Donna Karolchik

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The UCSC Genome Browser Database: 2008 update
    D 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
  2. pmc The UCSC Genome Browser Database
    D 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
  3. pmc The UCSC Table Browser data retrieval tool
    Donna 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
  4. pmc The UCSC Genome Browser database: update 2010
    Brooke 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
  5. pmc The UCSC Genome Browser database: extensions and updates 2011
    Timothy 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
  6. pmc ENCODE whole-genome data in the UCSC Genome Browser
    Kate 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
  7. pmc The UCSC Genome Browser database: 2014 update
    Donna Karolchik
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 42:D764-70. 2014
  8. pmc Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
    Brian J Raney
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Bioinformatics 30:1003-5. 2014
  9. pmc ENCODE whole-genome data in the UCSC Genome Browser: update 2012
    Kate 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
  10. pmc The UCSC Genome Browser
    Donna Karolchik
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA
    Curr Protoc Bioinformatics . 2009

Detail Information

Publications30

  1. pmc The UCSC Genome Browser Database: 2008 update
    D 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/...
  2. pmc The UCSC Genome Browser Database
    D 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...
  3. pmc The UCSC Table Browser data retrieval tool
    Donna 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...
  4. pmc The UCSC Genome Browser database: update 2010
    Brooke 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
    ....
  5. pmc The UCSC Genome Browser database: extensions and updates 2011
    Timothy 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...
  6. pmc ENCODE whole-genome data in the UCSC Genome Browser
    Kate 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...
  7. pmc The UCSC Genome Browser database: 2014 update
    Donna Karolchik
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 42:D764-70. 2014
    ..To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany. ..
  8. pmc Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
    Brian J Raney
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
    Bioinformatics 30:1003-5. 2014
    ..For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror...
  9. pmc ENCODE whole-genome data in the UCSC Genome Browser: update 2012
    Kate 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...
  10. pmc The UCSC Genome Browser
    Donna 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...
  11. pmc The UCSC Genome Browser database: extensions and updates 2013
    Laurence R Meyer
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz 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...
  12. pmc The UCSC Genome Browser database: update 2011
    Pauline 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...
  13. doi request reprint UCSC genome browser tutorial
    Ann 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/...
  14. pmc 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...
  15. pmc The ENCODE Project at UC Santa Cruz
    Daryl 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...
  16. pmc Exploring relationships and mining data with the UCSC Gene Sorter
    W 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...
  17. pmc The UCSC Genome Browser
    Donna 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...
  18. ncbi request reprint Comparative genomic analysis using the UCSC genome browser
    Donna 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...
  19. pmc ENCODE data in the UCSC Genome Browser: year 5 update
    Kate R Rosenbloom
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz 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...
  20. doi request reprint The UCSC Genome Browser
    Donna Karolchik
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA
    Curr Protoc Bioinformatics . 2012
    ..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...
  21. ncbi request reprint The UCSC Genome Browser
    Donna 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...
  22. pmc The UCSC Cancer Genomics Browser: update 2011
    J 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...
  23. pmc The UCSC Proteome Browser
    Fan 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...
  24. doi request reprint UCSC genome browser: deep support for molecular biomedical research
    Mary 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)...
  25. pmc What everybody should know about the rat genome and its online resources
    Simon N Twigger
    Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
    Nat Genet 40:523-7. 2008
    ....
  26. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard 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 lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  27. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert 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
    ....
  28. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  29. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott 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...
  30. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard 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...