Publications

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

2014

Science

A flock of genomes. Guojie Zhang, Erich D. Jarvis, M. Thomas P. Gilbert. Science 346 (6215) 1308. Commentary OBrien, 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. Cover photo.

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. Supplementary

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

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

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.

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.

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).

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

GigaScience

Genomic resources for the endangered Hawaiian honeycreepers. 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. (2014) GigaScience.

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. Supplementary 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. (2014) J Comp Neurol.

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

2013

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.

2012

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).

2011

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.

2010

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

2009

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.

2008

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

2007

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.

2006

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.

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)

2004

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).

2003

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

2002

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.

2000

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.

1999

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.

1998

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.

1997

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.

1995

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.

1994

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.

1993

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.

1990

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.

1988

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.

1986

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.