William J. Murphy - Publications

Affiliations: 
Texas A & M University, College Station, TX, United States 
Area:
evolutionary genomics

60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Li G, Hillier LW, Grahn R, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, ... Murphy WJ, et al. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (Bethesda, Md.). PMID 27172201 DOI: 10.1534/G3.116.028746  1
2016 Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: Partitioned coalescence support and a robust family-level tree for Mammalia Cladistics. DOI: 10.1111/Cla.12170  1
2015 Halley YA, Oldeschulte DL, Bhattarai EK, Hill J, Metz RP, Johnson CD, Presley SM, Ruzicka RE, Rollins D, Peterson MJ, Murphy WJ, Seabury CM. Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. Plos One. 10: e0144913. PMID 26713762 DOI: 10.1371/Journal.Pone.0144913  1
2015 Li G, Davis B, Eizirik E, Murphy W. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Research. PMID 26518481 DOI: 10.1101/Gr.186668.114  1
2015 Springer MS, Signore AV, Paijmans JL, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RD, Hofreiter M, et al. Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Molecular Phylogenetics and Evolution. 91: 178-93. PMID 26050523 DOI: 10.1016/J.Ympev.2015.05.022  1
2015 Davis BW, Seabury CM, Brashear WA, Li G, Roelke-Parker M, Murphy WJ. Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models. Molecular Biology and Evolution. PMID 26006188 DOI: 10.1093/Molbev/Msv124  1
2014 Soh YQ, Alföldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, Rozen S, Hughes JF, Owens E, Womack JE, Murphy WJ, et al. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell. 159: 800-13. PMID 25417157 DOI: 10.1016/J.Cell.2014.09.052  1
2014 Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, ... ... Murphy WJ, et al. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences of the United States of America. 111: 17230-5. PMID 25385592 DOI: 10.1073/Pnas.1410083111  1
2014 Gershony LC, Penedo MC, Davis BW, Murphy WJ, Helps CR, Lyons LA. 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. Animal Genetics. 45: 893-7. PMID 25143047 DOI: 10.1111/Age.12206  1
2014 Hayden S, Bekaert M, Goodbla A, Murphy WJ, Dávalos LM, Teeling EC. A cluster of olfactory receptor genes linked to frugivory in bats. Molecular Biology and Evolution. 31: 917-27. PMID 24441035 DOI: 10.1093/Molbev/Msu043  1
2013 Springer MS, Meredith RW, Teeling EC, Murphy WJ. Technical comment on "The placental mammal ancestor and the post-K-Pg radiation of placentals". Science (New York, N.Y.). 341: 613. PMID 23929967 DOI: 10.1126/Science.1238025  1
2013 Li G, Davis BW, Raudsepp T, Pearks Wilkerson AJ, Mason VC, Ferguson-Smith M, O'Brien PC, Waters PD, Murphy WJ. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Research. 23: 1486-95. PMID 23788650 DOI: 10.1101/Gr.154286.112  1
2013 Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC. Using Illumina next generation sequencing technologies to sequence multigene families in de novo species. Molecular Ecology Resources. 13: 510-21. PMID 23480365 DOI: 10.1111/1755-0998.12087  1
2012 Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. Plos One. 7: e49521. PMID 23166696 DOI: 10.1371/Journal.Pone.0049521  1
2011 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, ... ... Murphy WJ, et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science (New York, N.Y.). 334: 521-4. PMID 21940861 DOI: 10.1126/Science.1211028  1
2011 Mason VC, Li G, Helgen KM, Murphy WJ. Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. Genome Research. 21: 1695-704. PMID 21880778 DOI: 10.1101/Gr.120196.111  1
2011 Springer MS, Meredith RW, Janecka JE, Murphy WJ. The historical biogeography of Mammalia. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 366: 2478-502. PMID 21807730 DOI: 10.1098/Rstb.2011.0023  1
2011 Janečka JE, Munkhtsog B, Jackson RM, Naranbaatar G, Mallon DP, Murphy WJ. Comparison of noninvasive genetic and camera-trapping techniques for surveying snow leopards Journal of Mammalogy. 92: 771-783. DOI: 10.1644/10-Mamm-A-036.1  1
2010 Brinkmeyer-Langford CL, Murphy WJ, Childers CP, Skow LC. A conserved segmental duplication within ELA. Animal Genetics. 41: 186-95. PMID 21070294 DOI: 10.1111/J.1365-2052.2010.02137.X  1
2010 Davis BW, Li G, Murphy WJ. Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae). Molecular Phylogenetics and Evolution. 56: 64-76. PMID 20138224 DOI: 10.1016/J.Ympev.2010.01.036  1
2010 Eizirik E, Murphy WJ, Koepfli KP, Johnson WE, Dragoo JW, Wayne RK, O'Brien SJ. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Molecular Phylogenetics and Evolution. 56: 49-63. PMID 20138220 DOI: 10.1016/J.Ympev.2010.01.033  1
2010 Hayden S, Bekaert M, Crider TA, Mariani S, Murphy WJ, Teeling EC. Ecological adaptation determines functional mammalian olfactory subgenomes. Genome Research. 20: 1-9. PMID 19952139 DOI: 10.1101/Gr.099416.109  1
2009 Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS. Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. Plos Genetics. 5: e1000634. PMID 19730686 DOI: 10.1371/Journal.Pgen.1000634  1
2009 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, ... ... Murphy WJ, et al. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research. 19: 213-20. PMID 19139089 DOI: 10.1101/Gr.082628.108  1
2009 Collier GE, Murphy WJ, Espinoza M. Phylogeography of the genus Epiplatys (Aplocheiloidea: Cyprinodontiformes). Molecular Phylogenetics and Evolution. 50: 190-6. PMID 18984059 DOI: 10.1016/J.Ympev.2008.10.006  1
2009 Davis BW, Raudsepp T, Pearks Wilkerson AJ, Agarwala R, Schäffer AA, Houck M, Chowdhary BP, Murphy WJ. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. Genomics. 93: 299-304. PMID 18951970 DOI: 10.1016/J.Ygeno.2008.09.010  1
2009 Haussler D, O'Brien SJ, Ryder OA, Keith Barker F, Clamp M, Crawford AJ, Hanner R, Hanotte O, Johnson WE, McGuire JA, Miller W, Murphy RW, Murphy WJ, Sheldon FH, Sinervo B, et al. Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species Journal of Heredity. 100: 659-674. DOI: 10.1093/Jhered/Esp086  1
2008 Janecka JE, Helgen KM, Lim NT, Baba M, Izawa M, Boeadi, Murphy WJ. Evidence for multiple species of Sunda colugo. Current Biology : Cb. 18: R1001-2. PMID 19000793 DOI: 10.1016/J.Cub.2008.09.005  1
2008 Springer MS, Meredith RW, Eizirik E, Teeling E, Murphy WJ. Morphology and placental mammal phylogeny. Systematic Biology. 57: 499-503. PMID 18570041 DOI: 10.1080/10635150802164504  1
2007 Murphy WJ, O'Brien SJ. Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference Nature Protocols. 2: 3022-3030. PMID 18007639 DOI: 10.1038/Nprot.2007.429  1
2007 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, ... ... Murphy WJ, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/Gr.6761107  1
2007 Pontius JU, Mullikin JC, Smith DR, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, et al. Initial sequence and comparative analysis of the cat genome. Genome Research. 17: 1675-89. PMID 17975172 DOI: 10.1101/Gr.6380007  1
2007 Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ. Molecular and genomic data identify the closest living relative of primates. Science (New York, N.Y.). 318: 792-4. PMID 17975064 DOI: 10.1126/Science.1147555  1
2007 Springer MS, Burk-Herrick A, Meredith R, Eizirik E, Teeling E, O'Brien SJ, Murphy WJ. The adequacy of morphology for reconstructing the early history of placental mammals. Systematic Biology. 56: 673-84. PMID 17661234 DOI: 10.1080/10635150701491149  1
2007 Murphy WJ, Davis B, David VA, Agarwala R, Schäffer AA, Pearks Wilkerson AJ, Neelam B, O'Brien SJ, Menotti-Raymond M. A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics. 89: 189-96. PMID 16997530 DOI: 10.1016/J.Ygeno.2006.08.007  1
2007 Springer MS, Murphy WJ, Eizirik E, Madsen O, Scally M, Douady CJ, Teeling EC, Stanhope MJ, De Jong WW, O'Brien SJ. A molecular classification for the living orders of placental mammals and the phylogenetic placement of primates Primate Origins: Adaptations and Evolution. 1-28. DOI: 10.1007/978-0-387-33507-0_1  1
2006 Kohn MH, Murphy WJ, Ostrander EA, Wayne RK. Genomics and conservation genetics. Trends in Ecology & Evolution. 21: 629-37. PMID 16908089 DOI: 10.1016/J.Tree.2006.08.001  1
2006 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. An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Research. 16: 1084-90. PMID 16899656 DOI: 10.1101/Gr.5268806  1
2006 Murphy WJ, Pearks Wilkerson AJ, Raudsepp T, Agarwala R, Schäffer AA, Stanyon R, Chowdhary BP. Novel gene acquisition on carnivore Y chromosomes. Plos Genetics. 2: e43. PMID 16596168 DOI: 10.1371/Journal.Pgen.0020043  1
2006 Johnson WE, Eizirik E, Pecon-Slattery J, Murphy WJ, Antunes A, Teeling E, O'Brien SJ. The late Miocene radiation of modern Felidae: a genetic assessment. Science (New York, N.Y.). 311: 73-7. PMID 16400146 DOI: 10.1126/Science.1122277  1
2005 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, et al. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science (New York, N.Y.). 309: 613-7. PMID 16040707 DOI: 10.1126/Science.1111387  1
2005 Murphy WJ, Agarwala R, Schäffer AA, Stephens R, Smith C, Crumpler NJ, David VA, O'Brien SJ. A rhesus macaque radiation hybrid map and comparative analysis with the human genome. Genomics. 86: 383-95. PMID 16039092 DOI: 10.1016/J.Ygeno.2005.05.013  1
2005 Roca AL, Nash WG, Menninger JC, Murphy WJ, O'Brien SJ. Insertional polymorphisms of endogenous feline leukemia viruses. Journal of Virology. 79: 3979-86. PMID 15767400 DOI: 10.1128/Jvi.79.7.3979-3986.2005  1
2004 Murphy WJ, Pevzner PA, O'Brien SJ. Mammalian phylogenomics comes of age. Trends in Genetics : Tig. 20: 631-9. PMID 15522459 DOI: 10.1016/J.Tig.2004.09.005  1
2004 Roca AL, Bar-Gal GK, Eizirik E, Helgen KM, Maria R, Springer MS, O'Brien SJ, Murphy WJ. Mesozoic origin for West Indian insectivores. Nature. 429: 649-51. PMID 15190349 DOI: 10.1038/Nature02597  1
2003 O'Brien SJ, Murphy WJ. A dog's breakfast? Science. 301: 1854-1855. PMID 14512608 DOI: 10.1126/Science.1090531  1
2003 Menotti-Raymond M, David VA, Roelke ME, Chen ZQ, Menotti KA, Sun S, Schäffer AA, Tomlin JF, Agarwala R, O'Brien SJ, Murphy WJ. Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). The Journal of Heredity. 94: 95-106. PMID 12692169 DOI: 10.1093/Jhered/Esg008  1
2003 Springer MS, Murphy WJ, Eizirik E, O'Brien SJ. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proceedings of the National Academy of Sciences of the United States of America. 100: 1056-61. PMID 12552136 DOI: 10.1073/Pnas.0334222100  1
2001 Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science (New York, N.Y.). 294: 2348-51. PMID 11743200 DOI: 10.1126/Science.1067179  1
2001 O'Brien SJ, Eizirik E, Murphy WJ. Genomics. On choosing mammalian genomes for sequencing. Science (New York, N.Y.). 292: 2264-6. PMID 11423643 DOI: 10.1126/Science.1059393  1
2001 Murphy WJ, Stanyon R, O'Brien SJ. Evolution of mammalian genome organization inferred from comparative gene mapping Genome Biology. 2. PMID 11423011 DOI: 10.1186/Gb-2001-2-6-Reviews0005  1
2001 Eizirik E, Murphy WJ, O'Brien SJ. Molecular dating and biogeography of the early placental mammal radiation. The Journal of Heredity. 92: 212-9. PMID 11396581 DOI: 10.1093/Jhered/92.2.212  1
2001 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ. Molecular phylogenetics and the origins of placental mammals. Nature. 409: 614-8. PMID 11214319 DOI: 10.1038/35054550  1
2000 Pecon Slattery J, Murphy WJ, O'Brien SJ. Patterns of diversity among sine elements isolated from three Y- chromosome genes in carnivores [1] Molecular Biology and Evolution. 17: 825-829. PMID 10779543 DOI: 10.1093/Oxfordjournals.Molbev.A026361  1
1999 Murphy WJ, Thomerson JE, Collier GE. Phylogeny of the Neotropical killifish family Rivulidae (Cyprinodontiformes, Aplocheiloidei) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution. 13: 289-301. PMID 10603257 DOI: 10.1006/Mpev.1999.0656  1
1999 Murphy WJ, Collier GE. Phylogenetic relationships of African killifishes in the genera Aphyosemion and Fundulopanchax inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution. 11: 351-60. PMID 10196077 DOI: 10.1006/Mpev.1998.0566  1
1999 Murphy WJ, Nguyen TN, Taylor EB, Collier GE. Mitochondrial DNA phylogeny of West African aplocheiloid killifishes (Cyprinodontiformes, Aplocheilidae). Molecular Phylogenetics and Evolution. 11: 343-50. PMID 10196076 DOI: 10.1006/Mpev.1998.0567  1
1999 Murphy WJ, Menotti-Raymond M, Lyons LA, Thompson MA, O'Brien SJ. Development of a feline whole genome radiation hybrid panel and comparative mapping of human chromosome 12 and 22 loci Genomics. 57: 1-8. PMID 10191078 DOI: 10.1006/Geno.1998.5695  1
1997 Murphy WJ, Collier GE. A molecular phylogeny for aplocheiloid fishes (Atherinomorpha, Cyprinodontiformes): the role of vicariance and the origins of annualism. Molecular Biology and Evolution. 14: 790-9. PMID 9254916 DOI: 10.1093/Oxfordjournals.Molbev.A025819  1
1996 Murphy WJ, Collier GE. Phylogenetic relationships within the aplocheiloid fish genus Rivulus (Cyprinodontiformes, Rivulidae): implications for Caribbean and Central American biogeography. Molecular Biology and Evolution. 13: 642-9. PMID 8676738 DOI: 10.1093/Oxfordjournals.Molbev.A025624  1
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