Baertsch R, Diekhans M, Kent J, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics Accepted.

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

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

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

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