Adam A Margolin

Adam A Margolin

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Adam A Margolin

Adam A Margolin

Publications by authors named "Adam A Margolin"

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Complement C5a Fosters Squamous Carcinogenesis and Limits T Cell Response to Chemotherapy.

Cancer Cell 2018 10;34(4):561-578.e6

Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Research Building Room 3030, 2720 SW Moody Avenue, #KC-CDCB, Portland, OR 97201-5042, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6246036PMC
October 2018

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

BMC Bioinformatics 2018 01 31;19(1):28. Epub 2018 Jan 31.

Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, M5G 0A3, Canada.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-018-2046-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793408PMC
January 2018

Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies.

Bioinformatics 2017 05;33(9):1362-1369

Computational Biology Program, Oregon Health and Science University, Portland, OR 97239, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860077PMC
May 2017

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Nat Methods 2015 Jul 18;12(7):623-30. Epub 2015 May 18.

1] Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856034PMC
July 2015

Functional kinomics identifies candidate therapeutic targets in head and neck cancer.

Clin Cancer Res 2014 Aug;20(16):4274-88

Department of Otolaryngology: Head and Neck Surgery, University of Washington Medical Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington. Surgery and Perioperative Care Service, VA Puget Sound Health Care System, Seattle, Washington.

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http://dx.doi.org/10.1158/1078-0432.CCR-13-2858DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135446PMC
August 2014

Assessing the clinical utility of cancer genomic and proteomic data across tumor types.

Nat Biotechnol 2014 Jul 22;32(7):644-52. Epub 2014 Jun 22.

1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, USA. [2] Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA. [3].

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http://www.nature.com/articles/nbt.2940
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http://dx.doi.org/10.1038/nbt.2940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102885PMC
July 2014

Empirical Bayes analysis of quantitative proteomics experiments.

PLoS One 2009 Oct 14;4(10):e7454. Epub 2009 Oct 14.

Cancer program, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007454PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759080PMC
October 2009

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

Proc Natl Acad Sci U S A 2009 Jan 31;106(1):244-9. Epub 2008 Dec 31.

Department of Biomedical Informatics, Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0806445106
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http://dx.doi.org/10.1073/pnas.0806445106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613038PMC
January 2009

Theory and limitations of genetic network inference from microarray data.

Ann N Y Acad Sci 2007 Dec 9;1115:51-72. Epub 2007 Oct 9.

Department of Biomedical Informatics, 1130 St. Nicholas Avenue, Room 917, New York, NY 10032, USA.

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http://dx.doi.org/10.1196/annals.1407.019DOI Listing
December 2007

Reverse engineering cellular networks.

Nat Protoc 2006 ;1(2):662-71

Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA.

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http://dx.doi.org/10.1038/nprot.2006.106DOI Listing
September 2007

PEG10 is a c-MYC target gene in cancer cells.

Cancer Res 2006 Jan;66(2):665-72

Institute for Cancer Genetics, Columbia University Medical Center, 1150 St. Nicholas Avenue, New York, NY 10032, USA.

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http://cancerres.aacrjournals.org/content/66/2/665.full.pdf
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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
Publisher Site
http://dx.doi.org/10.1158/0008-5472.CAN-05-1553DOI Listing
January 2006

Boolean calculations made easy (for ribozymes).

Nat Biotechnol 2005 Nov;23(11):1374-6

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http://dx.doi.org/10.1038/nbt1105-1374DOI Listing
November 2005

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.

Bioinformatics 2005 Aug 19;21(15):3308-11. Epub 2005 May 19.

Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, 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/bti500DOI Listing
August 2005

Reverse engineering of regulatory networks in human B cells.

Nat Genet 2005 Apr 20;37(4):382-90. Epub 2005 Mar 20.

Institute for Cancer Genetics, 1300 St. Nicholas Avenue, Room 912, New York, New York 10032, USA.

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http://dx.doi.org/10.1038/ng1532DOI Listing
April 2005