Publications by authors named "John Koomen"

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Quantitative Proteomics of Nitrosylated Proteins in Melanoma Using the Biotin-Switch Technique Combined With Tandem Mass Tag Labeling.
Vipin K Yadav, Bin Fang, John M Koomen, Jyoti Srivastava, Sanjay Premi

Bio Protoc· December 2025

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Race-based differences in serum biomarkers for cancer-associated cachexia in a diverse cohort of patients with pancreatic ductal adenocarcinoma.
Margaret A Park, Evan W Davis, Solomon Alhassan, J Pablo Arnoletti, Toni L Basinski, John Koomen

Commun Med (Lond)· December 2025

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Cancer-associated fibroblasts confer ALK inhibitor resistance in -driven lung cancer by concurrent integrin and MET signaling.
Qianqian Hu, Lily L Remsing Rix, Bina Desai, Daria Miroshnychenko, Xueli Li, John M Koomen

Sci Signal· December 2025

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Evaluation of Proteinuria in Plasma Cell Disorders: Shortcomings of Measurements Based on 24-Hour Collections and Alternative Approaches.
Glen L Hortin, John M Koomen

J Appl Lab Med· November 2025

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Dual targeting of RET and SRC synergizes in RET fusion-positive cancer cells.
Juhyeon Son, Lily L Remsing Rix, Bin Fang, Eric A Welsh, Nicole V Bremer, John M Koomen

Mol Oncol· November 2025

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TAp73 mediates anti-tumor immunity through regulation of lipid metabolism in the lung tumor microenvironment.
Hayley D Ackerman, Vanessa Y Rubio, Andrew J Davis, John H Lockhart, Nicole Hackel, John M Koomen

bioRxiv· November 2025

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A machine learning framework for classifying lipids in untargeted metabolomics using mass-to-charge ratios and retention times.
Christelle Colin-Leitzinger, Yonatan Ayalew Mekonnen, Isis Narvaez-Bandera, Vanessa Y Rubio, Dalia Ercan, John M Koomen

Metabolomics· October 2025

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RAS-GTP Inhibition Overcomes Acquired Resistance to KRASG12C Inhibitors Mediated by Oncogenic and Wildtype RAS Activation in Non-Small Cell Lung Cancer.
Hitendra S Solanki, Harshit Shah, Denis Imbody, Bina Desai, Ryoji Kato, John M Koomen

Cancer Res· October 2025

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The Impact of Edema on Skeletal Muscle Changes among Patients with Pancreatic Ductal Adenocarcinoma.
Evan W Davis, Margaret A Park, Toni L Basinski, J Pablo Arnoletti, Mark Bloomston, John M Koomen

Cancer Epidemiol Biomarkers Prev· September 2025

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Acid ceramidase controls proteasome inhibitor resistance and is a novel therapeutic target for the treatment of relapsed/refractory multiple myeloma.
Ryan T Bishop, Tao Li, Praneeth Sudalagunta, Mostafa Nasr, Karl J Nyman, John Koomen

Haematologica· June 2025

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Blocking Nitrosylation Induces Immunogenic Cell Death by Sensitizing NRAS-Mutant Melanoma to MEK Inhibitors.
Jyoti Srivastava, Vipin K Yadav, Rachel V Jimenez, Pravin R Phadatare, Ninad A Inamdar, John M Koomen

Cancer Res· June 2025

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Reproducible Sectioning and Sample Preparation for Mass Spectrometry Imaging of Cancer Metabolism in Frozen Lung Tissue.
Vanessa Y Rubio, Hayley D Ackerman, Nicole Hackel, Christina L Carr, Jaden Baldwin, John M Koomen

Methods Mol Biol· June 2025

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Impaired T cell and neoantigen retention in time-serial analysis of metastatic non-small cell lung cancer in patients unresponsive to TIL cell therapy.
Chao Wang, Xiaoqing Yu, Jamie K Teer, Jiqiang Yao, Dongliang Du, John M Koomen

Nat Cancer· May 2025

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Ribosomal expansion segment contributes to translation fidelity via N-terminal processing of ribosomal proteins.
Riku Nagai, Olivia L Milam, Tatsuya Niwa, William J Howell, Jacob A Best, John M Koomen

Nucleic Acids Res· May 2025

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Tumor burden quantified by soluble B-cell maturation antigen and metabolic tumor volume determines myeloma CAR-T outcomes.
Ciara L Freeman, Jerald Noble, Meghan Menges, Ricardo Villanueva, Justyn Y Nakashima, John M Koomen

Blood· April 2025

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CAR T cell-driven induction of iNOS in tumor-associated macrophages promotes CAR T cell resistance in B cell lymphoma.
Marco Davila, Sae Bom Lee, Yun Pyo Kang, Justin Boucher, Jay Mandula, John Koomen

Res Sq· March 2025

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A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis.
Jennifer Guergues, Jessica Wohlfahrt, John M Koomen, Jonathan R Krieger, Sameer Varma

Proteomics· February 2025

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Race-based differences in serum biomarkers for cancer-associated cachexia in a diverse cohort of patients with pancreatic ductal adenocarcinoma.
Jennifer Permuth, Margaret Park, Evan Davis, Solomon Alhassan, J Arnoletti, John Koomen

Res Sq· February 2025

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Publisher Correction: Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution.
Santosh R Sukka, Patrick B Ampomah, Lancia N F Darville, David Ngai, Xiaobo Wang, John M Koomen

Nat Metab· November 2024

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Unveiling the Molecular Features of SCLC With a Clinical RNA Expression Panel.
Hilal Ozakinci, Aileen Y Alontaga, Pedro Cano, John M Koomen, Bradford A Perez

JTO Clin Res Rep· November 2024

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SART1 modulates poly-(ADP-ribose) chain accumulation and PARP1 chromatin localization.
Samuele Lodovichi, Thales C Nepomuceno, Nicholas T Woods, Uwe Rix, John M Koomen

iScience· November 2024

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Mapping the cancer surface proteome in search of target antigens for immunotherapy.
Francesco Di Meo, Brandon Kale, John M Koomen, Fabiana Perna

Mol Ther· September 2024

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Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution.
Santosh R Sukka, Patrick B Ampomah, Lancia N F Darville, David Ngai, Xiaobo Wang, John M Koomen

Nat Metab· September 2024

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Cancer-associated fibroblasts confer ALK inhibitor resistance in -driven lung cancer via concurrent integrin and MET signaling.
Qianqian Hu, Lily L Remsing Rix, Bina Desai, Daria Miroshnychenko, Xueli Li, John M Koomen

bioRxiv· August 2024

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A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.
Lancia N F Darville, John H Lockhart, Sudhir Putty Reddy, Bin Fang, Victoria Izumi, John M Koomen

Methods Mol Biol· July 2024

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