Skip Navigation

William Murphy

Professor

Send Email

Phone: (979) 458-0906

Mailstop: 4458

Department: VIBS

Photo of Murphy, William

Education

  • Post-doc Comparative Genomics, Laboratory of Genomic Diversity, NCI, NIH 2003
  • Ph.D. Biological Science, Tulsa University 1997
  • B.S. Biological Sciences, Illinois State University 1992

Publications

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution.
Li G, Davis BW, Raudsepp T, Pearks Wilkerson AJ, Mason VC, Ferguson-Smith M, O'Brien PC, Waters PD, Murphy WJ
Genome Res. 23(9):1486-95.
Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens.
Mason VC, Li G, Helgen KM, Murphy WJ
Genome Res. 21(10):1695-704.
A conserved segmental duplication within ELA.
Brinkmeyer-Langford CL, Murphy WJ, Childers CP, Skow LC
Anim Genet. 41 Suppl 2:186-95.
Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae).
Davis BW, Li G, Murphy WJ
Mol Phylogenet Evol. 56(1):64-76.
A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae.
Davis BW, Raudsepp T, Pearks Wilkerson AJ, Agarwala R, Schäffer AA, Houck M, Chowdhary BP, Murphy WJ
Genomics. 93(4):299-304.
The feline genome.
Murphy WJ
Genome Dyn. 2:60-8.
Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference.
Murphy WJ, O'Brien SJ
Nat Protoc. 2(11):3022-30.
Using genomic data to unravel the root of the placental mammal phylogeny.
Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W
Genome Res. 17(4):413-21.
Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome.
Pearks Wilkerson AJ, Raudsepp T, Graves T, Albracht D, Warren W, Chowdhary BP, Skow LC, Murphy WJ
Genomics. 92(5):329-38.
Molecular and genomic data identify the closest living relative of primates.
Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ
Science. 318(5851):792-4.
A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes.
Murphy WJ, Davis B, David VA, Agarwala R, Schäffer AA, Pearks Wilkerson AJ, Neelam B, O'Brien SJ, Menotti-Raymond M
Genomics. 89(2):189-96.
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps.
Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O'brien SJ, Pevzner PA, Lewin HA
Science. 309(5734):613-7.
Extensive conservation of sex chromosome organization between cat and human revealed by parallel radiation hybrid mapping.
Murphy WJ, Sun S, Chen ZQ, Pecon-Slattery J, O'Brien SJ
Genome Res. 9(12):1223-30.
Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor.
Holmes RS, Chan J, Cox LA, Murphy WJ, VandeBerg JL
BMC Evol Biol. 8:54.
Tracking genome organization in rodents by Zoo-FISH.
Graphodatsky AS, Yang F, Dobigny G, Romanenko SA, Biltueva LS, Perelman PL, Beklemisheva VR, Alkalaeva EZ, Serdukova NA, Ferguson-Smith MA, Murphy WJ, Robinson TJ
Chromosome Res. 16(2):261-74.
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ
Genome Res. 17(12):1797-808.
Initial sequence and comparative analysis of the cat genome.
Pontius JU, Mullikin JC, Smith DR, Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, NISC Comparative Sequencing Program, O'Brien SJ
Genome Res. 17(11):1675-89.
The adequacy of morphology for reconstructing the early history of placental mammals.
Springer MS, Burk-Herrick A, Meredith R, Eizirik E, Teeling E, O'Brien SJ, Murphy WJ
Syst Biol. 56(4):673-84.
Mammalian evolution and biomedicine: new views from phylogeny.
Springer MS, Murphy WJ
Biol Rev Camb Philos Soc. 82(3):375-92.
A cluster of olfactory receptor genes linked to frugivory in bats.
Hayden S, Bekaert M, Goodbla A, Murphy WJ, Dávalos LM, Teeling EC
Mol Biol Evol. 31(4):917-27.
Gene conversion between mammalian CCR2 and CCR5 chemokine receptor genes: a potential mechanism for receptor dimerization.
Vàzquez-Salat N, Yuhki N, Beck T, O'Brien SJ, Murphy WJ
Genomics. 90(2):213-24.
Technical comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals".
Springer MS, Meredith RW, Teeling EC, Murphy WJ
Science. 341(6146):613.
Using Illumina next generation sequencing technologies to sequence multigene families in de novo species.
Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC
Mol Ecol Resour. 13(3):510-21.
A family matter: conclusive resolution of the taxonomic position of the long-fingered bats, miniopterus.
Miller-Butterworth CM, Murphy WJ, O'Brien SJ, Jacobs DS, Springer MS, Teeling EC
Mol Biol Evol. 24(7):1553-61.
Genomics and conservation genetics.
Kohn MH, Murphy WJ, Ostrander EA, Wayne RK
Trends Ecol Evol. 21(11):629-37.
An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival.
Fyfe JC, Menotti-Raymond M, David VA, Brichta L, Schäffer AA, Agarwala R, Murphy WJ, Wedemeyer WJ, Gregory BL, Buzzell BG, Drummond MC, Wirth B, O'Brien SJ
Genome Res. 16(9):1084-90.
Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix.
Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ
PLoS One. 7(11):e49521.
Canine and feline parvoviruses can use human or feline transferrin receptors to bind, enter, and infect cells.
Parker JS, Murphy WJ, Wang D, O'Brien SJ, Parrish CR
J Virol. 75(8):3896-902.
Molecular phylogenetics and the origins of placental mammals.
Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ
Nature. 409(6820):614-8.
Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus).
Menotti-Raymond M, David VA, Roelke ME, Chen ZQ, Menotti KA, Sun S, Schäffer AA, Tomlin JF, Agarwala R, O'Brien SJ, Murphy WJ
J Hered. 94(1):95-106.
Placental mammal diversification and the Cretaceous-Tertiary boundary.
Springer MS, Murphy WJ, Eizirik E, O'Brien SJ
Proc Natl Acad Sci U S A. 100(3):1056-61.
Novel gene acquisition on carnivore Y chromosomes.
Murphy WJ, Pearks Wilkerson AJ, Raudsepp T, Agarwala R, Schäffer AA, Stanyon R, Chowdhary BP
PLoS Genet. 2(3):e43.
The late Miocene radiation of modern Felidae: a genetic assessment.
Johnson WE, Eizirik E, Pecon-Slattery J, Murphy WJ, Antunes A, Teeling E, O'Brien SJ
Science. 311(5757):73-7.
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification.
Meredith RW, Janečka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TL, Stadler T, Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub NA, Springer MS, Murphy WJ
Science. 334(6055):521-4.
The historical biogeography of Mammalia.
Springer MS, Meredith RW, Janecka JE, Murphy WJ
Philos Trans R Soc Lond B Biol Sci. 366(1577):2478-502.
A gene catalogue of the euchromatic male-specific region of the horse Y chromosome: comparison with human and other mammals.
Paria N, Raudsepp T, Pearks Wilkerson AJ, O'Brien PC, Ferguson-Smith MA, Love CC, Arnold C, Rakestraw P, Murphy WJ, Chowdhary BP
PLoS One. 6(7):e21374.
Phylogeny of the Neotropical killifish family Rivulidae (Cyprinodontiformes, Aplocheiloidei) inferred from mitochondrial DNA sequences.
Murphy WJ, Thomerson JE, Collier GE
Mol Phylogenet Evol. 13(2):289-301.
Genome maps 10. Comparative genomics. Mammalian radiations. Wall chart.
O'Brien SJ, Eisenberg JF, Miyamoto M, Hedges SB, Kumar S, Wilson DE, Menotti-Raymond M, Murphy WJ, Nash WG, Lyons LA, Menninger JC, Stanyon R, Wienberg J, Copeland NG, Jenkins NA, Gellin J, Yerle M, Andersson L, Womack J, Broad T, Postlethwait J, Serov O, Bailey E, James MR, Marshall Graves JA
Science. 286(5439):463-78.
The promise of comparative genomics in mammals.
O'Brien SJ, Menotti-Raymond M, Murphy WJ, Nash WG, Wienberg J, Stanyon R, Copeland NG, Jenkins NA, Womack JE, Marshall Graves JA
Science. 286(5439):458-62, 479-81.
The Feline Genome Project.
O'Brien SJ, Menotti-Raymond M, Murphy WJ, Yuhki N
Annu Rev Genet. 36:657-86.
A radiation hybrid mapping panel for the rhesus macaque.
Murphy WJ, Page JE, Smith C Jr, Desrosiers RC, O'Brien SJ
J Hered. 92(6):516-9.
A rhesus macaque radiation hybrid map and comparative analysis with the human genome.
Murphy WJ, Agarwala R, Schäffer AA, Stephens R, Smith C Jr, Crumpler NJ, David VA, O'Brien SJ
Genomics. 86(4):383-95.
Insertional polymorphisms of endogenous feline leukemia viruses.
Roca AL, Nash WG, Menninger JC, Murphy WJ, O'Brien SJ
J Virol. 79(7):3979-86.
A molecular phylogeny for bats illuminates biogeography and the fossil record.
Teeling EC, Springer MS, Madsen O, Bates P, O'brien SJ, Murphy WJ
Science. 307(5709):580-4.
Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.
Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ
Hum Genomics. 1(1):30-40.
The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region.
Beck TW, Menninger J, Murphy WJ, Nash WG, O'brien SJ, Yuhki N
Immunogenetics. 56(10):702-9.
Mammalian phylogenomics comes of age.
Murphy WJ, Pevzner PA, O'Brien SJ
Trends Genet. 20(12):631-9.
Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family.
Li G, Janecka JE, Murphy WJ
Mol Biol Evol. 28(2):911-20.
Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family felidae as a species tree.
Pecon-Slattery J, Pearks Wilkerson AJ, Murphy WJ, O'Brien SJ
Mol Biol Evol. 21(12):2299-309.
Mesozoic origin for West Indian insectivores.
Roca AL, Bar-Gal GK, Eizirik E, Helgen KM, Maria R, Springer MS, O'Brien SJ, Murphy WJ
Nature. 429(6992):649-51.
Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome.
Menotti-Raymond M, David VA, Agarwala R, Schäffer AA, Stephens R, O'Brien SJ, Murphy WJ
Cytogenet Genome Res. 102(1-4):272-6.
Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences.
Eizirik E, Murphy WJ, Koepfli KP, Johnson WE, Dragoo JW, Wayne RK, O'Brien SJ
Mol Phylogenet Evol. 56(1):49-63.
Ecological adaptation determines functional mammalian olfactory subgenomes.
Hayden S, Bekaert M, Crider TA, Mariani S, Murphy WJ, Teeling EC
Genome Res. 20(1):1-9.
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.
Genome 10K Community of Scientists
J Hered. 100(6):659-74.
Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals.
Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS
PLoS Genet. 5(9):e1000634.
Phylogenetic relationships of African killifishes in the genera Aphyosemion and Fundulopanchax inferred from mitochondrial DNA sequences.
Murphy WJ, Collier GE
Mol Phylogenet Evol. 11(3):351-60.
Mitochondrial DNA phylogeny of West African aplocheiloid killifishes (Cyprinodontiformes, Aplocheilidae).
Murphy WJ, Nguyen TN, Taylor EB, Collier GE
Mol Phylogenet Evol. 11(3):343-50.
Development of a feline whole genome radiation hybrid panel and comparative mapping of human chromosome 12 and 22 loci.
Murphy WJ, Menotti-Raymond M, Lyons LA, Thompson MA, O'Brien SJ
Genomics. 57(1):1-8.
Who's behind that mask and cape? The Asian leopard cat's Agouti (ASIP) allele likely affects coat colour phenotype in the Bengal cat breed.
Gershony LC, Penedo MC, Davis BW, Murphy WJ, Helps CR, Lyons LA
Anim Genet.
Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes
Alfoldi, J., Soh, Y.W.S., 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., D.C. Page.
Cell.
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication
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., Blackistone, 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
Proceedings of the National Academy of Sciences USA.
Characterization of 9 microsatellites and primers in snow leopards, and a species-specific PCR assay for identifying non-invasive samples.
Janečka JE, Jackson R, Munkhtsog B, MurphyWJ
Conservation Genetics Resources .
Phylogenetic relationships within the aplocheiloid fish genus Rivulus (Cyprinodontiformes, Rivulidae): implications for Caribbean and Central American biogeography.
Murphy WJ, Collier GE
Mol Biol Evol. 13(5):642-9.
A molecular phylogeny for aplocheiloid fishes (Atherinomorpha, Cyprinodontiformes): the role of vicariance and the origins of annualism.
Murphy WJ, Collier GE
Mol Biol Evol. 14(8):790-9.
A radiation hybrid map of the cat genome: implications for comparative mapping.
Murphy WJ, Sun S, Chen Z, Yuhki N, Hirschmann D, Menotti-Raymond M, O'Brien SJ
Genome Res. 10(5):691-702.
Patterns of diversity among SINE elements isolated from three Y-chromosome genes in carnivores.
Slattery JP, Murphy WJ, O'Brien SJ
Mol Biol Evol. 17(5):825-9.
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J, Zhao F, Gilbert MT, Dalén L, Arsuaga JL, Ericson PG, Huson DH, Helgen KM, Murphy WJ, Götherström A, Schuster SC
Genome Res. 19(2):213-20.
Evidence for multiple species of Sunda colugo.
Janecka JE, Helgen KM, Lim NT, Baba M, Izawa M, Boeadi, Murphy WJ
Curr Biol. 18(21):R1001-2.
Phylogeography of the genus Epiplatys (Aplocheiloidea: Cyprinodontiformes).
Collier GE, Murphy WJ, Espinoza M
Mol Phylogenet Evol. 50(1):190-6.
Raising the spectra of T-cell profiling.
Murphy WJ
Blood. 112(8):3008-9.
Construction of radiation hybrid panels.
Page JE, Murphy WJ
Methods Mol Biol. 422:51-64.
Morphology and placental mammal phylogeny.
Springer MS, Meredith RW, Eizirik E, Teeling E, Murphy WJ
Syst Biol. 57(3):499-503.
Resolution of the early placental mammal radiation using Bayesian phylogenetics.
Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS
Science. 294(5550):2348-51.
Genomics. On choosing mammalian genomes for sequencing.
O'Brien SJ, Eizirik E, Murphy WJ
Science. 292(5525):2264-6.
Evolution of mammalian genome organization inferred from comparative gene mapping.
Murphy WJ, Stanyon R, O'Brien SJ
Genome Biol. 2(6):REVIEWS0005.
Molecular dating and biogeography of the early placental mammal radiation.
Eizirik E, Murphy WJ, O'Brien SJ
J Hered. 92(2):212-9.
Integration of the feline radiation hybrid and linkage maps.
Sun S, Murphy WJ, Menotti-Raymond M, O'Brien SJ
Mamm Genome. 12(6):436-41.
Mapping of 53 loci in American mink (Mustela vison).
Kuznetsov SB, Matveeva NM, Murphy WJ, O'Brien SJ, Serov OL
J Hered. 94(5):386-91.
Genomics. A dog's breakfast?
O'Brien SJ, Murphy WJ
Science. 301(5641):1854-5.
Nuclear gene sequences confirm an ancient link between New Zealand's short-tailed bat and South American noctilionoid bats.
Teeling EC, Madsen O, Murphy WJ, Springer MS, O'Brien SJ
Mol Phylogenet Evol. 28(2):308-19.
The origin of human chromosome 1 and its homologs in placental mammals.
Murphy WJ, Frönicke L, O'Brien SJ, Stanyon R
Genome Res. 13(8):1880-8.


Request Update