0d02d453c1238599d373efd2052587feec62bc33 brianlee Fri Feb 19 11:10:26 2021 -0800 Rearranging pubs to alphabetical order and adding PMCIDs working towards Progress Report pubs. diff --git src/hg/htdocs/goldenPath/pubs.html src/hg/htdocs/goldenPath/pubs.html index e2fc817..3e237ac 100755 --- src/hg/htdocs/goldenPath/pubs.html +++ src/hg/htdocs/goldenPath/pubs.html @@ -18,84 +18,97 @@ <p> Gonzalez JN, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Powell CC, Nassar LR, Maulding ND, Lee CM, Lee BT, Hinrichs AS, Fyfe AC, Fernandes JD, Diekhans M, Clawson H, Casper J, Benet-Pagés A, Barber GP, Haussler D, Kuhn RM, Haeussler M, Kent WJ <a href="https://academic.oup.com/nar/article/49/D1/D1046/5998393" target="_blank"> 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> <h2>2020</h2> <!-- pending acceptance https://www.biorxiv.org/content/10.1101/2020.05.22.110833v1 does reference our grant "Towards complete and error-free genome assemblies of all vertebrate species" --> <p> -Aguet F, Ardlie KG, Lappalainen T, Haueussler M, Kent WJ, Lee CM, Powell CC, Rosenbloom KR, et. al. -<a href="https://science.sciencemag.org/content/369/6509/1318" target="_blank"> -The GTEx Consortium atlas of genetic regulatory effects across human tissues</a> -<em>Science</em>. 2020 Sep;369(6509):1318-1330 - +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> +</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> </p> <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> +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> -Fernandes, J.D., Zamudio-Hurtado, A., Clawson, H., Kent WJ., Haussler D., -Salama, SR., Haeussler M. -<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-020-00208-w" -target="_blank">The UCSC repeat browser allows discovery and visualization of -evolutionary conflict across repeat families</a>. -<em>Mobile DNA</em>. 2020 Mar 31;11(13). +GTEx Consortium.. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/32913098" target="_blank"> +The GTEx Consortium atlas of genetic regulatory effects across human tissues</a>. +<em>Science</em>. 2020 Sep 11;369(6509):1318-1330. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32913098" target="_blank">32913098</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7737656/" target="_blank">PMC7737656</a> </p> <p> Haeussler M. <a href="https://doi.org/10.1007/s10565-019-09497-1" target="_blank"> CRISPR off-targets: a question of context</a>. <em>Cell Biol Toxicol</em>. 2020 Feb;36(1):5-9. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31734746" target="_blank">31734746</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7056574/" target="_blank">PMC7056574</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> </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> + <!-- 2019 Publications --> <h2>2019</h2> <p> Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkz487" target="_blank"> Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double- strand break repair</a>. <em>Nucleic Acids Res</em>. 2019 Sep 5;47(15):7989-8003. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31165867" target="_blank">31165867</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735782/" target="_blank">PMC6735782</a> </p> <p> Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS,