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Publications

The following papers were produced by members of the Jarvis Lab or in collaboration with the Jarvis Lab. They are available for downloading.

2021

  • Towards Complete and Error-Free Genome Assemblies of All Vertebrate Species. Rhie, Arang, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O’Brien, Jonas Korlach, Harris A. Lewin, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, and Erich D. Jarvis. 2021. Towards Nature 592(7856):737–46. 

  • Universal Nomenclature for Oxytocin–Vasotocin Ligand and Receptor Families. Theofanopoulou, Constantina, Gregory Gedman, James A. Cahill, Cedric Boeckx, and Erich D. Jarvis. 2021. Nature 592(7856):747–55. 

  • Evolutionary and Biomedical Insights from a Marmoset Diploid Genome Assembly. Yang, Chentao, Yang Zhou, Stephanie Marcus, Giulio Formenti, Lucie A. Bergeron, Zhenzhen Song, Xupeng Bi, Juraj Bergman, Marjolaine Marie C. Rousselle, Chengran Zhou, Long Zhou, Yuan Deng, Miaoquan Fang, Duo Xie, Yuanzhen Zhu, Shangjin Tan, Jacquelyn Mountcastle, Bettina Haase, Jennifer Balacco, Jonathan Wood, William Chow, Arang Rhie, Martin Pippel, Margaret M. Fabiszak, Sergey Koren, Olivier Fedrigo, Winrich A. Freiwald, Kerstin Howe, Huanming Yang, Adam M. Phillippy, Mikkel Heide Schierup, Erich D. Jarvis, and Guojie Zhang. 2021. Nature. 

  • Complete Vertebrate Mitogenomes Reveal Widespread Repeats and Gene Duplications. Formenti, Giulio, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S. Horner, Eugene Myers, Richard Durbin, Alessandro Achilli, Edward L. Braun, Adam M. Phillippy, and Erich D. Jarvis. 2021. Genome Biology 22(1):120. 

  • Extended Haplotype-Phasing of Long-Read de Novo Genome Assemblies Using Hi-C. Kronenberg, Zev N., Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, David Porubsky, Kristen Kuhn, Kathryn A. Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo, Ivan Liachko, Richard J. Hall, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Timothy P. L. Smith, Erich D. Jarvis, Shawn T. Sullivan, and Sarah B. Kingan. 2021. Nature Communications 12(1):1935. 

  • Platypus and Echidna Genomes Reveal Mammalian Biology and Evolution.  Zhou, Yang, Linda Shearwin-Whyatt, Jing Li, Zhenzhen Song, Takashi Hayakawa, David Stevens, Jane C. Fenelon, Emma Peel, Yuanyuan Cheng, Filip Pajpach, Natasha Bradley, Hikoyu Suzuki, Masato Nikaido, Joana Damas, Tasman Daish, Tahlia Perry, Zexian Zhu, Yuncong Geng, Arang Rhie, Ying Sims, Jonathan Wood, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Qiye Li, Huanming Yang, Jian Wang, Stephen D. Johnston, Adam M. Phillippy, Kerstin Howe, Erich D. Jarvis, Oliver A. Ryder, Henrik Kaessmann, Peter Donnelly, Jonas Korlach, Harris A. Lewin, Jennifer Graves, Katherine Belov, Marilyn B. Renfree, Frank Grutzner, Qi Zhou, and Guojie Zhang. (2021) Nature.

  • Estrogen and Sex-Dependent Loss of the Vocal Learning System in Female Zebra Finches. Choe, Ha Na, Jeevan Tewari, Kevin W. Zhu, Matthew Davenport, Hiroaki Matsunami, and Erich D. Jarvis. (2021) Hormones and Behavior 129:104911.

  • A Spatially Resolved Brain Region- and Cell Type-Specific Isoform Atlas of the Postnatal Mouse Brain. Joglekar, Anoushka, Andrey Prjibelski, Ahmed Mahfouz, Paul Collier, Susan Lin, Anna Katharina Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, Ashley Hayes, Jennifer G. Chew, Neil I. Weisenfeld, Man Ying Wong, Alexander N. Stein, Simon A. Hardwick, Toby Hunt, Qi Wang, Christoph Dieterich, Zachary Bent, Olivier Fedrigo, Steven A. Sloan, Davide Risso, Erich D. Jarvis, Paul Flicek, Wenjie Luo, Geoffrey S. Pitt, Adam Frankish, August B. Smit, M. Elizabeth Ross, and Hagen U. Tilgner. (2021) Nature Communications 12(1):1–16. Supplementary Information

  • A New Duck Genome Reveals Conserved and Convergently Evolved Chromosome Architectures of Birds and Mammals. Li, Jing, Jilin Zhang, Jing Liu, Yang Zhou, Cheng Cai, Luohao Xu, Xuelei Dai, Shaohong Feng, Chunxue Guo, Jinpeng Rao, Kai Wei, Erich D. Jarvis, Yu Jiang, Zhengkui Zhou, Guojie Zhang, and Qi Zhou. (2021) GigaScience 10(1):1–15.

2020

  • Adaptive Radiation Genomics of Two Ecologically Divergent Hawai’ian Honeycreepers: The ’akiapōlCrossed D Sign ’Au and the Hawai’i ’Amakihi. Campana, Michael G., André Corvelo, Jennifer Shelton, Taylor E. Callicrate, Karen L. Bunting, Bridget Riley-Gillis, Frank Wos, Justin Degrazia, Erich D. Jarvis, and Robert C. Fleischer. (2020) Journal of Heredity 111(1):21–32.

  • Tempo and Pattern of Avian Brain Size Evolution. Ksepka, Daniel T., Amy M. Balanoff, N. Adam Smith, Gabriel S. Bever, Bhart Anjan S. Bhullar, Estelle Bourdon, Edward L. Braun, J. Gordon Burleigh, Julia A. Clarke, Matthew W. Colbert, Jeremy R. Corfield, Federico J. Degrange, Vanesa L. De Pietri, Catherine M. Early, Daniel J. Field, Paul M. Gignac, Maria Eugenia Leone Gold, Rebecca T. Kimball, Soichiro Kawabe, Louis Lefebvre, Jesús Marugán-Lobón, Carrie S. Mongle, Ashley Morhardt, Mark A. Norell, Ryan C. Ridgely, Ryan S. Rothman, R. Paul Scofield, Claudia P. Tambussi, Christopher R. Torres, Marcel van Tuinen, Stig A. Walsh, Akinobu Watanabe, Lawrence M. Witmer, Alexandra K. Wright, Lindsay E. Zanno, Erich D. Jarvis, and Jeroen B. Smaers. (2020) Current Biology 30(11):2026-2036.e3.

  • Building Genomic Infrastructure: Sequencing Platinum-Standard Reference-Quality Genomes of All Cetacean Species. Morin, Phillip A., Alana Alexander, Mark Blaxter, Susana Caballero, Olivier Fedrigo, Michael C. Fontaine, Andrew D. Foote, Shigehiro Kuraku, Brigid Maloney, Morgan L. McCarthy, Michael R. McGowen, Jacquelyn Mountcastle, Mariana F. Nery, Morten Tange Olsen, Patricia E. Rosel, and Erich D. Jarvis. (2020) Marine Mammal Science 36(4):1356–66.

  • Reference Genome and Demographic History of the Most Endangered Marine Mammal, the Vaquita. Morin, Phillip A., Frederick I. Archer, Catherine D. Avila, Jennifer R. Balacco, Yury V. Bukhman, William Chow, Olivier Fedrigo, Giulio Formenti, Julie A. Fronczek, Arkarachai Fungtammasan, Frances M. D. Gulland, Bettina Haase, Mads Peter Heide-Jorgensen, Marlys L. Houck, Kerstin Howe, Ann C. Misuraca, Jacquelyn Mountcastle, Whitney Musser, Sadye Paez, Sarah Pelan, Adam Phillippy, Arang Rhie, Jacqueline Robinson, Lorenzo Rojas-Bracho, Teri K. Rowles, Oliver A. Ryder, Cynthia R. Smith, Sacha Stevenson, Barbara L. Taylor, Jonas Teilmann, James Torrance, Randall S. Wells, Andrew J. Westgate, and Erich D. Jarvis. (2020) Molecular Ecology Resources (September):1–13.

  • Progressive Cactus Is a Multiple-Genome Aligner for the Thousand-Genome Era. Armstrong, Joel, Glenn Hickey, Mark Diekhans, Ian T. Fiddes, Adam M. Novak, Alden Deran, Qi Fang, Duo Xie, Shaohong Feng, Josefin Stiller, Diane Genereux, Jeremy Johnson, Voichita Dana Marinescu, Jessica Alföldi, Robert S. Harris, Kerstin Lindblad-Toh, David Haussler, Elinor Karlsson, Erich D. Jarvis, Guojie Zhang, and Benedict Paten. (2020) Nature 587(7833):246–51.

  • Dense Sampling of Bird Diversity Increases Power of Comparative Genomics. Feng, Shaohong, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant C. Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, Mark Diekhans, Wanjun Chen, Sergio Andreu-Sánchez, Ashot Margaryan, Jason Travis Howard, Carole Parent, George Pacheco, Mikkel Holger S. Sinding, Lara Puetz, Emily Cavill, Ângela M. Ribeiro, Leopold Eckhart, Jon Fjeldså, Peter A. Hosner, Robb T. Brumfield, Les Christidis, Mads F. Bertelsen, Thomas Sicheritz-Ponten, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul J. Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A. Ryder, Jérôme Fuchs, Michael Bunce, David W. Burt, Joel Cracraft, Guanliang Meng, Shannon J. Hackett, Peter G. Ryan, Knud Andreas Jønsson, Ian G. Jamieson, Rute R. da Fonseca, Edward L. Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B. Frandsen, Henriette van der Zwan, Rencia van der Sluis, Carina Visser, Christopher N. Balakrishnan, Andrew G. Clark, John W. Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B. Sackton, Scott V. Edwards, Dustin J. Foote, Subir B. Shakya, Frederick H. Sheldon, Alain Vignal, André E. R. Soares, Beth Shapiro, Jacob González-Solís, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalén, Araxi O. Urrutia, Tamás Székely, Yang Liu, Michael G. Campana, André Corvelo, Robert C. Fleischer, Kim M. Rutherford, Neil J. Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Milá, Ellen D. Ketterson, Andrew Eric Fidler, Guillermo Friis, Ángela M. Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A. Schlinger, Bette A. Loiselle, John G. Blake, Haw Chuan Lim, Lainy B. Day, Matthew J. Fuxjager, Maude W. Baldwin, Michael J. Braun, Morgan Wirthlin, Rebecca B. Dikow, T. Brandt Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Mark E. Hauber, Matthew I. M. Louder, Christopher C. Witt, Jimmy A. McGuire, Joann Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Ribeiro Vasconcelos, Claudio V. Mello, Jason T. Weir, David Haussler, Qiye Li, Huanming Yang, Jian Wang, Fumin Lei, Carsten Rahbek, M. Thomas P. Gilbert, Gary R. Graves, Erich D. Jarvis, Benedict Paten, and Guojie Zhang. (2020) Nature 587(7833):252–57.

  • A Draft Genome Sequence of the Elusive Giant Squid, Architeuthis Dux. Da Fonseca, Rute R., Alvarina Couto, Andre M. Machado, Brona Brejova, Carolin B. Albertin, Filipe Silva, Paul Gardner, Tobias Baril, Alex Hayward, Alexandre Campos, Ângela M. Ribeiro, Inigo Barrio-Hernandez, Henk Jan Hoving, Ricardo Tafur-Jimenez, Chong Chu, Barbara Frazão, Bent Petersen, Fernando Peñaloza, Francesco Musacchia, Graham C. Alexander, Hugo Osório, Inger Winkelmann, Oleg Simakov, Simon Rasmussen, M. Ziaur Rahman, Davide Pisani, Jakob Vinther, Erich Jarvis, Guojie Zhang, Jan M. Strugnell, L. Filipe C. Castro, Olivier Fedrigo, Mateus Patricio, Qiye Li, Sara Rocha, Agostinho Antunes, Yufeng Wu, Bin Ma, Remo Sanges, Tomas Vinar, Blagoy Blagoev, Thomas Sicheritz-Ponten, Rasmus Nielsen, and M. Thomas P. Gilbert. (2020) GigaScience 9(1):1–12.

  • Six Reference-Quality Genomes Reveal Evolution of Bat Adaptations. Jebb, David, Zixia Huang, Martin Pippel, Graham M. Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S. Jermiin, Emilia C. Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A. Ray, Kevin A. M. Sullivan, Juliana G. Roscito, Bogdan M. Kirilenko, Liliana M. Dávalos, Angelique P. Corthals, Megan L. Power, Gareth Jones, Roger D. Ransome, Dina K. N. Dechmann, Andrea G. Locatelli, Sébastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Michael Hiller, Sonja C. Vernes, Eugene W. Myers, and Emma C. Teeling. (2020) Nature 583(7817):578–84.

2019

2018

  • ​Earth BioGenome Project: Sequencing Life for the Future of Life. Lewin, Harris A., Gene E. Robinson, W. John Kress, William J. Baker, Jonathan Coddington, Keith A. Crandall, Richard Durbin, Scott V. Edwards, Félix Forest, M. Thomas P. Gilbert, Melissa M. Goldstein, Igor V. Grigoriev, Kevin J. Hackett, David Haussler, Erich D. Jarvis, Warren E. Johnson, Aristides Patrinos, Stephen Richards, Juan Carlos Castilla-Rubio, Marie Anne Van Sluys, Pamela S. Soltis, Xun Xu, Huanming Yang, and Guojie Zhang. (2018) Proceedings of the National Academy of Sciences of the United States of America 115(17):4325–33.

  • Bayesian Semiparametric Mixed Effects Markov Models With Application to Vocalization Syntax. Sarkar, Abhra, Jonathan Chabout, Joshua Jones Macopson, Erich D. Jarvis, and David B. Dunson. (2018) Journal of the American Statistical Association 113(524):1515–27.

  • Parrot Genomes and the Evolution of Heightened Longevity and Cognition. Wirthlin, Morgan, Nicholas C. B. Lima, Rafael Lucas Muniz Guedes, André E. R. Soares, Luiz Gonzaga P. Almeida, Nathalia P. Cavaleiro, Guilherme Loss de Morais, Anderson V. Chaves, Jason T. Howard, Marcus de Melo Teixeira, Patricia N. Schneider, Fabrício R. Santos, Michael C. Schatz, Maria Sueli Felipe, Cristina Y. Miyaki, Alexandre Aleixo, Maria P. C. Schneider, Erich D. Jarvis, Ana Tereza R. Vasconcelos, Francisco Prosdocimi, and Claudio V. Mello. (2018) Current Biology 28(24):4001-4008.e7.

  • Divergence in Problem-Solving Skills Is Associated with Differential Expression of Glutamate Receptors in Wild Finches. Audet, Jean Nicolas, Lima Kayello, Simon Ducatez, Sara Perillo, Laure Cauchard, Jason T. Howard, Lauren A. O’Connell, Erich D. Jarvis, and Louis Lefebvre. (2018) Science Advances 4(3).
     

2017

2016

2015

2014

Science

  • A flock of genomes. Guojie Zhang, Erich D. Jarvis, M. Thomas P. Gilbert. Science 346 (6215) 1308. Commentary O’Brien, Pennisi, Kress.

  • Core and region-enriched networks of behaviorally regulated genes and the singing genome. Osceola Whitney, Andreas R. Pfenning, Jason T. Howard, Charles A Blatti, Fang Liu, James M. Ward, Rui Wang, Jean-Nicoles Audet, Manolis Kellis, Sayan Mukherjee, Saurabh Sinha, Alexander J. Hartemink, Anne E. West, and Erich D. Jarvis. (2014) Science 346 (6215): 1334 & 1256780-1 to -11.

  • Convergent transcriptional specializations in the brains of humans and song-learning birds. Andreas R. Pfenning, Erina Hara, Osceola Whitney, Miriam V. Rivas, Rui Wang, Petra L. Roulhac, Jason T. Howard, Morgan Wirthlin, Peter V. Lovell, Ganeshkumar Ganapathy, Jacquelyn Mouncastle, M. Arthur Moseley, J. Will Thompson, Erik J. Soderblom, Atsushi Iriki, Masaki Kato, M. Thomas P. Gilbert, Guojie Zhang, Trygve Bakken, Angie Bongaarts, Amy Bernard, Ed Lein, Claudio V. Mello, Alexander J. Hartemink, and Erich D. Jarvis. (2014) Science 346 (6215): 1333 & 1256846-1 to -13.

  • Whole-genome analyses resolve early branches in the tree of life of modern birds. Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, Brant C. Faircloth, Benoit Nabholz, Jason T. Howard, Alexander Suh, Claudia C. Weber, Rute R. da Fonseca, Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, Ganesh Ganapathy, Bastien Boussau, Md. Shamsuzzoha Bayzid, Volodymyr Zavidovych, Sankar Subramanian, Toni Gabaldón, Salvador Capella-Gutiérrez, Jaime Huerta-Cepas, Bhanu Rekepalli, Kasper Munch, Mikkel Schierup, Bent Lindow, Wesley C. Warren, David Ray, Richard E. Green, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Shengbin Li, Ning Li, Yinhua Huang, Elizabeth P. Derryberry, Mads Frost Bertelsen, Frederick H. Sheldon, Robb T. Brumfield, Claudio V. Mello, Peter V. Lovell, Morgan Wirthlin, Maria Paula Cruz Schneider, Francisco Prosdocimi, José Alfredo Samaniego, Amhed Missael Vargas Velazquez, Alonzo Alfaro-Núñez, Paula F. Campos, Bent Petersen, Thomas Sicheritz-Ponten, An Pas, Tom Bailey, Paul Scofield, Michael Bunce, David M. Lambert, Qi Zhou, Polina Perelman, Amy C. Driskell, Beth Shapiro, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Qiuemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnea Smeds, Frank E. Rheindt, Michael Braun, Jon Fjeldsa, Ludovic Orlando, F. Keith Barker, Knud Andreas Jønsson, Warren Johnson, Klaus-Peter Koepfli, Stephen O’Brien, David Haussler, Oliver A. Ryder, Carsten Rahbek, Eske Willerslev, Gary R. Graves, Travis C. Glenn, John McCormack, Dave Burt, Hans Ellegren, Per Alström, Scott V. Edwards, Alexandros Stamatakis, David P. Mindell, Joel Cracraft, Edward L. Braun, Tandy Warnow, Wang Jun, M. Thomas P. Gilbert, and Guojie Zhang. †Co-first authors *Corresponding authors. (2014) Science 346 (6215): 1320-1331.

  • Comparative genomics reveals insights into avian genome evolution and adaptation. Guojie Zhang, Cai Li, Qiye Li, Bo Li, Denis M. Larkin, Chul Lee, Jay F. Storz, Agostinho Antunes, Matthew J. Greenwold, Robert W. Meredith, Anders Ödeen, Jie Cui, Qi Zhou, Luohao Xu, Hailin Pan, Zongji Wang, Lijun Jin, Pei Zhang, Haofu Hu, Wei Yang, Jiang Hu, Jin Xiao, Zhikai Yang, Yang Liu, Qiaolin Xie, Hao Yu, Jinmin Lian, Ping Wen, Fang Zhang, Hui Li, Yongli Zeng, Zijun Xiong, Shiping Liu, Long Zhou, Zhiyong Huang, Na An, Jie Wang, Qiumei Zheng, Yingqi Xiong, Guangbiao Wang, Bo Wang, Jingjing Wang, Yu Fan, Rute R. da Fonseca, Alonzo Alfaro-Núñez, Mikkel Schubert, Ludovic Orlando, Tobias Mourier, Jason T. Howard, Ganeshkumar Ganapathy, Andreas Pfenning, Osceola Whitney, Miriam V. Rivas, Erina Hara, Julia Smith, Marta Farré, Jitendra Narayan, Gancho Slavov, Michael N Romanov, Rui Borges, João Paulo Machado, Imran Khan, Mark S. Springer, John Gatesy, Federico G. Hoffmann, Juan C. Opazo, Olle Håstad, Roger H. Sawyer, Heebal Kim, Kyu-Won Kim, Hyeon Jeong Kim, Seoae Cho, Ning Li, Yinhua Huang, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Mads F. Bertelsen, Elizabeth Derryberry, Wesley Warren, Richard K Wilson, Shengbin Li, David A. Ray, Richard E. Green, Stephen J. O’Brien, Darren Griffin, Warren E. Johnson, David Haussler, Oliver A. Ryder, Eske Willerslev, Gary R. Graves, Per Alström, Jon Fjeldså, David P. Mindell, Scott V. Edwards, Edward L. Braun, Carsten Rahbek, David W. Burt, Peter Houde, Yong Zhang, Huanming Yang, Jian Wang, Avian Genome Consortium, Erich D. Jarvis, M. Thomas P. Gilbert, and Jun Wang. (2014) Science 346 (6215): 1311-1320.

  • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Richard E. Green, Edward L. Braun, Joel Armstrong, Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W. Vandewege, John A. St. John, Salvador Capella-Gutiérrez, Todd A. Castoe, Colin Kern, Matthew K. Fujita, Juan C. Opazo, Jerzy Jurka, Kenji K. Kojima, Juan Caballero, Robert M. Hubley, Arian F. Smit, Roy N. Platt, Christine A. Lavoie, Meganathan P. Ramakodi, John W. Finger Jr., Alexander Suh, Sally R. Isberg, Lee Miles, Amanda Y. Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C. Burgess, Scott V. Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T. Howard, Cathy R. Gresham, Daniel G. Peterson, Jürgen Schmitz, David D. Pollock, David Haussler, Eric W. Triplett, Guojie Zhang, Naoki Irie, Erich D. Jarvis, Christopher A. Brochu, Carl J. Schmidt, Fiona M. McCarthy, Brant C. Faircloth, Federico G. Hoffmann, Travis C. Glenn, Toni Gabaldón, Benedict Paten, and David A. Ray. (2014) Science 346 (6215): 1335 & 1254449-1 to -9.

  • Evidence for a single loss of mineralized teeth in the common avian ancestor. Robert W. Meredith, Guojie Zhang, M. Thomas P. Gilbert, Erich D. Jarvis, and Mark S. Springer. (2014) Science 346 (6215): 1336 & 1254390-1 to -6.

  • Complex evolutionary trajectories of sex chromosomes across bird taxa. Qi Zhou, Jilin Zhang, Doris Bachtrog, Na An, Quanfei Huang, Erich D. Jarvis, M. Thomas P. Gilbert, and Guojie Zhang. (2014) Science 346 (6215): 1332 & 1246338-1 to -8. 

 

Genome Biology

 

BMC journals

GigaScience

  • Comparative genomic data of the Avian Phylogenomics Project. Guojie Zhang, Bo Li, Cai Li, M. Thomas P. Gilbert, Erich D. Jarvis, Jun Wang, and The Avian Genome Consortium. (2014) GigaScience 3:26. DOI: 10.1186/2047-217X-3-26.

  • Phylogenomic analysis data of the Avian Phylogenomics Project. Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, Brant C. Faircloth, Benoit Nabholz, Jason T. Howard, Alexander Suh, Claudia C. Weber, Rute R. da Fonseca, Alonzo Alfaro-Núñez, Nitish Narula, Liang Liu, Dave Burt, Hans Ellegren, Scott V. Edwards, Alexandros Stamatakis, David P. Mindell, Joel Cracraft, Edward L. Braun, Tandy Warnow, Wang Jun, M Thomas P Gilbert, Guojie Zhang, and The Avian Phylogenomics Consortium. (Epub 2014; 2015) GigaScience 4:4.

  • High-coverage sequencing and annotated assemblies of the budgerigar genome. Ganeshkumar Ganapathy, Jason T. Howard, James M. Ward, Jianwen Li, Bo Li, Yingrui Li, Yingqi Xiong, Yong Zhang, Shiguo Zhou, David C. Schwartz, Michael Schatz, Robert Aboukhalil, Olivier Fedrigo6 Lisa Bukovnik, Ty Wang, Greg Wray, Isabelle Rasolonjatovo, Roger Winer, James R Knight, Sergey Koren, Wesley C Warren, Guojie Zhang, Adam M Phillippy, Erich D. Jarvis. (2014) Gigascience 3:11. doi: 10.1186/2047-217X-3-11. Supplemental figures.

  • Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the cold Antartic environment. Cai Li, Yong Zhang, Jianwen Li, Lesheng Kong, Haofu Hu, Hailin Pan, Luohao Xu, Yuan Deng, Qiye Li, Lijun Jin, Hao Yu, Yan Chen, Binghang Liu, Linfeng Yang, Shiping Liu, Yan Zhang, Yongshan Lang, Jinquan Xia, Weiming He, Qiong Shi, Sankar Subramanian, Craig D Millar, Stephen Meader, Chris M Rands, Matthew K Fujita, Matthew J Greenwold, Todd A Castoe, David D Pollock, Wanjun Gu, Kiwoong Nam, Hans Ellegren, Simon YW Ho, David W Burt, Chris P Ponting, Erich D Jarvis, M Thomas P Gilbert, Huanming Yang, JianWang, David M Lambert, Jun Wang, Guojie Zhang. (2014) GigaScience 3:27.

Other journals

2013

2012

2011

2010

2009

2008

2007

2006

2005

  • Rapid behavioral and genomic response to social opportunity. Sabrina S. Burmiester, Erich D. Jarvis, and Russell D. Fernald (2005) PLoS Biology 3: 1996-2004.

  • Night-vision brain area in migratory songbirds. Henrik Mouritsen, G Feenders, M Liedvogel, K Wada, ED Jarvis (2005). Proc. Natl. Acad. Sci. vol 102, no 23: 8339-8344. High Resolution Graphics: Figure 1 ( 6.3 MB pdf ), Figure 2 ( 1.5 MB pdf ), Figure 3 ( 2.5 MB pdf ).

  • Avian brains and a new understanding of vertebrate evolution. The Avian Brain Nomenclature Consortium: ED Jarvis, O Güntürkün, L Bruce, A Csillag, H Karten, W Kuenzel, L Medina, G Paxinos, DJ Perkel, T Shimizu, G Striedter, JM Wild, GF Ball, J Dugas-Ford, SE Durand, GE Hough, S Husband, L Kubikova, DW Lee, CV Mello, A Powers, C Siang, TV Smulders, K Wada, SA White, K Yamamoto, J Yu, A Reiner and AB Butler. Nature Rev. Neurosc. 6: 151-159 (2005).

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