W James Kent

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
    W J Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 10:1115-25. 2000
  2. pmc Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes
    W James Kent
    Center for Biomolecular Science and Engineering and Howard Hughes Medical Institute, Department of Computer Science, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 100:11484-9. 2003
  3. pmc The human genome browser at UCSC
    W James Kent
    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Genome Res 12:996-1006. 2002
  4. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
  5. pmc Assembly of the working draft of the human genome with GigAssembler
    W J Kent
    Department of Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 11:1541-8. 2001
  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: 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
  8. ncbi request reprint Ultraconserved elements in the human genome
    Gill Bejerano
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Science 304:1321-5. 2004
  9. ncbi request reprint The UCSC Known Genes
    Fan Hsu
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz Santa Cruz, CA 95064, USA
    Bioinformatics 22:1036-46. 2006
  10. 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

Detail Information

Publications57

  1. ncbi request reprint Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
    W J Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 10:1115-25. 2000
    ..The 3' and 5' intron splice sites have more similarity to each other in introns unique to one species than in C. elegans introns as a whole, suggesting a possible mechanism for intron removal...
  2. pmc Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes
    W James Kent
    Center for Biomolecular Science and Engineering and Howard Hughes Medical Institute, Department of Computer Science, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 100:11484-9. 2003
    ..To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments...
  3. pmc The human genome browser at UCSC
    W James Kent
    Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Genome Res 12:996-1006. 2002
    ..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...
  4. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    ..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...
  5. pmc Assembly of the working draft of the human genome with GigAssembler
    W J Kent
    Department of Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 11:1541-8. 2001
    ..7 billion base pairs and covering an estimated 88% of the genome that has been used for several recent studies of the genome. Here we describe the algorithm used by GigAssembler...
  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: 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
    ....
  8. ncbi request reprint Ultraconserved elements in the human genome
    Gill Bejerano
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Science 304:1321-5. 2004
    ....
  9. ncbi request reprint The UCSC Known Genes
    Fan Hsu
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz Santa Cruz, CA 95064, USA
    Bioinformatics 22:1036-46. 2006
    ..Although UCSC Known Genes offers the highest genomic and CDS coverage among major human and mouse gene sets, more detailed analysis suggests all of them could be further improved...
  10. 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...
  11. 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...
  12. 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/...
  13. 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...
  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 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...
  16. 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...
  17. 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...
  18. pmc The UCSC genome browser and associated tools
    Robert M Kuhn
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Brief Bioinform 14:144-61. 2013
    ..Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting...
  19. 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...
  20. 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...
  21. pmc Aligning multiple genomic sequences with the threaded blockset aligner
    Mathieu Blanchette
    Howard Hughes Medical Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 14:708-15. 2004
    ..We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser...
  22. 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...
  23. pmc Retrocopy contributions to the evolution of the human genome
    Robert Baertsch
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    BMC Genomics 9:466. 2008
    ..A subset of retroposed mRNAs (retrocopies) shows strong evidence of expression in primates, often yielding functional retrogenes...
  24. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    ..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
  25. 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...
  26. 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...
  27. pmc Variation resources at UC Santa Cruz
    Daryl J Thomas
    Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA, USA
    Nucleic Acids Res 35:D716-20. 2007
    ..The browsing and analysis tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/...
  28. doi request reprint 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. ..
  29. 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...
  30. 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...
  31. ncbi request reprint A distal enhancer and an ultraconserved exon are derived from a novel retroposon
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nature 441:87-90. 2006
    ....
  32. 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...
  33. pmc Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing
    Tracy Farrer
    Department of MCD Biology and Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 30:3360-7. 2002
    ....
  34. ncbi request reprint Computational screening of conserved genomic DNA in search of functional noncoding elements
    Gill Bejerano
    Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
    Nat Methods 2:535-45. 2005
  35. pmc The UCSC genome browser database: update 2007
    R M Kuhn
    Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 35:D668-73. 2007
    ..The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/...
  36. 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...
  37. pmc The UCSC Genome Browser Database: update 2009
    R M Kuhn
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 37:D755-61. 2009
    ..A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs...
  38. 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/...
  39. 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/...
  40. pmc BigWig and BigBed: enabling browsing of large distributed datasets
    W J Kent
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz UCSC, Santa Cruz, CA 95064, USA
    Bioinformatics 26:2204-7. 2010
    ..As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets...
  41. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
    ..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies...
  42. pmc Hotspots of mammalian chromosomal evolution
    Jeffrey A Bailey
    Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
    Genome Biol 5:R23. 2004
    ..With the availability of both the human and mouse genomic sequences, detailed analysis of the sequence properties underlying these breakpoints is now possible...
  43. ncbi request reprint The DNA sequence of human chromosome 7
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 424:157-64. 2003
    ..Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame...
  44. pmc Human-mouse alignments with BLASTZ
    Scott Schwartz
    Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genome Res 13:103-7. 2003
    ..This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results...
  45. 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...
  46. 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
    ....
  47. 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...
  48. pmc Reconstructing contiguous regions of an ancestral genome
    Jian Ma
    Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
    Genome Res 16:1557-65. 2006
    ..Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals...
  49. pmc Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
    Ross C Hardison
    Department of Biochemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Genome Res 13:13-26. 2003
    ..Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse...
  50. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  51. ncbi request reprint Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR
    Wanyuan Ao
    Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
    Science 305:1743-6. 2004
    ..Our combination of bioinformatics and in vivo analysis has provided a powerful means for genome-wide investigation of transcriptional control...
  52. 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...
  53. pmc 28-way vertebrate alignment and conservation track in the UCSC Genome Browser
    Webb Miller
    Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
    Genome Res 17:1797-808. 2007
    ..Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions...
  54. pmc Galaxy: a platform for interactive large-scale genome analysis
    Belinda Giardine
    Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
    Genome Res 15:1451-5. 2005
    ..Galaxy can be accessed at http://g2.bx.psu.edu...
  55. ncbi request reprint Piloting the zebrafish genome browser
    Anthony DiBiase
    Division of Hematology Oncology, Children s Hospital, Karp Research Laboratories, Boston, Massachusetts 02115, USA
    Dev Dyn 235:747-53. 2006
    ..This easy-to-use genome browser aims to display and download useful genome sequence information for zebrafish mutant mapping and cloning projects. Its user-friendly interface expedites annotation of the zebrafish genome sequence...
  56. pmc Over 20% of human transcripts might form sense-antisense pairs
    Jianjun Chen
    Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC2115, Chicago, IL 60637, USA
    Nucleic Acids Res 32:4812-20. 2004
    ....