5021f89a5ebb829503b4b900280862429c09bf92 markd Sat Nov 5 13:21:42 2022 -0700 change GENCODE credits to link directly to GENCODE page diff --git src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html index cb855a4..dbcc30b 100644 --- src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html +++ src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html @@ -1,110 +1,29 @@ <h2>Credits</h2> -<p> This GENCODE release is the result of a collaborative effort among -the following laboratories: (contact: <A HREF="mailto:gencode@sanger.ac.uk"> -GENCODE at the Sanger Institute</A>) -<!-- above address is gencode at sanger.ac.uk --> +<p> The GENCODE project is an international collaboration funded by NIH/NHGRI + grant U41HG007234. More information is available + at <a href="https://www.gencodegenes.org/" target="_blank">www.gencodegenes.org</a>, + Participating GENCODE institutions and personnel can be found + <a href="https://www.gencodegenes.org/pages/all_participants.html" target="_blank"> + here</a>. </p> -<table style="text-align: left; width: 100%;" border="1" cellpadding="2" cellspacing="2"> - <tbody> - <tr> - <td style="vertical-align: top; text-align: left;"><b>Lab/Institution</b></td> - <td style="vertical-align: top; text-align: left;"><b>Contributors</b></td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.ebi.ac.uk/about/people/paul-flicek" target="_blank">GENCODE Principal Investigator</a>, EMBL European Bioinformatics Institute, Cambridge, UK</td> - <td style="vertical-align: top;">Paul Flicek</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.sanger.ac.uk/person/frankish-adam/" target="_blank">GENCODE Co-Principal Investigator</a>, EMBL European Bioinformatics Institute, Cambridge, UK</td> - <td style="vertical-align: top;">Adam Frankish</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.researchgate.net/scientific-contributions/16169870_Bronwen_Aken" target="_blank">GENCODE Co-Principal Investigator</a>, Wellcome Trust Sanger Institute (WTSI), Cambridge, UK</td> - <td style="vertical-align: top;">Bronwen Aken</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://kclpure.kcl.ac.uk/portal/tim.hubbard.html" target="_blank">Kings College, London, UK</a></td> - <td style="vertical-align: top;">Tim Hubbard</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.sanger.ac.uk/group/vertebrate-annotation/" target="_blank">HAVANA manual annotation group</a>, EMBL European Bioinformatics Institute, Cambridge, UK</td> - <td style="vertical-align: top;"> - Timothy Cutts, Jyoti Choudhary, Ed Griffiths, Ewan Birney, Jose Manuel - Gonzalez, Stephen Fitzgerald, Andrew Berry, Alexandra Bignell, Claire - Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab - Mukherjee, Gemma Barson, Matt Hardy, Angela Macharia</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.ebi.ac.uk/services/teams/ensembl" target="_blank">Ensembl</a>, EMBL European Bioinformatics Institute, Cambridge, UK</td> - <td style="vertical-align: top;"> - Carlos Garcia, Fergal Martin, Osagie Izuogu</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.crg.eu//roderic_guigo" - target="_blank">Centre de Regulació Genòmica (CRG)</a>, Barcelona, Spain</td> - <td style="vertical-align: top;"> - Roderic Guigó, Julien Lagarde, Barbara Uszczyńska</td> - </tr> - <tr> - <td><a href="http://genome.ucsc.edu/" target="_blank">UC Santa Cruz Genomics Institute, University of California Santa Cruz</a> (UCSC), USA</td> - <td style="vertical-align: top;">David Haussler, Mark Diekhans, Benedict Paten, Joel Armstrong, Ian Fiddes</td> - </tr> - <tr> - <td><a href="https://www.csail.mit.edu/" target="_blank">Computer Science and Artificial Intelligence Lab</a>,<a href="https://www.broadinstitute.org/" target="_blank">Broad Institute of MIT and Harvard</a>, USA</td> - <td style="vertical-align: top;">Manolis Kellis, Irwin Jungreis</td> - </tr> - <tr> - <td><a href="https://medicine.yale.edu/bbs/computational/" target="_blank">Computational Biology and Bioinformatics, Yale University</a> (Yale), USA</td> - <td>Mark Gerstein, Ekta Khurana, Cristina Sisu, Baikang Pei, Yan Zhang, Mihali Felipe</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.unil.ch/cig/home.html" target="_blank">Center for Integrative Genomics</a>,University of Lausanne, Switzerland</td> - <td style="vertical-align: top;">Alexandre Reymond, Cedric Howald, Anne-Maud Ferreira, Jacqueline Chrast</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;"><a href="https://www.cnio.es/ing/index.asp" target="_blank">Structural Computational Biology Group</a>, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain</td> - <td style="vertical-align: top;">Alfonso Valencia, Michael Tress, José Manuel Rodríguez, Victor de la Torre</td> - </tr> - <tr> - <td style="vertical-align: top; text-align: left;">Former members of the GENCODE project</td> - <td style="vertical-align: top;"> - Jennifer Harrow, James Gilbert, Electra Tapanari, Stephen Searle, - Rachel Harte, Daniel Barrell, Felix Kokocinski, Veronika Boychenko, - Toby Hunt, Catherine Snow, Gary Saunders, Sarah Grubb, Thomas Derrien, - Andrea Tanzer, Gang Fang, Mihali Felipe, Joanne Howes, Reena Halai, - Pablo Roman-Garcia, Michael Brent, Randall Brown, Jeltje van Baren - </td> - </tr> - </tbody> -</table> - <h2>References</h2> - <p> -Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa -A, Searle S <em>et al</em>. -<a href="https://genome.cshlp.org/content/22/9/1760.long" target="_blank"> -GENCODE: the reference human genome annotation for The ENCODE Project</a>. -<em>Genome Res</em>. 2012 Sep;22(9):1760-74. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22955987" target="_blank">22955987</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431492/" target="_blank">PMC3431492</a> +Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong +J, Barnes I <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/33270111" target="_blank"> +GENCODE 2021</a>. +<em>Nucleic Acids Res</em>. 2021 Jan 8;49(D1):D916-D923. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33270111" target="_blank">33270111</a>; +PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778937/" target="_blank">PMC7778937</a>; +DOI: <a href="http://dx.doi.org/10.1093/nar/gkaa1087" target="_blank">10.1093/nar/gkaa1087</a> </p> -<p> -Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, -Swarbreck D <em>et al</em>. -<a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-s1-s4" target="_blank"> -GENCODE: producing a reference annotation for ENCODE</a>. -<em>Genome Biol</em>. 2006;7 Suppl 1:S4.1-9. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16925838" target="_blank">16925838</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810553/" target="_blank">PMC1810553</a> -</p> <p>A full list of GENCODE publications are available at <a href="https://www.gencodegenes.org/pages/publications.html" target="_blank">The GENCODE Project web site</a>. </p> <h2>Data Release Policy</h2> <p>GENCODE data are available for use without restrictions.</p>