Literature DB >> 22836096

Leveraging models of cell regulation and GWAS data in integrative network-based association studies.

Andrea Califano1, Atul J Butte, Stephen Friend, Trey Ideker, Eric Schadt.   

Abstract

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Year:  2012        PMID： 22836096      PMCID： PMC3593099          DOI： 10.1038/ng.2355

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


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  87 in total

1.  Inferring subnetworks from perturbed expression profiles.

Authors:  D Pe'er; A Regev; G Elidan; N Friedman
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2.  An integrative genomics approach to infer causal associations between gene expression and disease.

Authors:  Eric E Schadt; John Lamb; Xia Yang; Jun Zhu; Steve Edwards; Debraj Guhathakurta; Solveig K Sieberts; Stephanie Monks; Marc Reitman; Chunsheng Zhang; Pek Yee Lum; Amy Leonardson; Rolf Thieringer; Joseph M Metzger; Liming Yang; John Castle; Haoyuan Zhu; Shera F Kash; Thomas A Drake; Alan Sachs; Aldons J Lusis
Journal:  Nat Genet       Date:  2005-06-19       Impact factor: 38.330

3.  ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.

Authors:  Adam A Margolin; Teresa Palomero; Pavel Sumazin; Andrea Califano; Adolfo A Ferrando; Gustavo Stolovitzky
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-31       Impact factor: 11.205

Review 4.  Molecular networks as sensors and drivers of common human diseases.

Authors:  Eric E Schadt
Journal:  Nature       Date:  2009-09-10       Impact factor: 49.962

5.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

6.  Analysis of a functional BTNL2 polymorphism in type 1 diabetes, rheumatoid arthritis, and systemic lupus erythematosus.

Authors:  Gisela Orozco; Peter Eerligh; Elena Sánchez; Sasha Zhernakova; Bart O Roep; Miguel A González-Gay; Miguel A López-Nevot; Jose L Callejas; Carmen Hidalgo; Dora Pascual-Salcedo; Alejandro Balsa; María F González-Escribano; Bobby P C Koeleman; Javier Martín
Journal:  Hum Immunol       Date:  2006-03-09       Impact factor: 2.850

7.  Simultaneous clustering of multiple gene expression and physical interaction datasets.

Authors:  Manikandan Narayanan; Adrian Vetta; Eric E Schadt; Jun Zhu
Journal:  PLoS Comput Biol       Date:  2010-04-15       Impact factor: 4.475

8.  Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes.

Authors:  Hua Zhong; John Beaulaurier; Pek Yee Lum; Cliona Molony; Xia Yang; Douglas J Macneil; Drew T Weingarth; Bin Zhang; Danielle Greenawalt; Radu Dobrin; Ke Hao; Sangsoon Woo; Christine Fabre-Suver; Su Qian; Michael R Tota; Mark P Keller; Christina M Kendziorski; Brian S Yandell; Victor Castro; Alan D Attie; Lee M Kaplan; Eric E Schadt
Journal:  PLoS Genet       Date:  2010-05-06       Impact factor: 5.917

9.  Network-based model weighting to detect multiple loci influencing complex diseases.

Authors:  Wei Pan
Journal:  Hum Genet       Date:  2008-08-22       Impact factor: 4.132

10.  Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses.

Authors:  Marc R Birtwistle; Mariko Hatakeyama; Noriko Yumoto; Babatunde A Ogunnaike; Jan B Hoek; Boris N Kholodenko
Journal:  Mol Syst Biol       Date:  2007-11-13       Impact factor: 11.429
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  128 in total

1.  DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.

Authors:  Mariano J Alvarez; James C Chen; Andrea Califano
Journal:  Bioinformatics       Date:  2015-09-02       Impact factor: 6.937

2.  A neurogenetics approach to defining differential susceptibility to institutional care.

Authors:  Zoe H Brett; Margaret Sheridan; Kate Humphreys; Anna Smyke; Mary Margaret Gleason; Nathan Fox; Charles Zeanah; Charles Nelson; Stacy Drury
Journal:  Int J Behav Dev       Date:  2015-03

3.  Defining a comprehensive verotype using electronic health records for personalized medicine.

Authors:  Mary Regina Boland; George Hripcsak; Yufeng Shen; Wendy K Chung; Chunhua Weng
Journal:  J Am Med Inform Assoc       Date:  2013-09-03       Impact factor: 4.497

Review 4.  Principles and methods of integrative genomic analyses in cancer.

Authors:  Vessela N Kristensen; Ole Christian Lingjærde; Hege G Russnes; Hans Kristian M Vollan; Arnoldo Frigessi; Anne-Lise Børresen-Dale
Journal:  Nat Rev Cancer       Date:  2014-05       Impact factor: 60.716

Review 5.  Functional genomic screening approaches in mechanistic toxicology and potential future applications of CRISPR-Cas9.

Authors:  Hua Shen; Cliona M McHale; Martyn T Smith; Luoping Zhang
Journal:  Mutat Res Rev Mutat Res       Date:  2015-01-25       Impact factor: 5.657

Review 6.  A systems approach to drug discovery in Alzheimer's disease.

Authors:  Michael Shelanski; William Shin; Soline Aubry; Peter Sims; Mariano J Alvarez; Andrea Califano
Journal:  Neurotherapeutics       Date:  2015-01       Impact factor: 7.620

7.  Genetic Epidemiology of Complex Phenotypes.

Authors:  Darren D O'Rielly; Proton Rahman
Journal:  Methods Mol Biol       Date:  2021

8.  A network-based kernel machine test for the identification of risk pathways in genome-wide association studies.

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9.  Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases.

Authors:  Daniel Marbach; David Lamparter; Gerald Quon; Manolis Kellis; Zoltán Kutalik; Sven Bergmann
Journal:  Nat Methods       Date:  2016-03-07       Impact factor: 28.547

Review 10.  Genomics in cardiovascular disease.

Authors:  Robert Roberts; A J Marian; Sonny Dandona; Alexandre F R Stewart
Journal:  J Am Coll Cardiol       Date:  2013-03-21       Impact factor: 24.094
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