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Author Details

Pratik D Jagtap
University of Minnesota
1999
60
22
Mohammad Sadnan Al Manir (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36622853Galaxy Training: A powerful framework for teaching!PLoS Comput Biol2023
37787106A Galaxy of informatics resources for MS-based proteomics.Expert Rev Proteomics2023
38045370A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.bioRxiv2023
37969874The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).J Biomol Tech2023
37420292Integrative meta-omics in Galaxy and beyond.Environ Microbiome2023
37450889Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.J Proteome Res2023
37005570An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.Clin Proteomics2023
374353912019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.J Biomol Tech2023
36298760Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations.Viruses2022
35466851An overview of technologies for MS-based proteomics-centric multi-omics.Expert Rev Proteomics2022
35466239Quantitative Proteogenomic Characterization of Inflamed Murine Colon Tissue Using an Integrated Discovery, Verification, and Validation Proteogenomic Workflow.Proteomes2022
35484230Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome.Nat Microbiol2022
33393790Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.J Proteome Res2021
33683127Updates on metaQuantome Software for Quantitative Metaproteomics.J Proteome Res2021
33688669A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).medRxiv2021
34911965Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.Nat Commun2021
34930457The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes.Microbiome2021
34804501Perspectives on automated composition of workflows in the life sciences.F1000Res2021
33971807A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).Clin Proteomics2021
32396365A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases.J Proteome Res2020
31793300Challenges in Peptide-Spectrum Matching: A Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits.J Proteome Res2020
33170893Survey of metaproteomics software tools for functional microbiome analysis.PLoS One2020
32764642Novel protein pathways in development and progression of pulmonary sarcoidosis.Sci Rep2020
32650610Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform.Proteomes2020
32236523Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.Gigascience2020
30582332QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics.J Proteome Res2019
31235611metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.Mol Cell Proteomics2019
30980333The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.Methods Mol Biol2019
30702898Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.J Proteome Res2019
30511867Update on the moFF Algorithm for Label-Free Quantitative Proteomics.J Proteome Res2019
29385081Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.Proteomes2018
30130115Bridging 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.J Proteome Res2018
30022083Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome.Sci Rep2018
29953864Community-Driven Data Analysis Training for Biology.Cell Syst2018
30382775BAL Fluid Metaproteome in Acute Respiratory Failure.Am J Respir Cell Mol Biol2018
28785034Bronchoalveolar Lavage Fluid Protein Expression in Acute Respiratory Distress Syndrome Provides Insights into Pathways Activated in Subjects with Different Outcomes.Sci Rep2017
29092937An Accessible Proteogenomics Informatics Resource for Cancer Researchers.Cancer Res2017
26903422Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype.J Proteome Res2016
27155584Proteome Profiling in Lung Injury after Hematopoietic Stem Cell Transplantation.Biol Blood Marrow Transplant2016
25658277Multi-omic data analysis using Galaxy.Nat Biotechnol2015
26435507Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.J Proteome Res2015
26468045Microbiomes - embracing complexity.Proteomics2015
26684897Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.Microbiome2015
26058579Metaproteomic analysis using the Galaxy framework.Proteomics2015
25149441Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.BMC Genomics2014
25290099Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors.PLoS One2014
25301683Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.J Proteome Res2014
23412978A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.Proteomics2013
22623410Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm.Proteomics2012
22522805Deep metaproteomic analysis of human salivary supernatant.Proteomics2012
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Collaborators

Timothy J Griffin
University of Minnesota
Co-authored papers 42
Getiria Onsongo
Macalester College
Co-authored papers 4
Lennart Martens
Co-authored papers 4
Sean L Seymour
Co-authored papers 3
Magnus Palmblad
Center for Proteomics and Metabolomics, Leiden University Medical Center
Co-authored papers 3
Lloyd M Smith
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 3
John Chilton
The Pennsylvania State University, University Park
Co-authored papers 3
Philip C Andrews
Sydney Children's Hospital, University of New South Wales
Co-authored papers 2
Michael R Shortreed
University of Wisconsin-Madison
Co-authored papers 2
Hans-Rudolf Hotz
Friedrich Miescher Institute for Biomedical Research
Co-authored papers 2
Dave Clements
Johns Hopkins University
Co-authored papers 2
Folker Meyer
Institute for Artificial Intelligence, University of Duisburg-Essen
Co-authored papers 2
Paul Wilmes
University of Luxembourg
Co-authored papers 2
Mat???? Kala??
University of Bergen
Co-authored papers 1
Carole Goble
University of Manchester
Co-authored papers 1
Gianrico Farrugia
Mayo Clinic Gastroenterology and Hepatology, Mayo Clinic
Co-authored papers 1
Eric S Rasche
Clinical Bioinformatics Group, Erasmus Medical Center
Co-authored papers 1
Sanjeeva Srivastava
Indian Institute of Technology Bombay
Co-authored papers 1
James Taylor
Johns Hopkins University
Co-authored papers 1
Youri Hoogstrate
Erasmus MC Cancer Institute
Co-authored papers 1
Salvador Capella-Gutierrez
Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
Co-authored papers 1
Hans Ienasescu
Technical University of Denmark
Co-authored papers 1
Ilkay Altintas
Halicioglu Data Science Institute, University of California San Diego
Co-authored papers 1
Maria A Doyle
Peter MacCallum Cancer Centre
Co-authored papers 1
Peter Horvatovich
Groningen Research Institute of Pharmacy, University of Groningen
Co-authored papers 1
Fidel Ram??rez
Max Planck Institute of Immunobiology and Epigenetics
Co-authored papers 1
Vedran Kasalica
Utrecht University
Co-authored papers 1
Robin A Richardson
University College London
Co-authored papers 1
Susan T Weintraub
University of Texas Health Science Center at San Antonio Texas78229 USA.
Co-authored papers 1
Paul Groth
University of Amsterdam
Co-authored papers 1
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