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The UCSC genome browser database: update 2007
2007
Nucleic Acids Research
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The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. ...
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. ...
ACKNOWLEDGEMENTS The UCSC GBD project is funded by grants from the National Human Genome Research Institute (NHGRI), the Howard Hughes Medical Institute (HHMI) and the National Cancer Institute (NCI). ...
doi:10.1093/nar/gkl928
pmid:17142222
pmcid:PMC1669757
fatcat:5h65fma2trhvpcjy4glloar4ha
The UCSC Genome Browser Database: 2008 update
2007
Nucleic Acids Research
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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: 2016 update
2015
Nucleic Acids Research
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The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. ...
Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. ...
We would also like to acknowledge the dedicated system administrators who have provided an excellent ...
doi:10.1093/nar/gkv1275
pmid:26590259
pmcid:PMC4702902
fatcat:vpehyk3xujegfhqlaq7znr5rgi
The UCSC Genome Browser Database: update 2009
2009
Nucleic Acids Research
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The UCSC Genome Browser Database (GBD, http:// ...
We would also like to acknowledge the dedicated system administrators who have provided an excellent computing environment: Jorge Garcia, Erich Weiler, Chester Manuel and Victoria Lin. ...
ACKNOWLEDGEMENTS We would like to thank the many collaborators who have contributed data to our project, our Scientific Advisory Board for their valuable advice and recommendations, and our users for their ...
doi:10.1093/nar/gkn875
pmid:18996895
pmcid:PMC2686463
fatcat:gkmg6oyuc5fmjo46h422lvvqf4
The UCSC Genome Browser database: update 2011
2010
Nucleic Acids Research
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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 SARS-CoV-2 Genome Browser
[article]
2020
bioRxiv
pre-print
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Results: The UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID ...
We adapted our genome browser visualization tool to the viral genome for this purpose. ...
Armenta, Phil Berman, Nik Sgourakis and the rest of the scientists at UCSC and across the world for making these tracks of molecular information possible. ...
doi:10.1101/2020.05.04.075945
fatcat:yqmldbtnwbe43mb4yftpzy4ubi
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
2011
Nucleic Acids Research
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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
2012
Nucleic Acids Research
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, 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
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
2007
Genome Research
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Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability ...
and analyzed with the Galaxy server at http://g2.bx.psu.edu. This paper illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. ...
Sudhir Kumar and the reviewers provided many useful suggestions. Additional help was provided by Cathy Riemer and Heather Lawson. ...
doi:10.1101/gr.6761107
pmid:17984227
pmcid:PMC2099589
fatcat:dbrzsps2hzcztchnbfe6ro7yia
HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update
2007
Human Mutation
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These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful ...
genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype. ...
continuous improvement of the database and its contents. ...
doi:10.1002/humu.9479
pmid:17221864
fatcat:ehqehqcuqjc6ra7yi6fbd7s7zu
ECgene: an alternative splicing database update
2007
Nucleic Acids Research
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As for the human genome, we have also introduced several new applications to analyze differential expression. ...
The applications encompass the genome-based transcript modeling for alternative splicing (AS), domain analysis with Gene Ontology (GO) annotation and expression analysis based on the EST and SAGE data. ...
We also provide the ECgene genome browser that shows the genomic alignment of mRNA models and EST sequences as custom tracks in the UCSC genome browser (25) . ...
doi:10.1093/nar/gkl992
pmid:17132829
pmcid:PMC1716719
fatcat:cf67hvtpofec7hmnt5qrfhtpla
The Rat Genome Database, update 2007--Easing the path from disease to data and back again
2007
Nucleic Acids Research
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The Rat Genome Database (RGD, http://rgd.mcw. edu) is one of the core resources for rat genomics and recent developments have focused on providing support for disease-based research using the rat model ...
database. ...
ACKNOWLEDGEMENTS In addition to the listed authors RGD is built and maintained by the following group of dedicated people: Jiali Chen, Weihong Jin, Nataliya Nenasheva, Rajni Nigam, Andrew Patzer, Victoria ...
doi:10.1093/nar/gkl988
pmid:17151068
pmcid:PMC1761441
fatcat:2zdfnka2dfh7fgggb5ulwxznti
Automated Querying of Genome Databases
2007
PLoS Computational Biology
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The authors received no specific funding for this article. Competing interests. The author has declared that no competing interests exist. ...
UCSC Genome Browser Databases. ...
Moreover, if one's applications need genome annotations incorporating the most recent database updates, using a public mirror database may be advantageous. ...
doi:10.1371/journal.pcbi.0030001
pmid:17257048
pmcid:PMC1782033
fatcat:myarq5e5szhkjfuuswt3jye6z4
Choosing a genome browser for a Model Organism Database: surveying the Maize community
2010
Database: The Journal of Biological Databases and Curation
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we could not have created an implementation of the MaizeGDB Genome Browser customized to support our users' needs. ...
We thank the anonymous reviewers whose suggestions helped us improve this article. We very much appreciate the useful comments by Dr Patrick Armstrong. ...
The UCSC genome browser database The University of California Santa Cruz (UCSC) Genome Browser Database (28) started as part of the Human Genome Project (41) to make newly generated human genomic sequences ...
doi:10.1093/database/baq007
pmid:20627860
pmcid:PMC2911842
fatcat:6ihbvxcmdnfypo2clanjfma5vq
miRGen: a database for the study of animal microRNA genomic organization and function
2007
Nucleic Acids Research
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ACKNOWLEDGEMENTS We thank the reviewers and Shane Jensen for helpful commentary on this work. We also thank Julien Hirel for his contribution to the web interface style sheets. ...
Funding to pay the Open Access publication charges for this article was provided by xxxxx. Conflict of interest statement. None declared. ...
All genome annotation files are downloaded from the UCSC genome annotation database (36) and all genome browser views are through the UCSC Genome Browser. miRGen interfaces whole-genome collections of ...
doi:10.1093/nar/gkl904
pmid:17108354
pmcid:PMC1669779
fatcat:pubdpqmu3rdm5lzngg7budtv7y
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