Selected Publications
| 2011 Alfoldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011 Aug 31. doi: 10.1038/nature10390. [Epub ahead of print] Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Gene inactivation and its implications for annotation in the era of personal genomics. Genes Dev. 2011 Jan 1;25(1):1-10. Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. 2011 Feb 15;27(4):441-8. Epub 2010 Dec 15. Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2011 Nov 15. [Epub ahead of print] 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. Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A. 2011 Oct 14. [Epub ahead of print] Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82. Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011 Jan 27;469(7331):529-53. 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. Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2011 Nov 9. [Epub ahead of print] 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. 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. 2010 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. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 3;470(7332):59-65. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. Epub 2009 Oct 26. 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. 2009 Cline MS, Kent WJ. Understanding genome browsing. Nat Biotechnol. 2009 Feb;27(2):153-5. Genome 10K Community of Scientists. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009 Nov;100:659-674. 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. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009 Jan;37:D755-D761. Mangan ME, Williams JM, Kuhn RM, Lathe WC. The UCSC Genome Browser: what every molecular biologist should know In Curr. Protoc. Mol. Biol. 88:19.9.1-19.9.28. John Wiley & Sons, Inc., New York, 2009. 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. 2008 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. Buckley M, Walker A, Ho SY, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Koon H, Penkman K, Elsworth B, Ashford D, Solazzo C, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney B, Zylber MI, Gilbert MT, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, Collins MJ. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science. 2008 Jan 4;319(5859):33; author reply 33. Karolchik D, Kuhn, RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 2008 Jan;36:D773-9. Lathe W, Williams J, Mangan M, Karolchik D. Genomic data resources: challenges and promises. Nature Education. 2008;1(3). Ma J. Reconstructing ancient DNA sequences in silico. In Cooper DN and Kehrer-Sawatzki H. (ed): Handbook of Human Molecular Evolution, John Wiley & Sons, Inc., New Jersey, 2008. 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. Mangan ME, Williams JM, Lathe SM, Karolchik D, Lathe WC III. UCSC Genome Browser: Deep support for molecular biomedical research. In El-Gewely MR (ed): Biotechnology Annual Review. 14:63-108, Elsevier B.V., Amsterdam, 2008. 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. Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. UCSC genome browser tutorial. Genomics. 2008 Aug;92(2):75-84. 2007 Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. In Murphy WJ. (ed): Methods in Molecular Biology: Phylogenomics, Springer, New York, 2007. 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. The ENCODE Project Consortium et al. 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. 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. Karolchik D, Hinrichs AS, Kent WJ. The UCSC Genome Browser. Curr Protoc Bioinformatics. 2007 Mar;Chapter 1:Unit 1.4. Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human genome ultraconserved elements are ultraselected. Science. 2007 Aug 17;317(5840):915. [reprints] [supporting online materials] [materials and methods] Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent, WJ. The UCSC Genome Browser database: update 2007. Nucleic Acids Res. 2007 Jan;35(Database issue):D668-73. Li G, Ma J, Zhang L. Selecting genomes for reconstruction of ancestral genomes. 5th Annual RECOMB Satellite Workshop on Comparative Genomics. In McLysaght and A, Huson, DH. Lecture Notes in Computer Science: Comparative Genomics, 4751: 110-21, Springer, Berlin/Heidelberg, 2007. 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. Ma J, Ratan A, Zhang L, Miller W, Haussler D. A heuristic algorithm for reconstructing ancestral gene orders with duplications. In Lecture Notes in Computer Science: Comparative Genomics, Springer, Berlin/Heidelberg, 2007;4751:122-135. Margulies E, Cooper G, Asimenos G, Thomas D, Dewey C, Siepel A, Birney E, Keefe D, Schwartz A, Hou M, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun;17(6):760-74. 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. 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. Rhesus Macaque Genome Sequencing and Analysis Consortium et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13;316(5822):222-34. Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C et al. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 8;450(7167):219-232. Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs, AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS, The ENCODE Project Consortium, Haussler D, Kent WJ. The ENCODE project at UC Santa Cruz. Nucleic Acids Res. 2007 Jan;35(Database issue):D663-7. 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. Wang, T. Using PhyloCon to Identify Conserved Regulatory Motifs. Curr Protoc Bioinformatics. 2007 Sep;Chapter 2:Unit 2.12. 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. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 Jun;17(6):852-64. 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. Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle T, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. 2006 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. Darot J, Yeang CH, Haussler D. Detecting the dependent evolution of biosequences. In Proc. 10th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '06) (2006). DiBiase A, Harte RA, Zhou Y, Zon L, Kent WJ. Piloting the zebrafish genome browser. Dev Dyn. 2006 Mar;235(3):747-53. Drake JA, Bird C, Nemesh J, Thomas DJ, Newton-Cheh C, Reymond A, Excoffier L, Attar H, Antonarakis SE, Dermitzakis ET, Hirschhorn JN. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet. 2006 Feb;38(2):223-7. 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. 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. Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW et al. Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature. 2006 Mar 23;440(7083):497-500. 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. 2005 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. 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