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The UCSC Genome Browser database: update 2011

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik, M. S. Cline, M. Goldman, G. P. Barber, H. Clawson, A. Coelho, M. Diekhans, T. R. Dreszer (+15 others)
2010 Nucleic Acids Research  
Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome  ...  Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation  ...  Other tools The UCSC Genome Browser website provides additional tools to access the database and complement the Genome Browser.  ... 
doi:10.1093/nar/gkq963 pmid:20959295 pmcid:PMC3242726 fatcat:fnemefhmkbc65bmwbfxqlp7lpm

The UCSC Genome Browser database: extensions and updates 2011

T. R. Dreszer, D. Karolchik, A. S. Zweig, A. S. Hinrichs, B. J. Raney, R. M. Kuhn, L. R. Meyer, M. Wong, C. A. Sloan, K. R. Rosenbloom, G. Roe, B. Rhead (+17 others)
2011 Nucleic Acids Research  
In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011.  ...  The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms.  ...  ACKNOWLEDGEMENTS The authors would like to thank the many data contributors whose work makes the Genome Browser possible, our Scientific Advisory Board for steering our efforts, our users for their consistent  ... 
doi:10.1093/nar/gkr1055 pmid:22086951 pmcid:PMC3245018 fatcat:lnijxi7u4vclpjuharlr2wvkia

The UCSC cancer genomics browser: update 2011

J. Zachary Sanborn, Stephen C. Benz, Brian Craft, Christopher Szeto, Kord M. Kober, Laurence Meyer, Charles J. Vaske, Mary Goldman, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, W. James Kent (+3 others)
2010 Nucleic Acids Research  
The UCSC Cancer Genomics Browser (https://  ...  ACKNOWLEDGEMENTS We thank Eric Weiler, Victoria Lin and Jorge Garcia for computer support, the UCSC Genome Browser staff for advice on integration and support of the UCSC Genome Browser, database and source  ...  code library, Dr Eric Collisson and Dr Laura Esserman for their advice on the cancer browser development.  ... 
doi:10.1093/nar/gkq1113 pmid:21059681 pmcid:PMC3013705 fatcat:qywno5ztgre5vn35qcrp47splu

The UCSC Archaeal Genome Browser: 2012 update

P. P. Chan, A. D. Holmes, A. M. Smith, D. Tran, T. M. Lowe
2011 Nucleic Acids Research  
The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements  ...  The UCSC Archaeal Genome Browser (http:// archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes.  ...  ACKNOWLEDGEMENTS We thank Jim Kent and the Genome Bioinformatics Group of UC Santa Cruz for providing us with excellent assistance in developing the Archaeal Genome Browser.  ... 
doi:10.1093/nar/gkr990 pmid:22080555 pmcid:PMC3245099 fatcat:nbatgfqcjbfqbbwg7a5alvbcyq

The UCSC Genome Browser database: 2014 update

Donna Karolchik, Galt P. Barber, Jonathan Casper, Hiram Clawson, Melissa S. Cline, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steve Heitner (+13 others)
2013 Nucleic Acids Research  
The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms  ...  As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for 90 organisms.  ...  ACKNOWLEDGEMENTS The authors would like to thank the many data contributors and collaborators whose work makes the Genome Browser possible, our Scientific Advisory Board for guiding our efforts, our users  ... 
doi:10.1093/nar/gkt1168 pmid:24270787 pmcid:PMC3964947 fatcat:nqcltynd7zdgrml2ntspdj3v74

The UCSC Genome Browser Database: 2008 update

D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller (+13 others)
2007 Nucleic Acids Research  
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome. ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities  ...  The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line  ...  The UCSC Genome Browser team regularly updates data tracks and adds new annotations.  ... 
doi:10.1093/nar/gkm966 pmid:18086701 pmcid:PMC2238835 fatcat:zdlffcr2vvhpdhn5epwzsneyky

The UCSC Genome Browser database: extensions and updates 2013

Laurence R. Meyer, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Robert M. Kuhn, Matthew Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke Rhead, Brian J. Raney, Andy Pohl (+20 others)
2012 Nucleic Acids Research  
This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.  ...  The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms  ...  ACKNOWLEDGEMENTS The authors would like to thank the many data contributors whose work makes the Genome Browser possible, our Scientific Advisory Board for steering our efforts, our users for their consistent  ... 
doi:10.1093/nar/gks1048 pmid:23155063 pmcid:PMC3531082 fatcat:pernizd77fdijcyqc56eicrqzq

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

K. R. Rosenbloom, T. R. Dreszer, J. C. Long, V. S. Malladi, C. A. Sloan, B. J. Raney, M. S. Cline, D. Karolchik, G. P. Barber, H. Clawson, M. Diekhans, P. A. Fujita (+15 others)
2011 Nucleic Acids Research  
The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements  ...  The ENCODE Data  ...  We also acknowledge Hiram Clawson, a core Genome Browser engineer who has contributed greatly to its overall success by his work to keep the browser reliable, fast and annotationrich.  ... 
doi:10.1093/nar/gkr1012 pmid:22075998 pmcid:PMC3245183 fatcat:nzoqo62bbrhyzccqsag5ngl7ey

ENCODE Data in the UCSC Genome Browser: year 5 update

Kate R. Rosenbloom, Cricket A. Sloan, Venkat S. Malladi, Timothy R. Dreszer, Katrina Learned, Vanessa M. Kirkup, Matthew C. Wong, Morgan Maddren, Ruihua Fang, Steven G. Heitner, Brian T. Lee, Galt P. Barber (+9 others)
2012 Nucleic Acids Research  
, and its third year of investigations in the mouse genome.  ...  In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The  ...  FUNDING National Human Genome Research Institute [5P41HG002371-12, 3P41HG002371-12S1 to the UCSC  ... 
doi:10.1093/nar/gks1172 pmid:23193274 pmcid:PMC3531152 fatcat:ubjbo4yrofb75ibsxztzj2qp4e

The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser

Domenico Simone, Francesco Maria Calabrese, Martin Lang, Giuseppe Gasparre, Marcella Attimonelli
2011 BMC Genomics  
genome are debated issues.  ...  Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences), whose mode and time of insertion, as well as their functional/structural role within the  ...  Li of the UCSC tracks annotation staff who have allowed us to publish the NumtS tracks at the UCSC Genome Browser; G. Mineccia for contribution to primer design and NumtS sequences multialignment.  ... 
doi:10.1186/1471-2164-12-517 pmid:22013967 pmcid:PMC3228558 fatcat:jzmidilwjndd3d3mwzsguatjxi

The Pancreatic Expression database: 2011 update

Rosalind J. Cutts, Emanuela Gadaleta, Stephan A. Hahn, Tatjana Crnogorac-Jurcevic, Nicholas R. Lemoine, Claude Chelala
2010 Nucleic Acids Research  
The Pancreatic Expression database (PED, http:// www.pancreasexpression.org) has established itself as the main repository for pancreatic-derived -omics data.  ...  Here we describe several of its new and improved features, such as data content, which now includes over 60 000 measurements derived from transcriptomics, proteomics, genomics and miRNA profiles from various  ...  ACKNOWLEDGEMENTS The authors thank our colleagues who have suggested or contributed data for current or previous versions of the database.  ... 
doi:10.1093/nar/gkq937 pmid:20959292 pmcid:PMC3013788 fatcat:phrxd2u6mrcjzgtnnb4bu4gxti

The Comparative Toxicogenomics Database: update 2011

A. P. Davis, B. L. King, S. Mockus, C. G. Murphy, C. Saraceni-Richards, M. Rosenstein, T. Wiegers, C. J. Mattingly
2010 Nucleic Acids Research  
of CTD's curated information in other database products, such as STITCH (12) , ToppGene (13) , PhenoHM (14) , Chem2Bio2RDF (15) , UCSC Browser (16) , WhichGenes (17) , ChemSpider (http://www .chemspider.com  ...  Cluster and genome frequency calculations are also provided. Users can sort the table by the column headers: Ontology, GO level, GO term, Enrichment score and Annotated genes.  ... 
doi:10.1093/nar/gkq813 pmid:20864448 pmcid:PMC3013756 fatcat:5zrnoacyxjckvj6ae5oyhctrci

OriDB, the DNA replication origin database updated and extended

C. C. Siow, S. R. Nieduszynska, C. A. Muller, C. A. Nieduszynski
2011 Nucleic Acids Research  
The revised database structure underlies these improvements and will facilitate further expansion in the future. The updated OriDB for S. cerevisiae is available at  ...  OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites.  ...  We thank members of the Nieduszynski laboratory for helpful discussions and authors from the curated studies  ... 
doi:10.1093/nar/gkr1091 pmid:22121216 pmcid:PMC3245157 fatcat:nwvzqved6jah5kl6btmpl7fd7e

ConTra v2: a tool to identify transcription factor binding sites across species, update 2011

Stefan Broos, Paco Hulpiau, Jeroen Galle, Bart Hooghe, Frans Van Roy, Pieter De Bleser
2011 Nucleic Acids Research  
conservation scores of the genomic regions covered by the predicted TFBSs and strongest co-localizations with genomic regions exhibiting regulatory activity.  ...  The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region surrounding coding or non-coding genes.  ...  Genome Browser (http://genome.ucsc.edu) database.  ... 
doi:10.1093/nar/gkr355 pmid:21576231 pmcid:PMC3125763 fatcat:vsfcofovfvdctidme2ruvxguae

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

M. Y. Galperin, G. R. Cochrane
2010 Nucleic Acids Research  
The current 18th Database Issue of Nucleic Acids Research features descriptions of 96 new and 83 updated online databases covering various areas of molecular biology.  ...  It includes two editorials, one that discusses COMBREX, a new exciting project aimed at figuring out the functions of the  ...  ACKNOWLEDGEMENTS The authors thank Sir Richard Roberts  ... 
doi:10.1093/nar/gkq1243 pmid:21177655 pmcid:PMC3013748 fatcat:dwx6d5biofdudffruict23coby
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