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Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser

Judith E Stenger, Hong Xu, Carol Haynes, Elizabeth R Hauser, Margaret Pericak-Vance, Pascal J Goldschmidt-Clermont, Jeffery M Vance
2005 BMC Bioinformatics  
Statistical Viewer is an add-on package to the open-source Ensembl Genome Browser and Annotation System that displays disease study-specific linkage and/or association data as 2 dimensional plots in new  ...  To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath.  ...  to make Statistic View available through the public site.  ... 
doi:10.1186/1471-2105-6-95 pmid:15826305 pmcid:PMC1087836 fatcat:mpbejkdbmnaj5g7upboxoflfwu

Analysis of Complex Disease Association and Linkage Studies Using the University of California Santa Cruz Genome Browser

T. Wang, T. S. Furey
2009 Circulation: Cardiovascular Genetics  
The online-only Data Supplement is available at http://circgenetics.ahajournals.org/cgi/content/full/2/2/199/DC1.  ...  Disclosures Dr Furey is a partner in the Genome Browser Authors partnership, which licenses the UCSC Genome Browser software to profit entities.  ...  Sources of Funding This study was supported by the Duke Institute for Genome Sciences and Policy and National Institutes of Health grants HL073389 (Hauser), MH059528 (Hauser) and HL73042 (Goldschmidt,  ... 
doi:10.1161/circgenetics.108.843946 pmid:20031585 pmcid:PMC2798134 fatcat:mgy7kusauzdabhcesfnmiusqge

GenomeGraphs: integrated genomic data visualization with R

Steffen Durinck, James Bullard, Paul T Spellman, Sandrine Dudoit
2009 BMC Bioinformatics  
GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.  ...  We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets.  ...  The package has been tested and run on OS X, Windows, and a variety of Linux systems.  ... 
doi:10.1186/1471-2105-10-2 pmid:19123956 pmcid:PMC2629762 fatcat:vk4rd4vyy5airap55dckjyysuq

Exploring the Landscape of the Genome [chapter]

Michael R. Barnes
2010 Msphere  
The comprehensive range of information presented in tools such as the UCSC genome browser and Ensembl enables integrated queries of data that are otherwise reserved to the most skilled computational biologists  ...  While at a micro level, genome annotation can help to describe the full complexity of gene regulation, variation, and transcript diversity.  ...  Although there are many ways to access genomic information in an integrated manner, there are two primary tools that are the acknowledged leaders in the field, the UCSC human genome browser (1) and ENSEMBL  ... 
doi:10.1007/978-1-60327-367-1_2 pmid:20238074 fatcat:d37ygpseorcgnjfhsvtvbv4tey

A survey of tools for variant analysis of next-generation genome sequencing data

S. Pabinger, A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, Z. Trajanoski
2013 Briefings in Bioinformatics  
While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting  ...  We report an overview of the functionality, features and specific requirements of the individual tools.  ...  Acknowledgements We thank the reviewers for their numerous constructive suggestions, which helped us to considerably improve the article.  ... 
doi:10.1093/bib/bbs086 pmid:23341494 pmcid:PMC3956068 fatcat:zcunpg3i7bfrvhm5dixp6r6ofq

Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context

Markus Weniger, Julia C Engelmann, Jörg Schultz
2007 BMC Bioinformatics  
We provide an integration of statistical methods for data import and data analysis together with a biological interpretation for subsets of probes or single probes on the chip.  ...  GEPAT offers no linear work flow, but allows the usage of any subset of probes and samples as a start for a new data analysis.  ...  JE was funded by the IZKF of the University of Würzburg and by the BMBF project FUNCRYPTA (FKZ 0313838B). MW wants to thank P. Seibel for help with programming issues, S.  ... 
doi:10.1186/1471-2105-8-179 pmid:17543125 pmcid:PMC1896182 fatcat:bvmudnp27jbmzbwugigreq4y7m

easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies

Dominik G. Grimm, Damian Roqueiro, Patrice A. Salomé, Stefan Kleeberger, Bastian Greshake, Wangsheng Zhu, Chang Liu, Christoph Lippert, Oliver Stegle, Bernhard Schölkopf, Detlef Weigel, Karsten M. Borgwardt
2016 The Plant Cell  
The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments  ...  Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses.  ...  the uploading of summary statistics of GWAS obtained from third-party tools; (4) it provides a variety of different methods to correct for multiple hypothesis testing; and, most importantly, (5) it integrates  ... 
doi:10.1105/tpc.16.00551 pmid:27986896 pmcid:PMC5304348 fatcat:fbq5cwbwv5hovblsc5hkb5k7dq

Growing and cultivating the forest genomics database, TreeGenes

Taylor Falk, Nic Herndon, Emily Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M Baker, Risharde Ramnath, Stephen Ficklin, Margaret Staton, Frank A Feltus, Sook Jung (+2 others)
2018 Database: The Journal of Biological Databases and Curation  
This focus was paired with the development of tools to enable comparative genomics and data visualization.  ...  This migration enabled developments focused on data exchange, data transfer and improved analytical capacity, as well as providing TreeGenes the opportunity to communicate with the following partner databases  ...  Acknowledgements We would like to thank the Computational Biology Core within the Institute of Systems Genomics at the University of Connecticut and The High Performance Computing Facility at the UConn  ... 
doi:10.1093/database/bay084 pmid:30239664 pmcid:PMC6146132 fatcat:o5a5wj5ylvdkdncttoebsk3ni4

Online Resources for SNP Analysis: A Review and Route Map

Christopher Phillips
2007 Molecular Biotechnology  
The major online single nucleotide polymorphism (SNP) databases freely available as research tools for genetic analysis are explained, reviewed, and compared.  ...  the most appropriate data for the research needs of clinical genetics and population genetics research.  ...  Ensembl is one of the principal genome data repositories with extensive databases and search tools stemming from the integral role of The Sanger Centre and EMBL in HGP and the position of Ensembl in providing  ... 
doi:10.1385/mb:35:1:65 pmid:17401150 fatcat:3aifzadxlnd65pvn4zqxeas774

Analyzing Proteomes and Protein Function Using Graphical Comparative Analysis of Tandem Mass Spectrometry Results

K. Jill McAfee, Dexter T. Duncan, Michael Assink, Andrew J. Link
2006 Molecular & Cellular Proteomics  
Currently available applications are typically designed for displaying proteins and posttranslational modifications from the point of view of the mass spectrometrist and are not versatile enough to allow  ...  Our system, Bioinformatic Graphical Comparative Analysis Tools (BIGCAT), allows sophisticated analysis of tandem mass spectrometry results in a biologically intuitive format and provides a solution to  ...  The annotation page provides the user with the annotations for the protein as well as links to outside annotation services including Ensembl, RefSeq, Gene Ontology, Swiss-Prot, Saccharomyces Genome Database  ... 
doi:10.1074/mcp.t500027-mcp200 pmid:16707483 fatcat:orqf4pvq4rfvpgczejx3kaxofy

Visualizing the drug target landscape

Stephen J. Campbell, Anna Gaulton, Jason Marshall, Dmitri Bichko, Sid Martin, Cory Brouwer, Lee Harland
2010 Drug Discovery Today  
A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment.  ...  Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave  ...  Beyond predetermined content The major genome viewers (University of California Santa Cruz, or UCSC [5] ; Ensembl [6] ; and the Generic Genome Browser, or GBrowse [7] ) illustrate the benefits of systems  ... 
doi:10.1016/j.drudis.2009.09.011 pmid:19840866 fatcat:csd4hsaokjgbjjbq4azwdnf24q

RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse

Catherine M Farrell, Tamara Goldfarb, Sanjida H Rangwala, Alexander Astashyn, Olga D Ermolaeva, Vichet Hem, Kenneth S Katz, Vamsi K Kodali, Frank Ludwig, Craig L Wallin, Kim D Pruitt, Terence D Murphy
2021 biorxiv/medrxiv  
Comparisons to other gene regulatory datasets show that the RefSeqFE dataset includes a wider range of feature types representing more areas of biology, but it is comparatively smaller and subject to data  ...  The data have multiple uses for basic functional discovery, bioinformatics studies, genetic variant interpretation, as known positive controls for epigenomic data evaluation, and as reference standards  ...  details and data clarifications.  ... 
doi:10.1101/gr.275819.121 pmid:34876495 pmcid:PMC8744684 fatcat:dichersxxfcdfijtp33emabx3u

Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing

Michael A Bauer, Shweta S Chavan, Erich A Peterson, Christoph J Heuck, Donald J Johann
2014 BMC Bioinformatics  
A suite of custom software tools have been developed to rapidly integrate, explore, discover and validate molecular profiling data from the NGS modalities of Whole Exome Sequencing (WES) and RNA-seq with  ...  In this regard, necessity dictated a need to utilize and leverage the many years of historical microarray data with new NGS approaches.  ...  Acknowledgements Appreciation and thanks to Mr. Daniel Pollock for his programming assistance.  ... 
doi:10.1186/1471-2105-15-s11-s3 pmid:25350881 pmcid:PMC4251047 fatcat:5pxiqqrjvrbmdoyj7uujznkl4u

Visualizing the drug target landscape

Stephen J. Campbell, Anna Gaulton, Jason Marshall, Dmitri Bichko, Sid Martin, Cory Brouwer, Lee Harland
2012 Drug Discovery Today  
A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment.  ...  Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave  ...  Beyond predetermined content The major genome viewers (University of California Santa Cruz, or UCSC [5] ; Ensembl [6] ; and the Generic Genome Browser, or GBrowse [7] ) illustrate the benefits of systems  ... 
doi:10.1016/j.drudis.2011.12.005 pmid:22178891 fatcat:qvdkemacwbaibb42sb4om6dxke

Functional Annotation of Putative Regulatory Elements at Cancer Susceptibility Loci

Stephanie A. Rosse, Paul L. Auer, Christopher S. Carlson
2014 Cancer Informatics  
Most cancer-associated genetic variants identified from genome-wide association studies (GWAS) do not obviously change protein structure, leading to the hypothesis that the associations are attributable  ...  Translating genetic associations into mechanistic insights can be facilitated by knowledge of the causal regulatory variant (or variants) responsible for the statistical signal.  ...  The UCSC Cancer Genome Browser currently displays a growing catalog of data, including 201 datasets from 22 TCGA (The Cancer Genome Atlas) cancers as well as data from Cancer Cell Line Encyclopedia and  ... 
doi:10.4137/cin.s13789 pmid:25288875 pmcid:PMC4179605 fatcat:gitz7qou3ndlpbcwznuccorrcq
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