74c5e052d6546daa0cdf2962b1c1f11961832af5 gperez2 Tue Oct 29 12:42:40 2024 -0700 Adding the latest nar paper to the htdoc pages, No RM diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index 72ea59d..99fe387 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -1,212 +1,212 @@ <!DOCTYPE html> <!--#set var="TITLE" value="UCSC Genome Browser: Citing Us" --> <!--#set var="ROOT" value="." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Citing the UCSC Browser in a Publication or Web Page</h1> <p> <b>You are free to use all graphics produced by this website in your published work or on other websites</b>, there is no need to contact us to request permission. See the <a href="/license/">license page</a> for details.</p> <h2>How to cite the UCSC Genome Browser</h2> <p> The UCSC Genome Browser is exclusively funded by the NIH, please consider citing us properly so that we may report usage and continue to develop this resource.</p> <h3>What manuscript to cite?</h3> <p> Please cite our latest paper, currently <a target=_blank -href="https://pubmed.ncbi.nlm.nih.gov/37953330/">PMID 37953330</a>, -DOI 10.1093/nar/gkad987. In addition, you can reference the Genome Browser website +href="https://pubmed.ncbi.nlm.nih.gov/39460617/">PMID 39460617</a>, +DOI 10.1093/nar/gkae974. In addition, you can reference the Genome Browser website in your manuscript: <a href="index.html" target="_blank">http://genome.ucsc.edu</a> or mention in the text that you used the "UCSC Genome Browser". To cite one of our computational tools, see the <a href="#ref">reference section</a> below.</p> <h3>General best practices for publications</h3> <p> The following are recommendations to improve communication in your scientific manuscript and ensure readers in 10 years can still find the DNA sequence that you analyzed. This requires mention of the assembly, chromosome position, any transcripts, and ideally also a Genome Browser stable link:</p> <ol> <li><b>Assembly:</b> Provide a clear mention of which genome assembly you are working with, e.g. "hg19" or "hg38". It is often helpful to place the assembly name directly on any supplemental file names if they contain annotations. E.g. "promoters.hg38.bed".</li> <li><b>Chromosome Position:</b> References to nucleotides should have full chromosome positions in the publication text or a supplemental table, whenever possible. Including only the position on the transcript or coding sequence can be confusing later as transcript models change. E.g. mention "NC_000023.11:g.32389644G>A", in addition to the transcript-based description "NM_004006.2:c.4375C>T". Or, in the manuscript, you can add the chromosome location in brackets, such as "(hg38,chr11:32389644)", when nucleotide 4375 of NM_004006.2 is discussed.</li> <li><b>Transcript:</b> Transcripts change. Always mention the accession of a transcript, not only the gene name. E.g. "NM_004006.2", not just "the longest transcript of the gene DMD". Gene symbols and transcripts change over time, so any sort of accession is helpful. <li><b>Stable links:</b> A UCSC Genome Browser link is a great way to share results or regions of interest in a way readers and reviewers can explore. It includes the assembly, position, all transcripts, any tracks visible, all filter settings that you made and any other settings in the browser. If you would like to include a link, do not copy the URL directly from the address bar, the one with "hgsid=xxx". These links are long and expire after a few days. Instead, use the menu option <a href="../cgi-bin/hgSession">"My Data > My Sessions"</a>, to generate a short, stable link to your current genome browser view. For more information on how to add your own annotations to share this way see <a href="../cgi-bin/hgCustom">Custom Tracks</a> and <a href="https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html">Track Hubs</a>.</li> </ol> <a name="ref"></a> <h2>Genome Browser software and website references</h2> <p> <strong>Genome Browser screenshots:</strong><br> Journal-quality screenshots of the Genome Browser can be produced by using the View -> PDF utility in the top navigation bar from the tracks page. When including a screenshot in your manuscript, reference <em>http://genome.ucsc.edu</em> in the caption and cite the most recent Genome Browser paper in the manuscript. As mentioned above, we recommend including a <a href="goldenPath/help/hgSessionHelp.html#Introduction">My Data > My Sesssion URL</a> of your screenshot to allow readers to interact with your data and get more information.</p> <p> <strong>Most recent UCSC Genome Browser publication:</strong><br> Nassar et al. <a href="https://pubmed.ncbi.nlm.nih.gov/36420891/" target="_blank"> The UCSC Genome Browser database: 2023 update</a>. <em>Nucleic Acids Research</em> 2023 PMID: 36420891, DOI: 10.1093/nar/gkac1072 </p> <p> <strong>Original UCSC Genome Browser publication:</strong><br> 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 browser at UCSC</a>. <em>Genome Res.</em> 2002 Jun;12(6):996-1006.</p> <p> All present and past UCSC Genome Browser updates sorted by date can be shown with this <a target=_blank href="https://pubmed.ncbi.nlm.nih.gov/?term=%28%28UCSC+Genome+Browser%5BTitle%5D%29+AND+%28update%5BTitle%5D+OR+updates%5BTitle%5D%29+AND+%22Nucleic+acids+research%22%5BJournal%5D%29+NOT+ENCODE%5BTitle%5D&sort=date">PubMed search</a>. </p> <hr> <p> <strong>BLAT:</strong><br> Kent WJ. <a href="http://www.genome.org/cgi/content/abstract/12/4/656" target="_blank">BLAT - the BLAST-like alignment tool</a>. <em>Genome Res.</em> 2002 Apr;12(4):656-64.</p> <hr> <p> <strong>LiftOver:</strong><br> Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F <em>et al</em>. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkj144" target="_blank"> The UCSC Genome Browser Database: update 2006</a>. <em>Nucleic Acids Res</em>. 2006 Jan 1;34(Database issue):D590-8. </p> <hr> <p> <strong>UCSC Table Browser:</strong><br> Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. <a href="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D493?ijkey=06tIQcBr2VZNz&keytype=ref" target="_blank">The UCSC Table Browser data retrieval tool</a>. <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D493-6.</p> <hr> <p> <strong>UCSC Data Integrator and Variant Annotation Integrator:</strong><br> Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D <em>et al</em>. <a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv766" target="_blank"> UCSC Data Integrator and Variant Annotation Integrator</a>. <em>Bioinformatics</em>. 2016 May 1;32(9):1430-2. </p> <hr> <p> <strong>BigWig and BigBed tools:</strong><br> Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. <a href="http://bioinformatics.oxfordjournals.org/content/26/17/2204.long" target="_blank">BigWig and BigBed: enabling browsing of large distributed data sets</a>. <em>Bioinformatics</em>. 2010 Sep 1;26(17):2204-7.</p> <hr> <p> <strong>RESTful API:</strong><br> Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC <em>et al</em>. <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. </p> <hr> <p> <strong>Track Data Hubs:</strong><br> Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. <a href="http://bioinformatics.oxfordjournals.org/content/30/7/1003" target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser</a>. <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13.</p> <hr> <p> <strong>Genome Browser in a Box (GBiB):</strong><br> Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. <a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu712" target="_blank"> Navigating protected genomics data with UCSC Genome Browser in a Box</a>. <em>Bioinformatics</em>. 2015 Mar 1;31(5):764-6.</p> <hr> <p> <strong>UCSC Gene Sorter:</strong><br> 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 relationships and mining data with the UCSC Gene Sorter</a>. <em>Genome Res</em>. 2005 May;15(5):737-41.</p> <hr> <p> <strong>UCSC SARS-CoV-2 Genome Browser:</strong><br> Fernandes JD, Hinrichs AS, Clawson H, et al. <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 Sept 9; 52:991-998.</p> <hr> <p> <strong>GenArk: UCSC Genome Archive:</strong><br> Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM <em>et al</em>. <a href="https://doi.org/10.21203/rs.3.rs-2697398/v1" target="_blank"> GenArk: Towards a million UCSC Genome Browsers</a>. <em>Res Sq</em>. 2023 Apr 3;. </p> <p><strong>Other genome assemblies:</strong><br> Manuscripts that include the use of Genome Browser assembly data from organisms other than human should, e.g. one of the thousands of GenArk assemblies that we provide, should cite the relevant sequencing paper. Usually this information can be found on the assembly description that appears when the genome is selected on our gateway page or on the NCBI GenBank BioProject page of the assembly.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->