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Browsing by Author "Murphy, William J."

Browsing by Author "Murphy, William J."

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  • Wilder, Aryn P.; Supple, Megan A.; Subramanian, Ayshwarya; Mudide, Anish; Swofford, Ross; Serres-Armero, Aitor; Steiner, Cynthia; Koepfli, Klaus-Peter; Genereux, Diane P.; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Marques-Bonet, Tomas; Munoz Fuentes, Violeta; Foley, Kathleen; Meyer, Wynn K.; Zoonomia Consortium‡; Ryder, Oliver A.; Shapiro, Beth; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; Damas, Joana; Di Palma, Federica; Diekhans, Mark; Dong, Michael X.; Eizirik, Eduardo; Fan, Kaili; Fanter, Cornelia; Foley, Nicole M.; Forsberg-Nilsson, Karin; Garcia, Carlos J.; Gatesy, John; Gazal, Steven; Genereux, Diane P.; Goodman, Linda; Grimshaw, Jenna; Halsey, Michaela K.; Harris, Andrew J.; Hickey, Glenn; Hiller, Michael; Hindle, Allyson G.; Hubley, Robert M.; Hughes, Graham M.; Johnson, Jeremy; Juan, David; Kaplow, Irene M.; Karlsson, Elinor K.; Keough, Kathleen C.; Kirilenko, Bogdan; Koepfli, Klaus-Peter; Korstian, Jennifer M.; Kowalczyk, Amanda; Kozyrev, Sergey V.; Lawler, Alyssa J.; Lawless, Colleen; Lehmann, Thomas; Levesque, Danielle L.; Lewin, Harris A.; Li, Xue; Lind, Abigail; Lindblad-Toh, Kerstin; Mackay-Smith, Ava; Marinescu, Voichita D.; Marques-Bonet, Tomas; Mason, Victor C.; Meadows, Jennifer R. S.; Meyer, Wynn K.; Moore, Jill E.; Moreira, Lucas R.; Moreno-Santillan, Diana; Morrill, Kathleen M.; Muntané, Gerard; Murphy, William J.; Navarro, Arcadi; Nweeia, Martin; Ortmann, Sylvia; Osmanski, Austin; Paten, Benedict; Paulat, Nicole S.; Pfenning, Andreas R.; Phan, BaDoi N.; Pollard, Katherine S.; Pratt, Henry E.; Ray, David A.; Reilly, Steven K.; Rosen, Jeb R.; Ruf, Irina; Ryan, Louise; Ryder, Oliver A.; Sabeti, Pardis C.; Schäffer, Daniel E.; Serres, Aitor; Shapiro, Beth; Smit, Arian F. A.; Springer, Mark; Srinivasan, Chaitanya; Steiner, Cynthia; Storer, Jessica M.; Sullivan, Kevin A. M.; Sullivan, Patrick F.; Sundström, Elisabeth; Supple, Megan A.; Swofford, Ross; Talbot, Joy-El; Teeling, Emma; Turner-Maier, Jason; Valenzuela, Alejandro; Wagner, Franziska; Wallerman, Ola; Wang, Chao; Wang, Juehan; Weng, Zhiping; Wilder, Aryn P.; Wirthlin, Morgan E.; Xue, James R.; Zhang, Xiaomeng (2023)
    Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic ...
  • Haghani, Amin; Li, Caesar Z.; Robeck, Todd R.; Zhang, Joshua; Lu, Ake T.; Ablaeva, Julia; Acosta-Rodriguez, Victoria A.; Adams, Danielle M.; Alagaili, Abdulaziz N.; Almunia, Javier; Aloysius, Ajoy; Amor, Nabil M. S.; Ardehali, Reza; Arneson, Adriana; Baker, C. Scott; Banks, Gareth; Belov, Katherine; Bennett, Nigel C.; Black, Peter; Blumstein, Daniel T.; Bors, Eleanor K.; Breeze, Charles E.; Brooke, Robert T.; Brown, Janine L.; Carter, Gerald; Caulton, Alex; Cavin, Julie M.; Chakrabarti, Lisa; Chatzistamou, Ioulia; Chavez, Andreas S.; Chen, Hao; Cheng, Kaiyang; Chiavellini, Priscila; Choi, Oi-Wa; Clarke, Shannon; Cook, Joseph A.; Cooper, Lisa N.; Cossette, Marie-Laurence; Day, Joanna; DeYoung, Joseph; Dirocco, Stacy; Dold, Christopher; Dunnum, Jonathan L.; Ehmke, Erin E.; Emmons, Candice K.; Emmrich, Stephan; Erbay, Ebru; Erlacher-Reid, Claire; Faulkes, Chris G.; Fei, Zhe; Ferguson, Steven H.; Finno, Carrie J.; Flower, Jennifer E.; Gaillard, Jean-Michel; Garde, Eva; Gerber, Livia; Gladyshev, Vadim N.; Goya, Rodolfo G.; Grant, Matthew J.; Green, Carla B.; Hanson, M. Bradley; Hart, Daniel W.; Haulena, Martin; Herrick, Kelsey; Hogan, Andrew N.; Hogg, Carolyn J.; Hore, Timothy A.; Huang, Taosheng; Izpisua Belmonte, Juan Carlos; Jasinska, Anna J.; Jones, Gareth; Jourdain, Eve; Kashpur, Olga; Katcher, Harold; Katsumata, Etsuko; Kaza, Vimala; Kiaris, Hippokratis; Kobor, Michael S.; Kordowitzki, Pawel; Koski, William R.; Kruetzen, Michael; Kwon, Soo Bin; Larison, Brenda; Lee, Sang-Goo; Lehmann, Marianne; Lemaitre, Jean-Francois; Levine, Andrew J.; Li, Xinmin; Li, Cun; Lim, Andrea R.; Lin, David T. S.; Lindemann, Dana M.; Liphardt, Schuyler W.; Little, Thomas J.; Macoretta, Nicholas; Maddox, Dewey; Matkin, Craig O.; Mattison, Julie A.; McClure, Matthew; Mergl, June; Meudt, Jennifer J.; Montano, Gisele A.; Mozhui, Khyobeni; Munshi-South, Jason; Murphy, William J.; Naderi, Asieh; Nagy, Martina; Narayan, Pritika; Nathanielsz, Peter W.; Nguyen, Ngoc B.; Niehrs, Christof; Nyamsuren, Batsaikhan; O'Brien, Justine K.; Ginn, Perrie O'Tierney; Odom, Duncan T.; Ophir, Alexander G.; Osborn, Steve; Ostrander, Elaine A.; Parsons, Kim M.; Paul, Kimberly C.; Pedersen, Amy B.; Pellegrini, Matteo; Peters, Katharina J.; Petersen, Jessica L.; Pietersen, Darren W.; Pinho, Gabriela M.; Plassais, Jocelyn; Poganik, Jesse R.; Prado, Natalia A.; Reddy, Pradeep; Rey, Benjamin; Ritz, Beate R.; Robbins, Jooke; Rodriguez, Magdalena; Russell, Jennifer; Rydkina, Elena; Sailer, Lindsay L.; Salmon, Adam B.; Sanghavi, Akshay; Schachtschneider, Kyle M.; Schmitt, Dennis; Schmitt, Todd; Schomacher, Lars; Schook, Lawrence B.; Sears, Karen E.; Seifert, Ashley W.; Shafer, Aaron B. A.; Shindyapina, Anastasia V.; Simmons, Melanie; Singh, Kavita; Sinha, Ishani; Slone, Jesse; Snell, Russel G.; Soltanmohammadi, Elham; Spangler, Matthew L.; Spriggs, Maria; Staggs, Lydia; Stedman, Nancy; Steinman, Karen J.; Stewart, Donald T.; Sugrue, Victoria J.; Szladovits, Balazs; Takahashi, Joseph S.; Takasugi, Masaki; Teeling, Emma C.; Thompson, Michael J.; Van Bonn, Bill; Vernes, Sonja C.; Villar, Diego; Vinters, Harry V.; Vu, Ha; Wallingford, Mary C.; Wang, Nan; Wilkinson, Gerald S.; Williams, Robert W.; Yan, Qi; Yao, Mingjia; Young, Brent G.; Zhang, Bohan; Zhang, Zhihui; Zhao, Yang; Zhao, Peng; Zhou, Wanding; Zoller, Joseph A.; Ernst, Jason; Seluanov, Andrei; Gorbunova, Vera; Yang, X. William; Raj, Ken; Horvath, Steve (2023)
    Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, ...
  • Mason, Victor C.; Li, Gang; Helgen, Kristofer M.; Murphy, William J. (2011)
    The ability to uncover the phylogenetic history of recently extinct species and other species known only from archived museum material has rapidly improved due to the reduced cost and increased sequence capacity of ...
  • Janecka, Jan E.; Helgen, Kristofer M.; Lim, Norman T. -L; Baba, Minoru; Izawa, Masako; Boeadi; Murphy, William J. (2008)
  • Damas, Joana; Corbo, Marco; Kim, Jaebum; Turner-Maier, Jason; Farré, Marta; Larkin, Denis M.; Ryder, Oliver A.; Steiner, Cynthia; Houck, Marlys L.; Hall, Shaune; Shiue, Lily; Thomas, Stephen; Swale, Thomas; Daly, Mark; Korlach, Jonas; Uliano-Silva, Marcela; Mazzoni, Camila J.; Birren, Bruce W.; Genereux, Diane P.; Johnson, Jeremy; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Nweeia, Martin T.; Johnson, Rebecca N.; Consortium, Zoonomia; Lewin, Harris A.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; Damas, Joana; Palma, Federica Di; Diekhans, Mark; Dong, Michael X.; Eizirik, Eduardo; Fan, Kaili; Fanter, Cornelia; Foley, Nicole M.; Forsberg-Nilsson, Karin; Garcia, Carlos J.; Gatesy, John; Gazal, Steven; Genereux, Diane P.; Goodman, Linda; Grimshaw, Jenna; Halsey, Michaela K.; Harris, Andrew J.; Hickey, Glenn; Hiller, Michael; Hindle, Allyson G.; Hubley, Robert M.; Hughes, Graham M.; Johnson, Jeremy; Juan, David; Kaplow, Irene M.; Karlsson, Elinor K.; Keough, Kathleen C.; Kirilenko, Bogdan; Koepfli, Klaus-Peter; Korstian, Jennifer M.; Kowalczyk, Amanda; Kozyrev, Sergey V.; Lawler, Alyssa J.; Lawless, Colleen; Lehmann, Thomas; Levesque, Danielle L.; Lewin, Harris A.; Li, Xue; Lind, Abigail; Lindblad-Toh, Kerstin; Mackay-Smith, Ava; Marinescu, Voichita D.; Marques-Bonet, Tomas; Mason, Victor C.; Meadows, Jennifer R. S.; Meyer, Wynn K.; Moore, Jill E.; Moreira, Lucas R.; Moreno-Santillan, Diana; Morrill, Kathleen M.; Muntané, Gerard; Murphy, William J.; Navarro, Arcadi; Nweeia, Martin; Ortmann, Sylvia; Osmanski, Austin; Paten, Benedict; Paulat, Nicole S.; Pfenning, Andreas R.; Phan, BaDoi N.; Pollard, Katherine S.; Pratt, Henry E.; Ray, David A.; Reilly, Steven K.; Rosen, Jeb R.; Ruf, Irina; Ryan, Louise; Ryder, Oliver A.; Sabeti, Pardis C.; Schäffer, Daniel E.; Serres, Aitor; Shapiro, Beth; Smit, Arian F. A.; Springer, Mark; Srinivasan, Chaitanya; Steiner, Cynthia; Storer, Jessica M.; Sullivan, Kevin A. M.; Sullivan, Patrick F.; Sundström, Elisabeth; Supple, Megan A.; Swofford, Ross; Talbot, Joy-El; Teeling, Emma; Turner-Maier, Jason; Valenzuela, Alejandro; Wagner, Franziska; Wallerman, Ola; Wang, Chao; Wang, Juehan; Weng, Zhiping; Wilder, Aryn P.; Wirthlin, Morgan E.; Xue, James R.; Zhang, Xiaomeng (2022)
    Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale ...
  • Christmas, Matthew J.; Kaplow, Irene M.; Genereux, Diane P.; Dong, Michael X.; Hughes, Graham M.; Li, Xue; Sullivan, Patrick F.; Hindle, Allyson G.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Breit, Ana M.; Diekhans, Mark; Fanter, Cornelia; Foley, Nicole M.; Goodman, Daniel B.; Goodman, Linda; Keough, Kathleen C.; Kirilenko, Bogdan; Kowalczyk, Amanda; Lawless, Colleen; Lind, Abigail L.; Meadows, Jennifer R. S.; Moreira, Lucas R.; Redlich, Ruby W.; Ryan, Louise; Swofford, Ross; Valenzuela, Alejandro; Wagner, Franziska; Wallerman, Ola; Brown, Ashley R.; Damas, Joana; Fan, Kaili; Gatesy, John; Grimshaw, Jenna; Johnson, Jeremy; Kozyrev, Sergey V.; Lawler, Alyssa J.; Marinescu, Voichita D.; Morrill, Kathleen M.; Osmanski, Austin; Paulat, Nicole S.; Phan, BaDoi N.; Reilly, Steven K.; Schäffer, Daniel E.; Steiner, Cynthia; Supple, Megan A.; Wilder, Aryn P.; Wirthlin, Morgan E.; Xue, James R.; Zoonomia Consortium§; Birren, Bruce W.; Gazal, Steven; Hubley, Robert M.; Koepfli, Klaus-Peter; Marques-Bonet, Tomas; Meyer, Wynn K.; Nweeia, Martin; Sabeti, Pardis C.; Shapiro, Beth; Smit, Arian F. A.; Springer, Mark S.; Teeling, Emma C.; Weng, Zhiping; Hiller, Michael; Levesque, Danielle L.; Lewin, Harris A.; Murphy, William J.; Navarro, Arcadi; Paten, Benedict; Pollard, Katherine S.; Ray, David A.; Ruf, Irina; Ryder, Oliver A.; Pfenning, Andreas R.; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Andrews, Gregory; Armstrong, Joel C.; Bianchi, Matteo; Birren, Bruce W.; Bredemeyer, Kevin R.; Breit, Ana M.; Christmas, Matthew J.; Clawson, Hiram; Damas, Joana; Di Palma, Federica; Diekhans, Mark; Dong, Michael X.; Eizirik, Eduardo; Fan, Kaili; Fanter, Cornelia; Foley, Nicole M.; Forsberg-Nilsson, Karin; Garcia, Carlos J.; Gatesy, John; Gazal, Steven; Genereux, Diane P.; Goodman, Linda; Grimshaw, Jenna; Halsey, Michaela K.; Harris, Andrew J.; Hickey, Glenn; Hiller, Michael; Hindle, Allyson G.; Hubley, Robert M.; Hughes, Graham M.; Johnson, Jeremy; Juan, David; Kaplow, Irene M.; Karlsson, Elinor K.; Keough, Kathleen C.; Kirilenko, Bogdan; Koepfli, Klaus-Peter; Korstian, Jennifer M.; Kowalczyk, Amanda; Kozyrev, Sergey V.; Lawler, Alyssa J.; Lawless, Colleen; Lehmann, Thomas; Levesque, Danielle L.; Lewin, Harris A.; Li, Xue; Lind, Abigail; Lindblad-Toh, Kerstin; Mackay-Smith, Ava; Marinescu, Voichita D.; Marques-Bonet, Tomas; Mason, Victor C.; Meadows, Jennifer R. S.; Meyer, Wynn K.; Moore, Jill E.; Moreira, Lucas R.; Moreno-Santillan, Diana; Morrill, Kathleen M.; Muntané, Gerard; Murphy, William J.; Navarro, Arcadi; Nweeia, Martin; Ortmann, Sylvia; Osmanski, Austin; Paten, Benedict; Paulat, Nicole S.; Pfenning, Andreas R.; Phan, BaDoi N.; Pollard, Katherine S.; Pratt, Henry E.; Ray, David A.; Reilly, Steven K.; Rosen, Jeb R.; Ruf, Irina; Ryan, Louise; Ryder, Oliver A.; Sabeti, Pardis C.; Schäffer, Daniel E.; Serres, Aitor; Shapiro, Beth; Smit, Arian F. A.; Springer, Mark; Srinivasan, Chaitanya; Steiner, Cynthia; Storer, Jessica M.; Sullivan, Kevin A. M.; Sullivan, Patrick F.; Sundström, Elisabeth; Supple, Megan A.; Swofford, Ross; Talbot, Joy-El; Teeling, Emma; Turner-Maier, Jason; Valenzuela, Alejandro; Wagner, Franziska; Wallerman, Ola; Wang, Chao; Wang, Juehan; Weng, Zhiping; Wilder, Aryn P.; Wirthlin, Morgan E.; Xue, James R.; Zhang, Xiaomeng (2023)
    Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least ...
  • Haussler, David; O'Brien, Stephen J.; Ryder, Oliver A.; Barker, F. Keith; Clamp, Michele; Crawford, Andrew J.; Hanner, Robert; Hanotte, Olivier; McGuire, Jimmy A.; Miller, Webb; Murphy, Robert W.; Murphy, William J.; Sheldon, Frederick H.; Sinervo, Barry; Venkatesh, Byrappa; Wiley, Edward O.; Allendorf, Fred W.; Amato, George; Baker, C. Scott; Bauer, Aaron; Beja-Pereira, Albano; Bermingham, Eldredge; Bernardi, Giacomo; Bonvicino, Cibele R.; Brenner, Sydney; Burke, Terry; Cracraft, Joel; Diekhans, Mark; Edwards, Scott; Ericson, Per G. P.; Estes, James; Fjelsda, Jon; Flesness, Nate; Gamble, Tony; Gaubert, Philippe; Graphodatsky, Alexander S.; Graves, Jennifer A. Marshall; Green, Eric D.; Green, Richard E.; Hackett, Shannon; Hebert, Paul; Helgen, Kristofer M.; Joseph, Leo; Kessing, Bailey; Kingsley, David M.; Lewin, Harris A.; Luikart, Gordon; Martelli, Paolo; Moreira, Miguel A. M.; Nguyen, Ngan; Orti, Guillermo; Pike, Brian L.; Rawson, David Michael; Schuster, Stephan C.; Seuanez, Hector N.; Shaffer, H. Bradley; Springer, Mark S.; Stuart, Joshua Michael; Sumner, Joanna; Teeling, Emma; Vrijenhoek, Robert C.; Ward, Robert D.; Warren, Wesley C.; Wayne, Robert K.; Williams, Terrie M.; Wolfe, Nathan D.; Zhang, Ya-Ping; Graph-Odatsky, Alexander; Johnson, Warren E.; Felsenfeld, Adam; Turner, S. C. (2009)
    The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous ...
  • Trindade, Fernanda J.; Rodrigues, Maira R.; Figueiro, Henrique, V.; Li, Gang; Murphy, William J.; Eizirik, Eduardo (2021)
    Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when postspeciation gene flow is present. Leopardus is a Neotropical cat genus that has ...
  • Mason, Victor C.; Li, Gang; Minx, Patrick; Schmitz, Jü; Churakov, Gennady; Doronina, Liliya; Melin, Amanda D.; Dominy, Nathaniel J.; Lim, Norman T. -L; Springer, Mark S.; Wilson, Richard K.; Warren, Wesley C.; Helgen, Kristofer M.; Murphy, William J. (2016)
  • Springer, Mark S.; Signore, Anthony V.; Paijmans, Johanna L. A.; Vélez-Juarbe, Jorge; Domning, Daryl P.; Bauer, Cameron E.; He, Kai; Crerar, Lorelei; Campos, Paula F.; Murphy, William J.; Meredith, Robert W.; Gatesy, John; Willerslev, Eske; MacPhee, Ross D. E.; Hofreiter, Michael; Campbell, Kevin L. (2015)
    The recently extinct (ca. 1768) Steller s sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are ...
  • Jamieson, Alexandra; Carmagnini, Alberto; Howard-McCombe, Jo; Doherty, Sean; Hirons, Alexandra; Dimopoulos, Evangelos; Lin, Audrey T.; Allen, Richard; Anderson-Whymark, Hugo; Barnett, Ross; Batey, Colleen; Beglane, Fiona; Bowden, Will; Bratten, John; De Cupere, Bea; Drew, Ellie; Foley, Nicole M.; Fowler, Tom; Fox, Allison; Geigl, Eva-Maria; Gotfredsen, Anne Birgitte; Grange, Thierry; Griffiths, David; Groß, Daniel; Haruda, Ashleigh; Hjermind, Jesper; Knapp, Zoe; Lebrasseur, Ophélie; Librado, Pablo; Lyons, Leslie A.; Mainland, Ingrid; McDonnell, Christine; Muñoz-Fuentes, Violeta; Nowak, Carsten; O’Connor, Terry; Peters, Joris; Russo, Isa-Rita M.; Ryan, Hannah; Sheridan, Alison; Sinding, Mikkel-Holger S.; Skoglund, Pontus; Swali, Pooja; Symmons, Robert; Thomas, Gabor; Trolle Jensen, Theis Zetner; Kitchener, Andrew C.; Senn, Helen; Lawson, Daniel; Driscoll, Carlos; Murphy, William J.; Beaumont, Mark; Ottoni, Claudio; Sykes, Naomi; Larson, Greger; Frantz, Laurent (2023)
  • Miller, Webb; Drautz, Daniela I.; Janecka, Jan E.; Lesk, Arthur M.; Ratan, Aakrosh; Tomsho, Lynn P.; Packard, Mike; Zhang, Yeting; McClellan, Lindsay R.; Qi, Ji; Zhao, Fangqing; Gilbert, M. Thomas P.; Dalen, Love; Arsuaga, Juan Luis; Ericson, Per G. P.; Huson, Daniel H.; Helgen, Kristofer M.; Murphy, William J.; Gotherstrom, Anders; Schuster, Stephan C. (2009)
    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian ...
  • Janecka, Jan E.; Miller, Webb; Pringle, Thomas H.; Wiens, Frank; Zitzmann, Annette; Helgen, Kristofer M.; Springer, Mark S.; Murphy, William J. (2007)

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