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The UCSC genome browser database: update 2007

R. M. Kuhn, D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel, K. R. Rosenbloom, B. Rhead (+13 others)
2007 Nucleic Acids Research  
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

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: 2016 update

Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steve Heitner, Rachel A. Harte (+11 others)
2015 Nucleic Acids Research  
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

R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, L. Meyer, F. Hsu (+10 others)
2009 Nucleic Acids Research  
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

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 SARS-CoV-2 Genome Browser [article]

Jason D Fernandes, Angie S Hinrichs, Hiram Clawson, Jairo Navarro Gonzales, Brian T Lee, Luis R Nassar, Brian J Raney, Kate R Rosenbloom, Santrupti Nerli, Arjun A Rao, Daniel Schmelter, Ann S Zweig (+6 others)
2020 bioRxiv   pre-print
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

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

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

W. Miller, K. Rosenbloom, R. C. Hardison, M. Hou, J. Taylor, B. Raney, R. Burhans, D. C. King, R. Baertsch, D. Blankenberg, S. L. Kosakovsky Pond, A. Nekrutenko (+14 others)
2007 Genome Research  
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

Belinda Giardine, Sjozef van Baal, Polynikis Kaimakis, Cathy Riemer, Webb Miller, Maria Samara, Panagoula Kollia, Nicholas P. Anagnou, David H.K. Chui, Henri Wajcman, Ross C. Hardison, George P. Patrinos
2007 Human Mutation  
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

Y. Lee, Y. Lee, B. Kim, Y. Shin, S. Nam, P. Kim, N. Kim, W.-H. Chung, J. Kim, S. Lee
2007 Nucleic Acids Research  
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

S. N. Twigger, M. Shimoyama, S. Bromberg, A. E. Kwitek, H. J. Jacob
2007 Nucleic Acids Research  
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

Peter Schattner
2007 PLoS Computational Biology  
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

Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence
2010 Database: The Journal of Biological Databases and Curation  
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

M. Megraw, P. Sethupathy, B. Corda, A. G. Hatzigeorgiou
2007 Nucleic Acids Research  
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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