Author details

Full Name

John M Koomen

Affiliation

ORCID

Career Start Year

1996

Papers

184

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36922348	Differential Chemoproteomics Reveals MARK2/3 as Cell Migration-Relevant Targets of the ALK Inhibitor Brigatinib.		2023
37848034	Differential network analysis of ROS1 inhibitors reveals lorlatinib polypharmacology through co-targeting PYK2.		2023
38030596	HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis.		2023
37581943	Modulating the polyamine/hypusine axis controls generation of CD8+ tissue-resident memory T cells.		2023
37995180	Brain metastasis-associated fibroblasts secrete fucosylated PVR/CD155 that induces breast cancer invasion.		2023
37702657	CK1Î´ and CK1Îµ Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma.		2023
37286847	Associations of gut microbiome with endogenous estrogen levels in healthy postmenopausal women.		2023
36768152	Detectable Lipidomes and Metabolomes by Different Plasma Exosome Isolation Methods in Healthy Controls and Patients with Advanced Prostate and Lung Cancer.	Int J Mol Sci	2023
36630201	Chemical Proteomics with Novel Fully Functionalized Fragments and Stringent Target Prioritization Identifies the Glutathione-Dependent Isomerase GSTZ1 as a Lung Cancer Target.		2023
36690875	Fucosylation of HLA-DRB1 regulates CD4 T cell-mediated anti-melanoma immunity and enhances immunotherapy efficacy.		2023
37171072	Deciphering Phenotypes from Protein Biomarkers for Translational Research with PIPER.		2023
37042037	Dose-escalation trial of combination dabrafenib, trametinib, and AT13387 in patients with BRAF-mutant solid tumors.		2023
35149590	Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy.	Cancer Research	2022
36183837	Integrated proteomics identifies PARP inhibitor-induced prosurvival signaling changes as potential vulnerabilities in ovarian cancer.	Journal of Biological Chemistry	2022
35973030	IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells.	Sci Signal	2022
35969234	TCR-Independent Metabolic Reprogramming Precedes Lymphoma-Driven Changes in T-cell Fate.	Cancer Immunology Research	2022
36332889	A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer-Associated Stellate Cell Small Extracellular Vesicles.	Mol Cell Proteomics	2022
35361955	Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.	Nat Metab	2022
35861718	Inhibition of Epidermal Growth Factor Receptor Signaling by Antisense Oligonucleotides as a Novel Approach to Epidermal Growth Factor Receptor Inhibition.	Nucleic Acid Therapeutics	2022
35718636	Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma.	Eur Urol	2022
34329582	The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors.	Cell Chem Biol	2022
34988766	Associations of established breast cancer risk factors with urinary estrogens in postmenopausal women.	Cancer Causes and Control	2022
35311290	Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer.	ACS Chemical Biology	2022
35247927	Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy.	Clin Cancer Res	2022
35022314	Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration.	Molecular Cancer Research	2022
34385708	Tumor-infiltrating lymphocyte treatment for anti-PD-1-resistant metastatic lung cancer: a phase 1 trial.	Nat Med	2021
34070332	Fucosylated Proteome Profiling Identifies a Fucosylated, Non-Ribosomal, Stress-Responsive Species of Ribosomal Protein S3.	Cells	2021
34014671	Metabolic Changes Are Associated with Melphalan Resistance in Multiple Myeloma.	Journal of Proteome Research	2021
33619172	Cell Type-specific Adaptive Signaling Responses to KRAS Inhibition.	Clinical Cancer Research	2021
33879459	Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer.	Clin Cancer Res	2021
33978681	A Mutational Survey of Acral Nevi.	JAMA Dermatol	2021
34301759	Macrophage-Derived Cholesterol Contributes to Therapeutic Resistance in Prostate Cancer.	Cancer Research	2021
32926368	Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics.	Methods Mol Biol	2021
33346915	Reconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response.	Clin Exp Immunol	2021
32890629	Noncanonical EphA2 Signaling Is a Driver of Tumor-Endothelial Cell Interactions and Metastatic Dissemination in BRAF Inhibitorâ¿¿Resistant Melanoma.	J Invest Dermatol	2021
34671754	Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling.	Cell Rep Methods	2021
31199438	GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis.	Bioinformatics	2020
31689494	Translational pathology, genomics and the development of systemic therapies for acral melanoma.	Semin Cancer Biol	2020
32004476	Macrophage Metabolism of Apoptotic Cell-Derived Arginine Promotes Continual Efferocytosis and Resolution of Injury.		2020
32403132	Cereblon harnesses Myc-dependent bioenergetics and activity of CD8+ T lymphocytes.	Blood	2020
31936331	Network of Interactions between ZIKA Virus Non-Structural Proteins and Human Host Proteins.	Cells	2020
32156775	TAp63-Regulated miRNAs Suppress Cutaneous Squamous Cell Carcinoma through Inhibition of a Network of Cell-Cycle Genes.	Cancer Research	2020
31924735	Proteomic Analysis of CSF from Patients with Leptomeningeal Melanoma Metastases Identifies Signatures Associated with Disease Progression and Therapeutic Resistance.	Clinical Cancer Research	2020
31750881	HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms.	Blood	2020
32769047	LC-HRMS of derivatized urinary estrogens and estrogen metabolites in postmenopausal women.	Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences	2020
32768387	Sirt2 Inhibition Enhances Metabolic Fitness and Effector Functions of Tumor-Reactive T Cells.		2020
33255891	Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response.	Cancers	2020
32865326	Lowering Sample Requirements to Study Tyrosine Kinase Signaling Using Phosphoproteomics with the TMT Calibrator Approach.	Proteomics	2020
33108391	Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment.	PLoS ONE	2020
30987999	HDAC8 Regulates a Stress Response Pathway in Melanoma to Mediate Escape from BRAF Inhibitor Therapy.	Cancer Res	2019