Pratik D. Jagtap

Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.

Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery.

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

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

Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.

Multi-omic data analysis using Galaxy.

Metaproteomic analysis using the Galaxy framework.

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

Proteome Profiling in Lung Injury after Hematopoietic Stem Cell Transplantation.

An Accessible Proteogenomics Informatics Resource for Cancer Researchers.

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

Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome.

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 Variants Detected via Proteogenomics.

BAL Fluid Metaproteome in Acute Respiratory Failure.

Improve your Galaxy text life: The Query Tabular Tool.

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics.

metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.

A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases.

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

Survey of metaproteomics software tools for functional microbiome analysis.

Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.

Updates on metaQuantome Software for Quantitative Metaproteomics.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.

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

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

An overview of technologies for MS-based proteomics-centric multi-omics.

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

Galaxy Training: A powerful framework for teaching!

An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.

Integrative meta-omics in Galaxy and beyond.

2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.

Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.

A Galaxy of informatics resources for MS-based proteomics.

The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).

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

Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis.

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

Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19.

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

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.

Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.

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