. Murphy. 2011. Efficient cross-species capture hybridization and next-generation DNA sequencing of mitochondrial genomes from non-invasively sampled museum specimens. Genome Research 21: 1695-1704.

Springer, M. S., Meredith, R., Janecka, J.E., and W. J. Murphy. 2011. The Historical Biogeography of Mammalia.  Philosophical Transactions of the Royal Society, B: Biological Sciences 366: 2478-2502.

Janečka, J.E., Jackson, R.M., Munkhtsog, B., Mallon, D.P., Naranbaatar, G., and W. J. Murphy. 2011. Comparison of noninvasive genetic and camera-trapping techniques for surveying snow leopards. Journal of Mammalogy 92: 771-783.

Paria, N., Raudsepp, T., Pearks Wilkerson, A.J., O’Brien, P.C., Ferguson-Smith, M.A., Love, C.C., Arnold, C., Rakestraw, P., Murphy, W. J., Chowdhary, B.P. 2011. A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals. PLoS ONE  6: e21374.

Brinkmeyer-Langford, C., Murphy, W. J., Childers, C., and L.C. Skow. 2010. A conserved segmental duplication within ELA. Animal Genetics 41 Suppl. 2: 186-95.

Li, G., Janečka, J.E., and W. J. Murphy. 2011. Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family. Molecular Biology and Evolution 28: 911-920.

Davis, B.W., Li, G., and W. J. Murphy. 2010. Supermatrix and supertree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivore, Felidae). Molecular Phylogenetics and Evolution 56: 64-76.

Eizirik, E., Murphy, W. J., Koepfli, K.-P., Johnson, W.E., Dragoo, J., Wayne, R.K., and S.J. O’Brien. 2010. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Molecular Phylogenetics and Evolution 56: 49-63.

Hayden, S., Bekaert, M., Crider, T., Mariani, S., Murphy, W. J., and E.C. Teeling. 2010. Ecological adaptation determines functional mammalian olfactory subgenomes.  Genome Research 20: 1-9.

Meredith, R. W., Gatesy, J., Murphy, W. J., Ryder, O. A., and M. S. Springer. 2009. Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamelin in the fossil record of placental mammals. PLoS Genetics 5: e1000634.

Davis, B. W., Raudsepp, T., Pearks Wilkerson, A. J., Agarwala, R., Schäffer, A. A., Houck, M., Chowdhary, B. P., and W. J. Murphy. 2009. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics 93: 299-304.

Murphy, W. J. and E. Eizirik. 2009. “Placental Mammals (Eutheria)”. Pp. 471-474 In: The Timetree of Life, (S.B. Hedges and S. Kumar, eds.) Oxford University Press, Oxford.

Eizirik, E., and Murphy, W. J. 2009. “Carnivores (Carnivora)”. Pp. 504-507 In: The Timetree of Life (S.B. Hedges and S. Kumar, eds.) Oxford University Press, Oxford.

Miller, W., Drautz, D. I., Janečka, J. E., Lesk, A.M., Ratan, A., Tomsho, L.P., Packard, M., Zhang, Y., McClellan, L., Qi, J., Zhao, F., Gilbert, M.T.P., Dalén, L., Arsuaga, J.L., Ericson, P.G.P., Huson, D. H., Helgen, K. M., Murphy, W.J., Götherström, A., and S.C. Schuster. 2009. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research 19: 213-220.

Collier, G.E., Murphy, W.J., and M. Espinoza. 2009. Phylogeography of the genus Epiplatys (Aplocheiloidea: Cyprinodontiformes). Molecular Phylogenetics Evolution 50: 190-6.

Haussler, S. J. O’Brien, O.A. Ryder, F. K. Barker, M. Clamp, A. J. Crawford, R. Hanner, O. Hanotte, W. E. Johnson, J. A. McGuire, W. Miller, W. J. Murphy, F. H. Sheldon, B. Sinervo, B. Venkatesh, E. O. Wiley, F. W. Allendorf, C. S. Baker, A. Bauer, A. Beja-Pereira, E. Bermingham, G. Bernardi, C. R. Bonvicino, S. Brenner, T. Burke, J. Cracraft, M. Diekhans, S. Edwards, P. Ericson, J. Estes, J. Fjelsa, N. Flesness, T. Gamble, P. Gaubert, A. S. Graphodatsky, J. A. Marshall Graves, E. D. Green, R. E. Green, S. Hackett, P. Hebert, K. M. Helgen, L. Joseph, B. Kessing, D. M. Kingsley, H. A. Lewin, G. Luikart, P. Martelli, M. A.M. Moreira, N. Nguyen, G. Ortí, B. L. Pike, D. M. Rawson, S. C. Schuster, H. N. Seuánez, H. B. Shaffer, M. S. Springer, J. M. Stuart, J. Sumner, E. C. Teeling, R. C. Vrijenhoek, R. D. Ward, W. C. Warren, R. K. Wayne, T. M. Williams, N. D. Wolfe, Y.-P. Zhang. 2009. Genome 10K: A proposal to obtain whole genome sequence for 10,000 vertebrate species. Journal of Heredity 100: 659-674.

Pearks Wilkerson, A. J., Raudsepp, T., Graves, T., Warren, W., Chowdhary, B. P., Skow, L. C., and W. J. Murphy. 2008. Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Genomics 92: 329-338.

Janečka, J. E., Helgen, K. M., Lim, N., Baba, M., Izawa, M., Boeadi, and W. J. Murphy. 2008. Evidence for multiple species of Sunda colugo. Current Biology 18: pR1001-1003.

Janečka, J. E., Jackson, R., Li, D.-Q., Zhang, Y.-Q., F., Munkhtsog, B., Buckley-Beason, V., and W. J. Murphy. 2008. Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study. Animal Conservation 11: 401-411.

Springer, M. S., Meredith, R.W., Eizirik, E., Teeling, E., and W. J. Murphy. 2008. Morphology and placental mammal phylogeny. Systematic Biology 57: 499-503.

Graphodatsky, A. S., Yang, F., Dobigny, G., Biltueva, L., Romanenko, S., Perelman, P., Serdukova, N., Alkalaeva, E., Ferguson-Smith, M. A., Murphy, W. J., and T. J. Robinson. 2008. Tracking genome evolution in rodents by Zoo-FISH. Chromosome Research 16: 261-274.

Page, J.C. and W.J. Murphy. 2008. “Construction of radiation hybrid panels”. Pp. 51-64 In: Methods in Molecular Biology, Vol. 422: Phylogenomics (W. J. Murphy, ed.) Humana Press, Totowa, New Jersey.

Holmes, R. S., Chan, J., Cox, L.A., Murphy, W. J., and J. VandeBerg. 2008. Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor. BMC Evolutionary Biology 8:54.

Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D. C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Tyekucheva, S., Diekhans, M., Pringle, T. H., Murphy, W. J., Lesk, A., Weinstock, G. M., Lindblad-Toh, K., Gibbs, R. A., Lander, E. S., Siepel, A., Haussler, D., and W. J. Kent. 2007. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research 17: 1797-1808.

Janečka, J. E., Miller, W., Pringle, T. H., Wiens, F., Zitzmann, A., Helgen, K. M., Springer, M. S., and W. J. Murphy.  2007. Molecular and genomic data identify the closest living relative of primates. Science 318: 792-794.

Springer, M. S., Murphy, W. J., Eizirik, E., Madsen, O., Scally, M. S., Douady, C., Teeling, E., Stanhope, M. J., de Jong, W. W., and S. J. O’Brien. 2007. “A molecular classification for the living orders of placental mammals and the phylogenetic placement of primates.” Pp 1-28 In: Primate Origins: Adaptations & Evolution (M. Ravosa and M. Dagosta, eds.) Plenum Press, New York.

Murphy, W. J., and S. J. O’Brien. 2007. Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference in mammals. Nature Protocols 2: 3022-3030.

Pontius, J. U., Mullikin, J.C., Smith, D., Lindblad-Toh, K., Gnerre, S., Clamp, M., Stephens, R., Neelam, B., Volfovsky, N., Schäffer, A.A., Agarwala, R., Narfstrom, K., Murphy, W. J., Giger, U., Roca, A.L., O’hUigin, C., Antunes, A., Menotti-Raymond, M., Yuhki N., Pecon Slattery J., Johnson, W.E., Bourqe, G, Tesler, G. and S. J. O’Brien. 2007. Initial sequence and comparative analysis of the cat genome. Genome Research 17: 1675-1689.

Vasquez-Salat, N., Beck, T. W., Yuhki, N., O’Brien, S. J., and W. J. Murphy. 2007. Gene conversion within the mammalian CC chemokine receptor cluster promotes receptor dimerization. Genomics 90: 213-224.

Springer, M. S., Burk, A., Meredith, R., Eizirik, E., Teeling, E. C., O’Brien, S. J., and W. J. Murphy. 2007. The adequacy of morphology for reconstructing the early phylogenetic history of placental mammals. Systematic Biology 56: 673-684.

Springer, M. S., and W. J. Murphy. 2007. Mammalian evolution and biomedicine: new views from phylogeny. Biological Reviews 82: 375-392.

Miller-Butterworth, C. M., Murphy, W. J., O’Brien, S. J., Jacobs, D. S., Springer, M. S., and E. C. Teeling. 2007. A family matter: conclusive resolution of the taxonomic position of the long-fingered bats, Miniopterus. Molecular Biology and Evolution 24: 1553-1561.

Murphy, W. J., Pringle, T., Crider, T., Springer, M. S., and W. Miller. 2007. Using genomic data to unravel the root of the placental mammal phylogeny. Genome Research 17: 413-421.

Murphy, W. J., Davis, B., David, V. A., Agarwala, R., Schäffer, A. A., Pearks-Wilkerson, A. J., Neelam, B., O’Brien, S. J. and M. Menotti-Raymond. 2007. A 1.5-megabase-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics 89: 189-196.

Kohn, M. H., Murphy, W. J., Ostrander, E. A., and R. K. Wayne. 2006. Genomics and conservation genetics. Trends in Ecology and Evolution 21: 629-637.

Fyfe, J. C., M. Menotti-Raymond David, V., Schäffer, A. A., Brichta, L., Drummond, M. C., Buzzell, B. G., Gregory, B. L., Agarwala, R., Murphy, W. J., Wirth, B., and S. J. O’Brien. 2006. An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Research 16: 1084-1090.

Murphy, W. J. 2006. “The feline genome”. Pp. 60-68 in Genome Dynamics: Structure and Evolution of Vertebrate Genomes (Volff, J. N., ed.) Karger Press, Basel, Switzerland.

Murphy, W. J., Pearks Wilkerson, A. J., Raudsepp, T., Agarwala, R., Schäffer, A. A., Stanyon, R., and B. P. Chowdhary. 2006. Novel gene acquisition on carnivore Y chromosomes. PLoS Genetics 2: e43.

Johnson, W. E., Eizirik, E., Pecon-Slattery, J., Murphy, W. J., Antunes, A., Teeling, E. C., and S. J. O’Brien. 2006. The late Miocene radiation of modern Felidae: a genetic assessment. Science 311: 73-77.

Murphy, W. J., Stephens, R., Agarwala, R., Schaafer, A., Smith, C. J., Crumpler, N., David, V. A. and S. J. O’Brien. 2005. A rhesus macaque radiation hybrid map and comparative analysis with the human genome.  Genomics 86: 383-395.

Murphy, W. J., Larkin, D., Everts van-der Wind, A., Bourque, G., Tesler, G., Auvil, L., Beever, J. E., Chowdhary, B. P., Galibert, F., Gatzke, L., Hitte, C., Meyers, S. N., Ostrander, E. A., Pape, G., Parker, H. G., Raudsepp, T., Rogatcheva, M. B., Schook, L. B., Skow, L. C., Welge, M., Womack, J. E., O’Brien, S. J., Pevzner, P. A., H. A. Lewin. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309: 613-617.

Springer, M. S., Murphy, W. J., Eizirik, E., and S. J. O’Brien. 2005. “Evidence for major placental clades. Pp. 37-49 In The Rise of Placental Mammals (K.D. Rose & J.D. Archibald, eds.) The Johns Hopkins University Press, Baltimore, MD.

Roca, A. L., Nash, W. G., Menninger, J., Murphy, W. J., and S. J. O’Brien. 2005. Insertional polymorphisms of endogenous feline leukemia viruses.  Journal of Virology 79: 3979-3986.

He, Q., Lowrie, C., Shelton, G. D., Menotti-Raymond, M., Murphy, W. J., Swanson, W. F. and J. C. Fyfe. 2005. Inherited motor neuron disease in domestic cats: A model of spinal muscular atrophy. Pediatric Research 57: 324-330.

Teeling, E. C., Springer, M. S., Madsen, O., Bates, P., O’Brien, S. J., and W. J. Murphy. 2005. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307: 580-584.

Beck, T. W., Menninger, J. Murphy, W. J., Nash, W. G., O’Brien, S. J. and N. Yuhki. 2005. The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region. Immunogenetics 56: 702-709.

Murphy, W. J., Pevzner, P. and S. J. O’Brien.  2004. Mammalian phylogenomics comes of age. Trends in Genetics 20: 631-639. (Review).

Eizirik, E., Murphy, W. J., Springer, M. S., and S. J. O’Brien. 2004. “Molecular phylogeny and dating of early primate divergences.”  Pp. 45-64 in Anthropoid Origins, New Visions (R. Kay & C. Ross, eds.). Kluwer/Plenum.

Pecon-Slattery, J., Pearks Wilkerson, A. J., Murphy, W. J., and S. J. O’Brien.  2004. Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family Felidae as a species tree. Molecular Biology and Evolution 21: 2299-2309.

Roca, A. L.*, Kahila Bar-Gal, G.*, Eizirik, E., Helgen, K.M., Maria, R., Springer, M.S., O’Brien, S. J., and W. J. Murphy. 2004. Mesozoic origin for West Indian insectivores. Nature 429: 649-651.

Menotti-Raymond, M., David, V. A., Stephens, R., Agarwala, R., Schaffer, A., O’Brien, S. J., and W. J. Murphy. 2003. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Cytogenetics and Genome Research 102: 272-276.

Murphy, W. J., Bourque, G., Telser, G., Pevzner, P., and S. J. O’Brien.  2003. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Human Genomics 1: 30-40.

O’Brien, S. J. and W. J. Murphy. 2003.  Genomics. A dog’s breakfast?  Science 301: 1854-1855. (Review).

Kuznetsov, S. B., Matveeva, M. M., Murphy, W. J., O’Brien S. J. and O. L. Serov.  2003.  Mapping of 53 loci in American mink (Mustela vison). Journal of Heredity 94: 386-391.

Teeling, E. C., Madsen, O., Murphy, W. J., Springer, M. S., and S. J. O’Brien. 2003. Nuclear gene sequences confirm an ancient link between New Zealand’s short-tailed bat and South American noctilionoid bats. Molecular Phylogenetics and Evolution 28: 308-319.

Murphy, W. J., Fröenicke, L., O’Brien, S. J., and R. Stanyon. 2003. The origin of human chromosome 1 and its homologues in placental mammals. Genome Research 13: 1880-1888.

Springer, M. S., Murphy, W. J., Eizirik, E., and S. J. O’Brien. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proceedings of the National Academy of Sciences USA 100: 1056-1061.

Menotti-Raymond, M., David, V. A., Roelke-Parker, M., Sun, S., Schäffer, A., Agarwala, R., Tomlin, J.F., O’Brien, S. J. and W. J. Murphy.  2003.  Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Cytogenetics and Genome Research 102: 272-276.

Menotti-Raymond, M., David, V. A., Roelke-Parker, M., Sun, S., Schäffer, A., Agarwala, R., Tomlin, J.F., O’Brien, S. J. and W. J. Murphy.  2003.  Second generation integrated linkage and radiation hybrid maps of the domestic cat.  Journal of Heredity 94: 95-106.

O’Brien, S. J., Menotti-Raymond, M., Murphy, W. J., and N. Yuhki.  2002.  The feline genome project. Annual Reviews of Genetics 36: 657-686.

Murphy, W. J.*, Eizirik, E.*, O’Brien, S. J., Madsen, O., Scally, M., Douady, C., Teeling, E. C., Ryder, O. A., Stanhope, M., De Jong, W. W. and M. S. Springer.  2001.  Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.

Murphy, W. J., Page, J., Smith, C. J., Desrosiers, R. C. and S. J. O’Brien.  2001. A radiation hybrid mapping panel for the rhesus macaque.  Journal of Heredity 92: 516-519.

O’Brien, S. J., Eizirik, E., and W. J. Murphy.  2001.  Genomics. On choosing mammalian genomes for sequencing.  Science 292: 2264-2266.

Sun, S., Murphy, W. J., Menotti-Raymond, M., and S. J. O’Brien.  2001. Integration of the feline radiation hybrid and linkage maps.  Mammalian Genome 12: 436-441.

Murphy, W. J., Stanyon, R., and S. J. O’Brien. 2001.  Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biology 2: 0005.1-0005.8. (Review).

Parker, J. S. L., Murphy, W. J., Wang, D., O’Brien, S. J., and C. R. Parrish.  2001.  Canine and feline parvoviruses can use human or feline transferrin receptors to bind, enter, and infect cells.  Journal of Virology 75: 3896-3902.

Eizirik, E., Murphy, W. J., and S. J. O’Brien.  2001.  Molecular dating and biogeography of the early placental mammal radiation.  Journal of Heredity 92: 212-219.

Murphy, W. J., Eizirik, E., Johnson, W. J., Zhang, Y. P., Ryder, O. A., and S. J. O’Brien.  2001.  Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618.