6a89c12dbd7cc73c93e8be489d4e7fedf8b06670 jnavarr5 Mon Aug 3 16:25:26 2026 -0700 Fixing dead and unstable publisher links, refs #37986 diff --git src/hg/htdocs/goldenPath/pubs.html src/hg/htdocs/goldenPath/pubs.html index 2019a701316..c56e8a9b9f1 100755 --- src/hg/htdocs/goldenPath/pubs.html +++ src/hg/htdocs/goldenPath/pubs.html @@ -332,31 +332,31 @@ Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. <a href="http://dx.doi.org/10.1038/s41431-018-0219-y" target="_blank"> Registered access: authorizing data access</a>. <em>Eur J Hum Genet</em>. 2018 Dec;26(12):1721-1731. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30069064" target="_blank">30069064</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6244209/" target="_blank">PMC6244209</a> </p> <p> Howard JM, Lin H, Wallace AJ, Kim G, Draper JM, Haeussler M, Katzman S, Toloue M, Liu Y, Sanford JR. -<a href="http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=29650551" target="_blank"> +<a href="https://genome.cshlp.org/content/28/5/689" target="_blank"> HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo</a>. <em>Genome Res</em>. 2018 May;28(5):689-698. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29650551" target="_blank">29650551</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932609/" target="_blank">PMC5932609</a> </p> <!-- 2017 Publications --> <h2>2017</h2> <p> Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, Oliveira G, Raghavan N, Shedlock A, do Amaral LR, Arican-Goktas HD, Assis JG, Baba EH, Baron OL, Bayne CJ, Bickham-Wright U, Biggar KK, Blouin M, Bonning BC, Botka C, Bridger JM, Buckley KM, Buddenborg SK, Lima Caldeira R, Carleton J, Carvalho OS, Castillo MG, Chalmers IW, Christensens M, Clifton S, Cosseau C, Coustau C, Cripps RM, Cuesta-Astroz Y, Cummins SF, di Stephano L, Dinguirard N, Duval D, Emrich S, Feschotte C, Feyereisen @@ -405,31 +405,31 @@ </p> <p> He C, Hu X, Jung RS, Larsson M, Tu Y, Duarte-Vogel S, Kim P, Sandoval NP, Price TR, Allan CM, Raney B <em>et al</em>. <a href="https://doi.org/10.1172/jci.insight.96783" target="_blank"> Lipoprotein lipase reaches the capillary lumen in chickens despite an apparent absence of GPIHBP1</a>. <em>JCI Insight</em>. 2017 Oct 19;2(20). PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29046479" target="_blank">29046479</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5846916/" target="_blank">PMC5846916</a> </p> <p> Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, GTEx Consortium., Engelhardt BE, Battle A. -<a href="http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=29021288" target="_blank"> +<a href="https://genome.cshlp.org/content/27/11/1843" target="_blank"> Co-expression networks reveal the tissue-specific regulation of transcription and splicing</a>. <em>Genome Res</em>. 2017 Nov;27(11):1843-1858. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29021288" target="_blank">29021288</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668942/" target="_blank">PMC5668942</a> </p> <p> Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, GTEx Consortium., Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group., Statistical Methods groups—Analysis Working Group., Enhancing GTEx (eGTEx) groups., NIH Common Fund., NIH/NCI., NIH/NHGRI., NIH/NIMH., NIH/NIDA., Biospecimen Collection Source Site—NDRI., Biospecimen Collection Source Site—RPCI., Biospecimen Core Resource—VARI., Brain Bank Repository—University of Miami Brain Endowment Bank., Leidos Biomedical—Project Management., ELSI Study., Genome Browser Data Integration @@ -455,31 +455,31 @@ </p> <p> Vivian J, Rao AA, Nothaft FA, Ketchum C, Armstrong J, Novak A, Pfeil J, Narkizian J, Deran AD, Musselman-Brown A, Schmidt H, Amstutz P, Craft B, Goldman M, Rosenbloom K, Cline M, O'Connor B, Hanna M, Birger C, Kent WJ, Patterson DA, Joseph AD, Zhu J, Zaranek S, Getz G, Haussler D, Paten B. <a href="http://dx.doi.org/10.1038/nbt.3772" target="_blank"> Toil enables reproducible, open source, big biomedical data analyses</a>. <em>Nat Biotechnol</em>. 2017 Apr 11;35(4):314-316. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28398314" target="_blank">28398314</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546205/" target="_blank">PMC5546205</a> </p> <p> Yang F, Wang J, GTEx Consortium., Pierce BL, Chen LS. -<a href="http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=29021290" target="_blank"> +<a href="https://genome.cshlp.org/content/27/11/1859" target="_blank"> Identifying <i>cis</i>-mediators for <i>trans</i>-eQTLs across many human tissues using genomic mediation analysis</a>. <em>Genome Res</em>. 2017 Nov;27(11):1859-1871. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29021290" target="_blank">29021290</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668943/" target="_blank">PMC5668943</a> </p> <!-- 2016 Publications --> <h2>2016</h2> <p> Haeussler M, Concordet JP. <a href="http://linkinghub.elsevier.com/retrieve/pii/S1673-8527(16)30044-3" target="_blank">Genome Editing with CRISPR-Cas9: Can It Get Any Better?</a>. <em>J Genet Genomics</em>. 2016 May 20;43(5):239-50. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27210042" target="_blank">27210042</a>; PMC: <a @@ -1178,31 +1178,31 @@ 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. <a href="http://www.cell.com/AJHG/fulltext/S0002-9297(10)00208-9" target="_blank">Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies</a>. <em>Am J Hum Genet</em>. 2010 May 14;86(5):749-64.</p> <p> Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, et al. <a href="http://www.nature.com/nature/journal/v470/n7332/full/nature09708.html" target="_blank">Mapping copy number variation by population-scale genome sequencing</a>. <em>Nature</em>. 2011 Feb 3;470(7332):59-65.</p> <p> Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. -<a href="http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=19858363" +<a href="https://genome.cshlp.org/content/20/1/110" target="_blank">Detection of nonneutral substitution rates on mammalian phylogenies</a>. <em>Genome Res</em>. 2010 Jan;20(1):110-21. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19858363" target="_blank">19858363</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798823" target="_blank">PMC2798823</a></p> <p> Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. <a href="http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=19906737" target="_blank">The UCSC Genome Browser database: update 2010</a>. <em>Nucleic Acids Res</em>. 2010 Jan;38(Database issue):D613-9. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19906737" target="_blank">19906737</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808870" target="_blank">PMC2808870</a></p> <p> Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, @@ -1396,31 +1396,31 @@ Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. <a href="http://linkinghub.elsevier.com/retrieve/pii/S0888-7543(08)00045-1" target="_blank">UCSC genome browser tutorial</a>. <em>Genomics</em>. 2008 Aug;92(2):75-84. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18514479" target="_blank">18514479</a></p> <!-- 2007 Publications --> <h2>2007</h2> <p> Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. In Murphy WJ. (ed): <em>Methods in Molecular Biology: Phylogenomics</em>, Springer, New York, 2007.</p> <p> Dreszer TR, Wall GD, Haussler D, Pollard KS. -<a href="http://www.genome.org/cgi/content/abstract/gr.6395807v1" target="_blank">Biased clustered +<a href="https://genome.cshlp.org/content/17/10/1420" target="_blank">Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion</a>. <em>Genome Res</em>. 2007 Oct;17(10):1420-30.</p> <p> Drosophila 12 Genomes Consortium. <a href="http://www.nature.com/nature/journal/v450/n7167/full/nature06341.html" target="_blank">Evolution of genes and genomes on the Drosophila phylogeny</a>. <em>Nature</em>. 2007 Nov 8;450(7167):203-218.</p> <p> The ENCODE Project Consortium <em>et al</em>. <a href="http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html" target="_blank">Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project</a>. <em>Nature</em>. 2007 Jun 14;447(7146):799-816.</p> <p> Giardine B, Riemer C, Hefferon T, Thomas D, Hsu F, Zielenski J, Sang Y, Elnitski L, Cutting G, @@ -1473,61 +1473,61 @@ <p> Lowe CB, Bejerano G, Haussler D. <a href="http://www.pnas.org/cgi/content/abstract/104/19/8005" target="_blank">Thousands of human mobile element fragments undergo strong purifying selection near developmental genes</a>. <em>Proc Natl Acad Sci USA</em>. 2007 May 8;104(19):8005-10.</p> <p> Ma J, Ratan A, Zhang L, Miller W, Haussler D. <a href="http://www.springerlink.com/content/u531m71r72464p45/?p=b7bf5c849a504388a9c79d4e11291df4&pi=9" target="_blank">A heuristic algorithm for reconstructing ancestral gene orders with duplications</a>. In <em>Lecture Notes in Computer Science: Comparative Genomics</em>, Springer, Berlin/Heidelberg, 2007;4751:122-135.</p> <p> Margulies E, Cooper G, Asimenos G, Thomas D, Dewey C, Siepel A, Birney E, Keefe D, Schwartz A, Hou M, <em>et al</em>. -<a href="http://www.genome.org/cgi/content/full/17/6/760" target="_blank">Analyses of deep mammalian +<a href="https://genome.cshlp.org/content/17/6/760" target="_blank">Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome</a>. <em>Genome Res</em>. 2007 Jun;17(6):760-74.</p> <p> 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. <a href="https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=17984227&dopt=AbstractPlus" target="_blank">28-Way vertebrate alignment and conservation track in the UCSC Genome Browser</a>. <em>Genome Res</em>. 2007 Dec;17(12):1797-808.</p> <p> Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M Jr. <a href="http://www.genesdev.org/cgi/content/full/21/6/708" target="_blank">Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay</a>. <em>Genes Dev</em> 2007 Mar 15;21(6):708-18.</p> <p> Ohlson J, Pedersen JS, Haussler D, Öhman M. <a href="http://www.rnajournal.org/cgi/doi/10.1261/rna.349107" target="_blank">Editing modifies the GABAA receptor subunit a3</a>. <em>RNA</em>. 2007 Mar;13:1-6.</p> <p> Rhesus Macaque Genome Sequencing and Analysis Consortium <em>et al</em>. <a href="http://www.sciencemag.org/cgi/content/full/316/5822/222" target="_blank">Evolutionary and biomedical insights from the rhesus macaque genome</a>. <em>Science</em>. 2007 Apr 13;316(5822):222-34.</p> <p> Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C <em>et al.</em> -<a href="http://www.genome.org/cgi/content/abstract/gr.7128207v1" target="_blank">Targeted discovery +<a href="https://genome.cshlp.org/content/17/12/1763" target="_blank">Targeted discovery of novel human exons by comparative genomics</a>. <em>Genome Res.</em> 2007 Dec;17(12):1763-73.</p> <p> Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN <em>et al</em>. <a href="http://www.nature.com/nature/journal/v450/n7167/full/nature06340.html" target="_blank">Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures</a>. <em>Nature</em>. 2007 Nov 8;450(7167):219-232.</p> <p> 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. <a href="http://nar.oxfordjournals.org/cgi/content/full/gkl1017v1?ijkey=7DRhTvzo9DqRBLK&keytype=ref" target="_blank">The ENCODE project at UC Santa Cruz</a>. @@ -1537,47 +1537,47 @@ <a href="http://nar.oxfordjournals.org/cgi/content/full/gkl953?ijkey=YienxYPtROeTBrH&keytype=ref" target="_blank">Variation resources at UC Santa Cruz</a>. <em>Nucleic Acids Res</em>. 2007 Jan;35(Database issue):D716-20.</p> <p> Wang, T. Using PhyloCon to Identify Conserved Regulatory Motifs. <em>Curr Protoc Bioinformatics</em>. 2007 Sep;Chapter 2:Unit 2.12.</p> <p> Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. <a href="http://www.pnas.org/cgi/content/abstract/0703637104v1" target="_blank">Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53</a>. <em>Proc Natl Acad Sci USA</em>. 2007 Nov 20;104(47):18613-8.</p> <p> Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, <em>et al</em>. -<a href="http://www.genome.org/cgi/content/full/17/6/852" target="_blank">Structured RNAs in the +<a href="https://genome.cshlp.org/content/17/6/852" target="_blank">Structured RNAs in the ENCODE selected regions of the human genome</a>. <em>Genome Res</em>. 2007 Jun;17(6):852-64.</p> <p> Yeang CH, Darot JF, Noller HF, Haussler D. <a href="http://mbe.oxfordjournals.org/cgi/content/abstract/24/9/2119" target="_blank">Detecting the coevolution of biosequences--an example of RNA interaction prediction</a>. <em>Mol Biol Evol</em>. 2007 Sep;24(9):2119-31.</p> <p> Yeang CH and Haussler D. <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030211" target="_blank">Detecting coevolution in and among protein domains</a>. <em>PLoS Comput Biol</em>. 2007 Nov;3(11):e211.</p> <p> Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, <em>et al.</em> -<a href="http://www.genome.org/cgi/content/full/17/6/839" target="_blank">Pseudogenes in the ENCODE +<a href="https://genome.cshlp.org/content/17/6/839" target="_blank">Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription and evolution</a>. <em>Genome Res</em>. 2007 Jun;17(6):839-51.</p> <p> Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle T, Haussler D. <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247" target="_blank">Comparative genomics search for losses of long-established genes on the human lineage</a>. <em>PLoS Comput Biol</em>. 2007 Dec;3(12):e247.</p> <!-- 2006 Publications --> <h2>2006</h2> <p> Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. <a href="http://www.nature.com/nature/journal/v441/n7089/abs/nature04696.html" target="_blank">A distal enhancer and an ultraconserved exon are derived from a novel retroposon</a>. @@ -1615,31 +1615,31 @@ <em>Bioinformatics</em>. 2006 May 1;22(9):1036-46. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16500937" target="_blank">16500937</a></p> <p> Kabat JL, Barberan-Soler S, McKenna P, Clawson H, Farrer T, Zahler AM. <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020086" target="_blank">Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes</a>. <em>PLoS Comput Biol</em>. 2006 Jul 14;2(7):e86.</p> <p> Kent J. <a href="http://www.ddj.com/dept/database/193402895;jsessionid=31G1HTV04PNE2QSNDLRCKH0CJUNN2JVN" target=_blank">XML, SQL, and C</a>. <em>Dr. Dobb's</em>. 2006 Dec;31(12):32-9.</p> <p> Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. -<a href="http://www.genome.org/cgi/content/abstract/16/12/1557" target="_blank">Reconstructing +<a href="https://genome.cshlp.org/content/16/12/1557" target="_blank">Reconstructing contiguous regions of an ancestral genome</a>. <em>Genome Res</em>. 2006 Dec;16(12):1557-65.</p> <p> Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. <a href="http://dx.doi.org/10.1371/journal.pcbi.0020033" target="_blank">Identification and classification of conserved RNA secondary structures in the human genome</a>. <em>PLoS Comput Biol</em>. 2006 Apr;2(4):e33.</p> <p> 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. <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020168" target="_blank">Forces shaping the fastest evolving regions in the human genome</a>. <em>PLoS Genet</em>. 2006 Oct 13;2(10):e168.</p> <p> @@ -1677,63 +1677,63 @@ gene, is involved in cellular stress response</a>. <em>Oncogene</em>. 2006 May 11;25(20):2901-8. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16462772" target="_blank">16462772</a></p> <!-- 2005 Publications --> <h2>2005</h2> <p> Bejerano G, Siepel AC, Kent WJ, Haussler D. <a href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16170870&query_hl=4&itool=pubmed_docsum" target="_blank">Computational screening of conserved genomic DNA in search of functional noncoding elements</a>. <em>Nat Methods</em>. 2005 Jul;2(7):535-45. [<a href="http://www.soe.ucsc.edu/%7Ejill/papers/nmeth05.pdf" target="_blank">reprint</a>]</p> <p> Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA. -<a href="http://www.genome.org/cgi/content/abstract/15/11/1553" target="_blank">Genomic regions +<a href="https://genome.cshlp.org/content/15/11/1553" target="_blank">Genomic regions exhibiting positive selection identified from dense genotype data</a>. <em>Genome Res</em>. 2005 Nov;15(11):1553-65.</p> <p> The Chimpanzee Sequencing and Analysis Consortium. <a href="http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html" target="_blank">Initial sequence of the chimpanzee genome and comparison with the human genome</a>. <em>Nature</em>. 2005 Sep 1;437(7055):69-87.</p> <p> Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. -<a href="http://www.genome.org/cgi/content/abstract/15/6/800" target="_blank">Ultraconserved +<a href="https://genome.cshlp.org/content/15/6/800" target="_blank">Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of <em>homothorax</em> mRNA splicing</a>. <em>Genome Res</em>. 2005 Jun;15(6):800-8.</p> <p> Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. <a href="https://academic.oup.com/nar/article/33/suppl_1/D454/2505399/The-UCSC-Proteome-Browser" target="_blank">The UCSC Proteome Browser</a>. <em>Nucleic Acids Res</em>. 2005 Jan 1;33(Database issue):D454-8.</p> <p> The International HapMap Consortium. <a href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16255080&query_hl=15&itool=pubmed_docsum" target="_blank">A haplotype map of the human genome</a>. <em>Nature</em>. 2005 Oct 27;437(7063):1299-320.</p> <p> Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/full/bti442?ijkey=H2U6JPUziZVjHc5&keytype=ref" target="_blank">LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources</a>. <em>Bioinformatics</em>. 2005 Jun 15;21(12):2814-20.</p> <p> Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. -<a href="http://www.genome.org/cgi/content/abstract/15/5/737" target="_blank">Exploring +<a href="https://genome.cshlp.org/content/15/5/737" target="_blank">Exploring relationships and mining data with the UCSC Gene Sorter</a>. <em>Genome Res</em>. 2005 May;15(5):737-41.</p> <p> Lucena B, Haussler D. <a href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16126665&query_hl=1" target="_blank">Counterexample to a Claim About the Reconstruction of Ancestral Character States</a>. <em>Syst Biol</em>. 2005 Aug;54(4):693-5.</p> <p> Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K <em>et al</em>. <a href="http://www.nature.com/nature/journal/v437/n7058/abs/nature03983.html" target="_blank">DNA sequence and analysis of human chromosome 18</a>. <em>Nature</em>. 2005 Sep 22;437(7058):551-5.</p> <p> @@ -1750,41 +1750,41 @@ <em>Nature</em>. 2005 Mar 17;434(7031):325-37.</p> <p> Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. <a href="http://genomebiology.com/2005/6/2/R12" target="_blank">Identifying genetic networks underlying myometrial transition to labor</a>. <em>Genome Biol</em>. 2005;6(2):R12.</p> <p> Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA <em>et al</em>. <a href="http://www.nature.com/nature/journal/v440/n7082/full/nature04569.html" target="_blank">The finished DNA sequence of human chromosome 12</a>. <em>Nature</em>. 2006 Mar 16;440(7082):346-51.</p> <p> 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. -<a href="http://www.genome.org/cgi/doi/10.1101/gr.3715005" target="_blank">Evolutionarily conserved +<a href="https://genome.cshlp.org/content/15/8/1034" target="_blank">Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes</a>. <em>Genome Res</em>. 2005 Aug;15(8):1034-50.</p> <p> Siepel A, Haussler D. <a href="http://compgen.bscb.cornell.edu/~acs/phylohmm.pdf" target="_blank">Phylogenetic hidden Markov models</a>. In Nielsen R. (ed): <em>Statistical Methods in Molecular Evolution</em>, Springer, New York, 2005; 325-251.</p> <p> Smith AV, Thomas DJ, Munro HM, Abecasis GR. -<a href="http://www.genome.org/cgi/content/abstract/15/11/1519" target="_blank">Sequence features in +<a href="https://genome.cshlp.org/content/15/11/1519" target="_blank">Sequence features in regions of weak and strong linkage disequilibrium</a>. <em>Genome Res</em>. 2005 Nov;15(11):1519-34.</p> <!-- <p> Sugnet, C., Srinivasan. K., Clark, T., O'Brien, G., Cline, M., Williams, A., Kulp, D., Blume, J., Haussler, D., and Ares, M. Alternative exons identified by splicing microarrays are rich in adjacent blocks of extreme intron sequence conservation. In preparation. --> <!-- 2004 Publications --> <h2>2004</h2> <p> Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. <a href="http://genomebiology.com/2004/5/4/R23" target="_blank">Hotspots of mammalian chromosomal @@ -1804,90 +1804,90 @@ Bejerano G, Haussler D, Blanchette M. <a href="https://academic.oup.com/bioinformatics/article/20/suppl_1/i40/218154/" target="_blank">Into the heart of darkness: large-scale clustering of human non-coding DNA</a>. <em>Bioinformatics</em>. 2004 Aug 4;20 Suppl 1:I40-I48.</p> <p> <a name="ultra1"></a> Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. <a href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15131266&query_hl=1" target="_blank">Ultraconserved elements in the human genome</a>. <em>Science</em>. 2004 May 28;304(5675):1321-5. [<a href="http://www.soe.ucsc.edu/~jill/papers/science04.pdf" target="_blank">reprint</a>] [<a href="http://www.soe.ucsc.edu/~jill/papers/scienceSupple04.pdf" target="_blank">supplement</a>] [<a href="http://www.soe.ucsc.edu/~jill/ultra.html" target="_blank">website</a>]</p> <p> Blanchette M, Green ED, Miller W, Haussler D. -<a href="http://www.genome.org/cgi/content/abstract/14/12/2412" target="_blank">Reconstructing large +<a href="https://genome.cshlp.org/content/14/12/2412" target="_blank">Reconstructing large regions of an ancestral mammalian genome in silico</a>. <em>Genome Res</em>. 2004 Dec;14(12):2412-23.</p> <p> Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. -<a href="http://www.genome.org/cgi/content/abstract/14/4/708" target="_blank">Aligning multiple +<a href="https://genome.cshlp.org/content/14/4/708" target="_blank">Aligning multiple genomic sequences with the threaded blockset aligner</a>. <em>Genome Res</em>. 2004 Apr;14(4):708-15.</p> <p> Dudoit S, van der Laan MJ, Pollard KS. <a href="http://www.bepress.com/sagmb/vol3/iss1/art13/" target="_blank">Multiple testing. Part I. Single-step procedures for control of general type I error rates</a>. <em>Stat Appl Genet Mol Biol</em>. 2004;3(1):Article13.</p> <p> The ENCODE Project Consortium. <a href="http://www.sciencemag.org/cgi/content/full/306/5696/636" target="_blank">The ENCODE (ENCyclopedia Of DNA Elements) Project</a>. <em>Science</em>. 2004 Oct 22;306(5696):636-40.</p> <p> Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D. -<a href="http://www.genome.org/cgi/content/abstract/14/10b/2034" target="_blank">Analysis of human +<a href="https://genome.cshlp.org/content/14/10b/2034" target="_blank">Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing</a>. <em>Genome Res</em>. 2004 Oct;14(10B):2034-40.</p> <p> Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M <em>et al</em>. <a href="http://www.nature.com/nature/journal/v428/n6982/full/nature02399.html" target="_blank">The DNA sequence and biology of human chromosome 19</a>. <em>Nature</em>. 2004 Apr 1;428(6982):529-35.</p> <p> International Chicken Genome Sequencing Consortium. <a href="http://www.nature.com/nature/journal/v432/n7018/full/nature03154.html" target="_blank">Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution</a>. <em>Nature</em>. 2004 Dec 9;432(7018):695-716.</p> <p> International Human Genome Sequencing Consortium. <a href="http://www.nature.com/nature/journal/v431/n7011/full/nature03001.html" target="_blank">Finishing the euchromatic sequence of the human genome</a>. <em>Nature</em>. 2004 Oct 21;431(7011):931-45.</p> <p> Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. -<a href="http://www.genome.org/cgi/content/abstract/14/4/528" target="_blank">Comparative +<a href="https://genome.cshlp.org/content/14/4/528" target="_blank">Comparative recombination rates in the rat, mouse, and human genomes</a>. <em>Genome Res</em>. 2004 Apr;14(4):528-38.</p> <p> Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. <a href="https://academic.oup.com/bioinformatics/article/20/suppl_1/i161/217234/Efficient-approximations-for-learning-phylogenetic" target="_blank">Efficient approximations for learning phylogenetic HMM models from data</a>. <em>Proc of ISMB 2004</em> and <em>Bioinformatics</em>. 2004 Aug 4;20 Suppl 1:I161-I168.</p> <p> Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. <a href="https://academic.oup.com/nar/article/32/suppl_1/D493/2505322/The-UCSC-Table-Browser-data-retrieval-tool" target="_blank">The UCSC Table Browser data retrieval tool</a>. <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D493-6.</p> <p> MGC Project Team. -<a href="http://www.genome.org/cgi/content/abstract/14/10b/2121" target="_blank">The status, +<a href="https://genome.cshlp.org/content/14/10b/2121" target="_blank">The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)</a>. <em>Genome Res</em>. 2004 Oct;14(10B):2121-7.</p> <p> Pollard KS, van der Laan MJ. Choice of a null distribution in resampling-based multiple testing. <em>J Statistical Planning and Inference</em>. 2004;125: 85-100.</p> <p> Rat Genome Sequencing Project Consortium. <a href="http://www.nature.com/nature/journal/v428/n6982/full/nature02426.html" target="_blank">Genome sequence of the brown Norway rat yields insights into mammalian evolution</a>. <em>Nature</em>. 2004 Apr 1;428(6982):493-521.</p> <p> Roskin KM, Diekhans M, Haussler D. <a href="http://www.liebertonline.com/doi/pdfplus/10.1089/1066527041410328" @@ -1925,31 +1925,31 @@ mice</a>. <em>Pac Symp Biocomput</em>. 2004;:66-77.</p> <p> van der Laan MJ, Dudoit S, Pollard KS. <a href="http://www.bepress.com/sagmb/vol3/iss1/art15/" target="_blank">Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives</a>. <em>Stat Appl Genet Mol Biol</em>. 2004;3(1):Article15.</p> <p> van der Laan MJ, Dudoit S, Pollard KS. <a href="http://www.bepress.com/sagmb/vol3/iss1/art14/" target="_blank">Multiple testing. Part II. Step-down procedures for control of the family-wise error rate</a>. <em>Stat Appl Genet Mol Biol</em>. 2004;3(1):Article14.</p> <p> Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. -<a href="http://www.genome.org/cgi/content/abstract/14/4/517" target="_blank">Patterns of insertions +<a href="https://genome.cshlp.org/content/14/4/517" target="_blank">Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes</a>. <em>Genome Res</em>. 2004 Apr;14(4):517-27.</p> <!-- 2003 Publications --> <h2>2003</h2> <p> Blanchette M. <a href="http://portal.acm.org/citation.cfm?id=640082&dl=ACM" target="_blank">A comparative analysis method for detecting binding sites in coding regions</a>. <em>Proc. 7th Int'l Conf. on Research in Computational Molecular Biology</em> (RECOMB '03):57-65.</p> <p> Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D. <a href="../pubs/Symp68Chiaromonte.pdf" target="_blank">The share of human genomic DNA under selection estimated from human-mouse genomic alignments</a>. @@ -1960,71 +1960,71 @@ using an ion channel. <em>Biophys J</em>. 2003 84(2):490A-490A Part 2 Suppl.</p> <p> Furey TS, Haussler D. <a href="https://www.ncbi.nlm.nih.gov/pubmed/12700172" target="_blank">Integration of the cytogenic map with the draft human genome sequence</a>. <em>Hum Mol Genet</em>. 2003 May 1;12(9):1037-1044.</p> <p> Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C <em>et al</em>. <a href="../pubs/Symp68Hardison.pdf" target="_blank">Global predictions and tests of erythroid regulatory regions</a>. <em>Cold Spring Harb Symp Quant Biol</em>. 2003;68:335-44.</p> <p> Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D <em>et al</em>. -<a href="http://www.genome.org/cgi/content/abstract/13/1/13" target="_blank">Covariation in +<a href="https://genome.cshlp.org/content/13/1/13" target="_blank">Covariation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution</a>. <em>Genome Res</em>. 2003 Jan;13(1):13-26.</p> <p> Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R <em>et al</em>. <a href="http://www.nature.com/nature/journal/v424/n6945/full/nature01782.html" target="_blank">The DNA sequence of human chromosome 7</a>. <em>Nature</em> 2003 Jul 10;424(6945):157-64.</p> <p> 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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165576/" target="_blank">The UCSC Genome Browser database</a>. <em>Nucleic Acids Res</em>. 2003 Jan 1;31(1):51-4.</p> <p> Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. <a href="https://www.pnas.org/content/100/20/11484" target="_blank"> Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes</a>. <em>Proc Natl Acad Sci USA</em>. 2003 Sep 30;100(20):11484-9.</p> <p> Margulies EH, Blanchette M; NISC Comparative Sequencing Program; Haussler D, Green ED. -<a href="http://www.genome.org/cgi/content/abstract/13/12/2507?etoc" target="_blank">Identification +<a href="https://genome.cshlp.org/content/13/12/2507" target="_blank">Identification and characterization of multi-species conserved sequences</a>. <em>Genome Res</em>. 2003 Dec;13(12):2507-18.</p> <p> Pollard KS, van der Laan MJ. Multiple testing for gene expression data: an investigation of null distributions with consequences for the permutation test. <em>Proceedings of the 2003 International MultiConference in Computer Science and Engineering</em>, METMBS'03 Conference, pp.3-9.</p> <p> Roskin KM, Diekhans M, Haussler D. <a href="http://dl.acm.org/citation.cfm?id=640109" target="_blank">Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments</a>. <em>Proc. 7th Int'l Conf. on Research in Computational Molecular Biology</em> (RECOMB '03):257-266.</p> <p> Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. -<a href="http://www.genome.org/cgi/content/abstract/13/1/103" target="_blank">Human-mouse alignments +<a href="https://genome.cshlp.org/content/13/1/103" target="_blank">Human-mouse alignments with BLASTZ</a>. <em>Genome Res</em>. 2003 Jan;13(1):103-7.</p> <p> Siepel A, Haussler D. <a href="http://compgen.bscb.cornell.edu/~acs/JCB04.pdf" target="_blank">Combining phylogenetic and hidden markov models in biosequence analysis</a>. <em>Proc. 7th Int'l Conf. on Research in Computational Molecular Biology</em> (RECOMB '03):277-286.</p> <p> Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC <em>et al</em>. <a href="http://www.nature.com/nature/journal/v424/n6950/abs/nature01858.html" target="_blank">Comparative analyses of multi-species sequences from targeted genomic regions</a>. <em>Nature</em>. 2003 Aug 14;424(6950):788-93.</p> <p> @@ -2055,43 +2055,43 @@ <a href="http://www3.interscience.wiley.com/cgi-bin/abstract/97517898/START" target="_blank">Information theoretic dissection of pairwise contact potentials</a>. <em>Proteins</em>. 2002 Oct 1;49(1):7-14.</p> <p> Karchin R, Karplus K, Haussler D. <a href="https://academic.oup.com/bioinformatics/article/18/1/147/244018" target="_blank">Classifying G-protein coupled receptors with support vector machines</a>. <em>Bioinformatics</em>. 2002 Jan;18(1):147-59.</p> <p> Karolchik D, Kent WJ. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834533/" target="_blank">The UCSC Genome Browser</a>. <em>Curr Protoc Bioinformatics</em>. 2002;Chapter 1:Unit 1.4.</p> <p> Kent WJ. -<a href="http://www.genome.org/cgi/content/abstract/12/4/656" target="_blank">BLAT - the BLAST-like +<a href="https://genome.cshlp.org/content/12/4/656" target="_blank">BLAT - the BLAST-like alignment tool</a>. <em>Genome Res.</em> 2002 Apr;12(4):656-64. PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/11932250/" target="_blank">11932250</a> </p> <p> Kent WJ, Brumbaugh H. <a href="http://www.linuxjournal.com/article.php?sid=5949" target="_blank">autoSql and autoXml: code generators from the Genome Project</a>. <em>Linux J</em>. 2002;99:68-77.</p> <p> Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. -<a href="http://www.genome.org/cgi/content/abstract/12/6/996" target="_blank">The human genome +<a href="https://genome.cshlp.org/content/12/6/996" target="_blank">The human genome browser at UCSC</a>. <em>Genome Res.</em> 2002 Jun;12(6):996-1006. PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/12045153/" target="_blank">12045153</a> </p> <p> Mouse Genome Sequencing Consortium. <a href="http://www.nature.com/nature/mousegenome/" target="_blank">Initial sequencing and comparative analysis of the mouse genome</a>. <em>Nature</em>. 2002 Dec 5;420(6915):520-62.</p> <p> Roskin KM, Diekhans M, Kent WJ, Haussler D. <a href="https://www.soe.ucsc.edu/research/technical-reports/UCSC-CRL-02-30/" target="_blank">Score functions for assessing conservation in locally aligned regions of DNA from two species</a>. <em>UCSC Tech Report UCSC-CRL-02-30</em> Jul. 2002.</p> <p> @@ -2108,31 +2108,31 @@ target="_blank">Integration of cytogenetic landmarks into the draft sequence of the human genome</a>. <em>Nature</em>. 2001 Feb 15;409(6822):953-8.</p> <p> The Genome Sequencing Consortium. <a href="http://www.nature.com/nature/journal/v409/n6822/abs/409860a0.html" target="_blank">Initial sequencing and analysis of the human genome</a>. <em>Nature</em>. 2001 Feb 15;409(6822):860-921.</p> <p> International Human Genome Mapping Consortium. <a href="http://www.nature.com/nature/journal/v409/n6822/full/409934a0.html" target="_blank">A physical map of the human genome</a>. <em>Nature</em>. 2001 Feb 15;409(6822):934-941.</p> <p> Kent WJ, Haussler D. -<a href="http://www.genome.org/cgi/content/abstract/GR-1832Rv1" target="_blank">Assembly of the +<a href="https://genome.cshlp.org/content/11/9/1541" target="_blank">Assembly of the working draft of the human genome with gigAssembler</a>. <em>Genome Res</em>. 2001 Sep;11(9)1541-1548.</p> <p> Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN. <a href="http://noble.gs.washington.edu/papers/prom-svm.html" target="_blank">Promoter region-based classification of genes</a>. <em>Pac Symp Biocomput</em>. 2001;151-63.</p> <!-- 2000 Publications --> <h2>2000</h2> <p> Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D. <a href="http://www.pnas.org/cgi/content/abstract/97/1/262" target="_blank">Knowledge-based analysis of microarray gene expression data using support vector machines</a>. <em>Proc Natl Acad Sci USA</em>. 2000 Jan 4;97(1):262-7.</p>