Publications by authors named "David Gomez-Zepeda"

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Proteome dynamics of chilli pepper fruits during development and ripening from two Mexican cultivars of Capsicum annuum L.
David Gomez-Zepeda, Felipe Cervantes-Hernández, Octavio Martínez, Neftalí Ochoa-Alejo, José Juan Ordaz-Ortiz

J Proteomics· January 2026

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Benchmarking Software for DDA-PASEF Immunopeptidomics.
Yannic Chen, Annica Preikschat, Annette Arnold, Riccardo Pecori, David Gomez-Zepeda

Mol Cell Proteomics· December 2025

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Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set.
Ute Distler, Han Byul Yoo, Oliver Kardell, Dana Hein, Malte Sielaff, David Gomez-Zepeda

Nat Commun· October 2025

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High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MSRescore.
David Gomez-Zepeda, Julian Beyrle, Annica Preikschat, Arthur Declercq, Yannic Chen

Methods Mol Biol· October 2025

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Increased BNIP3-mediated mitophagy attenuates GDAP1 loss of function - implications for Charcot-Marie-Tooth disease 4A.
Li Zhang, Alireza Pouya, Janina Kopetzky, Sara Bitar, Christina Wolf, David Gomez-Zepeda

Neurobiol Dis· September 2025

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Correction to "Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum".
Oliver Kardell, Thomas Gronauer, Christine von Toerne, Juliane Merl-Pham, Ann-Christine König, David Gomez-Zepeda

J Proteome Res· September 2025

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Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.
David Teschner, David Gomez-Zepeda, Mateusz K Łącki, Thomas Kemmer, Anne Busch

J Proteome Res· May 2025

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TIMSRescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MSRescore.
Arthur Declercq, Robbe Devreese, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, David Gomez-Zepeda

J Proteome Res· March 2025

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Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum.
Oliver Kardell, Thomas Gronauer, Christine von Toerne, Juliane Merl-Pham, Ann-Christine König, David Gomez-Zepeda

J Proteome Res· March 2025

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Unveiling IRF4-steered regulation of context-dependent effector programs in CD4 T cells under Th17- and Treg-skewing conditions.
Anna Gabele, Maximilian Sprang, Mert Cihan, Mareen Welzel, Assel Nurbekova, David Gomez-Zepeda

Cell Rep· March 2025

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HowDirty: An R package to evaluate molecular contaminants in LC-MS experiments.
David Gomez-Zepeda, Thomas Michna, Tanja Ziesmann, Ute Distler, Stefan Tenzer

Proteomics· April 2024

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Fasting upregulates the monocarboxylate transporter MCT1 at the rat blood-brain barrier through PPAR δ activation.
Stéphanie Chasseigneaux, Véronique Cochois-Guégan, Lucas Lecorgne, Murielle Lochus, Sophie Nicolic, David Gomez-Zepeda

Fluids Barriers CNS· April 2024

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Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MSRescore with MSPIP timsTOF fragmentation prediction model.
David Gomez-Zepeda, Danielle Arnold-Schild, Julian Beyrle, Arthur Declercq, Ralf Gabriels

Nat Commun· March 2024

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Ionmob: a Python package for prediction of peptide collisional cross-section values.
David Teschner, David Gomez-Zepeda, Arthur Declercq, Mateusz K Łącki, Seymen Avci

Bioinformatics· September 2023

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Functional and targeted proteomics characterization of a human primary endothelial cell model of the blood-brain barrier (BBB) for drug permeability studies.
David Gomez-Zepeda, Nicolas Perrière, Fabienne Glacial, Meryam Taghi, Cérina Chhuon

Toxicol Appl Pharmacol· April 2023

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Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data.
Konstantin Bob, David Teschner, Thomas Kemmer, David Gomez-Zepeda, Stefan Tenzer

BMC Bioinformatics· July 2022

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GDAP1 loss of function inhibits the mitochondrial pyruvate dehydrogenase complex by altering the actin cytoskeleton.
Christina Wolf, Alireza Pouya, Sara Bitar, Annika Pfeiffer, Diones Bueno, David Gomez-Zepeda

Commun Biol· June 2022

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Mass spectrometry-based quantification and spatial localization of small organic acid exudates in plant roots under phosphorus deficiency and aluminum toxicity.
David Gomez-Zepeda, Moises Frausto, Héctor-Rogelio Nájera-González, Luis Herrera-Estrella, José-Juan Ordaz-Ortiz

Plant J· June 2021

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Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in and Its Influence on Metabolic Reprogramming.
Hugo Varela-Rodríguez, Diana G Abella-Quintana, Annie Espinal-Centeno, Luis Varela-Rodríguez, David Gomez-Zepeda

Front Cell Dev Biol· November 2020

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An Interspecies Molecular and Functional Study of Organic Cation Transporters at the Blood-Brain Barrier: From Rodents to Humans.
Catarina Chaves, Federica Campanelli, Hélène Chapy, David Gomez-Zepeda, Fabienne Glacial

Pharmaceutics· March 2020

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ABC Transporters at the Blood-Brain Interfaces, Their Study Models, and Drug Delivery Implications in Gliomas.
David Gomez-Zepeda, Méryam Taghi, Jean-Michel Scherrmann, Xavier Decleves, Marie-Claude Menet

Pharmaceutics· December 2019

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LC-MS/MS-based quantification of efflux transporter proteins at the BBB.
David Gomez-Zepeda, Meryam Taghi, Maria Smirnova, Philippe Sergent, Wang-Qing Liu

J Pharm Biomed Anal· February 2019

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Targeted unlabeled multiple reaction monitoring analysis of cell markers for the study of sample heterogeneity in isolated rat brain cortical microvessels.
David Gomez-Zepeda, Catarina Chaves, Méryam Taghi, Philippe Sergent, Wang-Qing Liu

J Neurochem· August 2017

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Generation and Characterization of a Breast Cancer Resistance Protein Humanized Mouse Model.
Shannon Dallas, Laurent Salphati, David Gomez-Zepeda, Thomas Wanek, Liangfu Chen

Mol Pharmacol· May 2016

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Effect of Subchronic Intravenous Morphine Infusion and Naloxone-Precipitated Morphine Withdrawal on P-gp and Bcrp at the Rat Blood-Brain Barrier.
Catarina Chaves, David Gómez-Zepeda, Sylvain Auvity, Marie-Claude Menet, Dominique Crété

J Pharm Sci· January 2016

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