5e27d82ebfe5ff7e366a47767f72965fcef09b5d brianlee Wed May 12 15:13:42 2021 -0700 Adding now available PMCIDs and new publication diff --git src/hg/htdocs/goldenPath/pubs.html src/hg/htdocs/goldenPath/pubs.html index bba8e24..645aa91 100755 --- src/hg/htdocs/goldenPath/pubs.html +++ src/hg/htdocs/goldenPath/pubs.html @@ -23,50 +23,62 @@ The UCSC Genome Browser database: 2021 update</a> <em>Nucleic Acids Res</em>. 2021 Jan 8;49(D1):D1046-D1057. PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/33221922/" target="_blank">33221922</a> PMCID: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7779060/" target="_blank">PMC7779060</a> </p> <p> Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33782609" target="_blank"> User-friendly, scalable tools and workflows for single-cell RNA-seq analysis</a>. <em>Nat Methods</em>. 2021 Apr;18(4):327-328. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33782609" target="_blank">33782609</a> </p> +<p> +Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan +A, Kim J <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/33911273" target="_blank"> +Towards complete and error-free genome assemblies of all vertebrate species</a>. +<em>Nature</em>. 2021 Apr;592(7856):737-746. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33911273" target="_blank">33911273</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081667/" target="_blank">PMC8081667</a> +</p> + <h2>2020</h2> <p> Birgmeier J, Deisseroth CA, Hayward LE, Galhardo LMT, Tierno AP, Jagadeesh KA, Stenson PD, Cooper DN, Bernstein JA, Haeussler M <em>et al</em>. <a href="http://dx.doi.org/10.1038/s41436-019-0643-6" target="_blank"> AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature</a>. <em>Genet Med</em>. 2020 Feb;22(2):362-370. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31467448" target="_blank">31467448</a> +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31467448" target="_blank">31467448</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7301356/" target="_blank">PMC7301356</a> </p> <p> Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, Ares M, Corbet-Detig R, Kent WJ, Haussler D, Haeussler M. <a href="https://www.nature.com/articles/s41588-020-0700-8" target="_blank">The UCSC SARS-CoV-2 Genome Browser</a>. <em>Nat Genet</em>. 2020 Sep 9;. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32908258" target="_blank">32908258</a> +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32908258" target="_blank">32908258</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8016453/" target="_blank">PMC8016453</a> </p> <p> Fernandes JD, Zamudio-Hurtado A, Clawson H, Kent WJ, Haussler D, Salama SR, Haeussler M. <a href="https://www.ncbi.nlm.nih.gov/pubmed/32266012" target="_blank"> The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families</a>. <em>Mob DNA</em>. 2020;11:13. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32266012" target="_blank">32266012</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110667/" target="_blank">PMC7110667</a> </p> <p> Ferraro NM, Strober BJ, Einson J, Abell NS, Aguet F, Barbeira AN, Brandt M, Bucan M, Castel SE, Davis JR <em>et al</em>. @@ -101,31 +113,32 @@ <a href="https://www.ncbi.nlm.nih.gov/pubmed/32913075" target="_blank"> Cell type-specific genetic regulation of gene expression across human tissues</a>. <em>Science</em>. 2020 Sep 11;369(6509). PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32913075" target="_blank">32913075</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8051643/" target="_blank">PMC8051643</a> </p> <p> Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkz1012" target="_blank"> UCSC Genome Browser enters 20th year</a>. <em>Nucleic Acids Res</em>. 2020 Jan 8;48(D1):D756-D761. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31691824" target="_blank">31691824</a> +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31691824" target="_blank">31691824</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145642/" target="_blank">PMC7145642</a> </p> <p> Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33206635" target="_blank"> Stability of SARS-CoV-2 phylogenies</a>. <em>PLoS Genet</em>. 2020 Nov;16(11):e1009175. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33206635" target="_blank">33206635</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721162/" target="_blank">PMC7721162</a> </p> <p> Turakhia Y, Thornlow B, Hinrichs AS, De Maio N, Gozashti L, Lanfear R, Haussler D, Corbett-Detig R. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33024970" target="_blank"> @@ -168,31 +181,32 @@ <em>Nature</em>. 2019 Sep;573(7772):75-82. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31316211" target="_blank">31316211</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731122/" target="_blank">PMC6731122</a> </p> <!-- 2018 Publications --> <h2>2018</h2> <p> Anderson KR, Haeussler M, Watanabe C, Janakiraman V, Lund J, Modrusan Z, Stinson J, Bei Q, Buechler A, Yu C, Thamminana SR, Tam L, Sowick MA, Alcantar T, O'Neil N, Li J, Ta L, Lima L, Roose-Girma M, Rairdan X, Durinck S, Warming S. <a href="http://dx.doi.org/10.1038/s41592-018-0011-5" target="_blank"> CRISPR off-target analysis in genetically engineered rats and mice</a>. <em>Nat Methods</em>. 2018 Jul;15(7):512-514. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29786090" target="_blank">29786090</a> +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29786090" target="_blank">29786090</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558654/" target="_blank">PMC6558654</a> </p> <p> Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L. <a href="http://dx.doi.org/10.1038/nprot.2018.005" target="_blank"> Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments</a>. <em>Nat Protoc</em>. 2018 May;13(5):946-986. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29651054" target="_blank">29651054</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182299/" target="_blank">PMC6182299</a> </p> <p> Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, @@ -356,31 +370,34 @@ <a href="http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=29021290" 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></p> +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27210042" target="_blank">27210042</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708852/" target="_blank">PMC5708852</a> +</p> + <p> Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J <em>et al</em>. <a href="http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1012-2" target="_blank">Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR</a>. <em>Genome Biol</em>. 2016 Jul 5;17(1):148. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27380939" target="_blank">27380939</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934014/" target="_blank">PMC4934014</a></p> <p> Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. <a href="https://academic.oup.com/bioinformatics/article/32/9/1430/1744314/" target="_blank">UCSC Data Integrator and Variant Annotation Integrator</a>. <em>Bioinformatics</em>. 2016 May 1;32(9):1430-2.