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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.

2022

 

  • The Human Pangenome Project: A Global Resource to Map Genomic Diversity. Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. Lawson, Julian K. Lucas, Adam M. Phillippy, Alice B. Popejoy, Mobin Asri, Caryn Carson, Mark J. P. Chaisson, Xian Chang, Robert Cook-Deegan, Adam L. Felsenfeld, Robert S. Fulton, Erik P. Garrison, Nanibaa’ A. Garrison, Tina A. Graves-Lindsay, Hanlee Ji, Eimear E. Kenny, Barbara A. Koenig, Daofeng Li, Tobias Marschall, Joshua F. McMichael, Adam M. Novak, Deepak Purushotham, Valerie A. Schneider, Baergen I. Schultz, Michael W. Smith, Heidi J. Sofia, Tsachy Weissman, Paul Flicek, Heng Li, Karen H. Miga, Benedict Paten, Erich D. Jarvis, Ira M. Hall, Evan E. Eichler, and David Haussler. 2022. Nature 604(7906):437–46. Supplementary Material.

 

  • The Complete Sequence of a Human Genome. Nurk, Sergey, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G. S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Ying Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, and Adam M. Phillippy. 2022. Science 376(6588):44–53. Supplement 1, Supplement 2, Supplement 3.

 

 

  • 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, Proceedings of the National Academy of Sciences. 119(4):1–10. Supplement.

  • Standards recommendations for the earth BioGenome project. Lawniczak, Mara K. N., Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose Victor Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Françoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, and Stephen Richards. 2022.  Proceedings of the National Academy of Sciences, 119(4). Supplement.

  • Why sequence all eukaryotes?. Blaxter, Mark, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, and Harris A. Lewin. 2022. Proceedings of the National Academy of Sciences, 119(4).

  • The earth BioGenome project 2020: Starting the clock. Lewin, H. A., Richards, S., Aiden, E. L., Allende, M. L., Archibald, J. M., Bálint, M., Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely , Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg , Sachiko Isobe, Kjetill Sigurd Jakobsen , Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin-Hyoung Kim, W. John Kre, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens-Mac, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O’Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Teders, Marcela Uliano-Silvan, Kun Wango, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder & Zhang, G. (2022). Proceedings of the National Academy of Sciences, 119(4). Supplement 1, Supplement 2.

  • Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Hardwick, S.A., Hu, W., Joglekar, A.Li Fan, Paul G. Collier, Careen Foord, Jennifer Balacco, Samantha Lanjewar, Maureen McGuirk Sampson, Frank Koopmans, Andrey D. Prjibelski, Alla Mikheenko, Natan Belchikov, Julien Jarroux, Anne Bergstrom Lucas, Miklós Palkovits, Wenjie Luo, Teresa A. Milner, Lishomwa C. Ndhlovu, August B. Smit, John Q. Trojanowski, Virginia M. Y. Lee, Olivier Fedrigo, Steven A. Sloan, Dóra Tombácz, M. Elizabeth Ross, Erich D. Jarvis, Zsolt Boldogkői, Li Gan & Hagen U. Tilgner.  Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01231-3 Supplementary information.

  • Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19. Sahajpal, N. S., Lai, C. Y. J., Hastie, A., Mondal, A. K., Dehkordi, S. R., van der Made, C. I., Olivier Fedrigo, Farooq Al-Ajli, Sawan Jalnapurkar, Marta Byrska-Bishop, Rashmi Kanagal-Shamanna, Brynn Levy, Maximilian Schieck, Thomas Illig, Silviu-Alin Bacanu, Janet S. Chou, Adrienne G. Randolph, Amyn M. Rojiani, Michael C. Zody, Catherine A. Brownstein, Alan H. Beggs, Vineet Bafna, Erich D. Jarvis, Alexander Hoischen, Alka Chaubey, Ravindra Kolhe & COVID19hostgenomesv Consortium. (2022).  Iscience, 25(2), 103760.

  • The era of reference genomes in conservation genomics. Formenti, Giulio, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklós Bálint, Fedor Čiampor, Jacob Hoglund, Per Palsbøll, María José Ruiz-López, Goujie Zhang, Erich Jarvis, Sargis A. Aghayan, Tyler S. Alioto, Isabel Almudi, Nadir Alvarez, Paulo C. Alves, Isabel R. Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul R. Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit L. Boštjančić, Bastien Boussau, Catherine M. Breton, Elena Buzan, Paula F. Campos, Carlos Carreras, L. FIlipe Castro, Luis J. Chueca, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica V. Cunha, Frédéric Delsuc, Alice B. Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier D. Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean François Flot, Toni Gabaldón, Dolores R. Galea Agius, Guido R. Gallo, Alice M. Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter D. Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill S. Jakobsen, Sissel Jentoft, Peter Klinga, Agnieszka Kloch, Claudius F. Kratochwil, Henrik Kusche, Kara K. S. Layton, Jennifer A. Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Florian Maumus, Ann M. Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael T. Monaghan, Matteo Montagna, Robert W. Mysłajek, Marco T. Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio S. Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig R. Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Simona Secomandi, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja C. Vernes, Cristiano Vernesi, David R. Vieites, Robert M. Waterhouse, Christopher W. Wheat, Gert Wörheide, Yannick Wurm, and Gabrielle Zammit. 2022. Trends in Ecology & Evolution.

2021

  • Population Genomics of the Critically Endangered Kākāpō. Dussex, Nicolas, Tom van der Valk, Hernán E. Morales, Christopher W. Wheat, David Díez-del-Molino, Johanna von Seth, Yasmin Foster, Verena E. Kutschera, Katerina Guschanski, Arang Rhie, Adam M. Phillippy, Jonas Korlach, Kerstin Howe, William Chow, Sarah Pelan, Joanna D. Mendes Damas, Harris A. Lewin, Alex R. Hastie, Giulio Formenti, Olivier Fedrigo, Joseph Guhlin, Thomas W. R. Harrop, Marissa F. Le Lec, Peter K. Dearden, Leanne Haggerty, Fergal J. Martin, Vamsi Kodali, Françoise Thibaud-Nissen, David Iorns, Michael Knapp, Neil J. Gemmell, Fiona Robertson, Ron Moorhouse, Andrew Digby, Daryl Eason, Deidre Vercoe, Jason Howard, Erich D. Jarvis, Bruce C. Robertson, and Love Dalén. 2021. Cell Genomics 1(1):100002. Supplement 1, Supplement 2, Supplement 3Supplement 4, Supplement 5Supplement 6, Supplement 7.

 

  • 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.

  • 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

  • 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). Nature 592(7856):737–46. 

  • Variation in predicted COVID-19 risk among lemurs and lorises. Melin, Amanda D., Joseph D. Orkin, Mareike C. Janiak, Alejandro Valenzuela, Lukas Kuderna, Frank Marrone, Hasinala Ramangason, Julie E. Horvath, Christian Roos, Andrew C. Kitchener, Chiea Chuen Khor, Weng Khong Lim, Jessica G. H. Lee, Patrick Tan, Govindhaswamy Umapathy, Muthuswamy Raveendran, R. Alan Harris, Ivo Gut, Marta Gut, Esther Lizano, Tilo Nadler, Dietmar Zinner, Minh D. Le, Sivakumara Manu, Clément J. Rabarivola, Alphonse Zaramody, Nicole Andriaholinirina, Steig E. Johnson, Erich D. Jarvis, Olivier Fedrigo, Dongdong Wu, Guojie Zhang, Kyle Kai How Farh, Jeffrey Rogers, Tomas Marques-Bonet, Arcadi Navarro, David Juan, Paramjit S. Arora, and James P. Higham. 2021. American Journal of Primatology 83(6):1–12.

2020

  • 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.

  • 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.

  • 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.

2017

2016

100&Change Citations 

2015

  • Core and Shell Song Systems Unique to the Parrot Brain. Chakraborty, Mukta, Solveig Walløe, Signe Nedergaard, Emma E. Fridel, Torben Dabelsteen, Bente Pakkenberg, Mads F. Bertelsen, Gerry M. Dorrestein, Steven E. Brauth, Sarah E. Durand, and Erich D. Jarvis. 2015. PLoS ONE 10(6):1–37.

  • The Genome 10K Project: A Way Forward. Koepfli, Klaus Peter, Benedict Paten, Stephen J. O’brien, Agostinho Antunes, Kathy Belov, Carlos Bustamante, Todd A. Castoe, Hiram Clawson, Andrew J. Crawford, Mark Diekhans, Dan Distel, Richard Durbin, Dent Earl, Matthew K. Fujita, Tony Gamble, Arthur Georges, Neil Gemmell, M. Thomas P. Gilbert, Jennifer Marshall Graves, Richard E. Green, Glenn Hickey, Erich D. Jarvis, Warren Johnson, Aleksey Komissarov, Ian Korf, Robert Kuhn, Denis M. Larkin, Harris Lewin, Jose V. Lopez, Jian Ma, Tomas Marques-Bonet, Webb Miller, Robert Murphy, Pavel Pevzner, Beth Shapiro, Cynthia Steiner, Gaik Tamazian, Byrappa Venkatesh, Jun Wang, Robert Wayne, Edward Wiley, Huanming Yang, Guojie Zhang, David Haussler, and Oliver Ryder. 2015. Annual Review of Animal Biosciences 3:57–111.

2014

Science

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

  • Convergent transcriptional specializations in the brains of humans and song-learning birds. Pfenning, Andreas R., 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. Jarvis, Erich D., 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. Zhang, Guojie, 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. Green, Richard E., 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.

 

Genome Biology

  • Genomic signatures of near-extinction and rebirth of the Crested Ibis and other endangered bird species. Li, Shengbin, Bo Li, Cheng Cheng, Zijun Xiong, Qingbo Liu, Jianghua Lai, Hannah V. Carey, Qiong Zhang, Haibo Zheng, Shuguang Wei, Hongbo Zhang, Liao Chang, Shiping Liu, Shanxin Zhang, Bing Yu, Xiaofan Zeng, Yong Hou, Wenhui Nie, Youmin Guo, Teng Chen, Jiuqiang Han, Jian Wang, Jun Wang, Chen Chen, Jiankang Liu, Peter J. Stambrook, Ming Xu, Guojie Zhang, M. Thomas P. Gilbert, Huanming Yang, Erich D. Jarvis, Jun Yu, Jianqun Yan. (2014) Genome Biology.

 

BMC journals

GigaScience

  • Phylogenomic analysis data of the Avian Phylogenomics Project. Jarvis, Erich D., 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. Ganapathy, Ganeshkumar, 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.

  • Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the cold Antartic environment. Li, Cai, 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

  • NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species. Striedter, Georg F., T. Grant Belgard, Chun Chun Chen, Fred P. Davis, Barbara L. Finlay, Onur Güntürkün, Melina E. Hale, Julie A. Harris, Erin E. Hecht, Patrick R. Hof, Hans A. Hofmann, Linda Z. Holland, Andrew N. Iwaniuk, Erich D. Jarvis, Harvey J. Karten, Paul S. Katz, William B. Kristan, Eduardo R. Macagno, Partha P. Mitra, Leonid L. Moroz, Todd M. Preuss, Clifton W. Ragsdale, Chet C. Sherwood, Charles F. Stevens, Maik C. Stüttgen, Tadaharu Tsumoto, and Walter Wilczynski. 2014. Brain, Behavior and Evolution 83(1):1–8

  • NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species. Striedter, Georg F., T. Grant Belgard, Chun-Chun Chen, Fred P. Davis, Barbara Finlay, Onur Güntürkün, Melina E. Hale, Julie A. Harris, Erin E. Hecht, Patrick Hof, Hans A. Hofmann, Linda Z. Holland, Andrew N. Iwaniuk, Erich D. Jarvis, Harvey J. Karten, Paul S. Katz, William B. Kristan, Eduardo R. Macagno, Partha P. Mitra, Leonid L. Moroz, Todd M. Preuss, Clifford W. Ragsdale, Chet C. Sherwood, Charles F. Stevens, Maik C. Stüttgen, Tadaharu Tsumoto, Water Wilczynski. (2014) J Comp Neurol. 522:1445-53.

2013

  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.  Bradnam, Keith R., Joseph N. Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod A. Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen Chi Chou, Jacques Corbeil, Cristian Del Fabbro, Roderick R. Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A. Fonseca, Ganeshkumar Ganapathy, Richard A. Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B. Hiatt, Isaac Y. Ho, Jason Howard, Martin Hunt, Shaun D. Jackman, David B. Jaffe, Erich D. Jarvis, Huaiyang Jiang, Sergey Kazakov, Paul J. Kersey, Jacob O. Kitzman, James R. Knight, Sergey Koren, Tak Wah Lam, Dominique Lavenier, François Laviolette, Yingrui Li, Zhenyu Li, Binghang Liu, Yue Liu, Ruibang Luo, Iain MacCallum, Matthew D. MacManes, Nicolas Maillet, Sergey Melnikov, Delphine Naquin, Zemin Ning, Thomas D. Otto, Benedict Paten, Octávio S. Paulo, Adam M. Phillippy, Francisco Pina-Martins, Michael Place, Dariusz Przybylski, Xiang Qin, Carson Qu, Filipe J. Ribeiro, Stephen Richards, Daniel S. Rokhsar, J. Graham Ruby, Simone Scalabrin, Michael C. Schatz, David C. Schwartz, Alexey Sergushichev, Ted Sharpe, Timothy I. Shaw, Jay Shendure, Yujian Shi, Jared T. Simpson, Henry Song, Fedor Tsarev, Francesco Vezzi, Riccardo Vicedomini, Bruno M. Vieira, Jun Wang, Kim C. Worley, Shuangye Yin, Siu Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou, and Ian F. Korf. 2013. GigaScience 2(1):1–31.

2012

  • Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. St John, John A., Edward L. Braun, Sally R. Isberg, Lee G. Miles, Amanda Y. Chong, Jaime Gongora, Pauline Dalzell, Christopher Moran, Bertrand Bed’Hom, Arkhat Abzhanov, Shane C. Burgess, Amanda M. Cooksey, Todd A. Castoe, Nicholas G. Crawford, Llewellyn D. Densmore, Jennifer C. Drew, Scott V. Edwards, Brant C. Faircloth, Matthew K. Fujita, Matthew J. Greenwold, Federico G. Hoffmann, Jonathan M. Howard, Taisen Iguchi, Daniel E. Janes, Shahid Y. Khan, Satomi Kohno, AP Jason de Koning, Stacey L. Lance, Fiona M. McCarthy, John E. McCormack, Mark E. Merchant, Daniel G. Peterson, David D. Pollock, Nader Pourmand, Brian J. Raney, Kyria A. Roessler, Jeremy R. Sanford, Roger H. Sawyer, Carl J. Schmidt, Eric W. Triplett, Tracey D. Tuberville, Miryam Venegas-Anaya, Jason T. Howard, Erich D. Jarvis, Louis J. Guillette, Travis C. Glenn, Richard E. Green, and David A. Ray. 2012. Genome Biology 13(1):1–12.

2011

2010

  • Empowering 21st Century Biology. Robinson, Gene E., Jody A. Banks, Dianna K. Padilla, Warren W. Burggren, C. Sarah Cohen, Charles F. Delwiche, Vicki Funk, Hopi E. Hoekstra, Erich D. Jarvis, et.al. (2010) BioScience. vol 60, no 11: 923-930.

  • Evolution of dynamic coordination. Balaban, Evan, Shimon Edelman, Sten Grillner, Uri Grodzinski, Erich D. Jarvis, Jon H. Kaas, Gilles Laurent, and Gordon Pipa. 2010. Dynamic Coordination in the Brain 5:59–82.

  • The genome of a songbird. Warren, Wesley C., David F. Clayton, Hans Ellegren, Arthur P. Arnold, Ladeana W. Hillier, Axel Künstner, Steve Searle, Simon White, Albert J. Vilella, Susan Fairley, Andreas Heger, Lesheng Kong, Chris P. Ponting, Erich D. Jarvis, Claudio V. Mello, Pat Minx, Peter Lovell, Tarciso A. F. Velho, Margaret Ferris, Christopher N. Balakrishnan, Saurabh Sinha, Charles Blatti, Sarah E. London, Yun Li, Ya Chi Lin, Julia George, Jonathan Sweedler, Bruce Southey, Preethi Gunaratne, Michael Watson, Kiwoong Nam, Niclas Backström, Linnea Smeds, Benoit Nabholz, Yuichiro Itoh, Osceola Whitney, Andreas R. Pfenning, Jason Howard, Martin Völker, Bejamin M. Skinner, Darren K. Griffin, Liang Ye, William M. McLaren, Paul Flicek, Victor Quesada, Gloria Velasco, Carlos Lopez-Otin, Xose S. Puente, Tsviya Olender, Doron Lancet, Arian F. A. Smit, Robert Hubley, Miriam K. Konkel, Jerilyn A. Walker, Mark A. Batzer, Wanjun Gu, David D. Pollock, Lin Chen, Ze Cheng, Evan E. Eichler, Jessica Stapley, Jon Slate, Robert Ekblom, Tim Birkhead, Terry Burke, David Burt, Constance Scharff, Iris Adam, Hugues Richard, Marc Sultan, Alexey Soldatov, Hans Lehrach, Scott V. Edwards, Shiaw Pyng Yang, Xiaoching Li, Tina Graves, Lucinda Fulton, Joanne Nelson, Asif Chinwalla, Shunfeng Hou, Elaine R. Mardis, and Richard K. Wilson. 2010. Nature 464(7289):757–62. Supplementary Information, Supplementary Accessory.

2009

  • Evolution of the Pallium in Birds and Reptiles. Erich D. Jarvis (2009) In: New Encyclopedia of Neuroscience. Marc D. Binder, Nobutaka Hirokawa and Uwe Windhorst (eds). Ann Butler (sub-ed). Springer-Verlag GmbH Berlin Heidelberg. 15 pages.

  • Bird Brain: Evolution. Jarvis, E. D. 2009. Evolution.” Encyclopedia of Neuroscience 2:209–15. Oxford: Academic Press.

2008

2007

2006

  • A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Wada, Kazuhiro, Jason T. Howard, Patrick McConnell, Osceola Whitney, Thierry Lints, Miriam V. Rivas, Haruhito Horita, Michael A. Patterson, Stephanie A. White, Constance Scharff, Sebastian Haesler, Shengli Zhao, Hironobu Sakaguchi, Masatoshi Hagiwara, Toshiyuki Shiraki, Tomoko Hirozane-Kishikawa, Pate Skene, Yoshihide Hayashizaki, Piero Carninci, and Erich D. Jarvis. 2006. Proceedings of the National Academy of Sciences of the United States of America 103(41):15212–17.

2005

  • Night-vision brain area in migratory songbirds. Mouritsen, Henrik, Gesa Feenders, Miriam Liedvogel, Kazuhiro Wada, and Erich D. Jarvis. 2005. Proceedings of the National Academy of Sciences of the United States of America 102(23):8339–44. 

  • Avian brains and a new understanding of vertebrate evolution. The Avian Brain Nomenclature Consortium: Jarvis, Erich, Onur Güntürkün, Laura Bruce, András Csillag, Harvey Karten, Wayne Kuenzel, Loreta Medina, George Paxinos, David J. Perkel, Toru Shimizu, Georg Striedter, J. Martin Wild, Gregory F. Ball, Jennifer Dugas-Ford, Sarah E. Durand, Gerald E. Hough, Scott Husband, Lubica Kubikova, Diane W. Lee, Claudio V. Mello, Alice Powers, Connie Siang, Tom V. Smulders, Kazuhiro Wada, Stephanie A. White, Keiko Yamamoto, Jing Yu, Anton Reiner, and Ann B. Butler. 2005.  Nature Reviews Neuroscience 6(2):151–59.

2004

 

  • Revised Nomenclature for Avian Telencephalon and Some Related Brainstem Nuclei. Reiner, Anton, David J. Perkel, Laura L. Bruce, Ann B. Butler, András Csillag, Wayne Kuenzel, Loreta Medina, George Paxinos, Toru Shimizu, Georg Striedter, Martin Wild, Gregory F. Ball, Sarah Durand, Onur Gütürkün, Diane W. Lee, Claudio V. Mello, Alice Powers, Stephanie A. White, Gerald Hough, Lubica Kubikova, Tom V. Smulders, Kazuhiro Wada, Jennifer Dugas-Ford, Scott Husband, Keiko Yamamoto, Jing Yu, Connie Siang, and Erich D. Jarvis. 2004. Journal of Comparative Neurology 473(3):377–414.

  • The Avian Brain Nomenclature Forum: Terminology for a New Century in Comparative Neuroanatomy. Reiner, Anton, David J. Perkel, Laura L. Bruce, Ann B. Butler, András Csillag, Wayne Kuenzel, Loreta Medina, George Paxinos, Toru Shimizu, Georg Striedter, Martin Wild, Gregory F. Ball, Sarah Durand, Onur Gütürkün, Diane W. Lee, Claudio V Mello, Alice Powers, Stephanie A. White, Gerald Hough, Lubica Kubikova, Tom V Smulders, Kazuhiro Wada, Jennifer Dugas-Ford, Scott Husband, Keiko Yamamoto, Jing Yu, Connie Siang, and Erich D. Jarvis. 2004. The Journal of Comparative Neurology 473:E1–6.

2003

  • Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System. Gustincich, Stefano, Serge Batalov, Kirk W. Beisel, Hidemasa Bono, Piero Carninci, Colin F. Fletcher, Sean Grimmond, Nobutaka Hirokawa, Erich D. Jarvis, Tim Jegla, Yuka Kawasawa, Julianna LeMieux, Harukata Miki, Elio Raviola, Rohan D. Teasdale, Naoko Tominaga, Ken Yagi, Andreas Zimmer, Takahiro Arakawa, Kazunori Waki, Jun Kawai, Yoshihide Hayashizaki, and Yasushi Okazaki. 2003. Genome Research 13(6 B):1395–1401.​

2002

  • A framework for integrating the songbird brain. Jarvis, E. D., V. A. Smith, K. Wada, M. V. Rivas, M. McElroy, T. V. Smulders, P. Carninci, Y. Hayashizaki, F. Dietrich, X. Wu, P. McConnell, J. Yu, P. P. Wang, A. J. Hartemink, and S. Lin. 2002. Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology 188(11–12):961–80.

2000

  • Modulation of movement by the basal ganglia. W Hall, M Nicolelis, ED Jarvis (2000). Neuroscience, 2nd edition. Purves, Augustine, Fitzpatrick, Katz, McNamara, Williams (eds). Sinauer Associates, MA. pp. 391-407.

  • Modulation of movement by the cerrebellum. W Hall, ED Jarvis (2000). Neuroscience, 2nd edition. Purves, Augustine, Fitzpatrick, Katz, McNamara, Williams (eds). Sinauer Associates, MA. pp. 409-426.

1999

1998

1997

1995

1994

1993

1990

  • The structure of the trpE, trpD and 5′ trpC genes of Bacillus pumilus. Rivas M.V., Erich D. Jarvis, Rudner R (1990). Gene 87: 71-78.

1988

1986