The genome sequence of Molossus alvarezi González-Ruiz, Ramírez-Pulido and Arroyo-Cabrales, 2011 (Chiroptera, Molossidae). Simmons NB, Ingala MR, Pieri M, O'Toole BP, Gray JL, Philge P, L Volkert T, Zhang N, Abueg L, Brajuka N, Jarvis E, Formenti G, McCaffrey K, Mai M, Teeling EC, C Vernes S; Bat Biology Foundation; Bat1K Consortium.Wellcome Open Res. 2024 Sep 12;9:522. doi: 10.12688/wellcomeopenres.22726.1. eCollection 2024.PMID: 39411461

A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes. Canesin LEC, Vilaça ST, Oliveira RRM, Al-Ajli F, Tracey A, Sims Y, Formenti G, Fedrigo O, Banhos A, Sanaiotti TM, Farias IP, Jarvis ED, Oliveira G, Hrbek T, Solferini V, Aleixo A. Sci Rep. 2024 Sep 12;14(1):19925. doi: 10.1038/s41598-024-70305-w.
PMID: 39261501

Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure. Ishigohoka J, Bascón-Cardozo K, Bours A, Fuß J, Rhie A, Mountcastle J, Haase B, Chow W, Collins J, Howe K, Uliano-Silva M, Fedrigo O, Jarvis ED, Pérez-Tris J, Illera JC, Liedvogel M.Evolution. 2024 Aug 29:qpae117. doi: 10.1093/evolut/qpae117. Online ahead of print.PMID: 39208288

Pronounced early differentiation underlies zebra finch gonadal germ cell development. Biegler MT, Belay K, Wang W, Szialta C, Collier P, Luo JD, Haase B, Gedman GL, Sidhu AV, Harter E, Rivera-López C, Amoako-Boadu K, Fedrigo O, Tilgner HU, Carroll T, Jarvis ED, Keyte AL.Dev Biol. 2024 Aug 28;517:73-90. doi: 10.1016/j.ydbio.2024.08.006. Online ahead of print.PMID: 39214328

The Ruminant Telomere-to-Telomere (RT2T) Consortium. Kalbfleisch TS, McKay SD, Murdoch BM, Adelson DL, Almansa-Villa D, Becker G, Beckett LM, Benítez-Galeano MJ, Biase F, Casey T, Chuong E, Clark E, Clarke S, Cockett N, Couldrey C, Davis BW, Elsik CG, Faraut T, Gao Y, Genet C, Grady P, Green J, Green R, Guan D, Hagen D, Hartley GA, Heaton M, Hoyt SJ, Huang W, Jarvis E, Kalleberg J, Khatib H, Koepfi KP, Koltes J, Koren S, Kuehn C, Leeb T, Leonard A, Liu GE, Low WY, McConnell H, McRae K, Miga K, Mousel M, Neibergs H, Olagunju T, Pennell M, Petry B, Pewsner M, Phillippy AM, Pickett BD, Pineda P, Potapova T, Rachagani S, Rhie A, Rijnkels M, Robic A, Rodriguez Osorio N, Safonova Y, Schettini G, Schnabel RD, Sirpu Natesh N, Stegemiller M, Storer J, Stothard P, Stull C, Tosser-Klopp G, Traglia GM, Tuggle CK, Van Tassell CP, Watson C, Weikard R, Wimmers K, Xie S, Yang L, Smith TPL, O'Neill RJ, Rosen BD.Nat Genet. 2024 Aug;56(8):1566-1573. doi: 10.1038/s41588-024-01835-2. Epub 2024 Aug 5.PMID: 39103649

Bayesian semiparametric Markov renewal mixed models for vocalization syntax. Wu Y, Jarvis ED, Sarkar A.Biostatistics. 2024 Jul 1;25(3):648-665. doi: 10.1093/biostatistics/kxac050.PMID: 36583955

The genome sequence of Rhynchonycteris naso, Peters, 1867 (Chiroptera, Emballonuridae, Rhynchonycteris). Alvarez van Tussenbroek I, Knörnschild M, Nagy M, O'Toole BP, Formenti G, Philge P, Zhang N, Abueg L, Brajuka N, Jarvis E, Volkert TL, Gray JL, Pieri M, Mai M, Teeling EC, Vernes SC; Bat Biology Foundation; Bat1K Consortium.Wellcome Open Res. 2024 Jul 10;9:361. doi: 10.12688/wellcomeopenres.19959.1. eCollection 2024.PMID: 39239167

Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain. Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Marrocco J, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU.Nat Neurosci. 2024 Jun;27(6):1051-1063. doi: 10.1038/s41593-024-01616-4. Epub 2024 Apr 9.PMID: 38594596

A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): Building genomic resources to study evolution in cave environments. Cadena CD, Pabón L, DoNascimiento C, Abueg L, Tilley T, O-Toole B, Absolon D, Sims Y, Formenti G, Fedrigo O, Jarvis ED, Torres M.J Hered. 2024 May 9;115(3):311-316. doi: 10.1093/jhered/esae019.PMID: 38513109

Complexity of avian evolution revealed by family-level genomes. Stiller J, Feng S, Chowdhury AA, Rivas-González I, Duchêne DA, Fang Q, Deng Y, Kozlov A, Stamatakis A, Claramunt S, Nguyen JMT, Ho SYW, Faircloth BC, Haag J, Houde P, Cracraft J, Balaban M, Mai U, Chen G, Gao R, Zhou C, Xie Y, Huang Z, Cao Z, Yan Z, Ogilvie HA, Nakhleh L, Lindow B, Morel B, Fjeldså J, Hosner PA, da Fonseca RR, Petersen B, Tobias JA, Székely T, Kennedy JD, Reeve AH, Liker A, Stervander M, Antunes A, Tietze DT, Bertelsen MF, Lei F, Rahbek C, Graves GR, Schierup MH, Warnow T, Braun EL, Gilbert MTP, Jarvis ED, Mirarab S, Zhang G.Nature. 2024 May;629(8013):851-860. doi: 10.1038/s41586-024-07323-1. Epub 2024 Apr 1.PMID: 38560995

Evolution and genetic architecture of sex-limited polymorphism in cuckoos. Merondun J, Marques CI, Andrade P, Meshcheryagina S, Galván I, Afonso S, Alves JM, Araújo PM, Bachurin G, Balacco J, Bán M, Fedrigo O, Formenti G, Fossøy F, Fülöp A, Golovatin M, Granja S, Hewson C, Honza M, Howe K, Larson G, Marton A, Moskát C, Mountcastle J, Procházka P, Red'kin Y, Sims Y, Šulc M, Tracey A, Wood JMD, Jarvis ED, Hauber ME, Carneiro M, Wolf JBW.Sci Adv. 2024 Apr 26;10(17):eadl5255. doi: 10.1126/sciadv.adl5255. Epub 2024 Apr 24.PMID: 38657058
A chromosome-level genome assembly for the dugong (Dugong dugon). Dorothy Nevé Baker, Linelle Abueg, Merly Escalona, Katherine A Farquharson, Janet M Lanyon, Diana Le Duc, Torsten Schöneberg, Dominic Absolon, Ying Sims, Olivier Fedrigo, Erich D Jarvis, Katherine Belov, Carolyn J Hogg, Beth Shapiro. March 2024. Journal of Heredity, Volume 115, Issue 2, Pages 212–220, https://doi.org/10.1093/jhered/esae003

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Bukhman, Y.V., Meyer, S., Chu, LF. et al. 2024. Sci Data 11, 176 https://doi.org/10.1038/s41597-024-03011-x

A region of suppressed recombination misleads neoavian phylogenomics. Siavash Mirarab, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey, Guangji Chen, Nadolina Brajuka, Olivier Fedrigo, Giulio Formenti, Jochen B. W. Wolf, Kerstin Howe, Agostinho Antunes, Mikkel H. Schierup, Benedict Paten, Erich D. Jarvis, Guojie Zhang, and Edward L. Braun. 2024. Proceedings of the National Academy of SciencesVol. 121, No. 15. https://doi.org/10.1073/pnas.2319506121

2023

A genomic basis of vocal rhythm in birds. Sebastianelli M, Lukhele SM, Secomandi S, de Souza SG, Haase B, Moysi M, Nikiforou C, Hutfluss A, Mountcastle J, Balacco J, Pelan S, Chow W, Fedrigo O, Downs CT, Monadjem A, Dingemanse NJ, Jarvis ED, Brelsford A, vonHoldt BM, Kirschel ANG.Nat Commun. 2024 Apr 23;15(1):3095. doi: 10.1038/s41467-024-47305-5.PMID: 38653976

Problem-solving skills are predicted by technical innovations in the wild and brain size in passerines. Audet JN, Couture M, Lefebvre L, Jarvis ED.Nat Ecol Evol. 2024 Apr;8(4):806-816. doi: 10.1038/s41559-024-02342-7. Epub 2024 Feb 22.PMID: 38388692

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R.Mol Biol Evol. 2024 Mar 1;41(3):msae036. doi: 10.1093/molbev/msae036.PMID: 38376487

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, Couture M, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Horan K, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Williams RW, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G.Nat Biotechnol. 2024 Mar;42(3):367-370. doi: 10.1038/s41587-023-02100-3.PMID: 38278971

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean. Lee YH, Abueg L, Kim JK, Kim YW, Fedrigo O, Balacco J, Formenti G, Howe K, Tracey A, Wood J, Thibaud-Nissen F, Nam BH, No ES, Kim HR, Lee C, Jarvis ED, Kim H.Sci Data. 2023 Dec 8;10(1):880. doi: 10.1038/s41597-023-02782-z.PMID: 38066002

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. Rice ES, Alberdi A, Alfieri J, Athrey G, Balacco JR, Bardou P, Blackmon H, Charles M, Cheng HH, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Gilbert MTP, Hearn CJ, Jarvis ED, Klopp C, Marcos S, Mason AS, Velez-Irizarry D, Xu L, Warren WC.BMC Biol. 2023 Nov 22;21(1):267. doi: 10.1186/s12915-023-01758-0.PMID: 37993882

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M.Nat Commun. 2023 Oct 19;14(1):6628. doi: 10.1038/s41467-023-42238-x.PMID: 37857613

The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Bond DM, Ortega-Recalde O, Laird MK, Hayakawa T, Richardson KS, Reese FCB, Kyle B, McIsaac-Williams BE, Robertson BC, van Heezik Y, Adams AL, Chang WS, Haase B, Mountcastle J, Driller M, Collins J, Howe K, Go Y, Thibaud-Nissen F, Lister NC, Waters PD, Fedrigo O, Jarvis ED, Gemmell NJ, Alexander A, Hore TA.Nat Commun. 2023 Oct 17;14(1):6364. doi: 10.1038/s41467-023-41784-8.PMID: 37848431

A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta). Squires TE, Rödin-Mörch P, Formenti G, Tracey A, Abueg L, Brajuka N, Jarvis E, Halapi EC, Melsted P, Höglund J, Magnússon KP.G3 (Bethesda). 2023 Jul 5;13(7):jkad099. doi: 10.1093/g3journal/jkad099.PMID: 37141262

A Draft Human Pangenome Reference. Liao, Wen Wei, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, Ho Joon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, and Benedict Paten. 2023. Nature 617(7960):312–24. doi: 10.1038/s41586-023-05896-x.

Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela Lutreola L., 1761., Jakub, Florian Brandes, Christian Seebass, Wolfgang Festl, Przemysław Śmietana, Jennifer Balacco, Nivesh Jain, Tatiana Tilley, Linelle Abueg, Jonathan Wood, Ying Sims, Giulio Formenti, Olivier Fedrigo, and Erich D. Jarvis. 2023. International Journal of Molecular Sciences 24(19):14816. doi: 10.3390/ijms241914816.

Songbird Species That Display More-Complex Vocal Learning Are Better Problem-Solvers and Have Larger Brains. Audet, Jean-Nicolas, Mélanie Couture, and Erich D. Jarvis. 2023. Science 381(6663):1170–75. doi: 10.1126/science.adh3428. Supplementary Materials 1, 2, 3.

Species-Wide Genomics of Kākāpō Provides Tools to Accelerate Recovery. Guhlin, Joseph, Marissa F. Le Lec, Jana Wold, Emily Koot, David Winter, Patrick J. Biggs, Stephanie J. Galla, Lara Urban, Yasmin Foster, Murray P. Cox, Andrew Digby, Lydia R. Uddstrom, Daryl Eason, Deidre Vercoe, Tāne Davis, Karen Andrew, Lisa Argilla, Karen Arnold, James Bohan, Liam Bolitho, Nichy Brown, Jo Carpenter, Jodie Crane, Margie Grant, Glen Greaves, Brett Halkett, Rory Hannan, Sam Haultain, Bryony Hitchcock, Leigh Joyce, Sara Larcombe, Jo Ledington, Jinty MacTavish, Phil Marsh, Gilbert Mingam, Freya Moore, Lyndsay Murray, Errol Nye, Jake Osborne, Lou Parker, Chris Phillips, Roy Phillips, Brodie Philp, Tim Raemaekers, Jenny Rickett, Rachel Rouse, Rachael Sagar, Alisha Sherriff, Theo Thompson, Jason Van de Wetering, Nicki van Zyl, Jen Waite, Jim Watts, Jason T. Howard, Erich D. Jarvis, Fiona E. Robertson, Bruce C. Robertson, Neil J. Gemmell, Tammy E. Steeves, Anna W. Santure, and Peter K. Dearden. 2023. Nature Ecology & Evolution. doi: 10.1038/s41559-023-02165-y.

A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa Tridactyla), a Declining Circumpolar Seabird. Sozzoni, Marcella, Joan Ferrer Obiol, Giulio Formenti, Anna Tigano, Josephine R. Paris, Jennifer R. Balacco, Nivesh Jain, Tatiana Tilley, Joanna Collins, Ying Sims, Jonathan Wood, Z. Morgan Benowitz-Fredericks, Kenneth A. Field, Eyuel Seyoum, Marie Claire Gatt, Don Jean Léandri-Breton, Chinatsu Nakajima, Shannon Whelan, Luca Gianfranceschi, Scott A. Hatch, Kyle H. Elliott, Akiko Shoji, Jacopo G. Cecere, Erich D. Jarvis, Andrea Pilastro, and Diego Rubolini. 2023. Genome Biology and Evolution 15(8). doi: 10.1093/gbe/evad153.

An Improved Germline Genome Assembly for the Sea Lamprey Petromyzon Marinus Illuminates the Evolution of Germline-Specific Chromosomes. Timoshevskaya, Nataliya, Kaan Eşkut, Vladimir A. Timoshevskiy, Sofia M. C. Robb, Carson Holt, Jon E. Hess, Hugo J. Parker, Cindy F. Baker, Allison K. Miller, Cody Saraceno, Mark Yandell, Robb Krumlauf, Shawn R. Narum, Ralph T. Lampman, Neil J. Gemmell, Jacquelyn Mountcastle, Bettina Haase, Jennifer R. Balacco, Giulio Formenti, Sarah Pelan, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D. Jarvis, and Jeramiah J. Smith. 2023. Cell Reports 42(3). doi: 10.1016/j.celrep.2023.112263.

A Chromosome-Level Reference Genome and Pangenome for Barn Swallow Population Genomics. Secomandi, Simona, Guido R. Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, Olivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, Graziella Messina, Anders P. Møller, Jacquelyn Mountcastle, Timothy A. Mousseau, Joan Ferrer Obiol, Anna Olivieri, Arang Rhie, Diego Rubolini, Marielle Saclier, Roscoe Stanyon, David Stucki, Françoise Thibaud-Nissen, James Torrance, Antonio Torroni, Kristina Weber, Roberto Ambrosini, Andrea Bonisoli-Alquati, Erich D. Jarvis, Luca Gianfranceschi, and Giulio Formenti. 2023. Cell Reports 42(1):111992.

The Swan Genome and Transcriptome, It Is Not All Black and White. Karawita, Anjana C., Yuanyuan Cheng, Keng Yih Chew, Arjun Challagulla, Robert Kraus, Ralf C. Mueller, Marcus Z. W. Tong, Katina D. Hulme, Helle Bielefeldt-Ohmann, Lauren E. Steele, Melanie Wu, Julian Sng, Ellesandra Noye, Timothy J. Bruxner, Gough G. Au, Suzanne Lowther, Julie Blommaert, Alexander Suh, Alexander J. McCauley, Parwinder Kaur, Olga Dudchenko, Erez Aiden, Olivier Fedrigo, Giulio Formenti, Jacquelyn Mountcastle, William Chow, Fergal J. Martin, Denye N. Ogeh, Françoise Thiaud-Nissen, Kerstin Howe, Alan Tracey, Jacqueline Smith, Richard I. Kuo, Marilyn B. Renfree, Takashi Kimura, Yoshihiro Sakoda, Mathew McDougall, Hamish G. Spencer, Michael Pyne, Conny Tolf, Jonas Waldenström, Erich D. Jarvis, Michelle L. Baker, David W. Burt, and Kirsty R. Short. 2023. Genome Biology 24(1):13.0.

Fourth Report on Chicken Genes and Chromosomes 2022. Smith, Jacqueline, James M. Alfieri, Nick Anthony, Peter Arensburger, Giridhar N. Athrey, Jennifer Balacco, Adam Balic, Philippe Bardou, Paul Barela, Yves Bigot, Heath Blackmon, Pavel M. Borodin, Rachel Carroll, Meya C. Casono, Mathieu Charles, Hans Cheng, Maddie Chiodi, Lacey Cigan, Lyndon M. Coghill, Richard Crooijmans, Neelabja Das, Sean Davey, Asya Davidian, Fabien Degalez, Jack M. Dekkers, Martijn Derks, Abigail B. Diack, Appolinaire Djikeng, Yvonne Drechsler, Alexander Dyomin, Olivier Fedrigo, Steven R. Fiddaman, Giulio Formenti, Laurent A. F. Frantz, Janet E. Fulton, Elena Gaginskaya, Svetlana Galkina, Rodrigo A. Gallardo, Johannes Geibel, Almas Gheyas, Cyrill John P. Godinez, Ashton Goodell, Jennifer A. M. Graves, Daren K. Griffin, Bettina Haase, Jian-Lin Han, Olivier Hanotte, Lindsay J. Henderson, Zhuo-Cheng Hou, Kerstin Howe, Lan Huynh, Evans Ilatsia, Erich Jarvis, Sarah M. Johnson, Jim Kaufman, Terra Kelly, Steve Kemp, Colin Kern, Jacob H. Keroack, Christophe Klopp, Sandrine Lagarrigue, Susan J. Lamont, Margaret Lange, Anika Lanke, Denis M. Larkin, Greger Larson, John King N. Layos, Ophélie Lebrasseur, Lyubov P. Malinovskaya, Rebecca J. Martin, Maria Luisa Martin Cerezo, Andrew S. Mason, Fiona M. McCarthy, Michael J. McGrew, Jacquelyn Mountcastle, Christine Kamidi Muhonja, William Muir, Kévin Muret, Terence Murphy, Ismael Ng’ang’a, Masahide Nishibori, Rebecca E. O’Connor, Moses Ogugo, Ron Okimoto, Ochieng Ouko, Hardip R. Patel, Francesco Perini, María Ines Pigozzi, Krista C. Potter, Peter D. Price, Christian Reimer, Edward S. Rice, Nicolas Rocos, Thea F. Rogers, Perot Saelao, Jens Schauer, Robert Schnabel, Valerie Schneider, Henner Simianer, Adrian Smith, Mark P. Stevens, Kyle Stiers, Christian Keambou Tiambo, Michele Tixier-Boichard, Anna A. Torgasheva, Alan Tracey, Clive A. Tregaskes, Lonneke Vervelde, Ying Wang, Wesley C. Warren, Paul D. Waters, David Webb, Steffen Weigend, Anna Wolc, Alison E. Wright, Dominic Wright, Zhou Wu, Masahito Yamagata, Chentao Yang, Zhong-Tao Yin, Michelle C. Young, Guojie Zhang, Bingru Zhao, and Huaijun Zhou. 2023. Cytogenetic and Genome Research. Supplementary Materials.

Divergent Sensory and Immune Gene Evolution in Sea Turtles with Contrasting Demographic and Life Histories. Bentley, Blair P., Tomás Carrasco-Valenzuela, Elisa K. S. Ramos, Harvinder Pawar, Larissa Souza Arantes, Alana Alexander, Shreya M. Banerjee, Patrick Masterson, Martin Kuhlwilm, Martin Pippel, Jacquelyn Mountcastle, Bettina Haase, Marcela Uliano-Silva, Giulio Formenti, Kerstin Howe, William Chow, Alan Tracey, Ying Sims, Sarah Pelan, Jonathan Wood, Kelsey Yetsko, Justin R. Perrault, Kelly Stewart, Scott R. Benson, Yaniv Levy, Erica V. Todd, H. Bradley Shaffer, Peter Scott, Brian T. Henen, Robert W. Murphy, David W. Mohr, Alan F. Scott, David J. Duffy, Neil J. Gemmell, Alexander Suh, Sylke Winkler, Françoise Thibaud-Nissen, Mariana F. Nery, Tomas Marques-Bonet, Agostinho Antunes, Yaron Tikochinski, Peter H. Dutton, Olivier Fedrigo, Eugene W. Myers, Erich D. Jarvis, Camila J. Mazzoni, and Lisa M. Komoroske. 2023. Proceedings of the National Academy of Sciences 120(7). Supplementary Materials.

Reply to: The Case for Standardizing Gene Nomenclature in Vertebrates. Theofanopoulou, Constantina, and Erich D. Jarvis. 2023. Nature 614(7948):E33–36.

How Genomics Can Help Biodiversity Conservation. Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J; European Reference Genome Atlas Consortium.Trends Genet. 2023 Jul;39(7):545-559. doi: 10.1016/j.tig.2023.01.005. Epub 2023 Feb 16.PMID: 36801111

A High-Quality Reference Genome for the Critically Endangered Aeolian Wall Lizard, Podarcis Raffonei. Gabrielli, Maëva, Andrea Benazzo, Roberto Biello, Lorena Ancona, Silvia Fuselli, Alessio Iannucci, Jennifer Balacco, Jacqueline Mountcastle, Alan Tracey, Gentile Francesco Ficetola, Daniele Salvi, Marco Sollitto, Olivier Fedrigo, Giulio Formenti, Erich D. Jarvis, Marco Gerdol, Claudio Ciofi, Emiliano Trucchi, and Giorgio Bertorelle. 2023. Journal of Heredity.

Three Amphioxus Reference Genomes Reveal Gene and Chromosome Evolution of Chordates. Huang, Zhen, Luohao Xu, Cheng Cai, Yitao Zhou, Jing Liu, Zaoxu Xu, Zexian Zhu, Wen Kang, Wan Cen, Surui Pei, Duo Chen, Chenggang Shi, Xiaotong Wu, Yongji Huang, Chaohua Xu, Yanan Yan, Ying Yang, Ting Xue, Wenjin He, Xuefeng Hu, Yanding Zhang, Youqiang Chen, Changwei Bi, Chunpeng He, Lingzhan Xue, Shijun Xiao, Zhicao Yue, Yu Jiang, Jr-Kai Yu, Erich D. Jarvis, Guang Li, Gang Lin, Qiujin Zhang, and Qi Zhou. 2023. Proceedings of the National Academy of Sciences 120(10).

2022

Birdsong neuroscience and the evolutionary substrates of learned vocalization. Davenport M, Jarvis E. 2022. Trends in Neurosciences 46(2) 97-99

A Haplotype-Resolved Genome Assembly of the Nile Rat Facilitates Exploration of the Genetic Basis of Diabetes. Toh, Huishi, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis, James A. Thomson, Ron Stewart, Mark J. P. Chaisson, and Yury V. Bukhman. 2022. BMC Biology 20(1):1–21.

Semi-Automated Assembly of High-Quality Diploid Human Reference Genomes. Jarvis, Erich D., Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang, Jonathan Wood, Alan Tracey, Francoise Thibaud-Nissen, Mitchell R. Vollger, David Porubsky, Haoyu Cheng, Mobin Asri, Glennis A. Logsdon, Paolo Carnevali, Mark J. P. Chaisson, Chen-Shan Chin, Sarah Cody, Joanna Collins, Peter Ebert, Merly Escalona, Olivier Fedrigo, Robert S. Fulton, Lucinda L. Fulton, Shilpa Garg, Jennifer L. Gerton, Jay Ghurye, Anastasiya Granat, Richard E. Green, William Harvey, Patrick Hasenfeld, Alex Hastie, Marina Haukness, Erich B. Jaeger, Miten Jain, Melanie Kirsche, Mikhail Kolmogorov, Jan O. Korbel, Sergey Koren, Jonas Korlach, Joyce Lee, Daofeng Li, Tina Lindsay, Julian Lucas, Feng Luo, Tobias Marschall, Matthew W. Mitchell, Jennifer McDaniel, Fan Nie, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Tamara Potapova, Daniela Puiu, Allison Regier, Jue Ruan, Steven L. Salzberg, Ashley D. Sanders, Michael C. Schatz, Anthony Schmitt, Valerie A. Schneider, Siddarth Selvaraj, Kishwar Shafin, Alaina Shumate, Nathan O. Stitziel, Catherine Stober, James Torrance, Justin Wagner, Jianxin Wang, Aaron Wenger, Chuanle Xiao, Aleksey V. Zimin, Guojie Zhang, Ting Wang, Heng Li, Erik Garrison, David Haussler, Ira Hall, Justin M. Zook, Evan E. Eichler, Adam M. Phillippy, Benedict Paten, Kerstin Howe, and Karen H. Miga. 2022. Nature.

Forebrain Nuclei Linked to Woodpecker Territorial Drum Displays Mirror Those That Enable Vocal Learning in Songbirds. Schuppe, Eric R., Lindsey Cantin, Mukta Chakraborty, Matthew T. Biegler, Electra R. Jarvis, Chun Chun Chen, Erina Hara, Mads F. Bertelsen, Christopher C. Witt, Erich D. Jarvis, and Matthew J. Fuxjager. 2022. PLoS Biology 20(9):e3001751. Supplementary Materials, Commentary.

False Gene and Chromosome Losses in Genome Assemblies Caused by GC Content Variation and Repeats. Kim, Juwan, Chul Lee, Byung June Ko, Dong Ahn Yoo, Sohyoung Won, Adam M. Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V Mello, Seoae Cho, Arang Rhie, and Heebal Kim. 2022. Genome Biology 1–29.

Widespread False Gene Gains Caused by Duplication Errors in Genome Assemblies. Ko, Byung June, Chul Lee, Juwan Kim, Arang Rhie, Dongahn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis, and Heebal Kim. 2022. BioRxiv 2021.04.09.438957.

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Hollis A Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony D Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa M Komoroske, Tanya Lama, Andrew J Crawford, Robert W Murphy, Samara Brown, Alan F Scott, Phillip A Morin, Erich D Jarvis, Olivier Fedrigo. GigaScience, Volume 11, 2022, giac068,

Reference Genomes for Conservation. Paez, Sadye, Robert H. S. Kraus, Beth Shapiro, M. Thomas P. Gilbert, Erich D. Jarvis, and Vertebrate Genomes. 2022. Science. Supplementary Materials

Oxytocin and Vasotocin Receptor Variation and the Evolution of Human Prosociality. Theofanopoulou, Constantina, Alejandro Andirkó, Cedric Boeckx, and Erich D. Jarvis. 2022. Comprehensive Psychoneuroendocrinology 11(April):100139. Supplementary Material.

Trends in Genetics genome of the month: The Kākāpō (Strigops Habroptilus). Dussex, Nicolas, Bruce C. Robertson, Love Dalén, and Erich D. Jarvis. 2022. Trends in Genetics. March 2022 :10–11.

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.

A High-Quality, Long-Read Genome Assembly of the Endangered Ring-Tailed Lemur (Lemur Catta). Palmada-Flores, Marc, Joseph D. Orkin, Bettina Haase, Jacquelyn Mountcastle, Mads F. Bertelsen, Olivier Fedrigo, Lukas F. K. Kuderna, Erich D. Jarvis, and Tomas Marques-Bonet. 2022. GigaScience 11:1–7. Supplementary Material, Supplement 1.

Merfin: Improved Variant Filtering, Assembly Evaluation and Polishing via k-Mer Validation. Formenti, Giulio, Arang Rhie, Brian P. Walenz, Françoise Thibaud-Nissen, Kishwar Shafin, Sergey Koren, Eugene W. Myers, Erich D. Jarvis, and Adam M. Phillippy. 2022. Nature Methods. Supplement 1.

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.

Haplotype-resolved assembly of diploid genomes without parental data. Cheng, Haoyu, Erich D. Jarvis, Olivier Fedrigo, Klaus-Peter Koepfli, Lara Urban, Neil J. Gemmell, and Heng Li. 2022. Nature Biotechnology, 1-4. Supplementary information.

Africa: sequence 100,000 species to safeguard biodiversity. Ebenezer, TGE., Anne W. T. Muigai, Simplice Nouala, Bouabid Badaoui, Mark Blaxter, Alan G. Buddie, Erich D. Jarvis, Jonas Korlach, Josiah O. Kuja, Harris A. Lewin, Roksana Majewska, Ntanganedzeni Mapholi, Suresh Maslamoney, Michèle Mbo’o-Tchouawou, Julian O. Osuji, Ole Seehausen, Oluwaseyi Shorinola, Christian Keambou Tiambo, Nicola Mulder, Cathrine Ziyomo & Appolinaire Djikeng. 2022. Nature.

Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9. Biegler, Matthew T., Olivier Fedrigo, Paul Collier, Jacquelyn Mountcastle, Bettina Haase, Hagen U. Tilgner, and Erich D. Jarvis. 2022. Scientific Reports 12(1):1–17 Supplement 1, Supplement 2.

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, European Reference Genome Atlas (ERGA) Consortium. (2022) Trends Ecol Evol. 37(3):197-202.

European Reference Genome Atlas (ERGA) Consortium: 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.

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 3, Supplement 4, Supplement 5, Supplement 6, Supplement 7.

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Mueller, Ralf C., Patrik Ellström, Kerstin Howe, Marcela Uliano-Silva, Richard I. Kuo, Katarzyna Miedzinska, Amanda Warr, Olivier Fedrigo, Bettina Haase, Jacquelyn Mountcastle, William Chow, James Torrance, Jonathan M. D. Wood, Josef D. Järhult, Mahmoud M. Naguib, Björn Olsen, Erich D. Jarvis, Jacqueline Smith, Lél Eöry, and Robert H. S. Kraus. 2021. GigaScience 10(12):1–15.

Oxytocin variation and brain region-specific geneexpression in a domesticated avian species. Tobari, Yasuko, Constantina Theofanopoulou, Chihiro Mori, Yoshimi Sato, Momoka Marutani, Sayaka Fujioka, Norifumi Konno, Kenta Suzuki, Akari Furutani, Shiomi Hakataya, Cheng Te Yao, En Yun Yang, Chia Ren Tsai, Pin Chi Tang, Chih Feng Chen, Cedric Boeckx, Erich D. Jarvis, and Kazuo Okanoya. 2022. Genes, Brain and Behavior. 21(2):1–15.

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans. Cahill, James A., Joel Armstrong, Alden Deran, Carolyn J. Khoury, Benedict Paten, David Haussler, and Erich D. Jarvis. 2021. Genome Research 31: 2035-2049.

Controlling for activity-dependent genes and behavioral states is critical for determining brain relationships within and across species. Biegler, Matthew T., Lindsey J. Cantin, Danielle L. Scarano, and Erich D. Jarvis. 2021. Journal of Comparative Neurology (2021); 529: 3206–3221.

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

A Relationship between the Characteristics of the Oval Nucleus of the Mesopallium and Parrot Vocal Response to Playback. Walløe, Solveig, Mukta Chakraborty, Thorsten J. S. Balsby, Erich D. Jarvis, Torben Dabelsteen, and Bente Pakkenberg. 2021. Brain, Behavior and Evolution 96(1):37–48.

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758 [version 1; peer review: 3 approved]. Hansen, Tom, Per Gunnar Fjelldal, Sigbjørn Lien, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A. McCarthy, William Chow, Kerstin Howe, James Torrance, Jonathan Wood, Ying Sims, Leanne Haggerty, Richard Challis, Jonathan Threlfall, Daniel Mead, and Richard Durbin. 2021. Wellcome Open Research 6:1–12.

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

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

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

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

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

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

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

At the beginning of speciation. Jarvis, Erich D. 2021. Science 371(6536):1312.

The role of sex chromosomes and sex hormones in vocal learning systems. Choe, Ha Na, and Erich D. Jarvis. 2021. Hormones and Behavior 132:104978.

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.

Hi-C scaffolded short-and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Peart, Claire R., Christina Williams, Saurabh D. Pophaly, Benjamin A. Neely, Frances M. D. Gulland, David J. Adams, Bee Ling Ng, William Cheng, Michael E. Goebel, Olivier Fedrigo, Bettina Haase, Jacquelyn Mountcastle, Arkarachai Fungtammasan, Giulio Formenti, Joanna Collins, Jonathan Wood, Ying Sims, James Torrance, Alan Tracey, Kerstin Howe, Arang Rhie, Joseph I. Hoffman, Jeremy Johnson, Erich D. Jarvis, Matthew Breen, and Jochen B. W. Wolf. 2021. Molecular Ecology Resources 21, 2455–2470.

Balanced imitation sustains song culture in zebra finches. Tchernichovski, Ofer, Sophie Eisenberg-Edidin, and Erich D. Jarvis. 2021. Nature Communications 12, 2562. Supplementary Information

As above, so below: Whole transcriptome profiling demonstrates strong molecular similarities between avian dorsal and ventral pallial subdivisions. Gedman, Gregory, Bettina Haase, Gillian Durieux, Matthew T. Biegler, Olivier Fedrigo, and Erich D. Jarvis. 2021. Journal of Comparative Neurology 529(12):3222–46

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.

Birdsong Learning and Culture: Analogies with Human Spoken Language. Hyland Bruno, Julia, Erich D. Jarvis, Mark Liberman, and Ofer Tchernichovski. 2021. Annual Review of Linguistics 2021 7:1, 449-472

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Liu, Jing, Zongji Wang, Jing Li, Luohao Xu, Jiaqi Liu, Shaohong Feng, Chunxue Guo, Shengchan Chen, Zhanjun Ren, Jinpeng Rao, Kai Wei, Yuezhou Chen, Erich D. Jarvis, Guojie Zhang, and Qi Zhou. 2021. Genome Research 31(3):497–511. Supplementary Information

2020

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

The Genome Sequence of the Eurasian Red Squirrel, Sciurus Vulgaris Linnaeus 1758. Blaxter, Mark, Daniel Mead, Kathryn Fingland, Rachel Cripps, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Dolucan, Olga Dudchenko, Arina D. Omer, David Weisz, Erez Lieberman Aiden, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A. McCarthy, Ying Sims, James Torrance, Alan Tracey, Kerstin Howe, Richard Challis, and Richard Durbin. 2020. Wellcome Open Research 5:1–12.

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

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

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

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

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

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

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

2019

Evolution of Vocal Learning and Spoken Language. Jarvis, Erich D. (2019) Science 366(6461):50–54. Supplementary Information.

Identification and Characterization of Primordial Germ Cells in a Vocal Learning Neoaves Species, the Zebra Finch. Jung, Kyung Min, Young Min Kim, Anna L. Keyte, Matthew T. Biegler, Deivendran Rengaraj, Hong Jo Lee, Claudio V. Mello, Tarciso A. F. Velho, Olivier Fedrigo, Bettina Haase, Erich D. Jarvis, and Jae Yong Han. (2019) FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology 33(12):13825–36.

Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype. Borges, Rui, João Fonseca, Cidália Gomes, Warren E. Johnson, Stephen J. O’Brien, Guojie Zhang, M. Thomas P. Gilbert, Erich D. Jarvis, Agostinho Antunes, and Sabyasachi Das. (2019) Genome Biology and Evolution 11(8):2244–55.

2018

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

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

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

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

2017

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Korlach, Jonas, Gregory Gedman, Sarah B. Kingan, Chen Shan Chin, Jason T. Howard, Jean Nicolas Audet, Lindsey Cantin, and Erich D. Jarvis. 2017. GigaScience, 6, 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. Lei, Huimeng, Zhangming Yan, Xiaohong Sun, Yue Zhang, Jianhong Wang, Caihong Ma, Qunyuan Xu, Rui Wang, Erich D. Jarvis, and Zhirong Sun. 2017. Brain & Language 174 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. Theofanopoulou, Constantina, Cedric Boeckx, and Erich D. Jarvis. 2017. Proceedings of the Royal Society B: Biological Sciences 284(1861).

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

Eliciting and Analyzing Male Mouse Ultrasonic Vocalization (USV) Songs. Chabout, Jonathan, Joshua Jones-Macopson, and Erich D. Jarvis. 2017. Journal of Visualized Experiments 2017(123):1–13.

Molecular Profiling Reveals Insight into Avian Brain Organization and Functional Columnar Commonalities with Mammals. Wada, Kazuhiro, Chun-Chun Chen, and Erich D. Jarvis. 2017. Pp. 273–89 in.

2016

A Foxp2 Mutation Implicated in Human Speech Deficits Alters Sequencing of Ultrasonic Vocalizations in Adult Male Mice. Chabout, Jonathan, Abhra Sarkar, Sheel R. Patel, Taylor Radden, David B. Dunson, Simon E. Fisher, and Erich D. Jarvis. 2016. Frontiers in Behavioral Neuroscience 10(OCT):1–18.

100&Change Citations

Bone-associated gene evolution and the origin of flight in birds. Machado, João Paulo, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, and Agostinho Antunes. 2016. BMC Genomics 17(1):1–15.

Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds. Almeida, Daniela, Emanuel Maldonado, Imran Khan, Liliana Silva, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O’Brien, Warren E. Johnson, and Agostinho Antunes. 2016. Genome Biology and Evolution 8(4):1115–31.

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

Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. Farré, Marta, Jitendra Narayan, Gancho T. Slavov, Joana Damas, Loretta Auvil, Cai Li, Erich D. Jarvis, David W. Burt, Darren K. Griffin, and Denis M. Larkin. 2016. Genome Biology and Evolution 8(8):2442–51.

2015

Surviving as an Underrepresented Minority Scientist in a Majority Environment. Jarvis, Erich D. 2015. Molecular Biology of the Cell 26(21):3692–96.

Brain evolution by brain pathway duplication. Chakraborty, Mukta, and Erich D. Jarvis. 2015. Philosophical Transactions of the Royal Society B: Biological Sciences 370(1684).

Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida. Khan, Imran, Zhikai Yang, Emanuel Maldonado, Cai Li, Guojie Zhang, M. Thomas P. Gilbert, Erich D. Jarvis, Stephen J. O’brien, Warren E. Johnson, and Agostinho Antunes. 2015. Molecular Biology and Evolution 32(11):2832–43.

Transsynaptic Tracing from Peripheral Targets with Pseudorabies Virus Followed by Cholera Toxin and Biotinylated Dextran Amines Double Labeling. Arriaga, Gustavo, Joshua J. Macopson, and Erich D. Jarvis. 2015. Journal of Visualized Experiments 2015(103):1–9.

Response to Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds.” Cracraft, Joel, 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, and Erich D. Jarvis. 2015. Science 349(6255):1460-b.

The Origin and Diversification of Birds. Brusatte, Stephen L., Jingmai K. O’Connor, and Erich D. Jarvis. 2015. Current Biology 25(19):R888–98.

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

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. Borges, Rui, 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).

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

The Basal Ganglia within a Cognitive System in Birds and Mammals. Petkov, Christopher I., and Erich D. Jarvis. 2015. Behavioral and Brain Sciences 37(6):568–69.

A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. Ribeiro, Ângela M., 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(1):1–8.

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.

Male mice song syntax depends on social contexts and influences female preferences. Chabout, Jonathan, Abhra Sarkar, David B. Dunson, and Erich D. Jarvis. 2015. Frontiers in Behavioral Neuroscience 9(APR):1–16

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.

Avianbase: A community resource for bird genomics. Eöry, Lél, M. Thomas P. Gilbert, Cai Li, Bo Li, Alan Archibald, Bronwen L. Aken, Guojie Zhang, Erich Jarvis, Paul Flicek, and David W. Burt. 2015. Genome Biology 16(1):2–5.

2014

Science

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

Core and region-enriched networks of behaviorally regulated genes and the singing genome. Whitney, Osceola, 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. 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.

Evidence for a single loss of mineralized teeth in the common avian ancestor. Meredith, Robert W., 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. Zhou, Qi, Jilin Zhang, Doris Bachtrog, Na An, Quanfei Huang, Erich D. Jarvis, M. Thomas P. Gilbert, and Guojie Zhang. (2014) Science 346 (6215): 1332 & 1246338-1 to -8.

Genome Biology

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.

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

Low frequency of paleoviral infiltration across the avian phylogeny. Cui, Jie, 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. Wirthlin, Morgan, 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. Greenwold, Matthew J., 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. Romanov, Michael N., 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. Callicrate, Taylor, Rebecca Dikow, James W Thomas, James C Mullikin, Erich D Jarvis, Robert Fleischer. (2014) BMC Genomics 15:1098.

GigaScience

Comparative genomic data of the Avian Phylogenomics Project. Zhang, Guojie, 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. 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

Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners. Wang, Rui, 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. Dai, Rui, 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, Lubica, Eva Bosikova, Martina Cvikova, Kristina Lukacova, Constance Scharff, and Erich D. Jarvis. 2014. Scientific Reports 4.

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.

Evolutionary genomics and adaptive evolution of the hedgehog gene family (SHH, IHH, and DHH) in vertebrates. Pereira, Joana, 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.

2013

Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities. Chen, Chun-Chun, Candace M. Winkler, Andreas R. Pfenning, and Erich D. Jarvis. 2013. Journal of Comparative Neurology 521(16):3666–3701.

Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns. Jarvis, Erich D., Jing Yu, Miriam V. Rivas, Haruhito Horita, Gesa Feenders, Osceola Whitney, Syrus C. Jarvis, Electra R. Jarvis, Lubica Kubikova, Ana E. P. Puck, Connie Siang-Bakshi, Suzanne Martin, Michael McElroy, Erina Hara, Jason Howard, Andreas Pfenning, Henrik Mouritsen, Chun Chun Chen, and Kazuhiro Wada. 2013. Journal of Comparative Neurology 521(16):3614–65.

Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species. Rosselló, Ricardo Antonio, Chun Chun Chen, Rui Dai, Jason T. Howard, Ute Hochgeschwender, and Erich D. Jarvis. 2013. ELife 2013(2):1–24.

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, 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.

Mouse vocal communication system: Are ultrasounds learned or innate? Arriaga, Gustavo, and Erich D. Jarvis. 2013. Brain and Language 124:96–116.

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

The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Parchman, T. L., Z. Gompert, M. J. Braun, R. T. Brumfield, D. B. McDonald, J. A. C. Uy, G. Zhang, E. D. Jarvis, B. A. Schlinger, and C. A. Buerkle. 2013. Molecular Ecology 22(12):3304–17.

2012

Dopamine regulation of human speech and bird song: A critical review. Simonyan, Kristina, 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. Koren, Sergey, 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, 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.

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

Convergent Differential Regulation of Parvalbumin in the Brains of Vocal Learners. Hara, Erina, 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. Arriaga, Gustavo, 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. Chen, Chun-Chun, 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. Horita, Haruhito, Masahiko Kobayashi, Wan chun Liu, Kotaro Oka, Erich D. Jarvis, and Kazuhiro Wada. 2012. PLoS ONE 7(8).

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. Nabholz, Benoit, 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. Roulhac, Petra L., 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 Nabholz, Benoit, Erich D. Jarvis, Hans Ellegren.(2010) Molecular Phylogenetics and Evolution. 57 (2010) 466–470.

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

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.

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Kunstner, Axel, 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 brain. Kubikova, Lubica, 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, Erina, Lubica Kubikova, Neal A. Hessler, and Erich D. Jarvis. 2009. Proceedings of the Royal Society B: Biological Sciences 276(1655):279–89.

Bird Song Systems: Evolution. Jarvis, E. D. 2009. Encyclopedia of Neuroscience 2:217–25. Oxford: Academic Press.

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

2008

Early onset of deafening-induced song deterioration and differential requirements of the pallial-basal ganglia vocal pathway. Horita, Haruhito, Kazuhiro Wada, and Erich D. Jarvis. 2008. European Journal of Neuroscience 28(12):2519–32.

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. Feenders, Gesa, Miriam Liedvogel, Miriam Rivas, Manuela Zapka, Haruhito Horita, Erina Hara, Kazuhiro Wada, Henrik Mouritsen, and Erich D. Jarvis. 2008. PLoS ONE 3(3).

Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics. Pinaud, Raphael, Cristina Osorio, Oscar Alzate, and Erich D. Jarvis. 2008. European Journal of Neuroscience 27(6):1409–22.

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. Hara, Erina, Lubica Kubikova, Neal A. Hessler, and Erich D. Jarvis. 2007. European Journal of Neuroscience 25(11):3406–16.

The pallial-basal ganglia pathway modulates the behaviorally-driven gene expression of the motor pathway. Kubikova, Lubica, Elena A. Turner, and Erich D. Jarvis. 2007. European Journal of Neuroscience 25(7):2145–60.

Lateralized activation of Cluster N in the brains of migratory songbirds. Liedvogel, Miriam, Gesa Feenders, Kazuhiro Wada, Nikolaus F. Troje, Erich D. Jarvis, and Henrik Mouritsen. 2007. European Journal of Neuroscience 25(4):1166–73.

2006

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

Computational inference of neural information flow networks. Smith, V. Anne, Jing Yu, Tom V. Smulders, Alexander J. Hartemink, and Erich D. Jarvis. 2006. PLoS Computational Biology 2(11):1436–49.
(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). Ferreira, Adriana R. J., Tom V. Smulders, Koichi Sameshima, Claudio V. Mello, and Erich D. Jarvis. 2006. Auk 123(4):1129–48.

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.

Social context-dependent singing-regulated dopamine. Sasaki, Aya, Tatyana D. Sotnikova, Raul R. Gainetdinov, and Erich D. Jarvis. 2006. Journal of Neuroscience 26(35):9010–14.

Selection for and against vocal learning in birds and mammals. Jarvis, Erich D. 2006. Ornithological Science 5(1):5–14. Special Issue on the Neuroecology of Birdsong.

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

2005

Rapid behavioral and genomic response to social opportunity. Burmeister, Sabrina S., Erich D. Jarvis, and Russell D. Fernald. 2005. PLoS Biology 3(11):1996–2004.

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

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

Differential Expression of Glutamate Receptors in Avian Neural Pathways for Learned Vocalization. Wada, Kazuhiro, 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. Yu, Jing, V. Anne Smith, Paul P. Wang, Alexander J. Hartemink, and Erich D. Jarvis. 2004. Bioinformatics 20(18):3594–3603. Supplementary Figures, Supplementary Table . Source Code.

Songbirds and the Revised Avian Brain Nomenclature. Reiner, Anton, 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. 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.

Fox P2 Expression in Avian Vocal Learners and Non-Learners. Haesler, Sebastian, Kazuhiro Wada, A. Nshdejan, Edward E. Morrisey, Thierry Lints, Eric D. Jarvis, and Constance Scharff. 2004. Journal of Neuroscience 24(13):3164–75.

Nature’s Music: The Science of BirdSong. Marler, Peter , Slabbekoorn, Hans (eds). Erich D. Jarvis (2004).

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.

Influence of Network Topology and Data Collection on Network Inference. Smith, V. A., E. D. Jarvis, and A. J. Hartemink. 2003. Pacific Symposium on Biocomputing 8 : 164-175 ( 2003 )

2002

Induction of Hippocampal Long-Term Potentiation during Waking Leads to Increased Extrahippocampal zif-268 Expression during Ensuing Rapid-Eye-Movement Sleep. Ribeiro, Sidarta, Claudio V. Mello, Tarciso Velho, Timothy J. Gardner, Erich D. Jarvis, and Constantine Pavlides. 2002. Journal of Neuroscience 22(24):10914–23.

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.

Evaluating functional network inference using simulation of complex biological systems. Smith, V. Anne, Erich D. Jarvis, and Alexander J. Hartemink. 2002. “Evaluating Functional Network Inference Using Simulations of Complex Biological Systems.” Bioinformatics 18 Suppl. 1: S216-S224.

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

Site-specific retinoic acid production in the brain of adult songbirds. Denisenko-Nehrbass, Natalia I., Erich Jarvis, Constance Scharff, Fernando Nottebohm, and Claudio V. Mello. 2000. Neuron 27(2):359–70.

A relationship between behavior, neurotrophin expression, and neuronal survival. Li, Xiao Ching, Erich D. Jarvis, Benjamin Alvarez-Borda, Daniel A. Lim, and Fernando Nottebohm. 2000. Proceedings of the National Academy of Sciences of the United States of America 97(15):8584–89.

Behaviorally-driven gene expression reveals hummingbird brain song nuclei. Jarvis, Erich D., Sidarta Ribeiro, Maria Luisa Da Silva, Dora Ventura, Jacques Vielliard, and Claudio V. Mello. 2000. Nature 406(6796):628–32.

Molecular mapping of brain areas involved in parrot vocal communication. Jarvis, Erich D., and Claudio V. Mello. 2000. Journal of Comparative Neurology 419(1):1–31.

A membrane-associated progesterone-binding protein, 25-Dx, is regulated by progesterone in brain regions involved in female reproductive behaviors. Krebs, Christopher J., Erich D. Jarvis, Johnny Chan, John P. Lydon, Sonoko Ogawa, and Donald W. Pfaff. 2000. Proceedings of the National Academy of Sciences of the United States of America 97(23):12816–21.

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. Krebs, Christopher J., Erich D. Jarvis, and Donald W. Pfaff. 1999. Proceedings of the National Academy of Sciences of the United States of America 96(4):1686–91.

Applying differential display to brain research. Mello, Claudio V., Erich D. 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. Jarvis, Erich D., Constance Scharff, Matthew R. Grossman, Joana A. Ramos, and Fernando Nottebohm. 1998. Neuron 21(4):775–88.

Classification and genetic characterization of pattern forming Bacilli. Rudner, Rivka, Oksana Martsinkevich, Wendy Leung, and Erich D. Jarvis. 1998. Molecular Microbiology 27(4):687–703.

1997

Selective expression of insulin-like growth factor II in the songbird brain. Holzenberger, Martin, Erich D. Jarvis, Christopher Chong, Matthew Grossman, Fernando Nottebohm, and Constance Scharff. 1997. Journal of Neuroscience 17(18):6974–87.

Isolation of song-regulated genes in the brain of songbirds. Mello, Claudio V., Erich D. 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. Jarvis, Erich D., Hubert Schwabl, Sidarta Ribeiro, and Claudio V. Mello Ca. 1997. 8(8):2073–77.

Motor-driven gene expression. Erich. D 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, Miriam V., Erich D. Jarvis, Seiichiro Morisaki, Henrietta Carbonado, Alice B. Gottleb, James G. Krueger. (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. Chew, Sek Jin, Claudio V. Mello, Fernando Nottebohm, Erich D. Jarvis & David S. 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. Jarvis, E. D., C. V. Mello, and F. Nottebohm. 1995. Learning & Memory (Cold Spring Harbor, N.Y.) 2(2):62–80.

1994

Determination of restriction fragment length polymorphisms in bacteria using ribosomal RNA genes. Rudner R., Studamire B., Erich D. 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., A. Chevrestt, S. R. Buchholz, B. Studamire, A. M. White, and E. D. Jarvis. 1993. Journal of Bacteriology 175(2):503–9.

1990

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

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

Chromosomal Organizations of rRNA operons in Bacillus subtilis. Jarvis, E. D., R. L. Widom, G. LaFauci, Y. Setoguchi, I. R. Richter, and R. Rudner. 1988. Genetics 120(3):625–35.

Instability of rRNA operons in Bacillus subtilis. Widom, R. L., E. D. Jarvis, G. LaFauci, and R. Rudner. 1988. Journal of Bacteriology 170(2):605–10.

1986

Mapping of rRNA genes with integrable plasmids in Bacillus subtilis. LaFauci, G., R. L. Widom, R. L. Eisner, E. D. Jarvis, and R. Rudner. 1986. Journal of Bacteriology 165(1):204–14.