Pratik D. Jagtap

Department of Biochemistry, University of Minnesota

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title	2025

Other Publications

Article	Year
Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. Journal of proteome research\| PubMed ID: 30702898	2019
Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery. Clinical proteomics\| PubMed ID: 21914210	2011
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. BMC genomics\| PubMed ID: 25149441	2014
Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors. PloS one\| PubMed ID: 25290099	2014
Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. Journal of proteome research\| PubMed ID: 25301683	2014
Multi-omic data analysis using Galaxy. Nature biotechnology\| PubMed ID: 25658277	2015
Metaproteomic analysis using the Galaxy framework. Proteomics\| PubMed ID: 26058579	2015
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. Microbiome\| PubMed ID: 26684897	2015
Proteome Profiling in Lung Injury after Hematopoietic Stem Cell Transplantation. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation\| PubMed ID: 27155584	2016
An Accessible Proteogenomics Informatics Resource for Cancer Researchers. Cancer research\| PubMed ID: 29092937	2017
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Proteomes\| PubMed ID: 29385081	2018
Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome. Scientific reports\| PubMed ID: 30022083	2018
Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence... Journal of proteome research\| PubMed ID: 30130115	2018
BAL Fluid Metaproteome in Acute Respiratory Failure. American journal of respiratory cell and molecular biology\| PubMed ID: 30382775	2018
Improve your Galaxy text life: The Query Tabular Tool. F1000Research\| PubMed ID: 30519459	2018
QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics. Journal of proteome research\| PubMed ID: 30582332	2019
metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes. Molecular & cellular proteomics : MCP\| PubMed ID: 31235611	2019
Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. GigaScience\| PubMed ID: 32236523	2020
A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases. Journal of proteome research\| PubMed ID: 32396365	2020
Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform. Proteomes\| PubMed ID: 32650610	2020
Survey of metaproteomics software tools for functional microbiome analysis. PloS one\| PubMed ID: 33170893	2020
Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms. Journal of proteome research\| PubMed ID: 33393790	2021
Updates on metaQuantome Software for Quantitative Metaproteomics. Journal of proteome research\| PubMed ID: 33683127	2021
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). medRxiv : the preprint server for health sciences\| PubMed ID: 33688669	2021
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). Clinical proteomics\| PubMed ID: 33971807	2021
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research\| PubMed ID: 34484688	2021
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome\| PubMed ID: 34930457	2021
Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow. Proteomes\| PubMed ID: 35466239	2022
An overview of technologies for MS-based proteomics-centric multi-omics. Expert review of proteomics\| PubMed ID: 35466851	2022
Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations. Viruses\| PubMed ID: 36298760	2022
Galaxy Training: A powerful framework for teaching! PLoS computational biology\| PubMed ID: 36622853	2023
An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples. Clinical proteomics\| PubMed ID: 37005570	2023
Integrative meta-omics in Galaxy and beyond. Environmental microbiome\| PubMed ID: 37420292	2023
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study. Journal of biomolecular techniques : JBT\| PubMed ID: 37435391	2023
Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients. Journal of proteome research\| PubMed ID: 37450889	2023
A Galaxy of informatics resources for MS-based proteomics. Expert review of proteomics\| PubMed ID: 37787106	2023
The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020). Journal of biomolecular techniques : JBT\| PubMed ID: 37969874	2023
A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. mSphere\| PubMed ID: 38780289	2024
Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis. Research square\| PubMed ID: 38883770	2024
An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. mSystems\| PubMed ID: 38934598	2024
Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 38941023	2024
Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis. Respiratory research\| PubMed ID: 39256809	2024
Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome. bioRxiv : the preprint server for biology\| PubMed ID: 39345414	2024
Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 39436599	2025
Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer. Scientific reports\| PubMed ID: 39755759	2025