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Institution

Science Applications International Corporation

CompanyMcLean, Virginia, United States
About: Science Applications International Corporation is a company organization based out in McLean, Virginia, United States. It is known for research contribution in the topics: Population & Virus. The organization has 7141 authors who have published 11747 publications receiving 696315 citations.
Topics: Population, Virus, Immune system, T cell, Cancer


Papers
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Journal ArticleDOI
TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
Abstract: DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.

31,015 citations

Journal ArticleDOI
TL;DR: The survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
Abstract: Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological processes most pertinent to their study. Approximately 68 bioinformatics enrichment tools that are currently available in the community are collected in this survey. Tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms. The comprehensive collections, unique tool classifications and associated questions/issues will provide a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends in a simpler tool-class level rather than by a tool-by-tool approach. Thus, the survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.

13,102 citations

Journal ArticleDOI
TL;DR: DAMID is a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries that assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.
Abstract: The distributed nature of biological knowledge poses a major challenge to the interpretation of genome-scale datasets, including those derived from microarray and proteomic studies. This report describes DAVID, a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries. Lists of gene or protein identifiers are rapidly annotated and summarized according to shared categorical data for Gene Ontology, protein domain, and biochemical pathway membership. DAVID assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.

8,849 citations

Journal ArticleDOI
John T. Lonsdale, Jeffrey Thomas, Mike Salvatore, Rebecca Phillips, Edmund Lo, Saboor Shad, Richard Hasz, Gary Walters, Fernando U. Garcia1, Nancy Young2, Barbara A. Foster3, Mike Moser3, Ellen Karasik3, Bryan Gillard3, Kimberley Ramsey3, Susan L. Sullivan, Jason Bridge, Harold Magazine, John Syron, Johnelle Fleming, Laura A. Siminoff4, Heather M. Traino4, Maghboeba Mosavel4, Laura Barker4, Scott D. Jewell5, Daniel C. Rohrer5, Dan Maxim5, Dana Filkins5, Philip Harbach5, Eddie Cortadillo5, Bree Berghuis5, Lisa Turner5, Eric Hudson5, Kristin Feenstra5, Leslie H. Sobin6, James A. Robb6, Phillip Branton, Greg E. Korzeniewski6, Charles Shive6, David Tabor6, Liqun Qi6, Kevin Groch6, Sreenath Nampally6, Steve Buia6, Angela Zimmerman6, Anna M. Smith6, Robin Burges6, Karna Robinson6, Kim Valentino6, Deborah Bradbury6, Mark Cosentino6, Norma Diaz-Mayoral6, Mary Kennedy6, Theresa Engel6, Penelope Williams6, Kenyon Erickson, Kristin G. Ardlie7, Wendy Winckler7, Gad Getz8, Gad Getz7, David S. DeLuca7, MacArthur Daniel MacArthur8, MacArthur Daniel MacArthur7, Manolis Kellis7, Alexander Thomson7, Taylor Young7, Ellen Gelfand7, Molly Donovan7, Yan Meng7, George B. Grant7, Deborah C. Mash9, Yvonne Marcus9, Margaret J. Basile9, Jun Liu8, Jun Zhu10, Zhidong Tu10, Nancy J. Cox11, Dan L. Nicolae11, Eric R. Gamazon11, Hae Kyung Im11, Anuar Konkashbaev11, Jonathan K. Pritchard12, Jonathan K. Pritchard11, Matthew Stevens11, Timothée Flutre11, Xiaoquan Wen11, Emmanouil T. Dermitzakis13, Tuuli Lappalainen13, Roderic Guigó, Jean Monlong, Michael Sammeth, Daphne Koller14, Alexis Battle14, Sara Mostafavi14, Mark I. McCarthy15, Manual Rivas15, Julian Maller15, Ivan Rusyn16, Andrew B. Nobel16, Fred A. Wright16, Andrey A. Shabalin16, Mike Feolo17, Nataliya Sharopova17, Anne Sturcke17, Justin Paschal17, James M. Anderson17, Elizabeth L. Wilder17, Leslie Derr17, Eric D. Green17, Jeffery P. Struewing17, Gary F. Temple17, Simona Volpi17, Joy T. Boyer17, Elizabeth J. Thomson17, Mark S. Guyer17, Cathy Ng17, Assya Abdallah17, Deborah Colantuoni17, Thomas R. Insel17, Susan E. Koester17, Roger Little17, Patrick Bender17, Thomas Lehner17, Yin Yao17, Carolyn C. Compton17, Jimmie B. Vaught17, Sherilyn Sawyer17, Nicole C. Lockhart17, Joanne P. Demchok17, Helen F. Moore17 
TL;DR: The Genotype-Tissue Expression (GTEx) project is described, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
Abstract: Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.

6,545 citations

Journal ArticleDOI
TL;DR: The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA with a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages.
Abstract: The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

5,294 citations


Authors

Showing all 7145 results

NameH-indexPapersCitations
David J. Hunter2131836207050
Elaine S. Jaffe156828112412
Ronald G. Crystal15599086680
Stephen J. Chanock1541220119390
Stephen J. O'Brien153106293025
Martin A. Nowak14859194394
Seth M. Steinberg13793680148
Bruce R. Blazar132100169622
Joost J. Oppenheim13045459601
Dan L. Longo12569756085
Sharon E. Straus12087972513
Warren Strober11642450247
Ruth Nussinov11472752320
Stefania Bandinelli11345055014
W. Marston Linehan11256850772
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20232
202219
2021100
202069
201971
201864