Research Topics
| W James KentSummaryAffiliation: University of California Country: USA Publications
| Collaborators
|
Detail Information
Publications
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignmentW 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...- Assembly of the working draft of the human genome with GigAssemblerW 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... - BLAT--the BLAST-like alignment toolW 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... - The human genome browser at UCSCW 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... - Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomesW 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... - 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... - 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.... - Ultraconserved elements in the human genomeGill Bejerano
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Science 304:1321-5. 2004.... - The UCSC Known GenesFan 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... - 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/... - 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... - 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 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... - 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... - Aligning multiple genomic sequences with the threaded blockset alignerMathieu 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... - 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 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 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... - 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
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... - Retrocopy contributions to the evolution of the human genomeRobert 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... - 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... - Variation resources at UC Santa CruzDaryl 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/... - 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... - Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomesAdam 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... - A distal enhancer and an ultraconserved exon are derived from a novel retroposonGill Bejerano
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
Nature 441:87-90. 2006.... - 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... - Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicingTracy 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.... - Computational screening of conserved genomic DNA in search of functional noncoding elementsGill Bejerano
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
Nat Methods 2:535-45. 2005 - 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 Genome Browser Database: update 2009R 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... - The UCSC Genome Browser Database: update 2006A 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/... - 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 2007R 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/... - BigWig and BigBed: enabling browsing of large distributed datasetsW 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..cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu... - 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.... - Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolutionRoss 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... - Human-mouse alignments with BLASTZScott 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... - The DNA sequence of human chromosome 7Ladeana 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... - Reconstructing contiguous regions of an ancestral genomeJian 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... - Hotspots of mammalian chromosomal evolutionJeffrey 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.... - 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... - Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHRWanyuan 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... - 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... - 28-way vertebrate alignment and conservation track in the UCSC Genome BrowserWebb 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... - Galaxy: a platform for interactive large-scale genome analysisBelinda 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... - Discovery of functional elements in 12 Drosophila genomes using evolutionary signaturesAlexander 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... - 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... - Piloting the zebrafish genome browserAnthony 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... - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:695-716. 2004..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture... - Assessing computational tools for the discovery of transcription factor binding sitesMartin 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... - Over 20% of human transcripts might form sense-antisense pairsJianjun Chen
Department of Medicine, University of Chicago, 5841 S Maryland Avenue, MC2115, Chicago, IL 60637, USA
Nucleic Acids Res 32:4812-20. 2004....