Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer

Authors: Jesenia M. Perez, Jolene M. Duda, Joohyun Ryu, Mihir Shetty, Subina Mehta, Pratik D. Jagtap, Andrew C. Nelson, Boris Winterhoff, Timothy J. Griffin, Timothy K. Starr, Stefani N. Thomas

Source: Scientific Reports, Vol 15, Iss 1, Pp 1-18 (2025)

Subject Terms: Patient-derived xenograft models (PDX), Ovarian cancer, Proteogenomics, Mass spectrometry, Proteomics, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/6ae2deb4ffbb434ea4e654f33c766270

Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes

Authors: Diana Samodova, Evelina Stankevic, Mathilde Sonne Søndergaard, Naiyu Hu, Tarunveer S. Ahluwalia, Daniel R. Witte, Daniel Belstrøm, Anniek Frederike Lubberding, Pratik D. Jagtap, Torben Hansen, Atul S. Deshmukh

Source: Microbiome, Vol 13, Iss 1, Pp 1-19 (2025)

Subject Terms: Metaproteomics, Microbiome, Saliva, Type-2 diabetes, DIA-PASEF, Genus, Microbial ecology, QR100-130

File Description: electronic resource

Relation: https://doaj.org/toc/2049-2618

Access URL: https://doaj.org/article/3f08bc3e5ff141a78abfdc7b76bbfb08

Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis

Authors: Sarah Samorodnitsky, Monica Kruk, Eric F. Lock, Ken M. Kunisaki, Alison Morris, Janice M. Leung, Danielle Weise, Subina Mehta, Laurie L. Parker, Pratik D. Jagtap, Timothy J. Griffin, Chris H. Wendt

Source: Respiratory Research, Vol 25, Iss 1, Pp 1-10 (2024)

Subject Terms: Diseases of the respiratory system, RC705-779

File Description: electronic resource

Relation: https://doaj.org/toc/1465-993X

Access URL: https://doaj.org/article/2aca99d787e348f2a5b0aec3b5cfc935

An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease

Authors: Monica E. Kruk, Subina Mehta, Kevin Murray, LeeAnn Higgins, Katherine Do, James E. Johnson, Reid Wagner, Chris H. Wendt, John B. O’Connor, J. Kirk Harris, Theresa A. Laguna, Pratik D. Jagtap, Timothy J. Griffin

Source: mSystems, Vol 9, Iss 7 (2024)

Subject Terms: microbiome, cystic fibrosis, host-pathogen interactions, metaproteomics, metagenomics, bioinformatics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/e36a430e5a754b0e804f12b6ccd9536c

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease

Authors: Katherine Do, Subina Mehta, Reid Wagner, Dechen Bhuming, Andrew T. Rajczewski, Amy P. N. Skubitz, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap

Source: mSphere, Vol 9, Iss 6 (2024)

Subject Terms: microbiome, metaproteomics, clinical analysis, bioinformatics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5042

Access URL: https://doaj.org/article/74b450ff3e6d49c5ae62dfa92b812727

Integrative meta-omics in Galaxy and beyond

Authors: Valerie C. Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin, Magnus Ø. Arntzen

Source: Environmental Microbiome, Vol 18, Iss 1, Pp 1-13 (2023)

Subject Terms: Integrated meta-omics, Metagenomics, Metatrascriptomics, Metaproteomics, Galaxy, Bioinformatics, Environmental sciences, GE1-350, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2524-6372

Access URL: https://doaj.org/article/5bda6fda2ac74a489dfbe9e3e1b39257

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Authors: Tim Van Den Bossche, Magnus Ø. Arntzen, Dörte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Céline Henry, Pratik D. Jagtap, Nico Jehmlich, Catherine Juste, Benoit J. Kunath, Bart Mesuere, Thilo Muth, Phillip B. Pope, Jana Seifert, Alessandro Tanca, Sergio Uzzau, Paul Wilmes, Robert L. Hettich, Jean Armengaud

Source: Microbiome, Vol 9, Iss 1, Pp 1-4 (2021)

Subject Terms: Microbiome, Metaproteomics, Multi-omics, Education, Interactions, Networking, Microbial ecology, QR100-130

File Description: electronic resource

Relation: https://doaj.org/toc/2049-2618

Access URL: https://doaj.org/article/ca63e99ef5e44ee6a7debf6b84b6ce6c

Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations

Authors: Subina Mehta, Valdemir M. Carvalho, Andrew T. Rajczewski, Olivier Pible, Björn A. Grüning, James E. Johnson, Reid Wagner, Jean Armengaud, Timothy J. Griffin, Pratik D. Jagtap

Source: Viruses, Vol 14, Iss 10, p 2205 (2022)

Subject Terms: SARS-CoV-2, variant detection, strain-specific, mass-spectrometry, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/14/10/2205; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/54b988d980714905b8379386a16a7840

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework [version 2; peer review: 2 approved]

Authors: Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap

Source: F1000Research, Vol 10 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/10-103/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/73e663f556a648a1931080c5ee40ac78

Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow

Authors: Andrew T. Rajczewski, Qiyuan Han, Subina Mehta, Praveen Kumar, Pratik D. Jagtap, Charles G. Knutson, James G. Fox, Natalia Y. Tretyakova, Timothy J. Griffin

Source: Proteomes, Vol 10, Iss 2, p 11 (2022)

Subject Terms: inflammation, proteogenomics, bioinformatics, colon cancer, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/2227-7382/10/2/11; https://doaj.org/toc/2227-7382

Access URL: https://doaj.org/article/d30189bf3c9641068ef1e79f1809d6ca

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform

Authors: Subina Mehta, Caleb W. Easterly, Ray Sajulga, Robert J. Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed, Lloyd M. Smith, Thomas McGowan, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap

Source: Proteomes, Vol 8, Iss 3, p 15 (2020)

Subject Terms: proteomics, label-free quantification, galaxy framework, workflows, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/2227-7382/8/3/15; https://doaj.org/toc/2227-7382

Access URL: https://doaj.org/article/d11a4e727c2c41819d9f94907c6c68fe

Improve your Galaxy text life: The Query Tabular Tool [version 2; referees: 2 approved, 1 approved with reservations]

Authors: James E. Johnson, Praveen Kumar, Caleb Easterly, Mark Esler, Subina Mehta, Arthur C. Eschenlauer, Adrian D. Hegeman, Pratik D. Jagtap, Timothy J. Griffin

Source: F1000Research, Vol 7 (2019)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/7-1604/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/604901802b674d0b9dc8eb8308629d96

Improve your Galaxy text life: The Query Tabular Tool [version 1; referees: 1 approved, 2 approved with reservations]

Authors: James E. Johnson, Praveen Kumar, Caleb Easterly, Mark Esler, Subina Mehta, Arthur C. Eschenlauer, Adrian D. Hegeman, Pratik D. Jagtap, Timothy J. Griffin

Source: F1000Research, Vol 7 (2018)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/7-1604/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/403fc11e965244a3a743aeaef8ae3bd7

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

Authors: Clemens Blank, Caleb Easterly, Bjoern Gruening, James Johnson, Carolin A. Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E. Elias, W. Judson Hervey, Thomas McGowan, Thilo Muth, Brook L. Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin, Pratik D. Jagtap

Source: Proteomes, Vol 6, Iss 1, p 7 (2018)

Subject Terms: metaproteomics, functional microbiome, bioinformatics, software workflow development, Galaxy platform, mass spectrometry, community development, Microbiology, QR1-502

File Description: electronic resource

Relation: http://www.mdpi.com/2227-7382/6/1/7; https://doaj.org/toc/2227-7382

Access URL: https://doaj.org/article/936ce48bfbba432e8e521b8ae6745693

Galaxy Training: A powerful framework for teaching!

Authors: Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, Galaxy Training Network, Björn Grüning, Bérénice Batut

Source: PLoS Computational Biology, Vol 19, Iss 1, p e1010752 (2023)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/418bd96910b049ef9a470281072747d4

Survey of metaproteomics software tools for functional microbiome analysis.

Authors: Ray Sajulga, Caleb Easterly, Michael Riffle, Bart Mesuere, Thilo Muth, Subina Mehta, Praveen Kumar, James Johnson, Bjoern Andreas Gruening, Henning Schiebenhoefer, Carolin A Kolmeder, Stephan Fuchs, Brook L Nunn, Joel Rudney, Timothy J Griffin, Pratik D Jagtap

Source: PLoS ONE, Vol 15, Iss 11, p e0241503 (2020)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/9da73087023c4018882f7a4da3170b7c

Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors.

Authors: Maneesh Bhargava, Trisha L Becker, Kevin J Viken, Pratik D Jagtap, Sanjoy Dey, Michael S Steinbach, Baolin Wu, Vipin Kumar, Peter B Bitterman, David H Ingbar, Christine H Wendt

Source: PLoS ONE, Vol 9, Iss 10, p e109713 (2014)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4188744?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/20866569ca6d47c8919d99c184f90756