pad

Current Work
MedBook live site
Tumor Map


Posters
AACR 2015 - Integrative genomic analysis to identify emergent enzalutamide resistance mechanisms in castration-resistant prostate cancer Josha Woodward, Carly King, Daniel Coleman, Robert Lisac, Jacob Schwartzman, Nicholas Wang, Martin Gleave, Joe Gray, George Thomas, Tomasz M. Beer, Katy Van Hook, Robert Baertsch, Ted Goldstein, Josh Stuart, Lina Gao, Joshua Urrutia, Laura Heiser, Joshi J. Alumkal.
ESMO 2014 - Neuroendocrine prostate cancer (NEPC) in patients (pts) with metastatic castration resistant prostate cancer (mCRPC) resistant to abiraterone (Abi)
ASCO 2014 - Identifying enzalutamide resistance mechanisms in men with castration-resistant prostate cancer.
ASCO 2014 - Molecular profiling of metastatic castration-resistant prostate cancer (mCRPC): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT).

Abstract describing MedBook

PhD

Customized Genome Browser   [pre-release "Retroposed Genes" data for retrocopy paper published below]


Code
MedBook source code uses Meteor
RetroFinder Pipeline

Climate Change in 31 seconds  or in 5 minutes  Science paper from Harvard


Publications

         h-index on Google Scholar pad
pad
Baertsch R, Diekhans M, Kent J, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics 2008, 9:466. Supplemental files

Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23.

Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, Schmitz J. Mosaic retroposon insertion patterns in placental mammals. Genome Res. 2009 May;19(5):868-75. Epub 2009 Mar 4.

Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. Epub 2008 Jan 24.

Deyou Zheng, Adam Frankish, Robert Baertsch, Philipp Kapranov, Alexandre Reymond , Siew Woh Choo , Yontao Lu , France Denoeud , Stylianos E Antonarakis , Michael Snyder , Yijun Ruan, Chia-Lin Wei , Thomas R. Gingeras , Roderic Guigo , Jennifer Harrow , and Mark B. Gerstein Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution. Genome Res. 2007 Jun;17(6):839-51.

ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 Dec;17(12):1797-808. Epub 2007 Nov 5.

Zhang Y, Luoh SM, Hon LS, Baertsch R, Wood WI, Zhang Z. GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W152-8. Epub 2007 Jun 1.

Katherine S. Pollard, Sofie R. Salama, Bryan King, Andrew Kern, Tim Dreszer, Sol Katzman, Adam Siepel, Jakob Skou Pedersen, Gill Bejerano, Robert Baertsch, Kate R. Rosenbloom, Jim Kent, David Haussler Forces Shaping the Fastest Evolving Regions in the Human Genome PLoS Genet. 2006 Oct 13;2(10):e168. Epub 2006 Aug 23.

Bowman BJ, McCall ME, Baertsch R, Bowman EJ. A model for the proteolipid ring and Bafilomycin / Concanamycin binding site in the vacuolar ATPase of Neurospora crassa. J Biol Chem. 2006 Aug 15; [Epub ahead of print]

Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. The UCSC Archaeal Genome Browser. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D407-10.

Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8.

Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, Scott WG. The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol. 2005 Jan;3(1):e5. Epub 2004 Dec 28.

W. James Kent, Robert Baertsch , Angie Hinrichs , Webb Miller and David Haussler. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes PNAS, September 30, 2003, vol. 100,no. 20 pp 11484-11489

Jeffrey A Bailey, Robert Baertsch, W James Kent, David Haussler and Evan E Eichler. Hotspots of mammalian chromosomal evolution" Genome Biology 2004, 5:R23

Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. "Human-mouse alignments with BLASTZ." Genome Research Vol. 13, Issue 1, 103-107, January 2003 [pdf] [ps] Software

Hillier et al."The DNA sequence of human chromosome 7" Nature 424, 157 - 164 (10 July 2003); doi:10.1038/nature01782

pad
Mouse Genome Sequencing Consortium. "Initial sequencing and comparative analysis of the mouse genome." Nature 420, 520-562. pad

pad
Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. "The UCSC Genome Browser Database." Nucleic Acids Res 2003 Jan 1;31(1):51-4 pad


pad



News Articles An Unusual RNA Structure In The SARS Virus Offers A Promising Target

Genome centers combine forces to validate a gene set for biomedical research