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List of works by Timothy Griffin

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva

scientific article

A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics.

scientific article

A functional screen provides evidence for a conserved, regulatory, juxtamembrane phosphorylation site in guanylyl cyclase a and B.

scientific article published on 9 May 2012

A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry.

scientific article

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

scientific article published on 15 March 2013

AminoxyTMT: A novel multi-functional reagent for characterization of protein carbonylation.

scientific article published on April 2016

An Accessible Proteogenomics Informatics Resource for Cancer Researchers

scientific article published on November 2017

An Approach to Predicting the Stabilities of Peptide Nucleic Acid:DNA Duplexes ⬇️

scientific article published on June 15, 1998

BAL Fluid Metaproteome in Acute Respiratory Failure

scientific article published on 01 November 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 Variants Detected via Proteogenomics

scientific article published on 05 September 2018

Calcium-binding protein S100A4 confers mesenchymal progenitor cell fibrogenicity in idiopathic pulmonary fibrosis

scientific article published on 22 May 2017

Challenges in Peptide-Spectrum Matching: A Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits

scientific article published on 20 December 2019

Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.

scientific article published on 5 October 2015

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

scientific article published on 15 December 2021

Deep metaproteomic analysis of human salivary supernatant.

scientific article

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

scientific article published on 31 January 2018

Distinct Cancer-Promoting Stromal Gene Expression Depending on Lung Function

scientific article published on 01 August 2019

Dynamic range compression: a solution for proteomic biomarker discovery?

scientific article published on 01 September 2011

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

scientific article published on 18 July 2018

Fibroblast Growth Factor Receptor 1 Activation in Mammary Tumor Cells Promotes Macrophage Recruitment in a CX3CL1-Dependent Manner ⬇️

scientific article published on September 24, 2012

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

scientific article

Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometry ⬇️

scientific article published on December 1, 1997

Global assessment of protein turnover in recombinant antibody producing myeloma cells.

scientific article published on 9 June 2010

Improve your Galaxy text life: The Query Tabular Tool

scientific article published on 05 October 2018

Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN).

scientific article published on 26 February 2014

Increased Indoleamine-2,3-Dioxygenase Activity Is Associated With Poor Clinical Outcome in Adults Hospitalized With Influenza in the INSIGHT FLU003Plus Study

Mass Spectrometric Identification of Phosphorylation Sites in Guanylyl Cyclase A and B ⬇️

scientific article published on November 8, 2010

Metaproteomic analysis using the Galaxy framework.

scientific article published on 9 June 2015

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

scientific article published on 04 January 2021

Microbiomes - embracing complexity

scientific article published in October 2015

Multi-omic data analysis using Galaxy.

scientific article

Multi-omic molecular profiling of lung cancer in COPD

scientific article published on 04 July 2018

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

scientific article published on 01 April 2020

Normalization of mass spectrometry data (NOMAD).

scientific article published on 20 November 2017

Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential ⬇️

scientific article published on July 25, 2010

Perspectives on automated composition of workflows in the life sciences

scientific article

Plasma sphingolipids in HIV-associated chronic obstructive pulmonary disease

scientific article

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

scientific article published on 08 July 2020

Protein carbonylation and adipocyte mitochondrial function.

scientific article

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

scientific article

Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype

scientific article

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

scientific article published on 04 January 2019

Quantitative proteomic analysis of oral brush biopsies identifies secretory leukocyte protease inhibitor as a promising, mechanism-based oral cancer biomarker.

scientific article

Quantitative 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

scientific article published on 03 October 2018

RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification

scientific article published on 18 February 2016

Salivary proteomics of healthy dogs: An in depth catalog

scientific article published on 12 January 2018

Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery.

scientific article published on 24 August 2011

Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression

scientific article published on 27 April 2016

The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

scientific article published on 07 February 2020

The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis

scientific article published on 01 January 2019

Three-dimensional peptide fractionation for highly sensitive nanoscale LC-based shotgun proteomic analysis of complex protein mixtures

scientific article published on 01 January 2011

Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease.

scientific article published on 29 September 2016

ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy induction.

scientific article published on 9 January 2018

Update on the moFF Algorithm for Label-Free Quantitative Proteomics

scientific article published on 14 December 2018

Updates on metaQuantome Software for Quantitative Metaproteomics

scientific article published on 08 March 2021

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

scientific article (publication date: 22 August 2014)

Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to detect monoclonal immunoglobulin light chains in serum and urine

scientific article published on 01 November 2015

Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm.

scientific article

mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation

scientific article

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

scientific article published on 24 June 2019

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