Jacob D Jaffe

Jacob D Jaffe

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Jacob D Jaffe

Jacob D Jaffe

Publications by authors named "Jacob D Jaffe"

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Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS.

Mol Cell Proteomics 2019 Oct 13;18(10):2089-2098. Epub 2019 Aug 13.

The Broad Institute of MIT and Harvard, Cambridge, MA.

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http://dx.doi.org/10.1074/mcp.RA119.001325DOI Listing
October 2019

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.

Cancer Cell 2018 12 21;34(6):939-953.e9. Epub 2018 Nov 21.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15356108183048
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http://dx.doi.org/10.1016/j.ccell.2018.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310147PMC
December 2018

Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.

Genome Res 2018 10 30;28(10):1455-1466. Epub 2018 Aug 30.

Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.230300.117
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http://dx.doi.org/10.1101/gr.230300.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169886PMC
October 2018

Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.

Mol Cell Proteomics 2018 06 27;17(6):1239-1244. Epub 2018 Feb 27.

From the ‡University of Washington, Seattle, Washington 98195;

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http://dx.doi.org/10.1074/mcp.RA117.000543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986241PMC
June 2018

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

Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms.

J Am Soc Mass Spectrom 2016 11 25;27(11):1745-1751. Epub 2016 Aug 25.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061621PMC
http://dx.doi.org/10.1007/s13361-016-1465-2DOI Listing
November 2016

Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of Peptides to Greater than 150 for Targeted MS-Based Assays.

Anal Chem 2016 08 12;88(15):7548-55. Epub 2016 Jul 12.

Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States.

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http://dx.doi.org/10.1021/acs.analchem.6b00946DOI Listing
August 2016

H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs.

Cell Rep 2016 Feb 21;14(5):1142-1155. Epub 2016 Jan 21.

Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.12.100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764991PMC
February 2016

Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.

Mol Cell Proteomics 2015 Jun 13;14(6):1435-46. Epub 2015 Feb 13.

From the ‡Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02143;

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http://dx.doi.org/10.1074/mcp.M114.044586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458711PMC
June 2015

Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.

Methods 2015 Jan 6;72:57-64. Epub 2014 Nov 6.

The Broad Institute of MIT and Harvard University, 415 Main St., Cambridge, MA 02142, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.10.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300274PMC
January 2015

Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.

Mol Cell 2015 Jan 8;57(2):304-316. Epub 2015 Jan 8.

Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10972765140095
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http://dx.doi.org/10.1016/j.molcel.2014.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305004PMC
January 2015

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

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.

Proc Natl Acad Sci U S A 2014 May 12;111(21):7741-6. Epub 2014 May 12.

Broad Institute, Cambridge, MA 02142;Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114;Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114;

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http://dx.doi.org/10.1073/pnas.1407001111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040621PMC
May 2014

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.

Mol Cell Proteomics 2012 Jun 30;11(6):M111.014423. Epub 2011 Dec 30.

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

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http://dx.doi.org/10.1074/mcp.M111.014423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433912PMC
June 2012

Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.

Mol Cell Proteomics 2012 May 14;11(5):148-59. Epub 2012 Apr 14.

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

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http://dx.doi.org/10.1074/mcp.M111.016857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418844PMC
May 2012

Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites.

Proc Natl Acad Sci U S A 2011 Jun 23;108(23):9378-83. Epub 2011 May 23.

Center for Biophysics and Computational Biology, Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1016460108
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http://dx.doi.org/10.1073/pnas.1016460108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111296PMC
June 2011

Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx).

J Proteome Res 2009 Jun;8(6):3154-60

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

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http://dx.doi.org/10.1021/pr801017aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753172PMC
June 2009

Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification.

Mol Cell Proteomics 2008 Oct 4;7(10):1952-62. Epub 2008 Jun 4.

The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1074/mcp.M800218-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559937PMC
October 2008

Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution.

Nature 2007 Sep;449(7158):83-6

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nature06130DOI Listing
September 2007

PEPPeR, a platform for experimental proteomic pattern recognition.

Mol Cell Proteomics 2006 Oct 19;5(10):1927-41. Epub 2006 Jul 19.

The Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, 02142, USA.

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http://dx.doi.org/10.1074/mcp.M600222-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649820PMC
October 2006

mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s.

Curr Biol 2006 Sep 17;16(18):1865-70. Epub 2006 Aug 17.

Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1016/j.cub.2006.08.001DOI Listing
September 2006

MapQuant: open-source software for large-scale protein quantification.

Proteomics 2006 Mar;6(6):1770-82

Harvard Medical School, Department of Genetics, Boston, MA 02115, USA.

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http://doi.wiley.com/10.1002/pmic.200500201
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http://dx.doi.org/10.1002/pmic.200500201DOI Listing
March 2006

Photosynthesis genes in marine viruses yield proteins during host infection.

Nature 2005 Nov 12;438(7064):86-9. Epub 2005 Oct 12.

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://www.nature.com/articles/nature04111
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http://dx.doi.org/10.1038/nature04111DOI Listing
November 2005

Cell surface differentiation of Mycoplasma mobile visualized by surface protein localization.

Microbiology 2004 Dec;150(Pt 12):4001-8

Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan.

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http://mic.microbiologyresearch.org/content/journal/micro/10
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http://dx.doi.org/10.1099/mic.0.27436-0DOI Listing
December 2004

Energetics of gliding motility in Mycoplasma mobile.

J Bacteriol 2004 Jul;186(13):4254-61

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1128/JB.186.13.4254-4261.2004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC421629PMC
July 2004

Proteogenomic mapping as a complementary method to perform genome annotation.

Proteomics 2004 Jan;4(1):59-77

Harvard Medical School Department of Genetics, Boston, MA 02115, USA.

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http://dx.doi.org/10.1002/pmic.200300511DOI Listing
January 2004