Aravind Subramanian

Aravind Subramanian

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Aravind Subramanian

Aravind Subramanian

Publications by authors named "Aravind Subramanian"

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52Publications

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Activation of WNT and CREB signaling pathways in human neuronal cells in response to the Omega-3 fatty acid docosahexaenoic acid (DHA).

Mol Cell Neurosci 2019 Sep 14;99:103386. Epub 2019 Jun 14.

Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America. Electronic address:

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http://dx.doi.org/10.1016/j.mcn.2019.06.006DOI Listing
September 2019

The Carcinogenome Project: In Vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity.

Environ Health Perspect 2019 Apr;127(4):47002

1 Computational Biomedicine, Boston University School of Medicine , Boston, Massachusetts, USA.

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https://ehp.niehs.nih.gov/doi/10.1289/EHP3986
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http://dx.doi.org/10.1289/EHP3986DOI Listing
April 2019

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Authors:
Alexandra B Keenan Sherry L Jenkins Kathleen M Jagodnik Simon Koplev Edward He Denis Torre Zichen Wang Anders B Dohlman Moshe C Silverstein Alexander Lachmann Maxim V Kuleshov Avi Ma'ayan Vasileios Stathias Raymond Terryn Daniel Cooper Michele Forlin Amar Koleti Dusica Vidovic Caty Chung Stephan C Schürer Jouzas Vasiliauskas Marcin Pilarczyk Behrouz Shamsaei Mehdi Fazel Yan Ren Wen Niu Nicholas A Clark Shana White Naim Mahi Lixia Zhang Michal Kouril John F Reichard Siva Sivaganesan Mario Medvedovic Jaroslaw Meller Rick J Koch Marc R Birtwistle Ravi Iyengar Eric A Sobie Evren U Azeloglu Julia Kaye Jeannette Osterloh Kelly Haston Jaslin Kalra Steve Finkbiener Jonathan Li Pamela Milani Miriam Adam Renan Escalante-Chong Karen Sachs Alex Lenail Divya Ramamoorthy Ernest Fraenkel Gavin Daigle Uzma Hussain Alyssa Coye Jeffrey Rothstein Dhruv Sareen Loren Ornelas Maria Banuelos Berhan Mandefro Ritchie Ho Clive N Svendsen Ryan G Lim Jennifer Stocksdale Malcolm S Casale Terri G Thompson Jie Wu Leslie M Thompson Victoria Dardov Vidya Venkatraman Andrea Matlock Jennifer E Van Eyk Jacob D Jaffe Malvina Papanastasiou Aravind Subramanian Todd R Golub Sean D Erickson Mohammad Fallahi-Sichani Marc Hafner Nathanael S Gray Jia-Ren Lin Caitlin E Mills Jeremy L Muhlich Mario Niepel Caroline E Shamu Elizabeth H Williams David Wrobel Peter K Sorger Laura M Heiser Joe W Gray James E Korkola Gordon B Mills Mark LaBarge Heidi S Feiler Mark A Dane Elmar Bucher Michel Nederlof Damir Sudar Sean Gross David F Kilburn Rebecca Smith Kaylyn Devlin Ron Margolis Leslie Derr Albert Lee Ajay Pillai

Cell Syst 2018 01 29;6(1):13-24. Epub 2017 Nov 29.

NIH, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.cels.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799026PMC
January 2018

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

Nat Commun 2017 10 30;8(1):1186. Epub 2017 Oct 30.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1038/s41467-017-01383-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662764PMC
October 2017

High-throughput validation of ceRNA regulatory networks.

BMC Genomics 2017 05 30;18(1):418. Epub 2017 May 30.

Columbia Department of Systems Biology, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864
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http://dx.doi.org/10.1186/s12864-017-3790-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5450082PMC
May 2017

Gene expression inference with deep learning.

Bioinformatics 2016 06 11;32(12):1832-9. Epub 2016 Feb 11.

Department of Computer Science, University of California, Irvine, CA 92697, USA Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908320PMC
June 2016

Genetic modifiers of EGFR dependence in non-small cell lung cancer.

Proc Natl Acad Sci U S A 2014 Dec 15;111(52):18661-6. Epub 2014 Dec 15.

Broad Institute of Harvard and MIT, Cambridge, MA 02142; Departments of Pathology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115; and

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http://dx.doi.org/10.1073/pnas.1412228112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284598PMC
December 2014

An unbiased approach to identify endogenous substrates of "histone" deacetylase 8.

ACS Chem Biol 2014 Oct 11;9(10):2210-6. Epub 2014 Aug 11.

Stanley Center for Psychiatric Research, ‡Proteomics Platform, §Cancer Program, and ∥Center for the Science of Therapeutics, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States.

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http://dx.doi.org/10.1021/cb500492rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201337PMC
October 2014

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.

Nucleic Acids Res 2014 Jul 6;42(Web Server issue):W449-60. Epub 2014 Jun 6.

Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York (SBCNY), One Gustave L. Levy Place, New York, NY 10029, USA

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http://dx.doi.org/10.1093/nar/gku476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086130PMC
July 2014

Molecular signatures database (MSigDB) 3.0.

Bioinformatics 2011 Jun 5;27(12):1739-40. Epub 2011 May 5.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106198PMC
June 2011

Selective killing of K-ras mutant cancer cells by small molecule inducers of oxidative stress.

Proc Natl Acad Sci U S A 2011 May 9;108(21):8773-8. Epub 2011 May 9.

Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1105941108
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http://dx.doi.org/10.1073/pnas.1105941108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102385PMC
May 2011

SNP-based pathway enrichment analysis for genome-wide association studies.

BMC Bioinformatics 2011 Apr 15;12:99. Epub 2011 Apr 15.

Department of Computer Science, University of California, Irvine, USA.

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http://dx.doi.org/10.1186/1471-2105-12-99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102637PMC
April 2011

Disease allele-dependent small-molecule sensitivities in blood cells from monogenic diabetes.

Proc Natl Acad Sci U S A 2011 Jan 23;108(2):492-7. Epub 2010 Dec 23.

Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.

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http://dx.doi.org/10.1073/pnas.1016789108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3021060PMC
January 2011

Wilms tumor 1 (WT1) regulates KRAS-driven oncogenesis and senescence in mouse and human models.

J Clin Invest 2010 Nov 25;120(11):3940-52. Epub 2010 Oct 25.

Cancer Biology Program, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1172/JCI44165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965578PMC
November 2010

A radiation-derived gene expression signature predicts clinical outcome for breast cancer patients.

Radiat Res 2009 Feb;171(2):141-54

Fred Hutchinson Cancer Research Center, Seattle Washington, USA.

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http://dx.doi.org/10.1667/RR1223.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662705PMC
February 2009

Perturbational profiling of nanomaterial biologic activity.

Proc Natl Acad Sci U S A 2008 May 20;105(21):7387-92. Epub 2008 May 20.

Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0802878105
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http://dx.doi.org/10.1073/pnas.0802878105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396702PMC
May 2008

GSEA-P: a desktop application for Gene Set Enrichment Analysis.

Bioinformatics 2007 Dec 20;23(23):3251-3. Epub 2007 Jul 20.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm369DOI Listing
December 2007

IFN-alpha-stimulated genes and Epstein-Barr virus gene expression distinguish WHO type II and III nasopharyngeal carcinomas.

Cancer Res 2007 Jan;67(2):474-81

Department of Pathology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA, and Graduate Institute of Microbiology, Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan.

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http://dx.doi.org/10.1158/0008-5472.CAN-06-1882DOI Listing
January 2007

Microarray-assisted pathway analysis identifies mitogen-activated protein kinase signaling as a mediator of resistance to the green tea polyphenol epigallocatechin 3-gallate in her-2/neu-overexpressing breast cancer cells.

Cancer Res 2006 May;66(10):5322-9

Department of Biochemistry and Women's Health Interdisciplinary Research Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-05-4287DOI Listing
May 2006

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

Proc Natl Acad Sci U S A 2005 Oct 30;102(43):15545-50. Epub 2005 Sep 30.

Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1073/pnas.0506580102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239896PMC
October 2005

An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis.

Nat Genet 2005 Jan 19;37(1):48-55. Epub 2004 Dec 19.

MIT Center for Cancer Research, Building E17-517, 40 Ames Street, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/ng1490DOI Listing
January 2005