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Jason T Howard
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 (link to http://www.unc.edu/depts/marzluff/Marzluff/Home.html) 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.
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 (link out to:
http://www.genomics.cn/en/index) and the University of Copenhagen (link out to:
http://geogenetics.ku.dk/research_groups/gilbert_groups/).
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 (link out to http://kakaporecovery.org.nz/), life technologies, and the Canon Research
Center (link out to http://www.carolinashealthcare.org/molecular-biology-facility) 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
https://www.linkedin.com/pub/jason-howard/13/445/36a
Lab Related Publications
Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C et al. 2006. A molecular
neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci U S A
103(41): 15212-15217.
Development of a transcript specific songbird oligo microarray for gene expression profiling. Howard JT, Pfenning AR, Rivas M,
Whitney, Hara E, Roulhac P, Ward JM, Agarwal P, Jarvis ED. SfN poster 197.27 2009
WC Warren et al. The genome of a Songbird Nature 464, 757-762 (2010)
Hybrid error correction and de novo assembly of single-molecule sequencing reads.
Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A
Rasko, W Richard McCombie, Erich D Jarvis & Adam M Phillippy (2012) Nature Biotechnology. 10.1038/nbt.2280.
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. St John et al. (2012) Genome
Biology. 13:415.
Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns.
Jarvis ED, Yu J, Rivas MV, Horita H, Feenders G, Whitney O, Jarvis SC, Jarvis ER, Kubikova L, Puck AE, Siang-Bakshi C, Martin S,
McElroy M, Hara E, Howard J, Pfenning A, Mouritsen H, Chen CC, Wada K. J Comp Neurol. 2013 Nov;521(16):3614-65. doi:
10.1002/cne.23404.
Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species.
Rosselló RA, Chen CC, Dai R, Howard JT, Hochgeschwender U, Jarvis ED. Elife. 2013 Sep 3;2:e00036. doi: 10.7554/eLife.00036.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Bradnam KR et.al. Gigascience. 2013
Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.
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. doi: 10.1186/2047-217X-3-11.
Comparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation. Guojie Zhang et. al. (in press 2014)
Whole Genome Analyses Resolve the Early Branches to the Tree of Life of Modern Birds. Erich D. Jarvis1, Siavash Mirarab, Andre J.
Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, Brant C. Faircloth, Benoit Nabholz1, Jason T. Howard, Alexander Suh, Claudia C.
Weber et. al (in press 2014)
Convergent transcriptional specializations in the brains of humans and song learning birds. Andreas R. Pfenning1*, Erina Hara1,
Osceola Whitney1, Miriam V. Rivas1, Rui Wang1, Petra L. Roulhac1, Jason T. Howard1, Morgan Wirthlin2, Peter V. Lovell2,
Ganeshkumar Ganapathy1, Jacquelyn Mouncastle1, et.al. (in press 2014)
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-Nicolas Audet, Manolis Kellis, Sayan Mukherjee, Saurabh
Sinha, Alexander J. Hartemink, Anne E. West, Erich D. Jarvis (in press 2014)
Three crocodilians genomes reveal ancestral patterns of evolution among archosaurs. Richard E Green, et. al. (in press 2014)
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, and Erich D. Jarvis J
Comparative Neurology (in press 2014)
Phylogenomic Analyses Data of the Avian Phylogenomics Project. Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer, Bo Li, Peter
Houde, Cai Li, Simon Y. W. Ho, Brant C. Faircloth, Benoit Nabholz, Jason T. Howard, Alexander Suh, Claudia C. Weber, Rute R. da
Fonseca, Alonzo Alfaro-Núñez, Nitish Narula, Liang Liu, Dave Burt, Hans Ellegren, Scott V. Edwards, Alexandros Stamatakis, David P.
Mindell, Joel Cracraft, Edward L. Braun, Tandy Warnow, Wang Jun, M Thomas P Gilbert, Guojie Zhang Gigascience 2014