Selected publications using Galaxy-P

Below is a selection of publications describing the development and application of the Galaxy-P platform.  For an updated list of all publications describing work enabled by the Galaxy-P platform, see this link.

The Galaxy platform for accessible, reproducible, and collaborative biomedical analyses: 2022 update. Galaxy Community. Nucleic Acids Res. 2022 Apr 21;50(W1):W345–51. doi: 10.1093/nar/gkac247. Epub ahead of print. Erratum in: Nucleic Acids Res. 2022 Aug 26;50(15):8999. PMID: 35446428; PMCID: PMC9252830.

Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow. Proteomes. Rajczewski AT, Han Q, Mehta S, Kumar P, Jagtap PD, Knutson CG, Fox JG, Tretyakova NY, Griffin TJ.  Proteomes 2022 Apr 14;10(2):11. doi: 10.3390/proteomes10020011. PMID: 35466239; PMCID: PMC9036229.

An overview of technologies for MS-based proteomics-centric multi-omics. Rajczewski AT, Jagtap PD, Griffin TJ. Expert Rev Proteomics. 2022 May 2:1-17. doi: 10.1080/14789450.2022.2070476. Epub ahead of print. PMID: 35466851.

Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome. Edwinson AL, Yang L, Peters S, Hanning N, Jeraldo P, Jagtap P, Simpson JB, Yang TY, Kumar P, Mehta S, Nair A, Breen-Lyles M, Chikkamenahalli L, Graham RP, De Winter B, Patel R, Dasari S, Kashyap P, Griffin T, Chen J, Farrugia G, Redinbo MR, Grover M. Nat Microbiol. 2022 May;7(5):680-694. doi: 10.1038/s41564-022-01103-1. Epub 2022 Apr 28. PMID: 35484230; PMCID: PMC9081267.

MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone. Pinter N, Glätzer D, Fahrner M, Fröhlich K, Johnson J, Grüning BA, Warscheid B, Drepper F, Schilling O, Föll MC.  J Proteome Res. 2022 Jun 3;21(6):1558-1565. doi: 10.1021/acs.jproteome.2c00051. Epub 2022 May 3. PMID: 35503992.

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform. 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
doi: 10.3390/proteomes8030015.

Novel protein pathways in development and progression of pulmonary sarcoidosis. Maneesh Bhargava, K J Viken, B Barkes, T J Griffin, M Gillespie, P D Jagtap, R Sajulga, E J Peterson, H E Dincer, L Li, C I Restrepo, B P O’Connor, T E Fingerlin, D M Perlman, L A Maier
doi: 10.1038/s41598-020-69281-8

Survey of metaproteomics software tools for functional microbiome analysis. 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
doi: 10.1371/journal.pone.0241503

Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms. Peter S. Thuy-Boun, Subina Mehta, Bjoern Gruening,Thomas McGowan,An Nguyen, Andrew T. Rajczewski, James. E Johnson, Timothy J. Griffin,  Dennis W. Wolan, and Pratik D. Jagtap
doi: 10.1021/acs.jproteome.0c00822.

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap
doi: 10.12688/f1000research.28608.1

Updates on metaQuantome Software for Quantitative Metaproteomics. Subina Mehta, Praveen Kumar, Marie Crane, James E Johnson, Ray Sajulga, Dinh Duy An Nguyen, Thomas McGowan, Magnus Ø Arntzen, Timothy J Griffin, Pratik D Jagtap
doi: 10.1021/acs.jproteome.0c00960

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization exploration. Thomas McGowan, James E Johnson, Praveen Kumar, Ray Sajulga, Subina Mehta, Pratik D Jagtap, Timothy J Griffin.
doi: 10.1093/gigascience/giaa025.

A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases. Praveen Kumar,James E Johnson, Caleb W Easterly, Subina Mehta, Ray Sajulga, Brooke Nunn, Pratik D Jagtap, Timothy J Griffin.
doi: 10.1021/acs.jproteome.0c00260

Challenges in Peptide-Spectrum Matching: A Robust and Reproducible statistical framework for removing low accuracy, high scoring hits. Shane L. Hubler, Praveen Kumar, Subina Mehta, Caleb Easterly, James E. Johnson, Pratik D. Jagtap and Timothy J. Griffin.
doi: 10.1021/acs.jproteome.9b00478

The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis. Paul A. Stewart, Brent M. Kuenzi, Subina Mehta, Praveen Kumar, James E. Johnson, Pratik Jagtap,Timothy J. Griffin, Eric B. Haura. doi: 10.1007/978-1-4939-9232-4_16

QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics. Praveen Kumar, Priyabrata Panigrahi, James Johnson, Wanda J. Weber, Subina Mehta, Ray Sajulga, Caleb Easterly, Brian A. Crooker, Mohammad Heydarian, Krishanpal Anamika, Timothy J. Griffin, Pratik D. Jagtap. doi: 10.1021/acs.jproteome. 8b00727

Improve your Galaxy text life: The Query tabular tool. James E. Johnson, Praveen Kumar, Caleb Easterly, Mark Esler, Subina Mehta, Arthur C. Eschenlauer, Adrian D. Hegeman, Pratik D. Jagtap, Timothy J. Griffin. f1000research.16450.1

Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics. Ray Sajulga, Subina Mehta, Praveen Kumar, James E. Johnson, Candace R. Guerrero, Michael C. Ryan, Rachel Karchin, Pratik D. Jagtap, and Timothy J. Griffin. doi: 10.1021/acs.jproteome.8b00404 PMID: 30130115

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. 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 Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin and Pratik D. Jagtap. doi: 110.3390/proteomes6010007 PMID:29385081

Comparative Metaproteomics to Study Environmental Changes. Sabine Matallana-Surget, Pratik D. Jagtap, Timothy J. Griffin, Mélanie Beraud, Ruddy Wattiez.

An Accessible Proteogenomics Informatics Resource for Cancer Researchers. Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, Björn Grüning, Ira R. Cooke, Mohammad Heydarian, Karen L. Reddy and Timothy J. Griffin. doi: 10.1158/0008-5472.CAN-17-0331 PMID:29092937

Bronchoalveolar Lavage Fluid Protein Expression in Acute Respiratory Distress Syndrome Provides Insights into Pathways Activated in Subjects with Different Outcomes. Bhargava M, Viken K, Wang Q, Jagtap P, Bitterman P, Ingbar D, Wendt C. Sci Rep. 2017 Aug 7;7(1):7464. doi: 10.1038/s41598-017-07791-8. PMID: 28785034 Free PMC Article

Proteome Profiling in Lung Injury after Hematopoietic Stem Cell Transplantation. Bhargava M, Viken KJ, Dey S, Steinbach MS, Wu B, Jagtap PD, Higgins L, Panoskaltsis-Mortari A, Weisdorf DJ, Kumar V, Arora M, Bitterman PB, Ingbar DH, Wendt CH. Biol Blood Marrow Transplant. 2016 Aug;22(8):1383-1390. doi: 10.1016/j.bbmt.2016.04.021. Epub 2016 May 5. PMID: 27155584 Free PMC Article

Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype.  Anderson KJ, Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT.  J Proteome Res. (2016) 15:1253-61.

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.  Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ. Microbiome. (2015) 3:69.

Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.  Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. J Proteome Res. (2015) 14:4792-804. (see also this  commentary in Chemical and Engineering News)

Metaproteomic analysis using the Galaxy framework. Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ.  Proteomics. (2015) 15:3553-65.

Multi-omic data analysis using Galaxy. Boekel J, Chilton JM, Cooke IR, Horvatovich PL, Jagtap PD, Käll L, Lehtiö J, Lukasse P, Moerland PD, Griffin TJ. Nat Biotechnol. (2015) 33:137-9.

Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ. J Proteome Res. (2014) 13:5898-908.

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM. BMC Genomics. (2014) 15:703.