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


De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Jonas Korlach, Gregory Gedman, Sarah B. Kingan, Chen-Shan Chin, Jason T. Howard, Jean-Nicolas Audet, Lindsey Cantin, and Erich D. Jarvis. GigaScience, 6, 2017, 1–16. doi: 10.1093/gigascience/gix085. Korlach et al supplementary figures v15 | Supplementary Figures Legend

Axon guidance pathways served as common targets for human speech/language evolution and related disorders. Huimeng Lei Zhangming Yan, Xiaohong Sun, Yue Zhang, Jianhong Wang, Caihong Ma, Qunyuan Xu, Rui Wang, Erich D. Jarvis, Zhirong Sun. Brain & Language 174 (2017) 1–8. http://dx.doi.org/10.1016/j.bandl.2017.06.007.

A hypothesis on a role of oxytocin in the social mechanisms of speech and vocal learning. Constantina Theofanopoulou, Cedric Boeckx, and Erich D. Jarvis. Proc. R. Soc. B (2017) 284: 20170988.

Overexpression of human NR2B receptor subunit in LMAN causes stuttering and song sequence changes in adult zebra finches. Mukta Chakraborty, Liang-Fu Chen, Emma E. Fridel, Marguerita E. Klein, Rebecca A. Senft, Abhra Sarkar & Erich D. Jarvis. Scientific Reports (2017). 7: 942 | DOI:10.1038/s41598-017-00519-8.

Eliciting and Analyzing Male Mouse Ultrasonic Vocalization (USV) Songs. Jonathan Chabout, Joshua Jones-Macopson, Erich D. Jarvis. J. Vis. Exp. (2017). doi:10.3791/54137.

Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. Marta Farre´, Jitendra Narayan, Gancho T. Slavov, Joana Damas, Loretta Auvil, Cai Li, Erich D. Jarvis, David W. Burt, Darren K. Griffin, and Denis M. Larkin. Genome Biol. Evol. 8(8):2442–2451. doi:10.1093/gbe/evw166.


A Foxp2 Mutation Implicated in Human Speech Deficits Alters Sequencing of Ultrasonic Vocalizations in Adult Male Mice. Chabout J, Sarkar A, Patel SR, Radden T, Dunson DB, Fisher SE and Jarvis ED. Front. Behav. Neurosci. (2016)  10:197. doi: 10.3389/fnbeh.2016.00197.

100&Change Citations 

Bone-associated gene evolution and the origin of flight in birds. João Paulo Machado, Warren E. Johnson , M. Thomas P. Gilbert , Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, and Agostinho Antunes. BMC Genomics (2016) 17:371 DOI 10.1186/s12864-016-2681-7.

Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds. Almeida D, Maldonado E, Khan I, Silva L, Gilbert MT, Zhang G, Jarvis ED, O’Brien SJ, Johnson WE, Antunes A. Genome Biol Evol. 2016. 8(4):1115-1131.

Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class. Erich D. Jarvis. (2016) Annu. Rev. Anim. Biosci. 2016. 4:45–59.


Brain evolution by brain pathway duplication. Mukta Chakraborty, and Erich D. Jarvis. (2015) Phil. Trans. R. Soc. B 370: 20150056.

Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in SauropsidaImran Khan, Zhikai Yangy, Emanuel Maldonado, Cai Li, Guojie Zhang, M. Thomas P. Gilbert, Erich D. Jarvis, Stephen J. O’Brien, Warren E. Johnson, and Agostinho Antunes. (2015) Mol. Biol. Evol. 32(11):2832–2843 doi:10.1093/molbev/msv155.

Transsynaptic Tracing from Peripheral Targets with Pseudorabies Virus Followed by Cholera Toxin and Biotinylated Dextran Amines Double Labeling. Gustavo Arriaga, Joshua J. Macopson, Erich D. Jarvis. (2015) J. Vis. Exp. (103), e50672, doi:10.3791/50672.

Response to Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds.” Joel Cracraft, Peter Houde, Simon Y. W. Ho, David P. Mindell, Jon Fjeldså, Bent Lindow, Scott V. Edwards, Carsten Rahbek, Siavash Mirarab, Tandy Warnow, M. Thomas P. Gilbert, Guojie Zhang, Edward L. Braun, Erich D. Jarvis. (2015) Science 349 (6255): 1460b-1 to -3.

The Origin and Diversification of Birds. Stephen L. Brussatte, Jingmai K. O’Connor, Erich D. Jarvis. (2015) Current Biology 25, R888-R898. In special issue on The History of Life on Earth.

Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates. Asher Haug-Baltzell , Erich D. Jarvis, Fiona M. McCarthy, Eric Lyons. (2015) Front. Neurosci. 9: Article 361, 1-16.

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. Rui Borges, Imran Khan, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, and Agostinho Antunes. (2015) BMC Genomics 16, 1-13.

Bird sequencing project takes off. Goujie Zhang, Carsten Rahbek, Erich D. Jarvis, and M. Thomas P. Gilbert. (2015) Nature 522:34.

The Basal Ganglia within a Cognitive System in Birds and MammalsChristopher I. Petkov, Erich D. Jarvis. (2015) Europe PMC Funders Group 1-5.

A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. Ângela M. Ribeiro , M. Lisandra Zepeda-Mendoza , Mads F. Bertelsen , Annemarie T. Kristensen , Erich D. Jarvis, M. Thomas P. Gilbert, and Rute R. da Fonseca. (2015) BMC Evolutionary Biology 15:124.

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

Male mice song syntax depends on social contexts and influences female preferences. Jonathan Chabout, Abhra Sarkar, David B. Dunson, and Erich D. Jarvis. (2015) Frontiers Behavioral Neuroscience 9:76.

The Genome 10K Project: A Way Forward. Klaus-Peter Koepfli, Benedict Paten, the Genome 10K Community of Scientists, and Stephen J. O’Brien. (2015) Annual Review of Animal Biosciences 3:57-111.

Avianbase: A community resource for bird genomics. Léi Eöry , M Thomas P. Gilbert, Cai Li, Bo Li, Alan Archibald, Bronwen L. Aken, Guojie Zhang, Erich D. Jarvis, Paul Flicek, and David W. Burt. (2015) Genome Biology 16:21.



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

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. Supplemental figures.

Genome Biology

Genomic signatures of near-extinction and rebirth of the Crested Ibis and other endangered bird species. Shengbin Li, 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. Supplemental figures.

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Claudia C. Weber, Bastien Boussau, Jonathan Romiguier, Erich D. Jarvis, and Hans Ellegren. (2014) Genome Biology. Supplemental figures.

Low frequency of paleoviral infiltration across the avian phylogeny. Jie Cui, Wei Zhao, Zhiyong Huang, Erich D. Jarvis, M. Thomas P. Gilbert, Peter J. Walker, Edward C. Holmes, Guojie Zhang. (2014) Genome Biology 15, 539. Supplemental figure 1, 2, 3, 4.

BMC journals

Comparative genomics reveals molecular features unique to the songbird lineage. Morgan Wirthlin, Peter V. Lovell, Erich D. Jarvis, Claudio V. Mello. (2014) BMC Genomics. Table. Supplemental figures.

Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. Matthew J. Greenwold, Weier Bao, Erich D. Jarvis, Haofu Hu, Cai Li, M. Thomas P. Gilbert, Guojie Zhang, Roger H. Sawyer. BMC Evolutionary Biology (2014) 14:249.

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. Michael N. Romanov, Marta Farré, Pamela E. Lithgow, Katie E. Fowler, Benjamin M. Skinner, Rebecca O’Connor, Gothami Fonseka, Niclas Backström, Yoichi Matsuda, Chizuko Nishida, Peter Houde, Erich D Jarvis, Hans Ellegren, David W. Burt, Denis M. Larkin, Darren K. Griffin. BMC Genomics (2014). Table.

Genomic resources for the endangered Hawaiian honeycreepersTaylor Callicrate, Rebecca Dikow, James W Thomas, James C Mullikin, Erich D Jarvis, Robert Fleischer. (2014) BMC Genomics 15:1098. Table.


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

Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners. Rui Wang, Chun-Chun Chen, Erina Hara, Miriam V. Rivas, Petra L. Roulhac, Jason T. Howard, Mukta Chakraborty, Jean-Nicolas Audet, Erich D. Jarvis. (Epub 2014; 2015) J. Comp. Neurol. 523:892-906.

Maintenance and Neuronal Differentiation of Chicken Induced Pluripotent Stem-Like Cells. Rui Dai, Ricardo Rossello, Chun-Chun Chen, Joeran Kessler, Ian Davison, Ute Hochgeschwender, Erich D. Jarvis. (2014) Stem Cell International Article 182737: 1-14. DOI

Basal ganglia function, stuttering, sequencing, and repair in adult songbirds. Kubikova L, Bosikova E, Cvikova M, Lukacova K, Scharff C, Jarvis ED. (2014) Scientific Reports. 4:6590.  Supplemental Movie Legends.

NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species. Georg F. Striedter, 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) Brain Behav Evol. 83:1-8.

NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species. Georg F. Striedter, 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.

Evolutionary genomics and adaptive evolution of the hedgehog gene family (SHH, IHH, and DHH) in vertebrates. Joana Pereira, Warren E. Johnson, Stephen J. O’Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vitor Vasconcelos, and Agostinho Antunes. (2014) PLoS ONE. 9:e74132. Table. Supplemental figure 123, 4, 5


Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities. Chen CC, Winkler CM, Pfenning AR, Jarvis ED. J Comp Neurol. (2013) Nov;521(16):3666-701. doi: 10.1002/cne.23406

Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns. Jarvis ED, Yu J, Rivas MV, Horita H, Feenders G, Whitney O, Jarvis SC, Jarvis ER, Kubikova L, Puck AE, Siang-Bakshi C, Martin S, McElroy M, Hara E, Howard J, Pfenning A, Mouritsen H, Chen CC, Wada K. J Comp Neurol. (2013) Nov;521(16):3614-65. doi: 10.1002/cne.23404.

Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species. Rosselló RA, Chen CC, Dai R, Howard JT, Hochgeschwender U, Jarvis ED. Elife. (2013) Sep 3;2:e00036. doi: 10.7554/eLife.00036.

Different mechanisms are responsible for dishabituation of electrophysiological auditory responses to a change in acoustic identity than to a change in stimulus location.  Smulders TV, Jarvis ED. Neurobiol Learn Mem. (2013) Nov;106:163-76. doi: 10.1016/j.nlm.2013.08.010. Epub 2013 Aug 30.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.  Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Gigascience. (2013) Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

Mouse vocal communication system: Are ultrasounds learned or innate? Gustavo Arriaga & Erich D. Jarvis. BRAIN AND LANGUAGE 124, 96–116 (2013).

Rudimentary substrates for vocal learning in a suboscine.  Wan-chun Liu, Kazuhiro Wada, Erich D. Jarvis & Fernando Nottebohm. Nature Communications 4, 1–12 (2013).

The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Thomas L. Parchman et al. Molecular Ecology 22, 3304–3317 (2013). Yeaman Commentary on Parchman et al 2013.


Dopamine regulation of human speech and bird song: A critical reviewKristina Simonyan, Barry Horwitz, Erich D. Jarvis (2012) Brain & Language. 10.1016/j.bandl.2011.12.009.

Hybrid error correction and de novo assembly of single-molecule sequencing reads. Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis & Adam M Phillippy (2012) Nature Biotechnology. 10.1038/nbt.2280.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. St John et al. (2012) Genome Biology. 13:415.

Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in TissueChun-Chun Chen, Kazuhiro Wada, Erich D. Jarvis (2012) Journal of Visualized Experiments. 10.3791/3764.

Convergent Differential Regulation of Parvalbumin in the Brains of Vocal LearnersErina Hara, Miriam V. Rivas, James M. Ward, Kazuo Okanoya, Erich D. Jarvis (2012) Public Library of Science ONE. 7(1):e29457.

Of Mice, Birds, and Men: The Mouse Ultrasonic Song System Has Some Features Similar to Humans and Song-Learning Birds. Gustavo Arriaga, Eric P. Zhou. & Erich D. Jarvis. PLoS ONE 7, e46610 (2012).

Interspecies Avian Brain Chimeras Reveal That Large Brain Size Differences Are Influenced by Cell–Interdependent Processes.  Chun-Chun Chen, Evan Balaban & Erich D. Jarvis. PLoS ONE 7, e42477 (2012).

Specialized Motor-Driven dusp1 Expression in the Song Systems of Multiple Lineages of Vocal Learning Birds. Haruhito Horita et al. PLoS ONE 7, e42173 (2012).

Birds, primates, and spoken language origins: behavioral phenotypes and neurobiological substrates. Christopher I. Petkov and Erich D. Jarvis. Frontiers in Evolutionary Neuroscience, 4(12), 1-24. (2012).


Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics. Benoit Nabholz, Axel Kunstner, Rui Wang, Erich D. Jarvis and Hans Ellegren (2011) Molecular Biology and Evolution. 28(8):2197–2210.

Microproteomics: Quantitative Proteomic Profiling of Small Numbers of Laser-Captured Cells. Petra L. Roulhac, James M. Ward, J. Will Thompson, Erik J. Soderblom, Michael Silva, M. Arthur Moseley III, and Erich D. Jarvis (2011) Cold Spring Harbor Protocols.


Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny Benoit Nabholz, Erich D. Jarvis, Hans Ellegren.(2010) Molecular Phylogenetics and Evolution. 57 (2010) 466–470.

Empowering 21st Century Biology. Gene E. Robinson, 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 E, Edelman S, Grillner S, Grodzinski U, Jarvis ED, Kaas JH, Laurent G, Pipa G. (2010). In: Dynamic Coordination in the Brain: From Neurons to Mind. Malsburg C von der, Phillips WA, Singer W (eds). Strungmann Forum Reports. Lupp J (series Ed.) MIT Press, Cambridge MA. 59-82.

The dusp1 Immediate Early Gene is Regulated by Natural Stimuli Predominantly in Sensory Input NeuronsHaruhito Horita, Kazuhiro Wada, Miriam V. Rivas, Erina Hara, Erich D. Jarvis (2010) The Journal of Comparative Neurology. 518:2873–2901

The genome of a songbirdWarren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, et al (2010) Nature. 464:757-762. Supplementary Information Supplementary Accessory.

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Axel Kunstner, Jochen B. W. Wolf, Niclas Backstrom, Osceola Whitney, Christopher N. Balakrishnan, Lainy Day, Scott V. Edwards, Daniel E. Janes, Barney A. Schlinger, Richard K. Wilson, Erich D. Jarvis, Wesley C. Warren and Hans Ellegran (2010) Molecular Ecology. 19 (Suppl. 1), 266–276.

Dopamine receptors in a songbird brainLubica Kubikova, Kazuhiro Wada, Erich D. Jarvis (2010) Journal of Comparative Neurology. 518:741-769. Supporting figures Cover Photo.


Behaviorally regulated mRNA and protein expression in the songbird brain. Rivas M, Jarvis ED (2009) In: Neuroproteomics. Frontiers in Neuroscience series. Alzate O (ed). pp. 239-262.

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.

Assessing visual requirements for social ceontext-dependent activation of the songbird song system. Hara E, Kubikova L, Hessler NA, Jarvis ED. (2009) Proc. R. Soc. B 276:279-289.

Bird Song Systems: Evolution. Erich D. Jarvis (2009) In: Encyclopedia of Neuroscience. Squire LR (eds). volume 2, pp. 217-225. Oxford: Academic Press.

Bird Brain: Evolution. Erich D. Jarvis (2009) In: Encyclopedia of Neuroscience. Squire LR (eds). volume 2, pp. 209-215. Oxford: Academic Press.


Early onset of deafening-induced song deterioration and differential requirements of the pallial-basal ganglia vocal pathway. Horita H, Wada K, Jarvis ED. (2008) Eur. J. Neurosci. 28:2519-2532.

Songbirds and the revised avian brain nomenclature. Reiner A, Perkel DJ, Mello CV, Jarvis ED. (2008) In: The Neuroscience of Birdsong. Zeigler and Marler (eds). Cambridge University Press. pp. 58-62.

Behavior-dependent expression of inducible genes in vocal learning birds. Mello CV, Jarvis ED (2008) In: The Neuroscience of Birdsong. Ziegler and Marler (eds). Cambridge University Press. pp. 381-397.

Molecular Mapping of Movement-Associated Areas in the Avian Brain: A Motor Theory for Vocal Learning Origin. Gesa Feenders, Miriam Liedvogel, Miriam Rivas, Manuela Zapka, Haruhito Horita, Erina Hara, Kazuhiro Wada, Henrik Mouritsen, Erich D. Jarvis. (2008) Public Library of Science ONE 3(3): e1768. doi:10.1371/journal.pone.0001768.
Supplementary materials

Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics. Raphael Pinaud, Cristina Osorio, Oscar Alzate, Erich D. Jarvis. (2008) European Journal of Neuroscience 27:1409-1422.


Neural systems for vocal learning in birds and humans: a synopsis. Erich. D Jarvis. (2007) Journal of Ornithology 143:S35-44. (Invited paper of a plenary lecture for the 24th international ornithology congress.)

Role of midbrain dopaminergic system in the modulation of vocal brain activation by social context. Erina Hara, Lubica Kubikova, Neal A Hessler, Erich D. Jarvis. (2007) European Journal of Neuroscience 25:3406-3416.
Supplementary figure and audios

The pallial-basal ganglia pathway modulates the behaviorally-driven gene expression of the motor pathway. Lubica Kubikova, Elena Turner , Erich D. Jarvis. (2007) European Journal of Neuroscience 25:2154-2160.

Lateralized activation of Cluster N in the brains of migratory songbirds. Miriam Liedvogel, Gesa Feenders, Kazuhiro Wada, Nikolaus F. Troje, Erich D. Jarvis and Henrik Mouritsen (2007) European Journal of Neuroscience 25:1166-1173.


Evolution of vocal learning systems in birds and humansJarvis ED (2006) In: Evolution of Nervous Systems. Kaas J (ed). 2:213-228.

Computational inference of neural information flow networksVictoria A. Smith, Jing Yu, Tom V. Smulders, Alexander J. Hartemink, Erich D. Jarvis (2006) PLoS Comp. Biol. 2:1436-1449.
Supplementary figures and text Powerpoint animation (Most viewed research article of this issue when published.)

Vocalizations and associated behaviors of the sombre hummingbird (aphantochroa cirrhoclhloris) and the rufous-breasted hermit (glaucis hirsutus)Adriana R.J. Ferreira, Tom V. Smulders, Koichi Sameshima, Claudio V. Mello, Erich D. Jarvis (2006) Auk 123: 1129-1148. Supplementary figures and sounds of of hummingbird vocalizations.

A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Kazuhiro Wada, 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) Proc Natl Acad Sci USA 103: 15212-15217. Supporting material: Supporting Appendix (pages 1-24), Supporting Figures 8-21, Supporting Tables 1-6.

Social context-dependent singing-regulated dopamineAya Sasaki, Tatyana D. Sotnikova, Raul R. Gainetdinov, and Erich D. Jarvis (2006) Journal of Neuroscience 26: 9010?014.

Selection for and against vocal learning in birds and mammals. Erich D. Jarvis (2006) Ornithology Science 5: 5-14. Special Issue on the Neuroecology of Birdsong.

Evolution of brain structures for vocal learning in birds: a synopsis. Erich D. Jarvis (2006) Acta Zoologica Sinica. Proc 23rd IOC Conf 52: 85-89.


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).


Learned Birdsong and the Neurobiology of Human LanguageErich D. Jarvis. Ann. N.Y. Acad. Sci. 1016: 749-777 (2004)

Differential Expression of Glutamate Receptors in Avian Neural Pathways for Learned VocalizationKazuhiro Wada, Hironobi Sakaguchi, Erich D. Jarvis, Masatoshi Hagiwara. J. Comp. Neurol. 476:44-64 (2004)

Advances to Bayesian Network Inference for Generating Causal Networks from Observational Biological Data. Jing Yu, VA Smith, PP Wang, AJ Hartemink, ED Jarvis. Bioinformatics Vol. 20, No. 18: 3594-3603 (2004)
Supplementary Figures. Source Code.

Songbirds and the Revised Avian Brain Nomenclature. A Reiner, DJ Perkel, CV Mello, ED Jarvis. Ann. N.Y. Acad. Sci. 1016: 77-108 (2004)

Revised Nomenclature for Avian Telencephalon and Some Related Brainstem Nuclei. A Reiner, DJ Perkel, L Bruce, AB Butler, A Csillag, W Kuenzel, L Medina, G Paxinos, T Shimizu, GF Striedter, M Wild, GF Ball, S Durand, O Güntürkün, DW Lee, CV Mello, A Powers, SA White, G Hough, L Kubikova, TV Smulders, K Wada, J Dugas-Ford, S Husband, K Yamamoto, J Yu, C Siang, ED Jarvis (2004) J. Comp. Neurol. 473:377-414.

The Avian Brain Nomenclature Forum: Terminology for a New Century in Comparative Neuroanatomy. A Reiner, DJ Perkel, et al. (2004) J. Comp. Neurol. 473: E1-E6.

Fox P2 Expression in Avian Vocal Learners and Non-Learners. S Haesler, K Wada, A Nshdejan, E Morriesey, T Lints, ED Jarvis, and C Scharff (2004) Journal of Neuroscience 24(13):3164-3175.
Supplementary Figures.

Nature’s Music: The Science of BirdSong. Marler P, Slaberkorn H (eds). ED Jarvis (2004).


Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System. Stefano Gustincich, 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, RIKEN GER Group and GSL Members, Yoshihide Hayashizaki, and Yasushi Okazaki (2003) Genome Research 13: 1395-1401.
Supplementary Material: Table 1 (Neurotransmitter Receptors) Table 2 (Channels) Table 3 (Neural RNAs)

Influence of Network Topology and Data Collection on Network Inference. VA Smith, ED Jarvis, AJ Hatermink.(2003) Pacific Symposium on Biocomputing 2003, pp. 164-175.


Induction of Hippocampal Long-Term Potentiation during Waking Leads to Increased Extrahippocampal zif-268 Expression during Ensuing Rapid-Eye-Movement Sleep. S Ribeiro, CV Mello, T Velho, TJ Gardner, ED Jarvis, and C Pavlides (2002) Journal of Neuroscience 22(24):10914-10923.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. The FANTOM Consortium, RIKEN Genome Exploration Research Group Phase I & II Team (2002) Nature 420: 563-573. Cover Photo. Supplementary.

Evaluating functional network inference using simulation of complex biological systems. VA Smith, ED Jarvis, AJ Hatermink.(2002) Bioinformatics 18 Suppl. 1: S216-S224.

A framework for integrating the songbird brain. ED Jarvis, VA Smith, MV Rivas, K Wada, M McElroy, TV Smulders, P Carnici, Y Hayashisaki, F Dietrich, X Wu, P Wang, S Lin (2002) J. Comp. Physiol. A 188:961-980.


Site-specific retinoic acid production in the brain of adult songbirds.  N Nehrbass, ED Jarvis, C Scharff, F Nottebohm & CV Mello (2000). Neuron 27:359-370.

A relation between behavior, neurotrophin expression, and neuronal survival. XC Li, ED Jarvis, B Alvarez-Bordo, D Lim, & F Nottebohm (2000). Proc. Natl. Acad. Sci. 97:8584-8589.

Behaviorally-driven gene expression reveals hummingbird brain song nuclei. ED Jarvis, S Ribeiro, J. Vielliard, M DaSilva, D. Ventura, CV Mello (2000). Nature 406:628-632.

Molecular mapping of brain areas involved in parrot vocal communication. ED Jarvis & CV Mello (2000). J. Comp. Neurol. 419:1-31. Cover Photo.

A membrane-associated progesterone-binding protein, 25-Dx, is regulated by progesterone in brain regions involved in female reproductive behaviors. CJ Krebs, ED Jarvis, J Chan, JP Lydon, S Ogawa, DW Pfaff (2000).Proc. Natl. Acad. Sci. 97:12816-12821.

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.


The 70-kDa heat shock cognate protein (Hsc73) gene is enhanced by ovarian hormones in the ventromedial hypothalamus. Christopher J. Krebs, E.D. Jarvis, D.W. Pfaff (1999) Proc. Natl. Acad. Sci. 96:1686-1691.

Applying differential display to brain research. CV Mello, ED Jarvis (1999). Techniques for Behavioral and Neural Sciences. WE Crusio & RT Gerlai (eds). Elsevier Science, Netherlands, Amsterdam. 13:200-211.


For whom the bird sings: context-dependent gene expression. ED Jarvis, C Scharff, M Grossman, JA Ramos & F Nottebohm (1998). Neuron 21:775-788. Commentary on Jarvis et al 1998 by Schmidt (1998). Neuron 21:645-642. Neuron.

Classification and genetic characterization of pattern forming Bacilli. Rudner R, Martsinkevich O, Leung W, ED Jarvis (1998). Molec. Microbio. 27:387-703. Commentary on Rudner et al. 1998.


Selective expression of insulin-like growth factor II in the songbird brain. M Holzenberger, ED Jarvis, C Chong, M Grossman, F Nottebohm & C Scharff (1997). J. Neurosci. 17:6974-6987.

Isolation of song-regulated genes in the brain of songbirds. CV Mello, ED Jarvis, N Denisenko, M Rivas (1997). In Methods in Molecular Biology, Differential Display Methods and Protocols vol. 85, pp205-217. P Liang, AB Pardee (eds), Humana Press, NJ.

Brain gene regulation by territorial singing behavior in freely ranging songbirds. ED Jarvis, H Schawbl, S Ribeiro, CV Mello (1997). NeuroReport 8:2073-2077.

Motor-driven gene expression. ED Jarvis & F Nottebohm (1997). Proc. Natl. Acad. Sci. 94:4097-4102.

Identification of aberrantly regulated genes in diseased skin using the cDNA differential display technique. Rivas M, ED Jarvis, Morisaki S, Carbonado H, Gottleb AB, Krueger J. (1997). J. Invest. Derm. 108:188-194.


Decrements in auditory responses to a repeated conspecific song are long-lasting and require two periods of protein synthesis in the songbird forebrain. SJ Chew, CV Mello, F Nottebohm, ED Jarvis & D Vicario (1995). Proc. Natl. Acad. Sci. 92:3406-3410.

Associative learning and stimulus novelty influence the song-induced expression of an immediate early gene in the canary forebrain. ED Jarvis, CV Mello, F Nottebohm (1995). Learning & Memory. 2:62-80.


Determination of restriction fragment length polymorphisms in bacteria using ribosomal RNA genes. Rudner R, Studamire B, ED Jarvis (1994). Methods in Enzymology. 235:184-196.


Two tRNA gene clusters associated with ribosomal RNA operons rrnD and rrnE in Bacillus subtilis. Rudner R, Severestt A, Buchholz S, Studamire B, White AM, ED Jarvis (1993). J. Bacteriol. 175: 503-509.


Genetic structure and DNA sequences at junctions involved in the rearrangements of Bacillus subtilis strains carrying the trpE26 mutation. ED Jarvis, Cheng S, Rudner R (1990). Genetics 126: 785-797.

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


Chromosomal Organizations of rRNA operons in Bacillus subtilis. ED Jarvis, Widom R, LaFauci G, Setoguchi Y, Richter IR, Rudner R (1988). Genetics 120: 625-635.

Instability of rRNA operons in Bacillus subtilis. Widom RL, ED Jarvis, LaFauci G, Rudner R (1988). J. Bacteriol. 170: 605-610.


Mapping of rRNA genes with integrable plasmids in Bacillus subtilis. LaFauci G, Widom RL, Eisner R, Jarvis ED, Rudner R (1986). J Bacteriol. 165: 204-214.