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Institution

Institute for Systems Biology

NonprofitSeattle, Washington, United States
About: Institute for Systems Biology is a nonprofit organization based out in Seattle, Washington, United States. It is known for research contribution in the topics: Population & Proteomics. The organization has 1277 authors who have published 2777 publications receiving 353165 citations.


Papers
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Journal ArticleDOI
TL;DR: The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data, and successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data.
Abstract: We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon Halobacterium NRC-1. The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data. The learned network successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data. Several specific regulatory predictions were experimentally tested and verified.

551 citations

Journal ArticleDOI
05 Apr 2018-Cell
TL;DR: The largest investigation of predisposition variants in cancer to date finds 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types, informing future guidelines of variant classification and germline genetic testing in cancer.

543 citations

Journal ArticleDOI
TL;DR: The use of iProphet in the Trans-Proteomics Pipeline increases the number of correctly identified peptides at a constant false discovery rate as compared with both PeptideProphet and another state-of-the-art tool Percolator.

535 citations

Journal ArticleDOI
TL;DR: The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the range of extant checklists.
Abstract: The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the range of extant checklists.

535 citations

Journal ArticleDOI
TL;DR: The PeptideAtlas Project is described, its contents and components are described, and it is shown how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.
Abstract: A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the system being studied. For proteomics to be a key part of such studies, it must deliver accurate quantification of all the components in the system for each tested perturbation without any gaps in the data. This will require a new approach to proteomics that is based on emerging targeted quantitative mass spectrometry techniques. The PeptideAtlas Project comprises a growing, publicly accessible database of peptides identified in many tandem mass spectrometry proteomics studies and software tools that allow the building of PeptideAtlas, as well as its use by the research community. Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.

534 citations


Authors

Showing all 1292 results

NameH-indexPapersCitations
Younan Xia216943175757
Ruedi Aebersold182879141881
David Haussler172488224960
Steven P. Gygi172704129173
Nahum Sonenberg167647104053
Leroy Hood158853128452
Mark H. Ellisman11763755289
Wei Zhang112118993641
John Ralph10944239238
Eric H. Davidson10645447058
James R. Heath10342558548
Alan Aderem9924646682
Anne-Claude Gingras9733640714
Trey Ideker9730672276
Michael H. Gelb9450634714
Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20233
202260
2021216
2020204
2019188
2018168