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Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biol. 2004;5(4):R23.

Bejerano G. Algorithms for variable length Markov chain modeling. Bioinformatics. 2004 Mar 22;20(5):788-9.

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.

Bejerano G, Haussler D, Blanchette M. Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics. 2004 Aug 4;20 Suppl 1:I40-I48.

Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science. 2004 May 28;304(5675):1321-5. [reprint] [supplement] [website]

Blanchette M, Green ED, Miller W, Haussler D. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 2004 Dec;14(12):2412-23.

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15.

Dudoit S, van der Laan MJ, Pollard KS. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol. 2004;3(1):Article13.

The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.

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.

International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716.

International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004 Oct 21;431(7011):931-45.

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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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.

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. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 2004;11(2-3):413-28.

Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. Proc. 8th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '04):177-186.

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.

van der Laan MJ, Dudoit S, Pollard KS. Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Stat Appl Genet Mol Biol. 2004;3(1):Article15.

van der Laan MJ, Dudoit S, Pollard KS. Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Stat Appl Genet Mol Biol. 2004;3(1):Article14.

Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes. Genome Res. 2004 Apr;14(4):517-27.

Blanchette M. A comparative analysis method for detecting binding sites in coding regions. Proc. 7th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '03):57-65.

Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D. The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol. 2003;68:245-54.

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.

Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R et al. The DNA sequence of human chromosome 7. Nature 2003 Jul 10;424(6945):157-64.

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.

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.

Roskin KM, Diekhans M, Haussler D. Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments. Proc. 7th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '03):257-266.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7.

Siepel A, Haussler D. Combining phylogenetic and hidden markov models in biosequence analysis. Proc. 7th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '03):277-286.

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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.

Wolfsberg TG, Wetterstrand KA, Guyer MS, Collins FS, Baxevanis AD. A user's guide to the human genome. Nat Genet. 2003 Sep;35 Suppl 1:4.

Clark TA, Sugnet CW, Ares M Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science. 2002 May 3;296(5569):907-10.

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.

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.

Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62.

Roskin KM, Diekhans M, Kent WJ, Haussler D. Score functions for assessing conservation in locally aligned regions of DNA from two species. UCSC Tech Report UCSC-CRL-02-30 Sep. 2002.

Wolfsberg TG, Wetterstrand KA, Guyer MS, Collins FS, Baxevanis AD. A user's guide to the human genome. Nat Genet. 2002 Sep;32 Suppl:1-79.

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The Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.

International Human Genome Mapping Consortium. A physical map of the human genome. Nature. 2001 Feb 15;409(6822):934-941.

Kent WJ, Haussler D. Assembly of the working draft of the human genome with gigAssembler. Genome Res. 2001 Sep;11(9)1541-1548.

Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN. Promoter region-based classification of genes. Pac Symp Biocomput. 2001;:151-63.

Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D. Knowledge-based analysis of microarray gene expression data using support vector machines. Proc Natl Acad Sci USA. 2000 Jan 4;97(1):262-7.

Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 2000 Oct;16(10):906-14.