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Author Details

Timothy J Griffin
University of Minnesota
1985
132
45
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
36949960Lung proteome and metabolome endotype in HIV-associated obstructive lung disease.ERJ Open Res2023
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
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
35849661Lung and Plasma Metabolome in HIV-Associated Obstructive Lung Disease.J Acquir Immune Defic Syndr2022
33413078Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics.Clin Proteomics2021
33683127Updates on metaQuantome Software for Quantitative Metaproteomics.J Proteome Res2021
33798209Metabolite profiles associated with disease progression in influenza infection.PLoS One2021
34911965Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.Nat Commun2021
34804501Perspectives on automated composition of workflows in the life sciences.F1000Res2021
34110810Novel 4-Hydroxybenzyl Adducts in Human Hemoglobin: Structures and Mechanisms of Formation.Chem Res Toxicol2021
33971807A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).Clin Proteomics2021
33393790Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms.J Proteome Res2021
32396365A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases.J Proteome Res2020
32101723The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.Trends Cancer2020
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
32804537Application of Proteomics in Sarcoidosis.Am J Respir Cell Mol Biol2020
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
30176067Quantitative proteomics of forebrain subcellular fractions in fragile X mental retardation 1 knockout mice following acute treatment with 2-Methyl-6-(phenylethynyl)pyridine: Relevance to developmental study of schizophrenia.Synapse2019
31235611metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.Mol Cell Proteomics2019
30742544Distinct Cancer-Promoting Stromal Gene Expression Depending on Lung Function.Am J Respir Crit Care Med2019
30980333The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.Methods Mol Biol2019
30511867Update on the moFF Algorithm for Label-Free Quantitative Proteomics.J Proteome Res2019
29313410ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy induction.Autophagy2018
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
30250409Plasma lipoproteome in Alzheimer's disease: a proof-of-concept study.Clin Proteomics2018
30382775BAL Fluid Metaproteome in Acute Respiratory Failure.Am J Respir Cell Mol Biol2018
29385081Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.Proteomes2018
29794131Multi-omic molecular profiling of lung cancer in COPD.Eur Respir J2018
29329347Salivary proteomics of healthy dogs: An in depth catalog.PLoS One2018
29174395Normalization of mass spectrometry data (NOMAD).Adv Biol Regul2018
28530639Calcium-binding protein S100A4 confers mesenchymal progenitor cell fibrogenicity in idiopathic pulmonary fibrosis.J Clin Invest2017
28409005Plasma sphingolipids in HIV-associated chronic obstructive pulmonary disease.BMJ Open Respir Res2017
29322062Increased Indoleamine-2,3-Dioxygenase Activity Is Associated With Poor Clinical Outcome in Adults Hospitalized With Influenza in the INSIGHT FLU003Plus Study.Open Forum Infect Dis2017
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
27729784Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease.Int J Chron Obstruct Pulmon Dis2016
27134171Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression.Cell Rep2016
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Collaborators

Pratik D Jagtap
University of Minnesota
Co-authored papers 42
Ruedi Aebersold
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 10
Getiria Onsongo
Macalester College
Co-authored papers 9
Lloyd M Smith
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 8
Steven P Gygi
Harvard Medical School
Co-authored papers 5
Beate Rist
Clinic for Swine, Ludwig-Maximilians-University
Co-authored papers 5
Lennart Martens
Co-authored papers 4
Sean L Seymour
Co-authored papers 3
David A Bernlohr
University of Minnesota-Twin Cities
Co-authored papers 3
John Chilton
The Pennsylvania State University, University Park
Co-authored papers 3
Ping Yang
Mayo Clinic
Co-authored papers 2
Michael R Shortreed
University of Wisconsin-Madison
Co-authored papers 2
Janne Lehti??
Karolinska Institutet
Co-authored papers 2
Jimmy K Eng
University of Washington
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
Fiona Ginty
GE Global Research Center
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
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
Jeffrey A Ranish
Institute for Systems Biology
Co-authored papers 1
Vedran Kasalica
Utrecht University
Co-authored papers 1
Robin A Richardson
University College London
Co-authored papers 1
Paul Wilmes
University of Luxembourg
Co-authored papers 1
Paul Groth
University of Amsterdam
Co-authored papers 1
Release 1.2