Pratik D. Jagtap
Department of Biochemistry,
Molecular Biology and Biophysics,
Department of Biochemistry, Molecular Biology and Biophysics
University of Minnesota
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Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.
Journal of proteome research 04, 2019 | Pubmed ID: 30702898
Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery.
Clinical proteomics Sep, 2011 | Pubmed ID: 21914210
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.
BMC genomics Aug, 2014 | Pubmed ID: 25149441
Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors.
PloS one , 2014 | Pubmed ID: 25290099
Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.
Journal of proteome research Dec, 2014 | Pubmed ID: 25301683
Multi-omic data analysis using Galaxy.
Nature biotechnology Feb, 2015 | Pubmed ID: 25658277
Metaproteomic analysis using the Galaxy framework.
Proteomics Oct, 2015 | Pubmed ID: 26058579
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.
Microbiome Dec, 2015 | Pubmed ID: 26684897
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 Aug, 2016 | Pubmed ID: 27155584
An Accessible Proteogenomics Informatics Resource for Cancer Researchers.
Cancer research Nov, 2017 | Pubmed ID: 29092937
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.
Proteomes Jan, 2018 | Pubmed ID: 29385081
Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome.
Scientific reports Jul, 2018 | Pubmed ID: 30022083
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.
Journal of proteome research Dec, 2018 | Pubmed ID: 30130115
BAL Fluid Metaproteome in Acute Respiratory Failure.
American journal of respiratory cell and molecular biology Nov, 2018 | Pubmed ID: 30382775
Improve your Galaxy text life: The Query Tabular Tool.
F1000Research , 2018 | Pubmed ID: 30519459
QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics.
Journal of proteome research Feb, 2019 | Pubmed ID: 30582332
metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.
Molecular & cellular proteomics : MCP Aug, 2019 | Pubmed ID: 31235611
Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.
GigaScience Apr, 2020 | Pubmed ID: 32236523
A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases.
Journal of proteome research Jul, 2020 | Pubmed ID: 32396365
Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform.
Proteomes Jul, 2020 | Pubmed ID: 32650610
Survey of metaproteomics software tools for functional microbiome analysis.
PloS one , 2020 | Pubmed ID: 33170893
Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.
Journal of proteome research Feb, 2021 | Pubmed ID: 33393790
Updates on metaQuantome Software for Quantitative Metaproteomics.
Journal of proteome research Apr, 2021 | Pubmed ID: 33683127
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 Mar, 2021 | Pubmed ID: 33688669
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).
Clinical proteomics May, 2021 | Pubmed ID: 33971807
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.
F1000Research , 2021 | Pubmed ID: 34484688
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes.
Microbiome Dec, 2021 | Pubmed ID: 34930457
Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow.
Proteomes Apr, 2022 | Pubmed ID: 35466239
An overview of technologies for MS-based proteomics-centric multi-omics.
Expert review of proteomics Mar, 2022 | Pubmed ID: 35466851
Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations.
Viruses Oct, 2022 | Pubmed ID: 36298760
Galaxy Training: A powerful framework for teaching!
PLoS computational biology Jan, 2023 | Pubmed ID: 36622853
An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.
Clinical proteomics Apr, 2023 | Pubmed ID: 37005570
Integrative meta-omics in Galaxy and beyond.
Environmental microbiome Jul, 2023 | Pubmed ID: 37420292
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.
Journal of biomolecular techniques : JBT Jul, 2023 | Pubmed ID: 37435391
Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.
Journal of proteome research Aug, 2023 | Pubmed ID: 37450889
A Galaxy of informatics resources for MS-based proteomics.
Expert review of proteomics , 2023 | Pubmed ID: 37787106
The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).
Journal of biomolecular techniques : JBT Sep, 2023 | Pubmed ID: 37969874
A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.
mSphere Jun, 2024 | Pubmed ID: 38780289
Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis.
Research square Jun, 2024 | Pubmed ID: 38883770
An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease.
mSystems Jul, 2024 | Pubmed ID: 38934598
Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19.
Methods in molecular biology (Clifton, N.J.) , 2024 | Pubmed ID: 38941023
Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.
Respiratory research Sep, 2024 | Pubmed ID: 39256809
Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.
bioRxiv : the preprint server for biology Sep, 2024 | Pubmed ID: 39345414
Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.
Methods in molecular biology (Clifton, N.J.) , 2025 | Pubmed ID: 39436599
Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.
Scientific reports Jan, 2025 | Pubmed ID: 39755759
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