Research Topics
| Donna KarolchikSummaryAffiliation: University of California Country: USA Publications
| Collaborators
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Detail Information
Publications
The UCSC Genome Browser DatabaseD Karolchik
Genome Bioinformatics Group, The University of California Santa Cruz UCSC, School of Engineering, 1156 High Street, Santa Cruz, CA 95064 1077, USA
Nucleic Acids Res 31:51-4. 2003..The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information...- The UCSC Table Browser data retrieval toolDonna Karolchik
Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, School of Engineering, 1156 High Street, Santa Cruz, CA 95064 1077, USA
Nucleic Acids Res 32:D493-6. 2004..The Table Browser User's Guide located on the UCSC website provides instructions and detailed examples for constructing queries and configuring output... - The UCSC Genome Browser Database: 2008 updateD Karolchik
Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
Nucleic Acids Res 36:D773-9. 2008..The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/... - The UCSC Genome Browser database: update 2010Brooke Rhead
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 38:D613-9. 2010.... - The UCSC Genome Browser database: extensions and updates 2011Timothy R Dreszer
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 40:D918-23. 2012..We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image... - ENCODE whole-genome data in the UCSC Genome BrowserKate R Rosenbloom
Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz, CA 95064, USA
Nucleic Acids Res 38:D620-5. 2010..The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access... - ENCODE whole-genome data in the UCSC Genome Browser: update 2012Kate R Rosenbloom
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 40:D912-7. 2012..ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http://encodeproject.org) provides specialized tools and information about the ENCODE data sets... - The UCSC Genome BrowserDonna Karolchik
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA
Curr Protoc Bioinformatics . 2009..This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks... - The UCSC Genome Browser database: update 2011Pauline A Fujita
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 39:D876-82. 2011..New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks... 
UCSC genome browser tutorialAnn S Zweig
UCSC Genome Bioinformatics Group, Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Genomics 92:75-84. 2008..The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/...- ENCODE whole-genome data in the UCSC genome browser (2011 update)Brian J Raney
Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 39:D871-5. 2011..ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access... 
The ENCODE Project at UC Santa CruzDaryl J Thomas
Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 35:D663-7. 2007..Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples...- Exploring relationships and mining data with the UCSC Gene SorterW J Kent
Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
Genome Res 15:737-41. 2005..Available on a selected subset of the genome assemblies found in the Genome Browser, it further enhances the usefulness of the UCSC tool set in interactive genomic exploration and analysis... 
Comparative genomic analysis using the UCSC genome browserDonna Karolchik
UCSC Genome Bioinformatics Group, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA
Methods Mol Biol 395:17-34. 2007..Here, we describe a procedure for examining a genomic region of interest in the Genome Browser, analyzing characteristics of the region, filtering the data, and downloading data sets for further study...- The UCSC Genome BrowserDonna Karolchik
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA
Curr Protoc Hum Genet . 2011..This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks... - The UCSC Genome Browser database: extensions and updates 2013Laurence R Meyer
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA, Centre for Genomic Regulation CRG, c Dr Aiguader, 88, 08003 Barcelona, Spain, Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
Nucleic Acids Res 41:D64-9. 2013..We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal... - The UCSC Genome BrowserDonna Karolchik
University of California Santa Cruz, Santa Cruz, California, USA
Curr Protoc Bioinformatics . 2007..This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks... - The UCSC Cancer Genomics Browser: update 2011J Zachary Sanborn
Department of Biomolecular Engineering, Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 39:D951-9. 2011..The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser's rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data... - ENCODE Data in the UCSC Genome Browser: year 5 updateKate R Rosenbloom
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA, Vertebrate Genomics Group, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK and Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA
Nucleic Acids Res 41:D56-63. 2013..ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets... - The UCSC Proteome BrowserFan Hsu
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
Nucleic Acids Res 33:D454-8. 2005..The browser may be accessed from any Known Genes details page of the Genome Browser at http://genome.ucsc.edu. A user's guide is also available on this website... - The UCSC Genome BrowserDonna Karolchik
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California
Curr Protoc Bioinformatics . 2012..Curr. Protoc. Bioinform. 40:1.4.1-1.4.33. © 2012 by John Wiley & Sons, Inc... - UCSC genome browser: deep support for molecular biomedical researchMary E Mangan
OpenHelix, LLC, Bellevue, WA 98006, USA
Biotechnol Annu Rev 14:63-108. 2008..The UCSC Genome Browser provides a source of deep support for a wide range of biomedical molecular research (http://genome.ucsc.edu)... - What everybody should know about the rat genome and its online resourcesSimon N Twigger
Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
Nat Genet 40:523-7. 2008.... - Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard A Gibbs
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA <http://www.hgsc.bcm.tmc.edu
Nature 428:493-521. 2004.... - Initial sequencing and comparative analysis of the mouse genomeRobert H Waterston
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 420:520-62. 2002.... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genomeElliott H Margulies
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Genome Res 17:760-74. 2007..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard A Gibbs
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
Science 316:222-34. 2007..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...