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Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. Epub 2010 Oct 18.

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Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 Aug 19;333(6045):1019-24.

Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons. J Comput Biol. 2011 Mar;18(3):469-81.

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5. Epub 2010 Oct 30.

Roskin KM, Paten B, Haussler D. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. BMC Bioinformatics. 2011 May 10;12(1):144.

Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. The UCSC Cancer Genomics Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D951-9. Epub 2010 Nov 8.

The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 30;474:609-615.

Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, Gordon PB, Jakkula L et al. Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17761-6.

Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P et al. The Human Epigenome Browser at Washington University. Nat Methods. 2011 Nov;8:989-90. Epub 2011 Nov 29.

1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct;28(10):1097-105. Epub 2010 Sep 19.

Harte, R. A., Diekhans, M., Kent, W. J. & Haussler, D. Guide to the UCSC Genome Browser. Cambridge, MA: NPG Education, 2010.

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics. 2010 Sep 1;26(17):2204-7. Epub 2010 Jul 17.

Kern AD, Haussler D. A population genetic hidden Markov model for detecting genomic regions under selection. Mol Biol Evol. 2010 Jul;27(7):1673-85. Epub 2010 Feb 25.

Lowe CB, Bejerano G, Salama SR, Haussler D. Endangered species hold clues to human evolution. J Hered. 2010 Jul-Aug;101(4):437-47. Epub 2010 Mar 23.

Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010 May 14;86(5):749-64.

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Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita P, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. Epub 2009 Nov 11.

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. Epub 2009 Nov 17.

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-6.

Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec;7(12):995-1001. Epub 2010 Nov 7.

Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010 Jun 15;26(12):i237-45.

Cline MS, Kent WJ. Understanding genome browsing. Nat Biotechnol. 2009 Feb;27(2):153-5.

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Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN. Posttranscriptional crossregulation between Drosha and DGCR8. Cell. 2009 Jan 9;136(1):75-84.

Harte RA, Karolchik D, Kuhn RM, Kent WJ, Haussler D. Databases and Genome Browsers. In Speicher M, Antonarakis S, Motulsky AG. (eds): Vogel and Motulsky's Human Genetics, Principles and Approaches, 4th Edition, Springer, New York, 2009.

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The MGC Project Team. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19:2324-33.

Pohl AA, Sugnet CW, Clark TA, Smith K, Fujita PA, Cline MS. Affy Exon Tissues: exon levels in normal tissues in human, mouse, and rat. Bioinformatics. 2009 Sept 15;25(18):2442-3.

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.

Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn R, Karolchik D, Archie J, Lenburg M, Esserman L, Kent J, Haussler D, Wang T. The UCSC Cancer Genomics Browser. Nat Methods. 2009 Apr;6(4):239-40.

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics. 2008 Oct 8;9(1):466.

Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. Methods Mol Biol. 2008;422:171-84.

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Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proc Natl Acad Sci USA. 2008 Sep 23;105(38):14254-61.

Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, and Haussler D. DUPCAR: Reconstructing contiguous ancestral regions with duplications. J Computational Biol. 2008 Oct;15(8):1007-27.

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Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S, Pringle T, Schuster SC. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008 Nov 20;456(7220):387-90.

Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. In Murphy WJ. (ed): Methods in Molecular Biology: Phylogenomics, Springer, New York, 2008.

Schattner P. Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases. Cambridge University Press, Cambridge, UK, 2008.

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.

Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ. What everybody should know about the rat genome and its online resources. Nat Genet. 2008 May;40(5):523-7.

Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci USA. 2007 Nov 20;104(47):18613-8.

Zheng J, Yan J, Wang T, Mosbrook-Davis D, Dolan K, Christensen R, Stormo G, Haussler D, Lathrop R, Brachmann R, Burgess SM. Genome wide screens in yeast to identify potential binding sites and target genes of DNA binding proteins. Nucleic Acids Res. 2008 Jan;36(1):e8.

Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247.

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Dreszer TR, Wall GD, Haussler D, Pollard KS. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 2007 Oct;17(10):1420-30.

Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-218.

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Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, Trumbower H, Kern A, Kuhn R, Patrinos GP, Hughes J, Higgs D, Chui D, Scriver C, Phommarinh M, Patnaik SK, Blumenfeld O, Gottlieb B, Vihinen M, Valiaho J, Kent J, Miller W, Hardison RC. PhenCode: connecting ENCODE data with mutations and phenotype. Hum Mutat. 2007 Jun;28(6):554-62.

The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-861.

Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Comparative genomic analysis using the UCSC Genome Browser. In Bergman NH. (ed): Methods in Molecular Biology: Comparative Genomics, Volume 1, Springer, New York, 2007.

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Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA. 2007 May 8;104(19):8005-10.

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Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M Jr. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 2007 Mar 15;21(6):708-18.

Ohlson J, Pedersen JS, Haussler D, Öhman M. Editing modifies the GABAA receptor subunit a3. RNA. 2007 Mar;13:1-6.

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Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ. Variation resources at UC Santa Cruz. Nucleic Acids Res. 2007 Jan;35(Database issue):D716-20.

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Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci USA. 2007 Nov 20;104(47):18613-8.

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Yeang CH, Darot JF, Noller HF, Haussler D. Detecting the coevolution of biosequences--an example of RNA interaction prediction. Mol Biol Evol. 2007 Sep;24(9):2119-31.

Yeang CH and Haussler D. Detecting coevolution in and among protein domains. PLoS Comput Biol. 2007 Nov;3(11):e211.

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, et al. Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription and evolution. Genome Res. 2007 Jun;17(6):839-51.

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Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 4;441(7089):87-90.

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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.

Kabat JL, Barberan-Soler S, McKenna P, Clawson H, Farrer T, Zahler AM. Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes. PLoS Comput Biol. 2006 Jul 14;2(7):e86.

Kent J. XML, SQL, and C. Dr. Dobb's. 2006 Dec;31(12):32-9.

Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. Reconstructing contiguous regions of an ancestral genome. Genome Res. 2006 Dec;16(12):1557-65.

Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLoS Comput Biol. 2006 Apr;2(4):e33.

Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006 Oct 13;2(10):e168.

Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14;443(7108):167-72.

Schattner P, Diekhans M. Regions of extreme synonymous codon selection in mammalian genes Nucleic Acids Res. 2006 Mar 23;34(6):1700-10.

Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection. In Proc. 10th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '06).

Smith DI, Zhu Y, McAvoy S, Kuhn R. Common fragile sites, extremely large genes, neural development and cancer. Cancer Lett. 2006 Jan 28;232(1):48-57.

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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.

Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods. 2005 Jul;2(7):535-45. [reprint]

Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 2005 Nov;15(11):1553-65.

The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87.

Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 2005 Jun;15(6):800-8.

Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. The UCSC Proteome Browser. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D454-8.

The International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320.

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.

Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K et al. DNA sequence and analysis of human chromosome 18. Nature. 2005 Sep 22;437(7058):551-5.

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.

Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP et al. The DNA sequence of the human X chromosome. Nature. 2005 Mar 17;434(7031):325-37.

Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005;6(2):R12.

Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA et al. The finished DNA sequence of human chromosome 12. Nature. 2006 Mar 16;440(7082):346-51.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50.

Siepel A, Haussler D. Phylogenetic hidden Markov models. In Nielsen R. (ed): Statistical Methods in Molecular Evolution, Springer, New York, 2005; 325-251.

Smith AV, Thomas DJ, Munro HM, Abecasis GR. Sequence features in regions of weak and strong linkage disequilibrium. Genome Res. 2005 Nov;15(11):1519-34.

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.

Pollard KS, van der Laan MJ. Choice of a null distribution in resampling-based multiple testing. J Statistical Planning and Inference. 2004;125: 85-100.

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.

She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C et al. The structure and evolution of centromeric transition regions within the human genome. Nature. 2004 Aug 19;430(7002):857-64.

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.

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 2003 Aug 14;424(6950):788-93.

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.

BAC Resource Consortium. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8.

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.