Brian J Raney

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. pmc Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
    John A St John
    Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
    Genome Biol 13:415. 2012
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. pmc The UCSC Genome Browser database: 2015 update
    Kate R Rosenbloom
    Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 43:D670-81. 2015

Collaborators

Detail Information

Publications16

  1. 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...
  2. pmc Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
    John A St John
    Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
    Genome Biol 13:415. 2012
    ..The status of these projects and our planned analyses are described...
  3. 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...
  4. 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...
  5. 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. ..
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. pmc The UCSC Genome Browser database: 2015 update
    Kate R Rosenbloom
    Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 43:D670-81. 2015
    ..As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled. ..
  11. pmc Navigating protected genomics data with UCSC Genome Browser in a Box
    Maximilian Haeussler
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Bioinformatics 31:764-6. 2015
    ..Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access...
  12. 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
    ....
  13. pmc Comparative assembly hubs: web-accessible browsers for comparative genomics
    Ngan Nguyen
    Center for Biomolecular Sciences and Engineering, CBSE ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA
    Bioinformatics 30:3293-301. 2014
    ..It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers...
  14. 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...
  15. pmc Alignathon: a competitive assessment of whole-genome alignment methods
    Dent Earl
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 24:2077-89. 2014
    ..We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments...
  16. pmc Three periods of regulatory innovation during vertebrate evolution
    Craig B Lowe
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA
    Science 333:1019-24. 2011
    ....