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UCSC Data Integrator and Variant Annotation Integrator

Angie S. Hinrichs, Brian J. Raney, Matthew L. Speir, Brooke Rhead, Jonathan Casper, Donna Karolchik, Robert M. Kuhn, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, W. James Kent
2016 Bioinformatics  
The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences  ...  Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs  ...  Acknowledgements We would like to acknowledge the work of the UCSC Genome Bioinformatics staff (http://genome.ucsc.edu/staff.html), our many collaborators and our users for their feedback and support.  ... 
doi:10.1093/bioinformatics/btv766 pmid:26740527 pmcid:PMC4848401 fatcat:76l7v2szq5g4dacohlcghn7joa

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  
New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype  ...  Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data.  ...  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: 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  
; and a new interactive tool, the "Data Integrator", for intersecting data from multiple tracks.  ...  The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently.  ...  ACKNOWLEDGEMENTS We would like to thank our many data contributors and collaborators whose work make the Genome Browser what it is, our loyal users for their support and vital feedback, and our exceptional  ... 
doi:10.1093/nar/gku1177 pmid:25428374 pmcid:PMC4383971 fatcat:sahorqoiejam7maduvqkqrh4de

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
; and a new interactive tool, the "Data Integrator", for intersecting data from multiple tracks.  ...  The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently.  ...  Data added to the Genome Browser through these methods are fully integrated with the other tools that UCSC offers, such as the Table Browser , Data Integrator, and the Variant Annotation Integrator.  ... 
doi:10.1101/027037 fatcat:5c7vac6nqbbftabnwrkprqljua

Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses

Geng Chen, Dianke Yu, Jiwei Chen, Ruifang Cao, Juan Yang, Huan Wang, Xiangjun Ji, Baitang Ning, Tieliu Shi
2015 Scientific Reports  
Acknowledgments We would like to thank Zhongchao Shen, Jianmin Yang, Qi Lv and Peng Li for their helpful discussions. The views presented in this article do not necessarily reflect those of the U.S.  ...  However, these studies did not combine different gene/regulatory annotation databases, high-throughput sequencing data and experimental assay to annotate noncoding genetic variants integratively.  ...  Moreover, our integrative approaches could be applied to characterize the genetic variants identified by genome/exome sequencing data as well.  ... 
doi:10.1038/srep09453 pmid:25819875 pmcid:PMC4377585 fatcat:s3qjgl5f3besrezmwyupuadabi

CNVannotator: A Comprehensive Annotation Server for Copy Number Variation in the Human Genome

Min Zhao, Zhongming Zhao, Yu Xue
2013 PLoS ONE  
Despite the growing demand to filter and classify CNVs by factors such as frequency in population, biological features, and function, surprisingly, no online web server for CNV annotations has been made  ...  The annotated results along with the server can be accessed at http://bioinfo.mc.vanderbilt. edu/CNVannotator/.  ...  Qingguo Wang for technical assistance and Ms. Rebecca Hiller Posey for polishing an earlier draft of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0080170 pmid:24244640 pmcid:PMC3828214 fatcat:7dxtul4fbrhlnph3gitcnvaa5e

CruzDB: software for annotation of genomic intervals with UCSC genome-browser database

Brent S. Pedersen, Ivana V. Yang, Subhajyoti De
2013 Computer applications in the biosciences : CABIOS  
Annotating a particular dataset with existing external data can provide insight into function.  ...  Results: We present CruzDB, a fast and intuitive programmatic interface to the University of California, Santa Cruz (UCSC) genome browser that facilitates integrative analyses of diverse local and remotely  ...  Integrating this locally hosted dataset with CpG island, and refGene data-tables from the UCSC genome browser, we find that early-replicating regions are enriched for gene bodies and for CpG islands relative  ... 
doi:10.1093/bioinformatics/btt534 pmid:24037212 pmcid:PMC3834799 fatcat:wmy2qat5lvezlgce7ggqjs3bhm

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  
The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets.  ...  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  ...  support and valuable feedback, and our outstanding team of system administrators: Jorge Garcia, Erich Weiler and Gary Moro.  ... 
doi:10.1093/nar/gks1048 pmid:23155063 pmcid:PMC3531082 fatcat:pernizd77fdijcyqc56eicrqzq

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  
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  ...  three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin  ...  The Variant Annotation Integrator (VAI) (42) annotates user-provided variant calls with predicted functional effects and data from other tracks. database to store track data.  ... 
doi:10.1093/nar/gkm966 pmid:18086701 pmcid:PMC2238835 fatcat:zdlffcr2vvhpdhn5epwzsneyky

OUP accepted manuscript

2016 Nucleic Acids Research  
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  ...  three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin  ...  The Variant Annotation Integrator (VAI) (42) annotates user-provided variant calls with predicted functional effects and data from other tracks. database to store track data.  ... 
doi:10.1093/nar/gkw1134 pmid:27899642 pmcid:PMC5210591 fatcat:h6hqicfojzaifoxt3ndyhoy5pi

CruzDB: software for annotation of genomic intervals with UCSC genome-browser data [article]

Brent S Pedersen, Ivana V Yang, Subhajyoti De
2013 arXiv   pre-print
We present CruzDB, a fast and intuitive programmatic interface to the UCSC genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets.  ...  Second, variants associated with cognitive functions map to lincRNA transcripts of relevant function. Third, lamina-associated domains are highly enriched in olfaction-related genes.  ...  Integrating this locally hosted dataset with CpG-island, and refGene data-tables from the UCSC genome browser, we find that early-replicating regions are enriched for gene-bodies and for CpG-islands relative  ... 
arXiv:1303.3332v2 fatcat:vbedk3b6njh7beenztxbfognry

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  
The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets.  ...  Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods.  ...  support and valuable feedback, and our outstanding team of system administrators: Jorge Garcia, Erich Weiler, Victoria Lin and Gary Moro.  ... 
doi:10.1093/nar/gkr1055 pmid:22086951 pmcid:PMC3245018 fatcat:lnijxi7u4vclpjuharlr2wvkia

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  
As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data  ...  assemblies and annotations to scientists and students worldwide.  ...  The Variant Annotation Integrator (VAI) allows users to upload variants and see potential functional effects on user-selected transcript sets and regulatory data sets in the Genome Browser database (e.g  ... 
doi:10.1093/nar/gkq963 pmid:20959295 pmcid:PMC3242726 fatcat:fnemefhmkbc65bmwbfxqlp7lpm

GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies

Wei Yu, Ajay Yesupriya, Anja Wulf, Lucia A Hindorff, Nicole Dowling, Muin J Khoury, Marta Gwinn
2011 European Journal of Human Genetics  
tool that offers a robust search capacity and a set of data mining functions by integrating information from the NHGRI GWAS Catalog, with data from other established bioinformatics resources including  ...  Data mining capacity A series of data mining capacities can be used to further explore search results. Variant-4proxy function.  ... 
doi:10.1038/ejhg.2011.91 pmid:21610748 pmcid:PMC3190251 fatcat:mjasfelvunbt5pevzh3vvx7om4

AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes

Young-Ji Na, Yonglae Cho, Ju Han Kim
2013 Healthcare Informatics Research  
The annotation data reported by the AnsNGS can meet this requirement. Integrating the AnsNGS into a human DNA sequencing pipeline is powerful and versatile in clinical applications of NGS.  ...  The AnsNGS takes text-based input files, obtains annotation information from the integrated databases, and returns the detailed annotation output to the user.  ... 
doi:10.4258/hir.2013.19.1.50 pmid:23626918 pmcid:PMC3633172 fatcat:lcpo3iptx5hetmojftlmgq76h4
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