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Browsing by Author "Ryder, Oliver A."

Browsing by Author "Ryder, Oliver A."

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  • Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates 
    Damas, Joana; Hughes, Graham M.; Keough, Kathleen C.; Painter, Corrie A.; Persky, Nicole S.; Corbo, Marco; Hiller, Michael; Koepfli, Klaus-Peter; Pfenning, Andreas R.; Zhao, Huabin; Genereux, Diane P.; Swofford, Ross; Pollard, Katherine S.; Ryder, Oliver A.; Nweeia, Martin T.; Lindblad-Toh, Kerstin; Teeling, Emma C.; Karlsson, Elinor K.; Lewin, Harris A. (2020)
    Abstract The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand ...
  • Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (<I>Mustela nigripes</I>) 
    Kliver, Sergei; Houck, Marlys L.; Perelman, Polina L.; Totikov, Azamat; Tomarovsky, Andrei; Dudchenko, Olga; Omer, Arina D.; Colaric, Zane; Weisz, David; Aiden, Erez Lieberman; Chan, Saki; Hastie, Alex; Komissarov, Aleksey; Ryder, Oliver A.; Graphodatsky, Alexander; Johnson, Warren E.; Maldonado, Jesús E.; Pukazhenthi, Budhan S.; Marinari, Paul E.; Wildt, David E.; Koepfli, Klaus-Peter (2023)
    The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex-situ conservation ...
  • Comparative genomics reveals insights into avian genome evolution and adaptation 
    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; Fonseca, Rute R. da; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N.; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth P.; Warren, Wesley; Wilson, Richard K.; Li, Shengbin; Ray, David A.; Green, Richard E.; O'Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. T.; Wang, Jun; Ye, Chen; Liang, Shaoguang; Yan, Zengli; Zepeda, M. L.; Campos, Paula F.; Velazquez, Amhed Missael Vargas; Samaniego, José Alfredo; Avila-Arcos, Mar; Martin, Michael D.; Barnett, Ross; Ribeiro, Angela M.; Mello, Claudio V.; Lovell, Peter V.; Almeida, Daniela; Maldonado, Emanuel; Pereira, Joana; Sunagar, Kartik; Philip, Siby; Dominguez-Bello, Maria; Bunce, Michael; Lambert, David; Brumfield, Robb T.; Sheldon, Frederick H.; Holmes, Edward C.; Gardner, Paul P.; Steeves, Tammy E.; Stadler, Peter F.; Burge, Sarah W.; Lyons, Eric; Smith, Jacqueline; McCarthy, Fiona; Pitel, Frederique; Rhoads, Douglas; Froman, David P. (2014)
    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant ...
  • 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 ...
  • Correcting parentage relationships in the endangered California Condor: Improving mean kinship estimates for conservation management 
    Moran, Brigid M.; Thomas, Steven M.; Judson, Jessica M.; Navarro, Asako; Davis, Heidi; Sidak-Loftis, Lindsay; Korody, Marisa; Mace, Michael; Ralls, Katherine; Callicrate, Taylor; Ryder, Oliver A.; Chemnick, Leona G.; Steiner, Cynthia C. (2021)
    Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. ...
  • Correcting parentage relationships in the endangered California condor: Improving mean kinship estimates for conservation management 
    Moran, Brigid M.; Thomas, Steven M.; Judson, Jessica M.; Navarro, Asako; Davis, Heidi; Sidak-Loftis, Lindsay; Korody, Marisa; Mace, Michael; Ralls, Katherine; Callicrate, Taylor; Ryder, Oliver A.; Chemnick, Leona G.; Steiner, Cynthia C. (Dryad, 2021)
    Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. ...
  • Darwinian genomics and diversity in the tree of life 
    Stephan, Taylorlyn; Burgess, Shawn M.; Cheng, Hans; Danko, Charles G.; Gill, Clare A.; Jarvis, Erich D.; Koepfli, Klaus-Peter; Koltes, James E.; Lyons, Eric; Ronald, Pamela; Ryder, Oliver A.; Schriml, Lynn M.; Soltis, Pamela; VandeWoude, Sue; Zhou, Huaijun; Ostrander, Elaine A.; Karlsson, Elinor K. (2022)
    Genomics encompasses the entire tree of life, both extinct and extant, and the evolutionary processes that shape this diversity. To date, genomic research has focused on humans, a small number of agricultural species, and ...
  • 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 ...
  • The Earth BioGenome Project 2020: Starting the clock 
    Lewin, Harris A.; Richards, Stephen; Lieberman Aiden, Erez; Allende, Miguel L.; Archibald, John M.; Bálint, Miklós; Barker, Katharine B.; Baumgartner, Bridget; Belov, Katherine; Bertorelle, Giorgio; Blaxter, Mark L.; Cai, Jing; Caperello, Nicolette D.; Carlson, Keith; Castilla-Rubio, Juan; Chaw, Shu-Miaw; Chen, Lei; Childers, Anna K.; Coddington, Jonathan A.; Conde, Dalia A.; Corominas, Montserrat; Crandall, Keith A.; Crawford, Andrew J.; DiPalma, Federica; Durbin, Richard; Ebenezer, ThankGod E.; Edwards, Scott V.; Fedrigo, Olivier; Flicek, Paul; Formenti, Giulio; Gibbs, Richard A.; Gilbert, M. T.; Goldstein, Melissa M.; Graves, Jennifer Marshall; Greely, Henry T.; Grigoriev, Igor V.; Hackett, Kevin J.; Hall, Neil; Haussler, David; Helgen, Kristofer M.; Hogg, Carolyn J.; Isobe, Sachiko; Jakobsen, Kjetill Sigurd; Janke, Axel; Jarvis, Erich D.; Johnson, Warren E.; Jones, Steven J. M.; Karlsson, Elinor K.; Kersey, Paul J.; Kim, Jin-Hyoung; Kress, W. John; Kuraku, Shigehiro; Lawniczak, Mara K. N.; Leebens-Mack, James; Li, Xueyan; Lindblad-Toh, Kerstin; Liu, Xin; Lopez, Jose V.; Marques-Bonet, Tomas; Mazard, Sophie; Mazet, Jonna A. K.; Mazzoni, Camila J.; Myers, Eugene W.; O'Neill, Rachel J.; Paez, Sadye; Park, Hyun; Robinson, Gene E.; Roquet, Cristina; Ryder, Oliver A.; Sabir, Jamal S. M.; Shaffer, H. B.; Shank, Timothy M.; Sherkow, Jacob S.; Soltis, Pamela S.; Tang, Boping; Tedersoo, Leho; Uliano-Silva, Marcela; Wang, Kun; Wei, Xiaofeng; Wetzer, Regina; Wilson, Julia L.; Xu, Xun; Yang, Huanming; Yoder, Anne D.; Zhang, Guojie (2022)
  • Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks 
    Farré, Marta; Kim, Jaebum; Proskuryakova, Anastasia A.; Zhang, Yang; Kulemzina, Anastasia I.; Li, Qiye; Zhou, Yang; Xiong, Yingqi; Johnson, Jennifer L.; Perelman, Polina; Johnson, Warren E.; Warren, Wesley C.; Kukekova, Anna V.; Zhang, Guojie; O'Brien, Stephen J.; Ryder, Oliver A.; Graphodatsky, Alexander S.; Ma, Jian; Lewin, Harris A.; Larkin, Denis M. (2019)
    The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution ...
  • 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 ...
  • Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis) 
    Brandt, Jessica R.; Van Coeverden, de Groot; Witt, Kelsey E.; Engelbrektsson, Paige K.; Helgen, Kristofer M.; Malhi, Ripan S.; Ryder, Oliver A.; Roca, Alfred L. (2018)
    The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control ...
  • 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 ...
  • Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (<I>Panthera uncia</I>, <I>Panthera pardus pardus</I>, and <I>Panthera tigris</I>) 
    Armstrong, Ellie E.; Campana, Michael G.; Solari, Katherine A.; Morgan, Simon R.; Ryder, Oliver A.; Naude, Vincent N.; Samelius, Gustaf; Sharma, Koustubh; Hadly, Elizabeth A.; Petrov, Dmitri A. (2022)
    The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution ...
  • Implications of different species concepts for conserving biodiversity 
    Frankham, Richard; Ballou, Jonathan D.; Dudash, Michele R.; Eldridge, Mark D. B.; Fenster, Charles B.; Lacy, Robert C.; Mendelson, Joseph R., III; Porton, Ingrid J.; Ralls, Katherine; Ryder, Oliver A. (2012)
    The ~26 definitions of species often yield different numbers of species and disparate groupings, with financial, legal, biological and conservation implications. Using conservation genetic considerations, we demonstrate ...
  • Phylogenomics of the world&#39;s otters 
    de Ferran, Vera; Figueiró, Henrique Vieira; Trindade, Fernanda de Jesus; Smith, Oliver; Sinding, Mikkel-Holger S.; Trinca, Cristine S.; Lazzari, Gabriele Zenato; Veron, Géraldine; Vianna, Juliana A.; Barbanera, Filippo; Kliver, Sergei; Serdyukova, Natalia; Bulyonkova, Tatiana; Ryder, Oliver A.; Gilbert, M. Thomas P.; Koepfli, Klaus-Peter; Eizirik, Eduardo (2022)
    Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized ...
  • Reference genomes for conservation 
    Paez, Sadye; Kraus, Robert H. S.; Shapiro, Beth; Gilbert, M. T.; Jarvis, Erich D.; Vertebrate Genomes Project, Conservation Group; Al-Ajli, Farooq; Ceballos, Gerardo; Crawford, Andrew J.; Fedrigo, Olivier; Johnson, Rebecca N.; Johnson, Warren E.; Marques-Bonet, Tomas; Morin, Phillip A.; Mueller, Ralf C.; Ryder, Oliver A.; Teeling, Emma C.; Venkatesh, Byrappa (2022)
    High-quality reference genomes for non–model species can benefit conservation , As of 2022, the International Union for Conservation of Nature (IUCN) Red List estimates that more than 32% of fungal, plant, and animal species ...
  • Response to Bakker et al 
    Robinson, Jacqueline A.; Bowie, Rauri C. K.; Dudchenko, Olga; Aiden, Erez Lieberman; Hendrickson, Sher L.; Steiner, Cynthia C.; Ryder, Oliver A.; Mindell, David P.; Wall, Jeffrey D. (2022)
  • Response to Bakker et al. Genetically based demographic reconstructions require careful consideration of generation time 
    Robinson, Jacqueline A.; Bowie, Rauri C. K.; Dudchenko, Olga; Aiden, Erez Lieberman; Hendrickson, Sher L.; Steiner, Cynthia C.; Ryder, Oliver A.; Mindell, David P.; Wall, Jeffrey D. (2022)

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