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Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006 May 1;22(9):1036-46. PMID: 16500937

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Zhu Y, McAvoy S, Kuhn R, Smith DI. RORA, a large common fragile site gene, is involved in cellular stress response. Oncogene. 2006 May 11;25(20):2901-8. PMID: 16462772

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Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15;21(12):2814-20.

Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 2005 May;15(5):737-41.

Lucena B, Haussler D. Counterexample to a Claim About the Reconstruction of Ancestral Character States. Syst Biol. 2005 Aug;54(4):693-5.

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Bejerano G, Friedman N, Tishby N. Efficient Exact p-Value Computation for Small Sample, Sparse and Surprising Categorical Data. J Comput Biol. 2004;11(5):867-86.

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Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D. Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Res. 2004 Oct;14(10B):2034-40.

Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M et al. The DNA sequence and biology of human chromosome 19. Nature. 2004 Apr 1;428(6982):529-35.

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Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 2004 Apr;14(4):528-38.

Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. Efficient approximations for learning phylogenetic HMM models from data. Proc of ISMB 2004 and Bioinformatics. 2004 Aug 4;20 Suppl 1:I161-I168.

Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7.

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Roskin KM, Diekhans M, Haussler D. Score functions for determining regional conservation in two-species local alignments. J Comput Biol. 2004;11(2-3):395-411.

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Siepel A, Haussler D. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol. 2004 Mar;21(3):468-88.

Sugnet CW, Kent WJ, Ares M Jr, Haussler D. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput. 2004;:66-77.

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DeGuzman V, Winters-Hilt S, Solbrig A, Sughrue W, Deamer D, Haussler D, Akeson M. Sequence-dependent fraying of single DNA molecules measured in real time at 5 angstrom resolution using an ion channel. Biophys J. 2003 84(2):490A-490A Part 2 Suppl.

Furey TS, Haussler D. Integration of the cytogenic map with the draft human genome sequence. Hum Mol Genet. 2003 May 1;12(9):1037-1044.

Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C et al. Global predictions and tests of erythroid regulatory regions. Cold Spring Harb Symp Quant Biol. 2003;68:335-44.

Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D et al. Covariation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution. Genome Res. 2003 Jan;13(1):13-26.

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Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA. 2003 Sep 30;100(20):11484-9.

Margulies EH, Blanchette M; NISC Comparative Sequencing Program; Haussler D, Green ED. Identification and characterization of multi-species conserved sequences. Genome Res. 2003 Dec;13(12):2507-18.

Pollard KS, van der Laan MJ. Multiple testing for gene expression data: an investigation of null distributions with consequences for the permutation test. Proceedings of the 2003 International MultiConference in Computer Science and Engineering, METMBS'03 Conference, pp.3-9.

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Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Siani-Rose MA, Ares M, Kulp DC, Haussler D. Gene structure-based splice variant deconvolution using a microarray platform. Proc. of ISMB 2003 and Bioinformatics. 2003;19 Suppl 1:i315-22.

Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D. Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophys J. 2003 Feb;84(2 Pt 1):967-76.

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Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG Jr, Haussler D. Information theoretic dissection of pairwise contact potentials. Proteins. 2002 Oct 1;49(1):7-14.

Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics. 2002 Jan;18(1):147-59.

Karolchik D, Kent WJ. The UCSC Genome Browser. Curr Protoc Bioinformatics. 2002;Chapter 1:Unit 1.4.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.

Kent WJ, Brumbaugh H. autoSQL and autoXml: code generators from the Genome Project. Linux J. 2002;99:68-77.

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