PUBLICATIONS
Guhlin J, Le Lec MF, Wold J, Koot E, Winter D, Biggs PJ, Galla SJ, Urban L, Foster Y, Cox MP, Digby A, Uddstrom LR, Eason D, Vercoe D, Davis T; Kākāpō Recovery Team; Howard JT, Jarvis ED, Robertson FE, Robertson BC, Gemmell NJ, Steeves TE, Santure AW, Dearden PK. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nature Ecology & Evolution. 2023 Oct;7(10):1693-1705.
Population genomics of the critically endangered kākāpō. Dussex N, van der Valk T, Morales HE, Wheat CW, Díez-Del-Molino D, von Seth J, Foster Y, Kutschera VE, Guschanski K, Rhie A, Phillippy AM, Korlach J, Vercoe D, Howard J, Jarvis ED, Robertson BC, Dalén L. Cell Genomics 2021 Sep 8;1(1):100002
Rhie A, et.al.. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28. PMID: 33911273; PMCID: PMC8081667.
Insights into the evolution of longevity and cognition from the genomes of the Blue-fronted Amazon (Amazona aestiva) and other birds. Wirthlin M, Lima NCB, Guedes RLM, Cavaleirv N, Gonzaga L, Loss G, Chaves AV, Howard JT, Teixeira MdM, Schneider P, et.al. Current Biology (2018).
Divergence in problem-solving skills is associated with differential expression of glutamate receptors in wild finches. Audet JN, Kayello L, Ducatez S, Perillo S, Cauchard L. Howard JT, Lauren A. O’Connell LA, Jarvis ED, Lefebvre L. Science Advances (2018).
Characterization and genetic manipulation of primed stem cells into a functional naïve state with ESRRB. Rossello RA, Pfenning A, Howard JT, Hochgeschwender U. World Journal of Stem Cells. 2016 Oct 26;8(10):355-366.
De Novo PacBio long-read and phased avian genome assemblies correct and add to genes important in neuroscience research. Korlach K, Gedman G, Kingman S, Chin J, Howard JT, Cantin L, Jarvis ED bioRxiv 2017 Jan 28
Whole Genome Analyses Resolve the Early Branches to the Tree of Life of Modern Birds. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC et. al Science 2014 Dec 12;346(6215):1320-31.
Core and region enriched networks of behaviorally regulated genes and the singing genome. Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Science 2014 Dec 12;346(6215).
High-coverage sequencing and annotated assemblies of the budgerigar genome. Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Phillippy AM, Jarvis ED. Gigascience. 2014 Jul 8; 3:11.
Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners. Wang R, Chen CC, Hara E, Rivas MV, Roulhac PL, Howard JT, Chakraborty M, Audet JN, Jarvis ED. Journal of Comparative Neurology 2014 Apr 15;523(6):892-906.
Comparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation. Guojie Zhang et. al. Science 2014 Dec 12;346(6215):1311-20.
Phylogenomic Analyses Data of the Avian Phylogenomics Project. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, et. al. Gigascience 2014.
Convergent transcriptional specializations in the brains of humans and song learning birds. Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED. Science 2014 Dec 12; 346 (6215): 1256846.
Three crocodilians genomes reveal ancestral patterns of evolution among archosaurs. Richard E Green, et. al. Science 2014 Dec 12;346(6215):1254449.
Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species. Rosselló RA, Chen CC, Dai R, Howard JT, Hochgeschwender U, Jarvis ED. Elife. 2013 Sep 3; 2:e00036.
Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns. Jarvis ED, Yu J, Rivas MV, Horita H, Feenders G, Whitney O, Jarvis SC, Jarvis ER, Kubikova L, Puck AE, Siang-Bakshi C, Martin S, McElroy M, Hara E, Howard J, Pfenning A, Mouritsen H, Chen CC, Wada K. Journal of Comparative Neurology. 2013 Nov;521(16):3614-65.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Bradnam KR et.al. Gigascience. 2013 Jul 22;2(1):10.
Hybrid error correction and de novo assembly of single-molecule sequencing reads. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam M Phillippy. (2012) Nature Biotechnology. 10.
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. St John et al. (2012) Genome Biology. 13:415.
The genome of a Songbird. Warren WC et al. Nature 464, 757-762 (2010).
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C et al. 2006 Proceedings of the National Academy of Sciences U S A 103(41): 15212-15217.