Author details

Full Name

Jacob D Jaffe

Affiliation

ORCID

Career Start Year

2001

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36409824	JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States.	Cancer Res	2023
34995493	Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors.	Cell Stem Cell	2022
34433823	Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds.	Sci Data	2021
33953401	Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity.	Nature	2021
33510483	Noncanonical open reading frames encode functional proteins essential for cancer cell survival.	Nat Biotechnol	2021
33273722	Author Correction: The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.	Nat Struct Mol Biol	2021
32747783	The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.	Nat Struct Mol Biol	2020
32004545	Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS.	Methods	2020
31662325	Phosphorylation of RAB7 by TBK1/IKKÎµ Regulates Innate Immune Signaling in Triple-Negative Breast Cancer.	Cancer Res	2020
33199889	Avant-garde: an automated data-driven DIA data curation tool.	Nat Methods	2020
31409669	Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS.	Mol Cell Proteomics	2019
30602589	Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis.	Mol Cell Proteomics	2019
30282776	Quantifying Homologous Proteins and Proteoforms.	Mol Cell Proteomics	2019
30872525	Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate.	Science	2019
30753830	KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.	Cancer Cell	2019
31068700	Next-generation characterization of the Cancer Cell Line Encyclopedia.	Nature	2019
31160565	Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma.	Nat Commun	2019
29233821	Activity of the PI3K-Î´,Î³ inhibitor duvelisib in a phase 1 trial and preclinical models of T-cell lymphoma.	Blood	2018
30166406	Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.	Genome Res	2018
30021779	A phosphoproteomic signature in endothelial cells predicts vascular toxicity of tyrosine kinase inhibitors used in CML.	Blood Adv	2018
29915188	GeNets: a unified web platform for network-based genomic analyses.	Nat Methods	2018
30472020	KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.	Cancer Cell	2018
29487113	Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.	Mol Cell Proteomics	2018
29655704	A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations.	Cell Syst	2018
29608554	Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics.	Nat Methods	2018
29199020	The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.	Cell Syst	2018
27899381	Castration Resistance in Prostate Cancer Is Mediated by the Kinase NEK6.	Cancer Res	2017
28701475	HIF activation causes synthetic lethality between the <i>VHL</i> tumor suppressor and the <i>EZH1</i> histone methyltransferase.	Sci Transl Med	2017
27684187	Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in Î²-Catenin-Active Cancers.	Cell Syst	2016
26804911	H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs.	Cell Rep	2016
26912667	Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.	Mol Cell Proteomics	2016
27321643	Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of Peptides to Greater than 150 for Targeted MS-Based Assays.	Anal Chem	2016
27562500	Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms.	Journal of the American Society for Mass Spectrometry	2016
26152395	Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis.	Proteomics	2015
25448295	Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.	Methods	2015
25578878	Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.	Mol Cell	2015
25680957	Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.	Mol Cell Proteomics	2015
25953088	Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow.	Mol Cell Proteomics	2015
26042473	Kinase-Independent Small-Molecule Inhibition of JAK-STAT Signaling.	J Am Chem Soc	2015
25089360	An unbiased approach to identify endogenous substrates of "histone" deacetylase 8.	ACS Chem Biol	2014
24821797	Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.	Proc Natl Acad Sci U S A	2014
24747640	Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation.	Nat Genet	2014
25102069	Panorama: a targeted proteomics knowledge base.	J Proteome Res	2014
23749302	Integrated proteomic analysis of post-translational modifications by serial enrichment.	Nat Methods	2013
24076604	Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia.	Nat Genet	2013
22210691	iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.	Mol Cell Proteomics	2012
22505724	Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.	Mol Cell Proteomics	2012
22908275	Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.	Proc Natl Acad Sci U S A	2012
22323609	STK33 kinase inhibitor BRD-8899 has no effect on KRAS-dependent cancer cell viability.	Proc Natl Acad Sci U S A	2012
22897849	ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.	Cancer Cell	2012