Publications

Oliver Ryder, Ph.D.

Damas, J., M. Corbo, J. Kim, J. Turner-Maier, M. Farré, D.M. Larkin, O.A. Ryder, C. Steiner, M.L. Houck, S. Hall, L. Shiue, S. Thomas, T. Swale, M. Daly, J. Korlach, M. Uliano-Silva, C.J. Mazzoni, B.W. Birren, D.P. Genereux, J. Johnson, K. Lindblad-Toh, E.K. Karlsson, M.T. Nweeia, R.N. Johnson, Zoonomia Consortium, H.A. Lewin. 2022. Evolution of the ancestral mammalian karyotype and syntenic regions. Evolution 119 (40). 1-12.

Shier, D.M., A.Y. Navarro, M. Tobler, S.M. Thomas, S.N.D. King, C.B. Mullaney, O.A. Ryder. 2021. Genetic and ecological evidence of long-term translocation success of the federally endangered Stephens' kangaroo rat. Conservation Science and Practice. DOI: https://doi.org/10.1111/csp2.478.

Damas, J., G.M. Hughes, K.C. Keough, C.A. Painter, N.S. Persky, M. Corbo, M. Hiller, K.P. Koepfli, A.R. Pfenning, H. Zhao, D.P. Genereux, R. Swofford, K.S. Pollard, O.A. Ryder, M.T. Nweeia, K. Lindblad-Toh, E.C. Teeling, E.K. Karlsson, H.A. Lewin. 2020. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.2010146117.

Hendricks, S., A.Y. Navarro, T. Wang, A. Wilder, O.A. Ryder, D.M. Shier. 2020. Patterns of genetic partitioning and gene flow in the endangered San Bernardino kangaroo rat (Dipodomys merriami parvus) and implications for conservation management. Conservation Genetics. DOI: 10.1007/s10592-020-01289-z.

Putnam, A.S., T.N. Nguyen, A. Mott, M.L. Korody, O.A. Ryder. 2020. Assessing possible hybridization among managed Nubian ibex in North America. Zoo Biology 39. 121–128.

Ryder, O.A., C. Friese, H.T. Greely, R. Sandler, J. Saragusty, B.S. Durrant, K.H. Redford. 2020. Exploring the limits of saving a subspecies: The ethics and social dynamics of restoring northern white rhinos (Ceratotherium simum cottoni). Conservation Science and Practice. DOI: 10.1111/csp2.241.

Watsa, M., G. Erkenswick, S. Prost, E.O. Davis, C. Moore, S. Kubiski, C. Witte, R. Ogden, A. Meredith, O.A. Ryder, C.C. Steiner, J.A. Phillips, M.A. Owen. 2020. Rigorous wildlife disease surveillance. Science 369 (6500). 145-147.

Wilder, A.P., A.Y. Navarro, S.N.D. King, W.B. Miller, S.M. Thomas, C.C. Steiner, O.A. Ryder, D.M. Shier. 2020. Fitness Costs Associated with Ancestry to Isolated Populations of an Endangered Species. Conservation Genetics 21(3). 589-601.

Chen, L., Q. Qiu, Y. Jiang, K. Wang, Z. Lin, Z. Li, F. Bibi, Y. Yang, J. Wang, W. Nie, W. Su, G. Liu, Q. Li, W. Fu, X. Pan, C. Liu, J. Yang, C. Zhang, Y. Yin, Y. Wang, Y. Zhao, C. Zhang, Z. Wang, Y. Qin, W. Liu, B. Wang, Y. Ren, R. Zhang, Y. Zeng, R.R. de Fonseca, B. Wei, R. Li, W. Wan, R. Zhao, W. Zhu, Y. Wang, S. Duan, Y. Gao, Y.E. Zhang, C. Chen, C. Hvilsom, C.W. Epps, L.G. Chemnick, Y. Dong, S. Mirarab, H.R. Siegismund, O.A. Ryder, M.T.P. Gilbert, H.A. Lewin, G. Zhang, R. Heller, W. Wang. 2019. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364(6446). 1152-1166.

Ryder, O.A. 2019. Announcements: In Memory of Kurt Benirschke, MD: Pioneer in mammalian cytogenetics, founder of the Frozen Zoo®, and champion of comparative medicine. Journal of Heredity. DOI: 10.1093/jhered/esz010.

Moodley, Y., I.M. Russo, J. Robovský, D.L. Dalton, A. Kotzé, J. Stejskal, O.A. Ryder, R. Hermes, C. Walzer, M.W. Bruford. 2018. Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum). Proceedings. Biological Sciences. The Royal Society. DOI: 10.1098/rspb.2018.1567.

Palkopoulou, E., M. Lipson, S. Mallick, S. Nielsen, N. Rohland, S. Baleka, E. Karpinski, A.M. Ivancevic, T.H. To, R.D. Kortschak, J.M. Raison, Z. Qu, T.J. Chin, K.W. Alt, S. Claesson, L. Dalen, R.D.E. MacPhee, H. Meller, A.L. Roca, O.A. Ryder, D. Heiman, S. Young, M. Breen, C. Williams, B.L. Aken, M. Ruffier, E. Karlsson, J. Johnson, F. Di Palma, J. Alfoldi, D.L. Adelson, T. Mailund, K. Munch, K. Lindblad-Toh, M. Hofreiter, H. Poinar, D. Reich. 2018. A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1720554115.

Ryder, O.A. 2018. Opportunities and Challenges for Conserving Small Populations: An Emerging Role for Zoos in Genetic Rescue. Pages 255-266 in The Ark and Beyond: The Evolution of Zoo and Aquarium Conservation. Edited by B.A. Minteer, Jane Maienschein, and J.P. Collins. University of Chicago Press, Chicago, Illinois.

Sutton, J.T., M. Helmkampf, C.C. Steiner, M.R. Bellinger, J. Korlach, R. Hall, P. Baybayan, J. Muehling, J. Gu, S. Kingan, B.M. Masuda, O.A. Ryder. 2018. A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaiiʻs Last Remaining Crow Species. Genes 9(8). 393.

Tunstall, T., R. Kock, J. Vahala, M. Diekhans, I. Fiddes, J. Armstrong, B. Paten, O.A. Ryder, C.C. Steiner. 2018. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Research 28. 780-788.

Zepeda Mendoza, M.L., Z. Xiong, M. Escalera-Zamudio, A.K. Runge, J. Thézé, D. Streicker, H.K. Frank, E. Loza-Rubio, S. Liu, O.A. Ryder, J.A. Samaniego Castruita, A. Katzourakis, G. Pacheco, B. Taboada, U. Löber, O.G. Pybus, Y. Li, E. Rojas-Anaya, K. Bohmann, A. Carmona Baez, C.F. Arias, S. Liu, A.D. Greenwood, M.F. Bertelsen, N.E. White, M. Bunce, G. Zhang, T. Sicheritz-Pontén, M.P.T. Gilbert. 2018. Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nature Ecology & Evolution. DOI: 10.1038/s41559-018-0476-8.

Steiner, C.C., M.L. Houck, O.A. Ryder. 2017. Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Conservation Genetics. DOI: 10.1007/s10592-017-1011-1.

Ivy, J.A., A.S. Putnam, A.Y. Navarro, J. Gurr, O.A. Ryder. 2016. Applying SNP-derived molecular ancestry estimates to captive breeding programs. Journal of Heredity 107(5). 403-412.

Li, H., J. Xiang-Yu, G. Dai, Z. Gu, C. Ming, Z. Yang, O.A. Ryder, W.H. Li, Y.X. Fu, Y.P. Zhang. 2016. Large numbers of vertebrates began rapid population decline in the late 19th century. Proceedings of the National Academy of Sciences USA 113. 14079-14084.

Saragusty, J., S. Diecke, M. Drukker, B.S. Durrant, I.F. Ben-Nun, C. Galli, F. Goritz, K. Hayashi, R. Hermes, S. Holtze, S. Johnson, G. Lazzari, P. Loi, J.F. Loring, K. Okita, M.B. Renfree, S. Seet, T. Voracek, J. Stejskal, O.A. Ryder, T.B. Hildebrandt. 2016. Rewinding the Process of Mammalian Extinction. Zoo Biology 9999. 1-13.

Yu, L., G-D. Wang, J. Ruan, Y-B. Chen, C-P. Yang, X. Cao, H. Wu, Y-H. Liu, Z-L. Du, X-P. Wang, J. Yang, S-C. Cheng, L. Zhong, L. Wang, X. Wang, J-Y. Hu, L. Fang, B. Bai, K-L. Wang, N. Yuan, S-F. Wu, B-G. Li, J-G. Zhang, Y-Q. Yang, C-L. Zhang, Y-C. Long, H-S. Li, J-Y. Yang, D.M. Irwin, O.A. Ryder, Y. Li, C-I. Wu, Y-P. Zhang. 2016. Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation. Nature Genetics 48(8). 947-955.

Bosse, M., H-J. Megens, O. Madsen, R.P.M.A. Crooijmans, O.A. Ryder, F. Austerlitz, M.A.M. Groenen, M.A.R. de Cara. 2015. Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations. Genome Research 25. 970-981.

Buchalski, M.R., A.Y. Navarro, W.M. Boyce, T. Winston Vickers, M.W. Tobler, L.A. Nordstrom, J.A. Garcia, D.A. Gille, M.C.T. Penedo, O.A. Ryder, H.B. Ernest. 2015. Genetic population structure of Peninsular bighorn sheep (Ovis canadensis nelsoni) indicates substantial gene flow across US–Mexico border. Biological Conservation 184. 218-228.

Fisch, K.M., C.C. Kozfkay, J.A. Ivy, O.A. Ryder. 2015. Fish hatchery genetic management techniques: Integrating theory with implementation. North American Journal of Aquaculture 77. 343-357.

Koepfli, K.-P., B. Paten, The Genome 10K Community of Scientists, C. Steiner, O. Ryder, S.J. O’Brien. 2015. The genome 10K project: A way forward. Annual Review of Animal Biosciences 3. 57-111.

Nam, K., K. Munch, A. Hobolth, J.Y. Dutheil, K.R. Veeramah, A.E. Woerner, M.F. Hammer, Great Ape Genome Diversity Project, O.A. Ryder, T. Mailund, M.H. Schierup. 2015. Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proceedings of the National Academy of Sciences 112. 6413-6418.

Steiner, C.C., S.J. Charter, N. Goddard, H. Davis, M. Brandt, M.L. Houck, O.A. Ryder. 2015. Chromosomal variation and perinatal mortality in San Diego Zoo Soemmerring’s gazelles. Zoo Biology 9999. 1-11.

Wisely, S.M., O.A. Ryder, J.F. Santymire, Engelhardt, B.J. Novak. 2015. A road map for 21st century genetic restoration: Gene pool enrichment of the black-footed ferret. Journal of Heredity 106. 581-592.

Jarvis, E.D., S. Mirarab, A.J. Aberer, B. Li, P. Houde, C. Li, S.Y.W Ho, B.C. Faircloth, B. Nabholz, J.T. Howard, A. Suh, C.C. Weber, R.R da Fonseca, H. Li, L. Zhou, N Narula, L. Liu, G. Ganapathy, B. Boussau, M.S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W.C. Warren, D. Ray, R.E. Green, M.W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E.P. Derryberry, M.F. Bertelsen, F.H. Sheldon, R.T. Brumfield, C.V. Mello, P.V. Lovell, M. Wirthlin, M.P.C. Schneider, F. Prosdocimi, J.A. Samaniego, A.M.V. Velazquez, A. Alfaro-Nunez, P.F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D.M. Lambert, Q. Zhou, P. Perelman, A.C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F.E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F.K. Barker, K.A. Jonsson, W. Johnson, K.-P. Koepfli, S. O’Brien, D. Haussler, O.A. Ryder, C. Rahbek, E. Willerslev, G.R. Graves, T.C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S.V. Edwards, A. Stamatakis, D.P. Mindell, J. Cracraft, E.L. Braun, T. Warnow, W. Jun, M.T.P. Gilbert, G. Zhang. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346. 1320-1331.

Liu, J., X. Wang, S. Cho, B.K. Lim, D.M. Irwin, O.A. Ryder, Y. Zhang, L. Yu. 2014. Evolutionary and functional novelty of pancreatic ribonuclease: A study of Musteloidea (order Carnivora). . Scientific Reports. DOI: 10.1038/srep05070.

O’Brien, S.J., D. Haussler, O.A. Ryder. 2014. The birds of Genome10K. GigaScience 3. 32.

Steiner, C.C., S.J. Charter, M.L. Houck, O.A. Ryder. 2014. Molecular phylogeny and chromosomal evolution of Alcelaphini (Antilopinae). Journal of Heredity 105. 324-333.

Zhang, G., C. Li, Q. Li, B. Li, D.M. Larkin, C. Lee, J.F. Storz, A. Antunes, M.J. Greenwold, R.W. Meredith, A. Odeen, J. Cui, Q. Zhou, L. Xu, H. Pan, Z. Wang, L. Jin, P. Zhang, H. Hu, W. Yang, J. Hu, J. Xiao, Z. Yang, Y. Liu, Q. Xie, H. Yu, J. Lian, P. Wen, F. Zhang, H. Li, Y. Zeng, Z. Xiong, S. Liu, L. Zhou, Z. Huang, N. An, J. Wang, Q. Zheng, Y. Xiong, G. Wang, B. Wang, J. Wang, Y. Fan, R.R. da Fonseca, A. Alfaro-Nunez, M. Schubert, L. Orlando, T. Mourier, J.T. Howard, G. Ganapathy, A. Pfenning, O. Whitney, M.V. Rivas, E. Hara, J. Smith, M. Farre, J. Narayan, G. Slavov, M.N. Romanov, R. Borges, J.P Machado, I. Khan, M.S. Springer, J. Gatesy, F.G. Hoffmann, J.C. Opazo, O. Hastad, R.H. Sawyer, H. Kim, K.-W. Kim, H.J. Kim, S. Cho, N. Li, Y. Huang, M.W. Bruford, X. Zhan, A. Dixon, M.F. Bertelsen, E. Derryberry, W. Warren, R.K. Wilson, S. Li, D.A. Ray, R.E. Green, S.J O’Brien, D. Griffin, W.E Johnson, D. Haussler, O.A. Ryder, E. Willerslev, G.R. Graves, P. Alstrom, J. Fjeldsa, D.P. Mindell, S.V. Edwards, E.L. Braun, C. Rahbek, D.W. Burt, P. Houde, Y. Zhang, H. Yang, J. Wang, Avian Genome Consortium, E.D. Jarvis, M.T.P. Gilbert, J. Wang, C. Ye, S. Liang, Z. Yan, M.L. Zepeda, P.F. Campos, A.M.V. Velazquez, J.A. Samaniego, M. Avila-Arcos, M.D. Martin, R. Barnett, A.M. Ribeiro, C.V. Mello, P.V. Lovell, D. Almeida, E. Maldonado, J. Pereira, K. Sunagar, S. Philip, M.G Dominguez-Bello, M. Bunce, D. Lambert, R.T. Brumfield, F.H. Sheldon, E.C. Holmes, P.P. Gardner, T.E. Steeves, P.F. Stadler, S.W. Burge, E. Lyons, J. Smith, F. McCarthy, F. Pitel, D. Rhoads, D.P. Froman. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. . Science 346. 1311-1320.

Evans, J.D., S.J. Brown, K.J. Hackett, G. Robinson, S. Richards, D. Lawson, C. Elsik, J. Coddington, O. Edwards, S. Emrich, T. Gabaldon, M. Goldsmith, G. Hanes, B. Misof, M. Munoz-Torres, O. Niehuis, A. Papanicolaou, M. Pfrender, M. Poelchau, M. Purcell-Miramontes, H.M. Robertson, O.A. Ryder, D. Tagu, T. Torres, E. Zdobnov, G. Zhang, X. Zhou. 2013. The i5K Initiative: Advancing arthropod genomics for knowledge, human health, agriculture, and the environment. Journal of Heredity 104. 594-600.

Luan, P.-T., O.A Ryder, H. Davis, Y.-P. Zhang, L. Yu. 2013. Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora). . Molecular Phylogenetics and Evolution 66. 748–756.

Moser, A.B., J. Hey, P.K. Dranchak, M.W. Karaman, J. Zhao, L.A. Cox, O.A. Ryder, J.G. Hacia. 2013. Diverse captive non-human primates with phytanic acid-deficient diets rich in plant products have substantial phytanic acid levels in their red blood cells. Lipids in Health and Disease. DOI: 10.1186/1476-511X-12-10.

Orlando, L., A. Ginolhac, G. Zhang, D. Froese, A. Albrechtsen, M. Stiller, M. Schubert, E. Cappellini, B. Petersen, I. Moltke, P.L. Johnson, M. Fumagalli, J.T. Vilstrup, M. Raghavan, T. Korneliussen, A.S. Malaspinas, J. Vogt, D. Szklarczyk, C.D. Kelstrup, J. Vinther, A. Dolocan, J. Stenderup, A.M. Velazquez, J. Cahill, M. Rasmussen, X. Wang, J. Min, G.D. Zazula, A. Seguin-Orlando, C. Mortensen, K. Magnussen, J.F. Thompson, J. Weinstock, K. Gregersen, K.H. Roed, V. Eisenmann, C.J. Rubin, D.C. Miller, D.F. Antcza, M.F. Bertelsen, S. Brunak, K.A. Al-Rasheid, O.A. Ryder, L. Andersson, J. Mundy, A. Krogh, M.T. Gilbert, K. Kjær, T. Sicheritz-Ponten, L.J. Jensen, J.V. Olsen, M. Hofreiter, R. Nielsen, B. Shapiro, J. Wang, E. Willerslev. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499. 74-78.

Prado-Martinez, J., P.H. Sudmant, J.M. Kidd, H. Li, J.L. Kelley, B. Lorente-Galdos, K.R. Veeramah, A.E. Woerner, T.D. O’Connor, G. Santpere, A. Cagan, C. Theunert, F. Casals, H. Laayouni, K. Munch, A. Hobolth, A.E. Halager, M. Malig, J. Hernandez-Rodriguez, I. Hernando-Herraez, K. Prufer, M. Pybus, L. Johnstone, M. Lachmann, C. Alkan, D. Twigg, N. Petit, C. Baker, F. Hormozdiari, M. Fernandez-Callejo, M. Dabad, M.L. Wilson, L. Stevison, C. Camprubí, T. Carvalho, A. Ruiz-Herrera, L. Vives, M. Mele, T. Abello, I. Kondova, R.E. Bontrop, A. Bontrop, F. Lankester, J.A. Kiyang, R.A. Bergl, E. Lonsdorf, S. Myers, M. Ventura, P. Gagneux, D. Comas, H. Siegismund, J. Blanc, L. Agueda-Calpena, M. Gut, L. Fulton, S.A. Tishkoff, J.C. Mullikin, R.K. Wilson, I.G. Gut, M.K. Gonder, O.A. Ryder, B.H. Hahn, A. Navarro, J.M. Akey, J. Bertranpetit, D. Reich, T. Mailund, M.H. Schierup, C. Hvilsom, A.M. Andres, J.D. Wall, C.D. Bustamante, M.F. Hammer, E.E. Eichler, T. Marques-Bonet. 2013. Great ape genetic diversity and population history. Nature 499. 471-475.

Steiner, C.C, O.A. Ryder. 2013. Characterization of Prdm9 in equids and sterility in mules. PLoS One 8. e61746.

Steiner, C.C, A.S. Putnma, P.E.A. Hoeck, O.A. Ryder. 2013. Conservation genomics of threatened animal species. Annual Review of Animal Biosciences 1. 261-281.

Bernardi, G., E.O. Wiley, H. Mansour, M.R. Miller, G. Orti, D. Haussler, S.J. O’Brien, O.A. Ryder, B. Venkatesh. 2012. The fishes of Genome 10K. Marine Genomics 7. 3-6.

Dennis, P., S. Ellis, J. Mellen, P. Lee, F. Olea-Popelka, A. Petric, O.A. Ryder. 2012. IOD in rhinos--epidemiology group report: Report from the epidemiology working group of the international workshop on iron overload disorder in browsing rhinoceros (February 2011). . Journal of Zoo and Wildlife Medicine 43. 114-116.

Frankham, R., J.D. Ballou, M.R. Dudash, M.D.B. Eldridge, C.B. Fenster, R.C. Lacy, J.R. Mendelson, I.J. Porton, K. Ralls, O.A. Ryder. 2012. Implications of different species concepts for conserving biodiversity. . Biological Conservation 153. 25-31.

McCue, M.E., D.L. Bannasch, J.L. Petersen, J. Gurr, E. Bailey, M.M Binns, O. Distl, G. Guerin, T. Hasegawa, E.W. Hill, T. Leeb, G. Lindgren, M.C.T. Penedo, K.H. Roed, O.A. Ryder, J.E. Swinburne, T. Tozaki, S.J. Valberg, M. Vaudin, K. Lindblad-Toh, C.M. Wade, J.R. Mickelson. 2012. A high density SNP array for the domestic horse and extant Perissodactyla: Utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genetics 8. e1002451.

Ryder, O.A. 2012. The Frozen Zoo. GeneWatch 25. 19-20.

Scally, A., J.Y. Dutheil, L.W. Hillier, G.E. Jordan, I. Goodhead, J. Herrero, A. Hobolth, T. Lappalainen, T. Mailund, T. Marques-Bonet, S. McCarthy, S.H. Montgomery, P.C. Schwalie, Y.A. Tang, M.C. Ward, Y. Xue, B. Yngvadottir, C. Alkan, L.N. Andersen, Q. Ayub, E.V. Ball, K. Beal, B.J. Bradley, Y. Chen, C.M. Clee, S. Fitzgerald, T.A. Graves, Y. Gu, P. Heath, A. Heger, E. Karakoc, A. Kolb-Kokocinski, G.K. Laird, G. Lunter, S. Meader, M. Mort, J.C. Mullikin, K. Munch, T.D. O’Connor, A.D. Phillips, J. Prado-Martinez, A.S. Rogers, S. Sajjadian, D. Schmidt, K. Shaw, J.T. Simpson, P.D. Stenson, D.J. Turner, L. Vigilan, A.J. Vilella, W. Whitener, B. Zhu, D.N. Cooper, P. de Jong, E.T. Dermitzakis, E.E. Eichler, P. Flicek, N. Goldman, N.I. Mundy, Z. Ning, D.T. Odom, C.P. Ponting, M.A. Quail, O.A. Ryder, S.M. Searle, W.C. Warren, R.K. Wilson, M.H. Schierup, J. Rogers, C. Tyler-Smith, R. Durbin. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483. 169-175.

Springer, M.S., R.W. Meredith, J. Gatesy, C.A. Emerling, J. Park, D.L. Rabosky, T. Stadler, C. Steiner, O.A. Ryder, J.E. Janecka, C.A. Fisher, W.J. Murphy. 2012. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One  7. e49521.

Steiner, C.C, A. Mitelberg, R. Tursi, O.A. Ryder. 2012. Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies. . Molecular Phylogenetics and Evolution 65. 573-581.

Walker, J.A., M.K. Konkel, B. Ullmer, C.P. Monceaux, O.A. Ryder, R. Hubley, A.F. Smit, M.A. Batzer. 2012. Orangutan Alu quiescence reveals possible source element: Support for ancient backseat drivers. Mobile DNA . DOI: 10.1186/1759-8753-3-8.

Wong, P.B.Y., E.O. Wiley, W.E. Johnson, O.A. Ryder, S.J. O’Brien, D. Haussler, K.-P. Koepfli, M.L. Houck, P. Perelman, G. Mastromonaco, A.C. Bentley, B. Venkatesh, Y-P. Zhang, R.W. Murphy, G10KCOS. 2012. Tissue sampling methods and standards for vertebrate genomics. GigaScience. DOI: 10.1186/2047-217X-1-8.

Ben-Nun, I.F., S.C. Montague, M.L. Houck, H.T. Tran, I. Garitaonandia, T.R. Leonardo, Y.-C. Wang, S.J. Charter, L.C. Laurent, O.A. Ryder, J.F. Loring. 2011. Induced pluripotent stem cells from highly endangered species. . Nature Methods 8. 829-831.

Gazave, E., F. Darre, C. Morcillo-Suarez, N. Petit-Marty, A. Carreno, U.M. Marigorta, O.A. Ryder, A. Blancher, M. Rocchi, E. Bosch, C. Baker, T. Marques-Bonet, E.E. Eichler, A. Navarro. 2011. Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Research  21. 1626-1639.

Gomes, N.M.V., O.A. Ryder, M.L. Houck, S.J. Charter, W. Walker, N.R. Forsyth, S.N. Austad, C. Venditti, M. Pagel, J.W. Shay, W.E. Wright. 2011. Comparative biology of mammalian telomeres: Hypotheses on ancestral states and the roles of telomeres in longevity determination. Aging Cell 10. 761-768.

Goto, H., O.A. Ryder, A.R. Fisher, B. Schultz, S.K. Pond, A. Nekrutenko, K.D. Makova. 2011. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski’s horses. Genome Biology and Evolution 3. 1096-1106.

Kulemzina, A.I., F. Yang, V.A. Trifonov, O.A. Ryder, M.A. Ferguson-Smith, A.S. Graphodatsky. 2011. Chromosome painting in Tragulidae facilitates the reconstruction of Ruminantia ancestral karyotype. Chromosome Research 19. 531-539.

Locke, D.P., L.W. Hillier, W.C. Warren, K.C. Worley, L.V. Nazareth, D.M. Muzny, S.-P. Yang, A.T. Chinwalla, P. Minx, M. Mitreva, L. Cook, K.D. Delehaunty, C. Fronick, H. Schmidt, L.A Fulton, R.S. Fulton, J.O. Nelson, V. Magrini, C. Pohl, T.A. Graves, C. Markovic, A Cree, H.H Dinh, J. Hume, C.L. Kovar, G.R. Fowler, G. Lunter, S. Meader, A. Heger, C.P. Ponting, T. Marques-Bonet, C. Alkan, L. Chen, Z. Cheng, J.M. Kidd, E.E. Eichler, S. White, S. Searle, A.J. Vilella, Y. Chen, P. Flicek, J. Ma, B. Raney, B. Suh, R. Burhans, J. Herrero, D. Haussler, R. Faria, O. Fernando, F. Darre, D. Farre, E. Gazave, M. Oliva, A. Navarro, R. Roberto, O. Capozzi, N. Archidiacono, G.D. Valle, S. Purgato, M. Rocchi, M.K. Konkel, J.A. Walker, B. Ullmer, M.A. Batzer, A.F.A Smit, R. Hubley, C. Casola, D.R. Schrider, M.W. Hahn, V. Quesada, X.S. Puente, G.R. Ordonez, C. Lopez-Otin, T. Vinar, B. Brejova, A. Ratan, R.S. Harris, W. Miller, C. Kosiol, H.A. Lawson, V. Taliwal, A.L. Martins, A. Siepel, A. RoyChoudhury, X. Ma, J. Degenhardt, C.D. Bustamante, R.N. Gutenkunst, T. Mailund, J.Y. Dutheil, A. Hobolth, M.H. Schierup, O.A. Ryder, Y. Yoshinaga, P.J. de Jong, G.M. Weinstock, J. Rogers, E.R. Mardis, R.K. Gibbs, R.K. Wilson. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469. 529-533.

Meredith, R.W., J.E. Janecka, J. Gatesy, O.A. Ryder, C.A Fisher, E.C. Teeling, A. Goodbla, E. Eizirik, T.L.L. Simao, T. Stadler, D.L. Rabosky, R.L. Honeycutt, J.J. Flynn, C.M. Ingram, C. Steiner, T.L. Williams, T.J. Robinson, A. Burk-Herrick, M. Westerman, N.A. Ayoub, M.S. Springer, W.J. Murphy. 2011. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334. 521-524.

Moser, A.B., S.J. Steinberg, P.A. Watkins, H.W. Moser, K. Ramaswamy, K.D. Siegmund, D.R. Lee, J.J. Ely, O.A. Ryder, J.G. Hacia. 2011. Human and great ape red blood cells differ in plasmalogen levels and composition. Lipids in Health and Disease. DOI: 10.1186/1476-511X-10-101.

Steiner, C.C., O.A. Ryder. 2011. Molecular phylogeny and evolution of the Perissodactyla. Zoological Journal of the Linnean Society 163. 1289-1303.

Steiner, C.C, M.L. Houck, O.A. Ryder. 2011. Species identification and chromosome variation of captive two-toed sloths. Zoo Biology 30. 623-635.

Yu, L., D. Peng, J. Liu, L. Luan, M. Lee, O.A. Ryder, Y. Zhang. 2011. On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes. BMC Evolutionary Biology . DOI: 10.1186/1471-2148-11-92.

Yu, L., P-T. Luan, W. Jin, O.A. Ryder, L.G. Chemnick, H.A. Davis, Y.-P. Zhang. 2011. Phylogenetic utility of nuclear introns in interfamilial relationships of Caniformia (order Carnivora). Systematic Biology 6. 175-187.

Alkan, C., M.F. Cardone, C.R. Catacchio, F. Antonacci, S.J. O’Brien, O.A. Ryder, S. Purgato, M. Zoli, G Della Valle, E.E. Eichler, M. Ventura. 2010. Genome-wide characterization of centromeric satellites from multiple mammalian genomes. Genome Research 21. 137-145.

Ellstrand, N.C., D. Biggs, A. Kaus, P. Lubinsky, L.A. McDade, K. Preston, L.M. Prince, H.M. Regan, V. Roriver, O.A. Ryder, K.A. Schierenbeck. 2010. Got hybridization? A multidisciplinary approach for informing science policy. BioScience 60. 384-388.

Puppione, D.L., C.M. Ryan, S. Bassilian, P. Souda, X. Souda, O.A. Ryder, J.P. Whitelegge. 2010. Detection of two distinct forms of apoC-I in great apes. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 5. 73-79.

Watkins, P.A., A.B. Moser, C.B. Toomer, S.J. Steinberg, H.W. Moser, M.W. Karaman, K. Ramaswamy, K.D. Siegmund, D.R. Lee, J.J. Ely, O.A. Ryder, J.G. Hacia. 2010. Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions. BMC Physiology. DOI: 10.1186/1472-6793-10-19.

Amato, G., R. DeSalle, O.A. Ryder, H.C. Rosenbaum. 2009. Conservation genetics in the age of genomics. Edited by G. Amato, R. DeSalle, O.A. Ryder, and H.C. Rosenbaum. Columbia University Press, New York, New York. 264 pp.

Chemnick, L.G., M.L. Houck, O.A. Ryder. 2009. Banking of genetic resources: The Frozen Zoo at the San Diego Zoo. Conservation Genetics in the Age of Genomics. Edited by G. Amato, R. DeSalle, O.A. Ryder, and H.C. Rosenbaum. Columbia University Press, New York, New York/United States of America.

Haussler, D., S.J. O'Brien, O.A. Ryder, F.K. Barker, M. Clamp, A.J. Crawford, R. Hanner, O. Hanotte, W.E. Johnson, J.A. McGuire, W. Miller, R.W. Murphy, W.J. Murphy, F.H. Sheldon, B. Sinervo, B. Venkatesh, E.O. Wiley, F.W. Allendorf, G. Amato, C.S. Baker, A. Bauer, A. Beja-Pereira, E. Bermingham, G. Bernardi, C.R. Bonvicino, S. Brenner, T. Burke, J. Cracraft, M. Diekhans, S. Edwards, P.G. Ericson, J. Estes, J. Fjelsda, N. Flesness, T. Gamble, P. Gaubert, A.S. Graphodatsky, J.A. Marshall Graves, E.D. Green, R.E. Green, S. Hackett, P. Hebert, K.M. Helgen, L. Joseph, B. Kessing, D.M. Kingsley, H.A. Lewin, G. Luikart, P. Martelli, M.A. Moreira, N. Nguyen, G. Ortí, B.L. Pike, D.M. Rawson, S.C. Schuster, H.N. Seuanez, H.B. Shaffer, M.S. Springer, J.M. Stuart, J. Sumner, E. Teeling, R.C. Vrijenhoek, R.D. Ward, W.C. Warren, R. Wayne, T.M. Williams, N.D. Wolfe, Y.P. Zhang. 2009. Genome 10K: A proposal to obtain whole-genome sequence for 10,000 vertebrate species. Journal of Heredity 100. 659-674.

Jing, J., K. Han, J. Xing, H-S. Kim, J. Rogers, O.A. Ryder, T. Disotell, B. Yue, M.A. Batzer. 2009. Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 448. 242-249.

Lau, J., A.C. Alberts, L.G. Chemnick, G.P. Gerber, K.C. Jones, A.A. Mitchell, O.A. Ryder. 2009. Isolation and characterization of 23 polymorphic microsatellite loci for a West Indian iguana (Cyclura pinguis) from the British Virgin Islands.  Molecular Ecology Resources 9. 1412-1414.

Lermen, D., B. Blomeke, R. Browne, A. Clarke, P.W. Dyce, T. Fixemer, G.R. Fuhr, W.V. Holt, K. Jewgenow, R.E. Lloyd, S. Lötters, M. Paulus, G.M. Reid, D.H. Rapoport, D. Rawson, J. Ringleb, O.A. Ryder, G. Sporl, T. Schmitt, M. Veith, P. Muller. 2009. Cryobanking of viable biomaterials: Implementation of new strategies for conservation purposes. Molecular Ecology 18. 1030-1033.

Li, R., W. Fan, G. Tian, H. Zhu, L. He, J. Cai, Q. Huang, Q. Cai, B. Li, Y. Bai, Z. Zhang, Y. Zhang, W. Wang, J. Li, F. Wei, H. Li, M. Jian, J. Li, Z. Zhang, R. Nielsen, D. Li, W. Gu, Z. Yang, Z. Xuan, O.A. Ryder, F.C.-C. Leung, Y. Zhou, J. Cao, X. Sun, Y. Fu, X. Fang, X. Guo, B. Wang, R. Hou, F. Shen, B. Mu, P. Ni, R. Lin, W. Qian, G. Wang, C. Yu, W. Nie, J. Wang, Z. Wu, H. Liang, J. Min, Q. Wu, S. Cheng, J. Ruan, M. Wang, Z. Shi, M. Wen, B. Liu, X. Ren, H. Zheng, D. Dong, K. Cook, G. Shan, H. Zhang, C. Kosiol, X. Xie, Z. Lu, H. Zheng, Y. Li, C.C. Steiner, T.T.-Y. Lam, S. Lin, Q. Zhang, G. Li, J. Tian, T. Gong, H. Liu, D. Zhang, L. Fang, C. Ye, J. Zhang, W. Hu, A. Xu, Y. Ren, G. Zhang, M.W. Bruford, Q. Li, L. Ma, Y. Guo, N. An, Y. Hu, Y. Zheng, Y. Shi, Z. Li, Q. Liu, Y. Chen, J. Zhao, N. Qu, S. Zhao, F. Tian, X. Wang, H. Wang, L. Xu, X. Liu, T. Vinar, Y. Wang, T.-W. Lam, S.-M. Yiu, S. Liu, H. Zhang, D. Li, Y. Huang, X. Wang, G. Yang, Z. Jiang, J. Wang, N. Qin, L. Li, J. Li, L. Bolund, K. Kristiansen, G.K.-S. Wong, M. Olson, X. Zhang, S. Li, H. Yang, J. Wang, J. Wang. 2009. The sequence and de novo assembly of the giant panda genome. Nature 463. 311-317.

Marques-Bonet, T., O.A. Ryder, E.E. Eichler. 2009. Sequencing primate genomes: What have we learned? Annual Review of Genomics and Human Genetics 10. 355-386.

Meredith, R.W., J. Gatesy, W.J. Murphy, O.A. Ryder, M.S. Springer. 2009. Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS Genetics  5. e1000634.

Modi, W.S., M. Romanov, E.D. Green, O.A. Ryder. 2009. Molecular cytogenetics of the California condor: Evolutionary and conservation implications. Cytogenetic and Genome Research 2009. 26-32.

Nsubuga, A.M., J. Holzman, L.G. Chemnick, O.A. Ryder. 2009. The cryptic genetic structure of the North American captive gorilla population. Conservation Genetics 11. 161-172.

Pessier, A., J. Mendelson, O.A. Ryder. 2009. Amphibian disease testing and bioresource banking at the San Diego Zoo. Connect 51.

Piras, F.M., S.G. Nergadze, V. Poletto, F. Cerutti, O.A. Ryder, T. Leeb, E. Raimondi, E. Giulotto. 2009. Phylogeny of horse chromosome 5q in the genus Equus and centromere repositioning. Cytogenetic and Genome Research 126. 165-172.

Puppione, D.L., L.D. Donna, A.D. Laganowsky, S. Bassilian, P. Souda, O.A. Ryder, J.P. Whitelegge. 2009. Mass spectral analyses of the two major apolipoproteins of great ape high density lipoproteins. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics 4. 305-309.

Rogers, D.L., C.O. Qualset, P.E. McGuire, O.A. Ryder. 2009. The silent biodiversity crisis: Loss of genetic resource collections. Pages 141-59 in Conservation Genetics in the Age of Genomics. Edited by G. Amato, R. DeSalle, O.A. Ryder, and H.C. Rosenbaum. Columbia University Press, New York, New York/United States of America.

Romanov, M.N., E.M. Tuttle, M.L. Houck, W.S. Modi, L.G. Chemnick, M.L. Korody, E.M.S. Mork, C.A. Otten, T. Renner, K.C. Jones, S. Dandekar, J.C. Papp, Y. Da, E.D. Green, V. Magrini, M.T. Hickenbotham, J. Glasscock, S. McGrath, E.R. Mardis, O.A. Ryder. 2009. The value of avian genomics to the conservation of wildlife. BMC Genomics. DOI: 10.1186/1471-2164-10-S2-S10.

Ryder, O.A., C.C. Steiner. 2009. How much hybridization and in what direction? Animal Conservation 12. 516-517.

Ryder, O.A. 2009. Forests of the night: Refugia of genetic diversity in wild tigers. PLoS Genetics 5. e1000603.

Wade, C.M., E. Giulotto, S. Sigurdsson, M. Zoli, S. Gnerre, F. Imsland, T.L. Lear, D.L. Adelson, E. Bailey, R.R. Bellone, H. Blocker, O. Distl, R.C. Edgar, M. Garber, T. Leeb, E. Mauceli, J.N. MacLeod, M.C.T. Penedo, J.M. Raison, T. Sharpe, J. Vogel, L. Andersson, D.F. Antczak, T. Biagi, M.M. Binns, B.P. Chowdhary, S.J. Coleman, G. Della Valle, S. Fryc, G. Guerin, T. Hasegawa, E.W. Hill, J. Jurka, A. Kiialainen, G. Lindgren, J. Liu, E. Magnani, J.R. Mickelson, J. Murray, S.G. Nergadze, R. Onofrio, S. Pedroni, M.F. Piras, T. Raudsepp, M. Rocchi, K.H. Roed, O.A. Ryder, S. Searle, L. Skow, J.E. Swinburne, A.C. Syvanen, T. Tozaki, S.J. Valberg, M. Vaudin, J.R. White, M.C. Zody, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, E.S. Lander, K. Lindblad-Toh. 2009. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326. 865-867.

Lau, A.N., L. Peng, H. Goto, L.G. Chemnick, O.A. Ryder, K.D. Makova. 2008. Horse domestication and conservation genetics of Przewalski’s horse inferred from sex chromosomal and autosomal sequences. Molecular Biology and Evolution 26. 199-208.

Yu, L., J. Liu, P.-tao. Luan, H. Lee, M. Lee, M-S. Min, O.A. Ryder, L.G. Chemnick, H. Davis, Y.-P. Zhang. 2008. New insights into the evolution of intronic sequences of the beta-fibrinogen gene and their application in reconstructing mustelid phylogeny. Zoological Science 25. 662-672.

Baena, A., A.R. Mootnick, J.V. Falvo, A.V. Tsytsykova, F. Ligeiro, O.M. Diop, C. Brieva, P. Gagneux, S.J. O’Brien, O.A. Ryder, A.E. Goldfeld. 2007. Primate TNF promoters reveal markers of phylogeny and evolution of innate immunity. . PLOS ONE 2. e621.

Pan, D., J.-H. Chen, C. Groves, Y.-X. Wang, E. Narushima, H. Fitch-Snyder, P. Crow, X. Jinggong, V.N. Thanh, O.A. Ryder, L.G. Chemnick, H.-W. Zhang, Y.-X. Fu, Y.-P. Zhang. 2007. Mitochondrial control region and population genetic patterns of Nycticebus bengalensis and N. pygmaeus. International Journal of Primatology 28. 791-799.

Schmidt, C.J., M. Romanov, O.A. Ryder, V. Magrini, M. Hickenbotham, J. Glasscock, S. McGrath, E. Mardis, L.D. Stein. 2007. Gallus GBrowse: A unified genomic database for the chicken. Nucleic Acids Research 36. D719-D723.

Yu, L., Y.-W. Li, O.A. Ryder, Y.-P. Zhang. 2007. Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evolutionary Biology. DOI: 10.1186/1471-2148-7-198.

Amor, D.C., S.O. Kolokotronis, R.R. Ramey, R.A. Medellin, O.A. Ryder. 2006. Genética de la conservación del berrendo. El Berrendo En México: Acciones De Conservación. Edited by P.R. Gil. Instituto Nacional de Ecología (INE-Semarnat), Mexico, Mexico.

Chen, J.-H., D. Pan, C. Groves, Y.-X. Wang, E. Narushima, H. Fitch-Snyder, P. Crow, V.N. Thanh, O.A. Ryder, H.-W. Zhang, Y.-X. Fu, Y.-P. Zhang. 2006. Molecular phylogeny of Nycticebus inferred from mitochondrial genes. International Journal of Primatology 27. 1187-1200.

David, V.A., S. Sun, Z. Zhang, F. Shen, G. Zhong, H. Zhang, Z. Xie, Y.-P. Zhang, O.A. Ryder, S. Ellis, D.E. Wildt, A. Zhang, S.J. O’Brien. 2006. Parentage assessment among captive giant pandas in China. . Giant Pandas: Biology, Veterinary Medicine and Management. Edited by D.E. Wildt, A. Zhang, H. Zhang, D.L. Janssen, and S. Ellis. Cambridge University Press, New York, New York/United States of America.

Dorus, S., J.R. Anderson, E.J. Vallender, S.L. Gilbert, L. Zhang, L.G. Chemnick, O.A. Ryder, W. Li, B.T. Lahn. 2006. Sonic Hedgehog, a key development gene, experienced intensified molecular evolution in primates. Human Molecular Genetics 15. 2031-2037.

Dulloo, E., Y. Nagamura, O.A. Ryder. 2006. DNA storage as a complementary conservation strategy. DNA Banks — providing novel options for genebanks. Edited by M.C. de Vicente, and M.S. Andersson. International Plant Genetic Resources Institute, Rome, Italy.

Durnin, M.E., P.J. Palsbøll, O.A. Ryder, D.R. McCullough. 2006. A reliable genetic technique for sex determination of giant panda (Ailuropoda melanoleuca) from non-invasively collected hair samples. Conservation Genetics 8. 715-720.

Houck, M.L., O.A. Ryder. 2006. Order Perissodactyla introduction. Atlas of Mammalian Chromosomes. Edited by S.J. O’Brien, J.C. Menninger, and W.G. Nash. Wiley, Somerset, New Jersey/United States of America.

Houck, M.L., O.A. Ryder. 2006. Die Genetik der Tapiridae. Die Tapire. Edited by S. Todd, and U. Ganslosser. Filander Verlag, Furth, Germany.

Houck, M.L., O.A. Ryder. 2006. Die Genetik der Tapiridae. Pages 47-58 in Die Tapire. Edited by S. Todd, and U. Ganslosser. Filander Verlag, Furth, Germany.