Andrey Sivachenko

Andrey Sivachenko

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Andrey Sivachenko

Andrey Sivachenko

Publications by authors named "Andrey Sivachenko"

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40Publications

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Isogenic cell models of cystic fibrosis-causing variants in natively expressing pulmonary epithelial cells.

J Cyst Fibros 2019 Jul 15;18(4):476-483. Epub 2018 Dec 15.

Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jcf.2018.12.001DOI Listing
July 2019

Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.

PLoS One 2014 9;9(5):e96094. Epub 2014 May 9.

Program in Membrane Biology, Division of Nephrology & Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096094PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015934PMC
October 2015

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events.

PLoS One 2014 31;9(1):e87361. Epub 2014 Jan 31.

Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America ; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America ; Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087361PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3909098PMC
October 2014

PRADA: pipeline for RNA sequencing data analysis.

Bioinformatics 2014 Aug 1;30(15):2224-6. Epub 2014 Apr 1.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103589PMC
August 2014

Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients.

J Clin Oncol 2014 Jan 9;32(2):121-8. Epub 2013 Dec 9.

Youngwook Kim, Ji-ae Yoon, Yoomi Lee, Yeong Kyung Yoo, and Keunchil Park, Samsung Medical Center, Samsung Biomedical Research Institute; Jong-Mu Sun, Hong Kwan Kim, Yong Soo Choi, Kwhanmien Kim, Young Mog Shim, Yoon-La Choi, Jhingook Kim, Jin Seok Ahn, Myung-Ju Ahn, and Keunchil Park, Samsung Medical Center, Sungkyunkwan University School of Medicine; Sukki Cho, Seoul National University Bundang Hospital, College of Medicine, Seoul National University, Seoul; In-Jae Oh, Kyu-Sik Kim, Sang-Yun Song, Kook-Ju Na, and Young-Chul Kim, Chonnam National University Hwasun Hospital, Jeonnam, Republic of Korea; Peter S. Hammerman, Jaegil Kim, Chandra Sekhar Pedamallu, Kristian Cibulskis, Michael S. Lawrence, Petar Stojanov, Scott L. Carter, Aaron McKenna, Chip Stewart, Andrey Y. Sivachenko, Gad Getz, and Matthew Meyerson, Broad Institute of Harvard and MIT, Cambridge; Matthew Meyerson, Harvard Medical School; Peter S. Hammerman and Chandra Sekhar Pedamallu, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital Cancer Center, Boston, MA; and Matthew D. Wilkerson and D. Neil Hayes, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.

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http://dx.doi.org/10.1200/JCO.2013.50.8556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062710PMC
January 2014

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Genome Res 2010 Sep 19;20(9):1297-303. Epub 2010 Jul 19.

Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/gr.107524.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928508PMC
September 2010

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

BMC Bioinformatics 2008 Aug 12;9 Suppl 9:S5. Epub 2008 Aug 12.

School of Informatics, Indiana University - Purdue University, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1186/1471-2105-9-S9-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2537576PMC
August 2008

Molecular networks in microarray analysis.

J Bioinform Comput Biol 2007 Apr;5(2B):429-56

Ariadne Genomics, Inc., 9430 Key West avenue, Suite 113, Rockville, MD 20850, USA.

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April 2007

Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism.

Expert Opin Ther Targets 2007 Mar;11(3):411-21

Ariadne Genomics, Inc., 9430 Key West Avenue, Rockville, MD 20850, USA.

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http://www.tandfonline.com/doi/full/10.1517/14728222.11.3.41
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http://dx.doi.org/10.1517/14728222.11.3.411 DOI Listing
March 2007

Mining Alzheimer disease relevant proteins from integrated protein interactome data.

Pac Symp Biocomput 2006 :367-78

Indiana University School of Informatics, Purdue University School of Science, Dept. of Computer and Information Science Indianapolis, IN 46202, USA.

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January 2007

Pathway analysis for design of promiscuous drugs and selective drug mixtures.

Curr Drug Discov Technol 2006 Dec;3(4):269-77

Ariadne Genomics Inc, Rockville, MD 20850, USA.

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December 2006

Initial large-scale exploration of protein-protein interactions in human brain.

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:229-34

Myriad Proteomics, Inc., Salt Lake City, UT 84116, USA.

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August 2006

Data mining in protein interactomics. Six computational research challenges and opportunities.

IEEE Eng Med Biol Mag 2005 May-Jun;24(3):95-102

Indiana University School of Informatics, USA.

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August 2005