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Article ; Online: Variant interpretation: UCSC Genome Browser Recommended Track Sets.

Benet-Pagès, Anna / Rosenbloom, Kate R / Nassar, Luis R / Lee, Christopher M / Raney, Brian J / Clawson, Hiram / Schmelter, Daniel / Casper, Jonathan / Gonzalez, Jairo Navarro / Perez, Gerardo / Lee, Brian T / Zweig, Ann S / Kent, W James / Haeussler, Maximillian / Kuhn, Robert M

Human mutation

2022 Volume 43, Issue 8, Page(s) 998–1011

Abstract: The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, ... ...

Abstract	The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, which are dispersed at many locations worldwide, are collected into one view on the Browser, where the graphical interface presents the data in one location. This supports the expertise of the researcher to interpret variants in the genome. Because the analysis of single nucleotide variants and copy number variants require interpretation of data at very different genomic scales, different data resources are required. We present here several Recommended Track Sets designed to facilitate the interpretation of variants in the clinic, offering quick access to datasets relevant to the appropriate scale.
MeSH term(s)	DNA Copy Number Variations ; Databases, Genetic ; Genome, Human/genetics ; Genomics ; Humans ; Internet ; Software
Language	English
Publishing date	2022-02-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.24335
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: GenArk: Towards a million UCSC Genome Browsers.

Research square

2023

Abstract: Interactive graphical genome browsers are essential tools for biologists working with DNA sequences. Although tens of thousands of new genome assemblies have become available over the last decade, accessibility is limited by the work involved in manually ...

Abstract	Interactive graphical genome browsers are essential tools for biologists working with DNA sequences. Although tens of thousands of new genome assemblies have become available over the last decade, accessibility is limited by the work involved in manually creating browsers and curating annotations. The results can push the limits of data storage infrastructure. To facilitate managing this increasing number of genome assemblies, we created the Genome Archive (GenArk) collection of UCSC Genome Browsers from assemblies hosted at NCBI(1). Built on our established assembly hub system, this collection enables fast, on-demand visualization of chromosome regions without requiring a database server. Available annotations include gene models, some mapped through whole-genome alignments, repeat masks, GC content, and others. We also modified our popular BLAT(2) aligner and in-silico PCR to support a large number of genomes using limited RAM. Users can upload additional annotations themselves via track hubs(3) and custom tracks. We can import more annotations in bulk from third-party resources, demonstrated here with TOGA(4) gene models. 2,430 GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be found by searching on the main UCSC gateway page. We will continue to add human high-quality assemblies and for other organisms, we are looking forward to receiving requests from the research community for ever more browsers and whole-genome alignments via http://genome.ucsc.edu/assemblyRequest.html.
Language	English
Publishing date	2023-04-03
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-2697398/v1
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Article ; Online: GenArk: towards a million UCSC genome browsers.

Genome biology

2023 Volume 24, Issue 1, Page(s) 217

Abstract: Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub ...

Abstract	Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies.Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page.
MeSH term(s)	Software ; Genome ; Genomics ; Archives ; Nucleic Acid Amplification Techniques ; Databases, Genetic ; Internet
Language	English
Publishing date	2023-10-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-023-03057-x
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Article ; Online: The UCSC Genome Browser database: 2024 update.

Raney, Brian J / Barber, Galt P / Benet-Pagès, Anna / Casper, Jonathan / Clawson, Hiram / Cline, Melissa S / Diekhans, Mark / Fischer, Clayton / Navarro Gonzalez, Jairo / Hickey, Glenn / Hinrichs, Angie S / Kuhn, Robert M / Lee, Brian T / Lee, Christopher M / Le Mercier, Phillipe / Miga, Karen H / Nassar, Luis R / Nejad, Parisa / Paten, Benedict /

Perez, Gerardo / Schmelter, Daniel / Speir, Matthew L / Wick, Brittney D / Zweig, Ann S / Haussler, David / Kent, W James / Haeussler, Maximilian

Nucleic acids research

2023 Volume 52, Issue D1, Page(s) D1082–D1088

Abstract: The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to ...

Abstract	The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to SARS-CoV2. This year, we have introduced new data from the Human Pangenome Reference Consortium and on viral genomes including SARS-CoV2. We have added 1,200 new genomes to our GenArk genome system, increasing the overall diversity of our genomic representation. We have added support for nine new user-contributed track hubs to our public hub system. Additionally, we have released 29 new tracks on the human genome and 11 new tracks on the mouse genome. Collectively, these new features expand both the breadth and depth of the genomic knowledge that we share publicly with users worldwide.
MeSH term(s)	Animals ; Humans ; Mice ; Databases, Genetic ; Genome, Human ; Genome, Viral ; Genomics ; Internet ; Molecular Sequence Annotation ; RNA, Viral ; Software
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-10-20
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad987
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Article ; Online: The UCSC Genome Browser database: 2023 update.

Nassar, Luis R / Barber, Galt P / Benet-Pagès, Anna / Casper, Jonathan / Clawson, Hiram / Diekhans, Mark / Fischer, Clay / Gonzalez, Jairo Navarro / Hinrichs, Angie S / Lee, Brian T / Lee, Christopher M / Muthuraman, Pranav / Nguy, Beagan / Pereira, Tiana / Nejad, Parisa / Perez, Gerardo / Raney, Brian J / Schmelter, Daniel / Speir, Matthew L /

Wick, Brittney D / Zweig, Ann S / Haussler, David / Kuhn, Robert M / Haeussler, Maximilian / Kent, W James

Nucleic acids research

2022 Volume 51, Issue D1, Page(s) D1188–D1195

Abstract: The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with ...

Abstract	The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.
MeSH term(s)	Humans ; COVID-19/epidemiology ; COVID-19/genetics ; Databases, Genetic ; Genomics/methods ; Internet ; Phylogeny ; SARS-CoV-2/genetics ; Software ; Web Browser
Language	English
Publishing date	2022-11-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac1072
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The UCSC SARS-CoV-2 Genome Browser.

Nature genetics

2020 Volume 52, Issue 10, Page(s) 991–998

MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/virology ; Databases, Genetic ; Genome, Viral/genetics ; Humans ; Internet ; Pandemics ; Pneumonia, Viral/virology ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-09-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-020-0700-8
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Article ; Online: The UCSC Genome Browser database: 2021 update.

Nucleic acids research

2020 Volume 49, Issue D1, Page(s) D1046–D1057

Abstract: For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, ... ...

Abstract	For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.
MeSH term(s)	Animals ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Computational Biology/methods ; Data Curation/methods ; Databases, Genetic ; Epidemics ; Genome/genetics ; Genomics/methods ; Humans ; Internet ; Mice ; Molecular Sequence Annotation/methods ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Software
Language	English
Publishing date	2020-11-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa1070
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The UCSC Genome Browser database: 2022 update.

Lee, Brian T / Barber, Galt P / Benet-Pagès, Anna / Casper, Jonathan / Clawson, Hiram / Diekhans, Mark / Fischer, Clay / Gonzalez, Jairo Navarro / Hinrichs, Angie S / Lee, Christopher M / Muthuraman, Pranav / Nassar, Luis R / Nguy, Beagan / Pereira, Tiana / Perez, Gerardo / Raney, Brian J / Rosenbloom, Kate R / Schmelter, Daniel / Speir, Matthew L /

Wick, Brittney D / Zweig, Ann S / Haussler, David / Kuhn, Robert M / Haeussler, Maximilian / Kent, W James

Nucleic acids research

2021 Volume 50, Issue D1, Page(s) D1115–D1122

Abstract: The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. The website provides integrated tools for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic datasets. ...

Abstract	The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. The website provides integrated tools for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic datasets. Data highlights this year include a collection of easily accessible public hub assemblies on new organisms, now featuring BLAT alignment and PCR capabilities, and new and updated clinical tracks (gnomAD, DECIPHER, CADD, REVEL). We introduced a new Track Sets feature and enhanced variant displays to aid in the interpretation of clinical data. We also added a tool to rapidly place new SARS-CoV-2 genomes in a global phylogenetic tree enabling researchers to view the context of emerging mutations in our SARS-CoV-2 Genome Browser. Other new software focuses on usability features, including more informative mouseover displays and new fonts.
MeSH term(s)	Animals ; Databases, Genetic ; Genome, Human ; Humans ; Phylogeny ; Polymerase Chain Reaction ; SARS-CoV-2/genetics ; User-Computer Interface ; Web Browser ; Exome Sequencing
Language	English
Publishing date	2021-10-29
Publishing country	England
Document type	Dataset ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab959
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The UCSC Genome Browser database: 2019 update.

Haeussler, Maximilian / Zweig, Ann S / Tyner, Cath / Speir, Matthew L / Rosenbloom, Kate R / Raney, Brian J / Lee, Christopher M / Lee, Brian T / Hinrichs, Angie S / Gonzalez, Jairo Navarro / Gibson, David / Diekhans, Mark / Clawson, Hiram / Casper, Jonathan / Barber, Galt P / Haussler, David / Kuhn, Robert M / Kent, W James

Nucleic acids research

2018 Volume 47, Issue D1, Page(s) D853–D858

Abstract: The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. ... ...

Abstract	The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.
MeSH term(s)	Animals ; Chromosome Mapping ; Databases, Genetic ; Genome/genetics ; Genome, Human/genetics ; Genomics ; Humans ; Molecular Sequence Annotation ; Software ; Web Browser
Language	English
Publishing date	2018-11-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky1095
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Article ; Online: UCSC Genome Browser enters 20th year.

Lee, Christopher M / Barber, Galt P / Casper, Jonathan / Clawson, Hiram / Diekhans, Mark / Gonzalez, Jairo Navarro / Hinrichs, Angie S / Lee, Brian T / Nassar, Luis R / Powell, Conner C / Raney, Brian J / Rosenbloom, Kate R / Schmelter, Daniel / Speir, Matthew L / Zweig, Ann S / Haussler, David / Haeussler, Maximilian / Kuhn, Robert M / Kent, W James

Nucleic acids research

2019 Volume 48, Issue D1, Page(s) D756–D761

Abstract: The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new ... ...

Abstract	The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a 'lollipop' plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.
MeSH term(s)	Databases, Genetic ; Genome, Human ; Genomics ; Humans ; Internet ; Software
Language	English
Publishing date	2019-11-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkz1012
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