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Browsing by Author "Diekhans, Mark"

Browsing by Author "Diekhans, Mark"

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  • The contribution of historical processes to contemporary extinction risk in placental mammals 
    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 ...
  • Dense sampling of bird diversity increases power of comparative genomics 
    Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart; Xie, Duo; Chen, Guangji; Guo, Chunxue; Faircloth, Brant C.; Petersen, Bent; Wang, Zongji; Zhou, Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Pacheco, George; Sinding, Mikkel-Holger S.; Puetz, Lara; Cavill, Emily; Ribeiro, Ângela M.; Eckhart, Leopold; Fjeldså, Jon; Hosner, Peter A.; Brumfield, Robb T.; Christidis, Les; Bertelsen, Mads F.; Sicheritz-Ponten, Thomas; Tietze, Dieter Thomas; Robertson, Bruce C.; Song, Gang; Borgia, Gerald; Claramunt, Santiago; Lovette, Irby J.; Cowen, Saul J.; Njoroge, Peter; Dumbacher, John Philip; Ryder, Oliver A.; Fuchs, Jérôme; Bunce, Michael; Burt, David W.; Cracraft, Joel; Meng, Guanliang; Hackett, Shannon J.; Ryan, Peter G.; Jønsson, Knud Andreas; Jamieson, Ian G.; da Fonseca, Rute R.; Braun, Edward L.; Houde, Peter; Mirarab, Siavash; Suh, Alexander; Hansson, Bengt; Ponnikas, Suvi; Sigeman, Hanna; Stervander, Martin; Frandsen, Paul B.; van der Zwan, Henriette; van der Sluis, Rencia; Visser, Carina; Balakrishnan, Christopher N.; Clark, Andrew G.; Fitzpatrick, John W.; Bowman, Reed; Chen, Nancy; Cloutier, Alison; Sackton, Timothy B.; Edwards, Scott V.; Foote, Dustin J.; Shakya, Subir B.; Sheldon, Frederick H.; Vignal, Alain; Soares, André E. R.; Shapiro, Beth; González-Solís, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Riutort, Marta; Tigano, Anna; Friesen, Vicki; Dalén, Love; Urrutia, Araxi O.; Székely, Tamás; Liu, Yang; Campana, Michael G.; Corvelo, André; Fleischer, Robert C.; Rutherford, Kim M.; Gemmell, Neil J.; Dussex, Nicolas; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Hoeppner, Marc P.; Krone, Oliver; Fudickar, Adam M.; Milá, Borja; Ketterson, Ellen D.; Fidler, Andrew Eric; Friis, Guillermo; Parody-Merino, Ángela M.; Battley, Phil F.; Cox, Murray P.; Lima, Nicholas Costa Barroso; Prosdocimi, Francisco; Parchman, Thomas Lee; Schlinger, Barney A.; Loiselle, Bette A.; Blake, John G.; Lim, Haw Chuan; Day, Lainy B.; Fuxjager, Matthew J.; Baldwin, Maude W.; Braun, Michael J.; Wirthlin, Morgan; Dikow, Rebecca B.; Ryder, T. B.; Camenisch, Glauco; Keller, Lukas F.; DaCosta, Jeffrey M.; Hauber, Mark E.; Louder, Matthew I. M.; Witt, Christopher C.; McGuire, Jimmy A.; Mudge, Joann; Megna, Libby C.; Carling, Matthew D.; Wang, Biao; Taylor, Scott A.; Del-Rio, Glaucia; Aleixo, Alexandre; Vasconcelos, Ana Tereza Ribeiro; Mello, Claudio V.; Weir, Jason T.; Haussler, David; Li, Qiye; Yang, Huanming; Wang, Jian; Lei, Fumin; Rahbek, Carsten; Gilbert, M. T.; Graves, Gary R.; Jarvis, Erich D.; Paten, Benedict; Zhang, Guojie (2020)
    Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a ...
  • Evolution of the ancestral mammalian karyotype and syntenic regions 
    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 ...
  • Evolutionary constraint and innovation across hundreds of placental mammals 
    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 ...
  • Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species 
    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 ...
  • Genomic legacy of the African cheetah, Acinonyx jubatus 
    Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A.; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-Küntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren E.; Kuderna, Lukas F. K.; García-Pérez, Raquel; Manuel, Marc de; Godinez, Ricardo; Komissarov, Aleksey; Makunin, Alexey; Brukhin, Vladimir; Qiu, Weilin; Zhou, Long; Li, Fang; Yi, Jian; Driscoll, Carlos; Antunes, Agostinho; Oleksyk, Taras K.; Eizirik, Eduardo; Perelman, Polina; Roelke, Melody; Wildt, David E.; Diekhans, Mark; Marques-Bonet, Tomas; Marker, Laurie; Bhak, Jong; Wang, Jun; Zhang, Guojie; O'Brien, Stephen J. (2015)
    BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs ...
  • Towards complete and error-free genome assemblies of all vertebrate species 
    Rhie, Arang; McCarthy, Shane A.; Fedrigo, Olivier; Damas, Joana; Formenti, Giulio; Koren, Sergey; Uliano-Silva, Marcela; Chow, William; Fungtammasan, Arkarachai; Kim, Juwan; Lee, Chul; Ko, Byung June; Chaisson, Mark; Gedman, Gregory L.; Cantin, Lindsey J.; Thibaud-Nissen, Francoise; Haggerty, Leanne; Bista, Iliana; Smith, Michelle; Haase, Bettina; Mountcastle, Jacquelyn; Winkler, Sylke; Paez, Sadye; Howard, Jason; Vernes, Sonja C.; Lama, Tanya M.; Grutzner, Frank; Warren, Wesley C.; Balakrishnan, Christopher N.; Burt, Dave; George, Julia M.; Biegler, Matthew T.; Iorns, David; Digby, Andrew; Eason, Daryl; Robertson, Bruce; Edwards, Taylor; Wilkinson, Mark; Turner, George; Meyer, Axel; Kautt, Andreas F.; Franchini, Paolo; Detrich, H. William; Svardal, Hannes; Wagner, Maximilian; Naylor, Gavin J. P.; Pippel, Martin; Malinsky, Milan; Mooney, Mark; Simbirsky, Maria; Hannigan, Brett T.; Pesout, Trevor; Houck, Marlys; Misuraca, Ann; Kingan, Sarah B.; Hall, Richard; Kronenberg, Zev; Sovi, Ivan; Dunn, Christopher; Ning, Zemin; Hastie, Alex; Lee, Joyce; Selvaraj, Siddarth; Green, Richard E.; Putnam, Nicholas H.; Gut, Ivo; Ghurye, Jay; Garrison, Erik; Sims, Ying; Collins, Joanna; Pelan, Sarah; Torrance, James; Tracey, Alan; Wood, Jonathan; Dagnew, Robel E.; Guan, Dengfeng; London, Sarah E.; Clayton, David F.; Mello, Claudio, V.; Friedrich, Samantha R.; Lovell, Peter, V.; Osipova, Ekaterina; Al-Ajli, Farooq O.; Secomandi, Simona; Kim, Heebal; Theofanopoulou, Constantina; Hiller, Michael; Zhou, Yang; Harris, Robert S.; Makova, Kateryna D.; Medvedev, Paul; Hoffman, Jinna; Masterson, Patrick; Clark, Karen; Martin, Fergal; Howe, Kevin; Flicek, Paul; Walenz, Brian P.; Kwak, Woori; Clawson, Hiram; Diekhans, Mark; Nassar, Luis; Paten, Benedict; Kraus, Robert H. S.; Crawford, Andrew J.; Gilbert, M. Thomas P.; Zhang, Guojie; Venkatesh, Byrappa; Murphy, Robert W.; Koepfli, Klaus-Peter; Shapiro, Beth; Johnson, Warren E.; Di Palma, Federica; Marques-Bonet, Tomas; Teeling, Emma C.; Warnow, Tandy; Graves, Jennifer Marshall; Ryder, Oliver A.; Haussler, David; O'Brien, Stephen J.; Korlach, Jonas; Lewin, Harris A.; Howe, Kerstin; Myers, Eugene W.; Durbin, Richard; Phillippy, Adam M.; Jarvis, Erich D. (2021)
    The Vertebrate Genome Project has used an optimized pipeline to generate high-quality genome assemblies for sixteen species (representing all major vertebrate classes), which have led to new biological insights. High-quality ...

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