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Jason T Howard

Recent Publications

  • Core and region enriched networks of behaviorally regulated genes and the singing genome. Science 2014
  • Convergent transcriptional specializations in the brains of humans and song learning birds. Science 2014
  • High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 2014
  • Comparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation. Science 2014
  • Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners.  J Comparative Neurology Science 2014
  • Whole Genome Analyses Resolve the Early Branches to the Tree of Life of Modern Birds. Science 2014
  • Three crocodilians genomes reveal ancestral patterns of evolution among archosaurs. Science 2014
  • Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species. Elife 2013

Research Interests

I consider myself the go to person in the lab when it comes to molecular biology work done in the lab. When I was an undergraduate, I worked in the Immunology lab of Kenneth Roux. During my work in the Roux lab, I did a lot of PCR and downstream cloning. Most of my work was focused on comparative genomics of the RAG1 gene in the immune system of lower vertebrates. Although I did not realize at it the time, I was doing comparative genomics! This was well before genome sequencing took off. For graduate school, I worked in the lab of William Marzluff studying the post transcriptional regulation of histone transcripts by SLBP (Stem Loop Binding Protein). My interest in histone regulation and histone modification is one of the reasons that drew me into looking at histone acetylation in song nuclei. We are using the regions where H3 histone is acetylated to identify regions in the genome where song nuclei are active. This will help us identify promoters that are specific or common to the song nuclei.


From Ann West’s Door of Fame (Data of the Week)

From Ann West’s Door of Fame (Data of the Week)

Before I joined the Jarvis lab I worked at Cogent Neuroscience. This startup biotech company was founded by faculty members from Department of Neurobiology at Duke University. During my time at Cogent Neuroscience I work on developing high throughput assays for discovering theuropeutics for Huntingtons disease. I also worked on identifying promoters that drive region specific gene expression in the brain.

I joined the Jarvis lab because I was interested in how behavior can alter gene expression in specific regions of the brain. For my work in the lab, I have focus on the song nuclei. For my first project in the lab I worked with Kazuhiro Wada on a songbird transcriptome sequencing project. I also worked with Patrick McConnell and Pankaj Agarwal on developing the songbirdtranscriptome.net database. I also supervised students who manually annotated the genes in the database. I later used our transcriptome along with two other published songbird transcriptomes to make an Agilent oligo array. This array was used by Osceola Whitney for his singing driven gene expression work. I also worked with Andreas Pfhenning when he identified human homologs to the genes we found in the songbird brain. He used this information to identify homologous regions in the songbird song nuclei and areas of the human brain by comparing the gene expression profiles. The human gene expression profiles were obtain from the Allan Brain Institute.

Currently, I am collecting tissue and blood samples from birds for genomic DNA isolation and downstream genome sequencing. We are attempting to sequence the genomes from all 30+ bird orders in an effort to better understand the phylogeny of birds.   We are also using the genomes to study the genetic basis of vocal learning using comparative genomics. This project is being done in collaboration with BGI and the University of Copenhagen.

A fun side project that I have is genome sequencing and analysis of endangered animals. I am finishing up a genome sequencing project on the critically endangered Kakapo. I am working closely with the New Zealand Kakapo recovery team, life technologies, and the Canon Research Center on this project. I would like use the genome information to better find markers for genetic diversity. The aim is to facilitate breeding that will help the survival of the Kakapo. I also have several other similar collaborations with other conservation biologists to help species survival.

Contact me:

howard [at] neuro.duke.edu
Lab phone number: 919-668-3537
Visit me at Linkedin

Lab Related Publications

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

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

Convergent transcriptional specializations in the brains of humans and song-learning birds. Andreas R. Pfenning, 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.

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

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

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

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

Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species Ricardo A. Rosselló, Chun C. Chen, Dai R, Jason T. Howard, Ute Hochgeschwender U, Erich D. Jarvis ED. Elife. (2013) Sep 3;2:e00036. doi: 10.7554/eLife.00036.

Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species. Bradnam Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod A Chapman, Guillaume Chpuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T Roderick 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 T. 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 Vieira31, Jun Wang, Kim C Worley, Shuangye Yin, Siu-Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou and Ian F Korf. Gigascience. (2013) Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns. Erich D. Jarvis, 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 T. Howard, Andreas Pfenning, Henrik Mouritsen, Chun-Chun Chen, and Kazuhiro Wada J. Comp Neurol. (2013) Nov;521(16):3614-65. doi: 10.1002/cne.23404.

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

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. John A St John, 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 Yar 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. 13:415.

The genome of a songbird. Wesley C. Warren, 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 T. 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. 464:757-762.

A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Kazuhiro Wada, Jason T. Howard, Patrick McConnell, Osceola Whitney, Thierry Lints, Miriam V. Rivas, Haruhito Horita, Michael A. Patterson, Stephanie A. White, Constance Scharff, Sebastian Haesler, Shengli Zhao, Hironobu Sakaguchi, Masatoshi Hagiwara, Toshiyuki Shiraki, Tomoko Hirozane-Kishikawa, Pate Skene, Yoshihide Hayashizaki, Piero Carninci, and Erich D. Jarvis (2006) Proc Natl Acad Sci USA 103: 15212-15217.