f109d04eb4371b671b4d2810f0b3403320d800d3 markd Mon Aug 3 06:31:30 2026 -0700 Add PMID and DOI to all references on cite.html, move screenshot guidance into the best practices section. refs #37986 Every entry under "Genome Browser software and website references" now lists both a PMID and a DOI, verified against PubMed via NCBI E-utilities. Replace the superseded GenArk Res Sq preprint citation with the published Genome Biology version (PMID 37784172). Update the 2026 NAR update citation from the epub stub to the final 54(D1):D1331-D1335, and the SARS-CoV-2 entry to its issue citation. Move the Genome Browser screenshots paragraph out of the reference list and into "General best practices for publications" as a list item, and extend that section's intro sentence to mention screenshots. diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index ce4a4ae4ed9..bb907f75556 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -17,198 +17,220 @@

What manuscript to cite?

Please cite our latest paper, currently PMID 41251146, DOI 10.1093/nar/gkaf1250. In addition, you can reference the Genome Browser website in your manuscript: http://genome.ucsc.edu or mention in the text that you used the "UCSC Genome Browser". To cite one of our computational tools, see the reference section below.

General best practices for publications

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:

+Genome Browser stable link. We also have recommendations for screenshots used as figures:

  1. Assembly: 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".
  2. Chromosome Position: 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.
  3. Transcript: 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.
  4. Stable links: 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 "My Data > My Sessions", 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 Custom Tracks and Track Hubs.
    5. +
  5. Screenshots: 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 http://genome.ucsc.edu in the caption and cite +the most recent Genome Browser paper in the manuscript. As mentioned above, we recommend including +a My Data > My Session URL +of your screenshot to allow readers to interact with your data and get more information.

Genome Browser software and website references

-

-Genome Browser screenshots:
-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 http://genome.ucsc.edu in the caption and cite -the most recent Genome Browser paper in the manuscript. As mentioned above, we recommend including a My Data > My Session URL -of your screenshot to allow readers to interact with your data and get more information.

-

Most recent UCSC Genome Browser publication:
Casper J, Speir ML, Raney BJ, Perez G, Nassar LR, Lee CM, Hinrichs AS, Gonzalez JN, Fischer C, Diekhans M et al. The UCSC Genome Browser database: 2026 update. -Nucleic Acids Res. 2025 Nov 18;. -PMID: 41251146 +Nucleic Acids Res. 2026 Jan 6;54(D1):D1331-D1335. +PMID: 41251146; +DOI: 10.1093/nar/gkaf1250

Original UCSC Genome Browser publication:
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. -Genome Res. 2002 Jun;12(6):996-1006.

+Genome Res. 2002 Jun;12(6):996-1006. +PMID: 12045153; +DOI: 10.1101/gr.229102

All present and past UCSC Genome Browser updates sorted by date can be shown with this PubMed search.

BLAT:
Kent WJ. BLAT - the BLAST-like alignment tool. -Genome Res. 2002 Apr;12(4):656-64.

+Genome Res. 2002 Apr;12(4):656-64. +PMID: 11932250; +DOI: 10.1101/gr.229202

LiftOver:
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8. +PMID: 16381938; +DOI: 10.1093/nar/gkj144

UCSC Table Browser:
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. -Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

+Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. +PMID: 14681465; +DOI: 10.1093/nar/gkh103

UCSC Data Integrator and Variant Annotation Integrator:
Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D et al. UCSC Data Integrator and Variant Annotation Integrator. Bioinformatics. 2016 May 1;32(9):1430-2. +PMID: 26740527; +DOI: 10.1093/bioinformatics/btv766

BigWig and BigBed tools:
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. -Bioinformatics. 2010 Sep 1;26(17):2204-7.

+Bioinformatics. 2010 Sep 1;26(17):2204-7. +PMID: 20639541; +DOI: 10.1093/bioinformatics/btq351

RESTful API:
Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC et al. UCSC Genome Browser enters 20th year. Nucleic Acids Res. 2020 Jan 8;48(D1):D756-D761. +PMID: 31691824; +DOI: 10.1093/nar/gkz1012

Track Data Hubs:
Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. -Bioinformatics. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13.

+Bioinformatics. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13. +PMID: 24227676; +DOI: 10.1093/bioinformatics/btt637

Genome Browser in a Box (GBiB):
Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Navigating protected genomics data with UCSC Genome Browser in a Box. -Bioinformatics. 2015 Mar 1;31(5):764-6.

+Bioinformatics. 2015 Mar 1;31(5):764-6. +PMID: 25348212; +DOI: 10.1093/bioinformatics/btu712

UCSC Gene Sorter:
Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. -Genome Res. 2005 May;15(5):737-41.

+Genome Res. 2005 May;15(5):737-41. +PMID: 15867434; +DOI: 10.1101/gr.3694705

UCSC SARS-CoV-2 Genome Browser:
Fernandes JD, Hinrichs AS, Clawson H, et al. The UCSC SARS-CoV-2 Genome Browser. -Nat Genet. 2020 Sept 9; 52:991-998.

+Nat Genet. 2020 Oct;52(10):991-998. +PMID: 32908258; +DOI: 10.1038/s41588-020-0700-8

GenArk: UCSC Genome Repository:
Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM et al. - -GenArk: Towards a million UCSC Genome Browsers. -Res Sq. 2023 Apr 3;. + +GenArk: towards a million UCSC genome browsers. +Genome Biol. 2023 Oct 2;24(1):217. +PMID: 37784172; +DOI: 10.1186/s13059-023-03057-x

Other genome assemblies:
Manuscripts that include the use of Genome Browser assembly data from organisms other than human, 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.