Publications by authors named "Mahmoud Ghandi"

28Publications

Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes.

Cell Rep 2017 12;21(13):3700-3707

BioFrontiers Institute, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747321PMC
December 2017

Defining a Cancer Dependency Map.

Cell 2017 Jul;170(3):564-576.e16

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5667678PMC
July 2017

gkmSVM: an R package for gapped-kmer SVM.

Bioinformatics 2016 07 19;32(14):2205-7. Epub 2016 Apr 19.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937197PMC
July 2016

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

Cell Syst 2015 Dec;1(6):417-425

Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA; Department of Medicine, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.cels.2015.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4707969PMC
December 2015

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.

Cancer Cell 2014 Dec;26(6):813-825

Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2014.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302418PMC
December 2014

ERK mutations confer resistance to mitogen-activated protein kinase pathway inhibitors.

Cancer Res 2014 Dec 15;74(23):7079-89. Epub 2014 Oct 15.

Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute, Cambridge, Massachusetts.

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http://dx.doi.org/10.1158/0008-5472.CAN-14-2073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300142PMC
December 2014

Enhanced regulatory sequence prediction using gapped k-mer features.

PLoS Comput Biol 2014 Jul 17;10(7):e1003711. Epub 2014 Jul 17.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102394PMC
July 2014

ARID1B is a specific vulnerability in ARID1A-mutant cancers.

Nat Med 2014 Mar 23;20(3):251-4. Epub 2014 Feb 23.

1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA. [4] Broad Institute of Harvard and MIT, Boston, Massachusetts, USA. [5] Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nm.3480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954704PMC
March 2014

Robust k-mer frequency estimation using gapped k-mers.

J Math Biol 2014 Aug 17;69(2):469-500. Epub 2013 Jul 17.

Department of Biomedical Engineering and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA,

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http://dx.doi.org/10.1007/s00285-013-0705-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895138PMC
August 2014

Group normalization for genomic data.

PLoS One 2012 13;7(8):e38695. Epub 2012 Aug 13.

McKusick-Nathans Institute of Genetic Medicine and the Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038695PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418286PMC
April 2013

A mechanistic study on the effect of dexamethasone in moderating cell death in Chinese Hamster Ovary cell cultures.

Biotechnol Prog 2012 Mar-Apr;28(2):490-6. Epub 2011 Dec 2.

Biologics Process and Product Development, Technical Operations, Bristol-Myers Squibb Company, East Syracuse, NY 13057, USA.

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http://doi.wiley.com/10.1002/btpr.747
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http://dx.doi.org/10.1002/btpr.747DOI Listing
July 2012