The UCSC Genome Browser database: 2027 update
5 affiliations
- 1Genomics Institute, University of California Santa Cruz , Santa Cruz, CA 95064 ,
- 2Institute of Neurogenomics, Helmholtz Zentrum München GmbH—German Research Center for Environmental Health , Neuherberg 85764 ,
- 3Medical Genetics Center (Medizinisch Genetisches Zentrum) , Munich 80335 ,
- 4Tricode Genomics , Santa Cruz, CA 95064 ,
- 5Quantitative and Computational Biology, University of Southern California , Los Angeles, CA 90089 ,
Abstract
Since 2000, the UCSC Genome Browser (https://genome.ucsc.edu) has served as a standard tool for visualizing and comparing annotations across thousands of genome assemblies. Users can browse and visualize a wide range of data types from gene annotations to regulatory regions and comparative genome alignments. Once the data view is configured, the Genome Browser image can be exported for use in publications. Beyond visualization, users can use our tools to compare and export the annotations for further analysis. This year’s feature updates include the full release of a tool to copy annotations between related assemblies, QuickLift; feature additions to our data-hosting service HubSpace to enable live editing of configuration files; two new display configurability options: “My Annotations” and custom item coloring; and several improvements to genome assembly discovery and track management. Beyond these new features, 28 new annotation tracks have been added across three broad categories: variant databases and interpretation, gene regulation, and transcriptome and gene expression. These include ENCODE4 cCREs and other ENCODE4 regulatory annotations, variant frequencies and phased variants from national sequencing projects, and two massively parallel reporter assay tracks.
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BibTeX
@article{speir2026ucsc,
title = {{The UCSC Genome Browser database: 2027 update}},
author = {Matthew L Speir and Marijke J van Baren and Galt P Barber and Anna Benet-Pages and Johannes Birgmeier and Jonathan Casper and Hiram Clawson and Mark Diekhans and Clay Fischer and Jairo Navarro Gonzalez and Angie S Hinrichs and Christopher M Lee and Luis R Nassar and Gerardo Perez and Brian J Raney and James Robinson and Andrew D Smith and Eliza Alde and Barali Kitiyakara and David Haussler and William James Kent and Maximilian Haeussler},
journal = {Nucleic Acids Research},
year = {2026},
month = nov,
doi = {10.1093/nar/gkag1115},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1115/9013043},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - The UCSC Genome Browser database: 2027 update
AU - Matthew L Speir
AU - Marijke J van Baren
AU - Galt P Barber
AU - Anna Benet-Pages
AU - Johannes Birgmeier
AU - Jonathan Casper
AU - Hiram Clawson
AU - Mark Diekhans
AU - Clay Fischer
AU - Jairo Navarro Gonzalez
AU - Angie S Hinrichs
AU - Christopher M Lee
AU - Luis R Nassar
AU - Gerardo Perez
AU - Brian J Raney
AU - James Robinson
AU - Andrew D Smith
AU - Eliza Alde
AU - Barali Kitiyakara
AU - David Haussler
AU - William James Kent
AU - Maximilian Haeussler
PY - 2026
DA - 2026/11/05
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1115
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1115/9013043
AB - Since 2000, the UCSC Genome Browser (https://genome.ucsc.edu) has served as a standard tool for visualizing and comparing annotations across thousands of genome assemblies. Users can browse and visualize a wide range of data types from gene annotations to regulatory regions and comparative genome alignments. Once the data view is configured, the Genome Browser image can be exported for use in publications. Beyond visualization, users can use our tools to compare and export the annotations for further analysis. This year’s feature updates include the full release of a tool to copy annotations between related assemblies, QuickLift; feature additions to our data-hosting service HubSpace to enable live editing of configuration files; two new display configurability options: “My Annotations” and custom item coloring; and several improvements to genome assembly discovery and track management. Beyond these new features, 28 new annotation tracks have been added across three broad categories: variant databases and interpretation, gene regulation, and transcriptome and gene expression. These include ENCODE4 cCREs and other ENCODE4 regulatory annotations, variant frequencies and phased variants from national sequencing projects, and two massively parallel reporter assay tracks.
SN - 0305-1048
SN - 1362-4962
ER -