Angie S Hinrichs

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
    Danielle G Lemay
    Genome Center, University of California Davis, 451 Health Science Dr, Davis, CA, 95616, United States of America
    BMC Bioinformatics 13:253. 2012
  2. pmc The UCSC Genome Browser Database: update 2006
    A S Hinrichs
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 34:D590-8. 2006
  3. pmc The bovine lactation genome: insights into the evolution of mammalian milk
    Danielle G Lemay
    Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
    Genome Biol 10:R43. 2009
  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 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

  • Donna Karolchik
  • W James Kent
  • Brian J Raney
  • Brooke Rhead
  • Maximilian Haeussler
  • Fan Hsu
  • Benedict Paten
  • David Gibson
  • Ngan Nguyen
  • Glenn Hickey
  • Ting Wang
  • D J Thomas
  • Melissa S Cline
  • Krishna M Roskin
  • R M Kuhn
  • Jeffrey C Long
  • Gill Bejerano
  • Kate R Rosenbloom
  • Ann S Zweig
  • David Haussler
  • Galt P Barber
  • Pauline A Fujita
  • Mark Diekhans
  • Hiram Clawson
  • Katrina Learned
  • Timothy R Dreszer
  • Rachel A Harte
  • Laurence R Meyer
  • Luvina Guruvadoo
  • Andy Pohl
  • Matthew L Speir
  • Brian T Lee
  • Steve Heitner
  • Chin H Li
  • Mary Goldman
  • Danielle G Lemay
  • Jonathan Casper
  • Venkat S Malladi
  • Cricket A Sloan
  • Vanessa Kirkup
  • Belinda M Giardine
  • Cath Tyner
  • Parisa Nejad
  • Christopher Eisenhart
  • Greg Roe
  • Monique Rijnkels
  • William F Martin
  • Katherine S Pollard
  • J Bruce German
  • Kayla E Smith
  • Chris Villarreal
  • Christopher M Lee
  • Jairo Navarro Gonzalez
  • Clayton M Fischer
  • John Vivian
  • Joel Armstrong
  • Robert Hubley
  • Arian F A Smit
  • Karen H Miga
  • Matthew Wong
  • Matthew C Wong
  • Morgan Maddren
  • Mathew Wong
  • W James Kent
  • Vanessa M Kirkup
  • Robert C Gravell
  • Ian Korf
  • Jennifer Hillman-Jackson
  • Antonio Coelho
  • Michael Pheasant
  • Evgeny M Zdobnov
  • Gonzalo Rincon
  • Regan Murney
  • Adrian J Molenaar
  • Ross L Tellam
  • Juan F Medrano
  • Wesley C Barris
  • Margaret C Neville
  • Kuljeet Singh
  • Evgenia V Kriventseva
  • Nauman J Maqbool
  • Theresa M Casey
  • David J Lynn

Detail Information

Publications22

  1. pmc G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
    Danielle G Lemay
    Genome Center, University of California Davis, 451 Health Science Dr, Davis, CA, 95616, United States of America
    BMC Bioinformatics 13:253. 2012
    ....
  2. pmc The UCSC Genome Browser Database: update 2006
    A S Hinrichs
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 34:D590-8. 2006
    ..These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/...
  3. pmc The bovine lactation genome: insights into the evolution of mammalian milk
    Danielle G Lemay
    Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
    Genome Biol 10:R43. 2009
    ..The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes...
  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 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...
  6. 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. ..
  7. 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...
  8. 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...
  9. 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
    ....
  10. 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...
  11. pmc UCSC Data Integrator and Variant Annotation Integrator
    Angie S Hinrichs
    Genomics Institute, University of California, Santa Cruz, CA, USA
    Bioinformatics 32:1430-2. 2016
    ..When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores...
  12. 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...
  13. 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...
  14. 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. ..
  15. 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...
  16. 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...
  17. pmc The UCSC Genome Browser database: 2016 update
    Matthew L Speir
    Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 44:D717-25. 2016
    ....
  18. 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...
  19. 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...
  20. 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...
  21. pmc The UCSC Genome Browser database: 2017 update
    Cath Tyner
    Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res . 2016
    ....
  22. 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...