Publications by authors named "Subina Mehta"

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Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.
Andrew T Rajczewski, Subina Mehta, Reid Wagner, Wassim Gabriel, James Johnson

J Proteomics· January 2026

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A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.
Subina Mehta, Reid Wagner, Katherine T Do, James E Johnson, Fengchao Yu

bioRxiv· December 2025

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Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.
Engy Nasr, Nikos Pechlivanis, Nikolaos Strepis, Pierre Amato, Matthias Bernt, Subina Mehta

bioRxiv· September 2025

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The microbiologist's guide to metaproteomics.
Tim Van Den Bossche, Jean Armengaud, Dirk Benndorf, Jose Alfredo Blakeley-Ruiz, Madita Brauer, Subina Mehta

Imeta· June 2025

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Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset.
Andrew T Rajczewski, Subina Mehta, Reid Wagner, Wassim Gabriel, James Johnson

bioRxiv· May 2025

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Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.
Jesenia M Perez, Jolene M Duda, Joohyun Ryu, Mihir Shetty, Subina Mehta

Sci Rep· January 2025

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A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease.
Katherine Do, Subina Mehta, Reid Wagner, Timothy J Griffin, Pratik D Jagtap

J Vis Exp· January 2025

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Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.
Praveen Kumar, James E Johnson, Thomas McGowan, Matthew C Chambers, Mohammad Heydarian, Subina Mehta

Methods Mol Biol· October 2024

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Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.
Sarah Samorodnitsky, Monica Kruk, Eric F Lock, Ken M Kunisaki, Alison Morris, Subina Mehta

Respir Res· September 2024

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An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease.
Monica E Kruk, Subina Mehta, Kevin Murray, LeeAnn Higgins, Katherine Do

mSystems· July 2024

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A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.
Katherine Do, Subina Mehta, Reid Wagner, Dechen Bhuming, Andrew T Rajczewski

mSphere· June 2024

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Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis.
Sarah Samorodnitsky, Monica Kruk, Eric F Lock, Ken M Kunisaki, Alison Morris, Subina Mehta

Res Sq· June 2024

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Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19.
Surbhi Bihani, Aryan Gupta, Subina Mehta, Andrew Rajczewski, Timothy Griffin

Methods Mol Biol· June 2024

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A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.
Katherine Do, Subina Mehta, Reid Wagner, Dechen Bhuming, Andrew T Rajczewski

bioRxiv· December 2023

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A Galaxy of informatics resources for MS-based proteomics.
Subina Mehta, Matthias Bernt, Matthew Chambers, Matthias Fahrner, Melanie Christine Föll

Expert Rev Proteomics· November 2023

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Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.
Surbhi Bihani, Aryan Gupta, Subina Mehta, Andrew T Rajczewski, James Johnson

J Proteome Res· August 2023

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Integrative meta-omics in Galaxy and beyond.
Valerie C Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta

Environ Microbiome· July 2023

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An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.
Danielle O Weise, Monica E Kruk, LeeAnn Higgins, Todd W Markowski, Pratik D Jagtap, Subina Mehta

Clin Proteomics· April 2023

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Galaxy Training: A powerful framework for teaching!
Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Subina Mehta

PLoS Comput Biol· January 2023

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Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations.
Subina Mehta, Valdemir M Carvalho, Andrew T Rajczewski, Olivier Pible, Björn A Grüning

Viruses· October 2022

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Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome.
Adam L Edwinson, Lu Yang, Stephanie Peters, Nikita Hanning, Patricio Jeraldo, Subina Mehta

Nat Microbiol· May 2022

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Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow.
Andrew T Rajczewski, Qiyuan Han, Subina Mehta, Praveen Kumar, Pratik D Jagtap

Proteomes· April 2022

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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.
Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann

F1000Res· September 2021

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A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).
Andrew T Rajczewski, Subina Mehta, Dinh Duy An Nguyen, Björn Grüning, James E Johnson

Clin Proteomics· May 2021

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A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).
Andrew T Rajczewski, Subina Mehta, Dinh Duy An Nguyen, Björn A Grüning, James E Johnson

medRxiv· March 2021

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