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The UCSC Genome Browser database: 2015 update

Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steve Heitner (+17 others)
2014 Nucleic Acids Research  
The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently.  ...  For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a  ...  group of system administrators who keep the Genome Browser running.  ... 
doi:10.1093/nar/gku1177 pmid:25428374 pmcid:PMC4383971 fatcat:sahorqoiejam7maduvqkqrh4de

The UCSC Cancer Genomics Browser: update 2015

Mary Goldman, Brian Craft, Teresa Swatloski, Melissa Cline, Olena Morozova, Mark Diekhans, David Haussler, Jingchun Zhu
2014 Nucleic Acids Research  
The UCSC Cancer Genomics Browser (https:// genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their  ...  The Cancer Genomics Browser currently hosts 575 public datasets from genome-wide analyses of over 227 000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET.  ...  ACKNOWLEDGEMENT We would like to thank Erich Weiler, Jorge Garcia and the UCSC Genome Browser for their support.  ... 
doi:10.1093/nar/gku1073 pmid:25392408 pmcid:PMC4383911 fatcat:engeo7umabdqrdqupnemmwgucu

The UCSC Genome Browser database: 2016 update [article]

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 bioRxiv   pre-print
The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently.  ...  For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a  ...  added over 200 new and updated tracks to the UCSC Genome Browser database for our existing assemblies (Table 2) , as well as 7 public track and assembly hubs (Table 3) .  ... 
doi:10.1101/027037 fatcat:5c7vac6nqbbftabnwrkprqljua

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.  ...  Genome Browser wiki site.  ...  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: 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: 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

An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools

Jing Gong, Chunjie Liu, Wei Liu, Yuliang Wu, Zhaowu Ma, Hu Chen, An-Yuan Guo
2015 Database: The Journal of Biological Databases and Curation  
An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools.  ...  In addition, as a supplement of the database, we have set up three flexible online tools to analyse the influence of novel variants on miRNA:mRNA binding.  ...  We retrieved the genomic locations and sequences of mRNA 3 0 UTRs from the Refgene table of UCSC genome browser (hg19, http://genome.ucs c.edu/).  ... 
doi:10.1093/database/bav029 pmid:25877638 pmcid:PMC4397995 fatcat:ckkcq3xgsnbi3ghapcrtozowca

Repbase Update, a database of repetitive elements in eukaryotic genomes

Weidong Bao, Kenji K. Kojima, Oleksiy Kohany
2015 Mobile DNA  
Repbase Update (RU) is a database of representative repeat sequences in eukaryotic genomes.  ...  Here, we introduce recent updates of RU, focusing on technical issues concerning the submission and updating of Repbase entries and will give short examples of using RU data.  ...  The authors would like to thank the reviewer for many valuable comments and Karolina Walichiewicz for the help with editing the manuscript.  ... 
doi:10.1186/s13100-015-0041-9 pmid:26045719 pmcid:PMC4455052 fatcat:pke4bh5w65eafgy3tnqologkfa

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

Mulin Jun Li, Zipeng Liu, Panwen Wang, Maria P. Wong, Matthew R. Nelson, Jean-Pierre A. Kocher, Meredith Yeager, Pak Chung Sham, Stephen J. Chanock, Zhengyuan Xia, Junwen Wang
2015 Nucleic Acids Research  
These updates include: (i) Up to August 2015, we collected 2479 unique publications from PubMed and other resources; (ii) We further curated moderate SNP-trait associations (P-value < 1.0×10 −3 ) from  ...  ; (vii) Last, we improved the user interface of website.  ...  several convenient external links to DMDM (47), SNPedia, Regulomedb (48) , HaploReg (49) , rSNPBase (50), UCSC Genome Browser (51) and GWAS Central ( Figure 1E ).  ... 
doi:10.1093/nar/gkv1317 pmid:26615194 pmcid:PMC4702921 fatcat:44jy3nlrpfg73j2scgx3gnjk3e

DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites

Marcin Jąkalski, Hiroyuki Wakaguri, Tabea G. Kischka, Yoshifumi Nishikawa, Shin-ichiro Kawazu, Makoto Matsubayashi, Fumiya Kawahara, Naotoshi Tsuji, Shinuo Cao, Fujiko Sunaga, Xuenan Xuan, Kazuhiro Okubo (+8 others)
2014 Nucleic Acids Research  
The 2015 update witnesses the major shift in the databases content with focus on diverse transcriptomes of the apicomplexan parasites.  ...  To adequately reflect the recent modifications and the current content we have changed the database name to DB-AT--DataBase of Apicomplexa Transcriptomes.  ...  Abe for constructing the RNA-seq libraries; H. Suganuma for cultivation of the parasites and to K. Imamura, A. Kanai and M. Tosaka for performing the RNA-seq sequencing. FUNDING  ... 
doi:10.1093/nar/gku1240 pmid:25414358 pmcid:PMC4383994 fatcat:ewd3dmrjzjbhdnc6ml3s27xcqu

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Hana Imrichová, Gert Hulselmans, Zeynep Kalender Atak, Delphine Potier, Stein Aerts
2015 Nucleic Acids Research  
Whereas the original version of i-cisTarget was focused on Drosophila data, the 2015 update also provides support for human and mouse data. i-cisTarget detects transcription factor motifs (position weight  ...  i-cisTarget is a web tool to predict regulators of a set of genomic regions, such as ChIP-seq peaks or co-regulated/similar enhancers. i-cisTarget can also be used to identify upstream regulators and their  ...  We thank Rekin's Janky and Dmitry Svetlichnyy for compiling the PWM database.  ... 
doi:10.1093/nar/gkv395 pmid:25925574 pmcid:PMC4489282 fatcat:zdqbi56ggfgblet64dgzh3fhqu

ZFIN, The zebrafish model organism database: Updates and new directions

Leyla Ruzicka, Yvonne M. Bradford, Ken Frazer, Douglas G. Howe, Holly Paddock, Sridhar Ramachandran, Amy Singer, Sabrina Toro, Ceri E. Van Slyke, Anne E. Eagle, David Fashena, Patrick Kalita (+8 others)
2015 Genesis  
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research.  ...  ZFIN collaborates with major bioinformatics organizations to verify and integrate genomic sequence data, provide nomenclature support, establish reciprocal links and participate in the development of standardized  ...  Acknowledgments Grant Support: This work was supported by the National Human Genome Research Institute (HG002659, and HG004834) of the National Institutes of Health.  ... 
doi:10.1002/dvg.22868 pmid:26097180 pmcid:PMC4545674 fatcat:tba5jdejl5grxavmzhzgzjfcpa

The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

Michael Y. Galperin, Daniel J. Rigden, Xosé M. Fernández-Suárez
2015 Nucleic Acids Research  
The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously  ...  This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets.  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their help in compiling this issue.  ... 
doi:10.1093/nar/gku1241 pmid:25593347 pmcid:PMC4383995 fatcat:rpqeohyapre5rijy7vfn7r2p7a

Databases and Web Tools for Cancer Genomics Study

Yadong Yang, Xunong Dong, Bingbing Xie, Nan Ding, Juan Chen, Yongjun Li, Qian Zhang, Hongzhu Qu, Xiangdong Fang
2015 Genomics, Proteomics & Bioinformatics  
The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge.  ...  Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience.  ...  UCSC Cancer Genomics Browser The UCSC Cancer Genomics Browser is an online analysis tool for hosting, visualizing, and analyzing information on cancer genomics and clinical research [9] .  ... 
doi:10.1016/j.gpb.2015.01.005 pmid:25707591 pmcid:PMC4411507 fatcat:nn4g76i3b5gbln2cqqkzs2irza
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