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Research Output 1997 2019

2019
1 Citation (Scopus)

Distinct cancer-promoting stromal gene expression depending on lung function

Sandri, B. J., Masvidal, L., Murie, C., Bartish, M., Avdulov, S. V., Higgins, L., Markowski, T. W., Peterson, M., Bergh, J., Yang, P., Rolny, C., Limper, A. H., Griffin, T. J., Bitterman, P. B., Wendt, C. H. & Larsson, O., Aug 1 2019, In : American journal of respiratory and critical care medicine. 200, 3, p. 348-358 11 p.

Research output: Contribution to journalArticle

Gene Expression
Lung
Lung Neoplasms
Neoplasms
Sirolimus

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

Easterly, C. W., Sajulga, R., Mehta, S., Johnson, J. E., Kumar, P., Hubler, S., Mesuere, B., Rudney, J. D., Griffin, T. J. & Jagtap, P. D., Aug 9 2019, In : Molecular & cellular proteomics : MCP. 18, 8, p. S82-S91

Research output: Contribution to journalArticle

Open Access
Microbiota
Taxonomies
Benchmarking
Proteins
Galaxies
Subcellular Fractions
Prosencephalon
Knockout Mice
Intellectual Disability
Proteomics

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

Kumar, P., Panigrahi, P., Johnson, J. E., Weber, W. J., Mehta, S., Sajulga, R., Easterly, C., Crooker, B. A., Heydarian, M., Anamika, K., Griffin, T. J. & Jagtap, P. D., Feb 1 2019, In : Journal of Proteome Research. 18, 2, p. 782-790 9 p.

Research output: Contribution to journalArticle

Informatics
Galaxies
Software
Proteins
Visualization

The galaxy platform for reproducible affinity proteomic mass spectrometry data analysis

Stewart, P. A., Kuenzi, B. M., Mehta, S., Kumar, P., Johnson, J. E., Jagtap, P. D., Griffin, T. J. & Haura, E. B., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 249-261 13 p. (Methods in Molecular Biology; vol. 1977).

Research output: Chapter in Book/Report/Conference proceedingChapter

Galaxies
Proteomics
Mass Spectrometry
Workflow
Software
1 Citation (Scopus)

Update on the moFF Algorithm for Label-Free Quantitative Proteomics

Argentini, A., Staes, A., Grüning, B., Mehta, S., Easterly, C., Griffin, T. J., Jagtap, P. D., Impens, F. & Martens, L., Feb 1 2019, In : Journal of Proteome Research. 18, 2, p. 728-731 4 p.

Research output: Contribution to journalArticle

Proteomics
Labels
Search Engine
Peptides
Workflow
2018
Open Access
Dimercaprol
Respiratory Insufficiency
Fluids
4 Citations (Scopus)
Proteome
Chromosomes
Galaxies
Proteins
Workflow

Chronic Obstructive Pulmonary Disease Phenotype Dictates Cancer-Promoting Stromal Gene Expression Programs

Wendt, C. H., Sandri, B. J., Masvidal, L., Murie, C., Bartish, M., Avdulov, S. V., Higgins, L., Markowski, T., Peterson, M., Bergh, J., Yang, P., Rolny, C., Limper, A. H., Griffin, T. J., Bitterman, P. B. & Larsson, O., Dec 1 2018, In : Annals of the American Thoracic Society. 15, 4, p. S290-S291

Research output: Contribution to journalArticle

Chronic Obstructive Pulmonary Disease
Phenotype
Gene Expression
Neoplasms
Lung Neoplasms
10 Citations (Scopus)

Disseminating metaproteomic informatics capabilities and knowledge using the galaxy-P framework

Blank, C., Easterly, C., Gruening, B., Johnson, J. E., Kolmeder, C. A., Kumar, P., May, D., Mehta, S., Mesuere, B., Brown, Z., Elias, J. E., Hervey, W. J., McGowan, T., Muth, T., Nunn, B. L., Rudney, J. D., Tanca, A., Griffin, T. J. & Jagtap, P. D., Mar 1 2018, In : Proteomes. 6, 1, 7.

Research output: Contribution to journalArticle

Open Access
Galaxies
Informatics
Workflow
Software
Microbiota
Open Access
Papanicolaou Test
Microbiota
Fixatives
Protein Databases
Proteins

Improve your Galaxy text life: The Query Tabular Tool [version 1; referees: 1 approved, 2 approved with reservations]

Johnson, J. E., Kumar, P., Easterly, C., Esler, M., Mehta, S., Eschenlauer, A. C., Hegeman, A. D., Jagtap, P. D. & Griffin, T. J., Jan 1 2018, In : F1000Research. 7, 1604.

Research output: Contribution to journalArticle

Open Access
Galaxies
Workflow
Software
Processing
Research Personnel
1 Citation (Scopus)

Increased indoleamine-2,3-dioxygenase activity is associated with poor clinical outcome in adults hospitalized with influenza in the INSIGHT FLU003Plus study

Pett, S. L., Kunisaki, K. M., Wentworth, D., Griffin, T. J., Kalomenidis, I., Nahra, R., Sanchez, R. M., Hodgson, S. W., Ruxrungtham, K., Dwyer, D., Davey, R. T., Wendt, C. H., Lundgren, J., Jansson, P., Pearson, M., Aagaard, B., Hudson, F., Bennet, R., Pacciarini, F., Angus, B. & 31 others, Paton, N., Collaco Moraes, Y., Cooper, D., Pett, S., Emery, S., Courtney-Rogers, D., Robson, R., Gordin, F., Sanchez, A., Standridge, B., Vjecha, M., Moricz, A., Delfino, M., Belloso, W., Losso, M., Tillmann, K., Touloumi, G., Gioukari, V., Anagnostou, O., La Rosa, A., Saenz, M. J., Lopez, P., Herrero, P., Portas, B., Avihingsanon, A., Ruxrungtham, K., Kaewon, P., Denning, E., Engen, N., Neaton, J. D. & For the INSIGHT FLU003 Plus Study Group, Jan 1 2018, In : Open Forum Infectious Diseases. 5, 1, ofx228.

Research output: Contribution to journalArticle

Indoleamine-Pyrrole 2,3,-Dioxygenase
Human Influenza
Disease Progression
Tryptophan
Kynurenine
2 Citations (Scopus)

Multi-omic molecular profiling of lung cancer in COPD

Sandri, B. J., Kaplan, A., Hodgson, S. W., Peterson, M., Avdulov, S. V., Higgins, L., Markowski, T., Yang, P., Limper, A. H., Griffin, T. J., Bitterman, P. B., Lock, E. & Wendt, C. H., Jul 1 2018, In : European Respiratory Journal. 52, 1, 1702665.

Research output: Contribution to journalArticle

Chronic Obstructive Pulmonary Disease
Lung Neoplasms
Neoplasms
Joints
Proto-Oncogene Proteins c-akt
2 Citations (Scopus)

Normalization of mass spectrometry data (NOMAD)

Murie, C., Sandri, B., Sandberg, A. S., Griffin, T. J., Lehtiö, J., Wendt, C. & Larsson, O., Jan 1 2018, In : Advances in Biological Regulation. 67, p. 128-133 6 p.

Research output: Contribution to journalArticle

Open Access
Mass Spectrometry
Linear Models
Sample Size
Proteomics
Analysis of Variance
2 Citations (Scopus)

Plasma lipoproteome in Alzheimer's disease: A proof-of-concept study

Li, D., Huang, F., Zhao, Y., Villata, P. W., Griffin, T. J., Zhang, L., Li, L. & Yu, F., Sep 20 2018, In : Clinical Proteomics. 15, 1, 31.

Research output: Contribution to journalArticle

Alzheimer Disease
Plasmas
Lipoproteins
Peptides
Complement C3
6 Citations (Scopus)

Salivary proteomics of healthy dogs: An in depth catalog

Torres, S. M. F., Furrow, E., Souza, C. P., Granick, J. L., De Jong, E. P., Griffin, T. J. & Wang, X., Jan 2018, In : PloS one. 13, 1, e0191307.

Research output: Contribution to journalArticle

Proteomics
proteomics
Dogs
Peptides
Phylogeny
17 Citations (Scopus)

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

Park, J-M., Seo, M., Jung, C. H., Grunwald, D., Stone, M., Otto, N. M., Toso, E., Ahn, Y., Kyba, M., Griffin, T. J., Higgins, L. & Kim, D-H., Apr 3 2018, In : Autophagy. 14, 4, p. 584-597 14 p.

Research output: Contribution to journalArticle

Autophagy
Phosphotransferases
Phosphorylation
Starvation
Amino Acids
2017
7 Citations (Scopus)

An accessible proteogenomics informatics resource for cancer researchers

Chambers, M. C., Jagtap, P. D., Johnson, J. E., McGowan, T., Kumar, P., Onsongo, G., Guerrero, C. R., Barsnes, H., Vaudel, M., Martens, L., Grüning, B., Cooke, I. R., Heydarian, M., Reddy, K. L. & Griffin, T. J., Nov 1 2017, In : Cancer Research. 77, 21, p. e43-e46

Research output: Contribution to journalArticle

Open Access
Informatics
Software
Workflow
Research Personnel
Galaxies
14 Citations (Scopus)
Open Access
Idiopathic Pulmonary Fibrosis
Calcium-Binding Proteins
Mesenchymal Stromal Cells
Fibrosis
Myofibroblasts

Carbonylated Proteins and Their Metabolic Regulation: Overview of Mechanisms, Target Proteins, and Characterization Using Proteomic Methods

Afiuni-Zadeh, S. & Griffin, T. J., Apr 20 2017, Protein Carbonylation: Principles, Analysis, and Biological Implications. wiley, p. 110-130 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carbonylation
Proteins
Oxidative stress
Avidin
Biomarkers
1 Citation (Scopus)

Chapter 13: Using Galaxy for Proteomics

Guerrero, C. R., Jagtap, P. D., Johnson, J. E. & Griffin, T. J., Jan 1 2017, Proteome Informatics. Bessant, C. & Gaskell, S. J. (eds.). 5 ed. Royal Society of Chemistry, p. 289-320 32 p. (New Developments in Mass Spectrometry; vol. 2017-January, no. 5).

Research output: Chapter in Book/Report/Conference proceedingChapter

Galaxies
Mass spectrometry
Bioinformatics
Proteomics
Scalability

Comparative Metaproteomics to Study Environmental Changes

Matallana-Surget, S., Jagtap, P. D., Griffin, T. J., Beraud, M. & Wattiez, R., Oct 29 2017, Metagenomics: Perspectives, Methods, and Applications. Elsevier Inc., p. 327-363 37 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Aquatic ecosystems
Microorganisms
Ecosystems
Ecosystem
Workflow
4 Citations (Scopus)
Open Access
Sphingolipids
Chronic Obstructive Pulmonary Disease
HIV
Tryptophan
Kynurenine
2016
7 Citations (Scopus)

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

Afiuni-Zadeh, S., Rogers, J. C., Snovida, S. I., Bomgarden, R. D. & Griffin, T. J., Apr 1 2016, In : BioTechniques. 60, 4, p. 186-196 11 p.

Research output: Contribution to journalArticle

Protein Carbonylation
Carbonylation
Tandem Mass Spectrometry
Mass spectrometry
Complex Mixtures
15 Citations (Scopus)

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

Anderson, K. J., Vermillion, K. L., Jagtap, P., Johnson, J. E., Griffin, T. J. & Andrews, M. T., Apr 1 2016, In : Journal of Proteome Research. 15, 4, p. 1253-1261 9 p.

Research output: Contribution to journalArticle

Hibernation
Mammals
Physiology
Muscle
Skeletal Muscle
7 Citations (Scopus)

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

Van Riper, S. K., Higgins, L., Carlis, J. V. & Griffin, T. J., Jul 1 2016, In : Bioinformatics. 32, 13, p. 2035-2037 3 p.

Research output: Contribution to journalArticle

Metabolomics
Proteomics
Mass Spectrometry
Quantification
Mass spectrometry
8 Citations (Scopus)

Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression

Thu, Y-M., Van Riper, S. K., Higgins, L., Zhang, T., Becker, J., Markowski, T. W., Nguyen, H. D., Griffin, T. J. & Bielinsky, A. K., May 10 2016, In : Cell Reports. 15, 6, p. 1254-1265 12 p.

Research output: Contribution to journalArticle

Minichromosome Maintenance Proteins
M Phase Cell Cycle Checkpoints
Ligases
Methyl Methanesulfonate
Protein Deficiency
6 Citations (Scopus)

Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease

Gulcev, M., Reilly, C. S., Griffin, T. J., Broeckling, C. D., Sandri, B. J., Witthuhn, B. A., Hodgson, S. W., Woodruff, P. G. & Wendt, C. H., Sep 29 2016, In : International Journal of COPD. 11, 1, p. 2435-2446 12 p.

Research output: Contribution to journalArticle

Tryptophan
Chronic Obstructive Pulmonary Disease
Indoleamine-Pyrrole 2,3,-Dioxygenase
Metabolomics
Mass Spectrometry
2015
17 Citations (Scopus)

Characterizing cardiac molecular mechanisms of mammalian hibernation via quantitative proteogenomics

Vermillion, K. L., Jagtap, P. D., Johnson, J. E., Griffin, T. J. & Andrews, M. T., Jan 1 2015, In : Journal of Proteome Research. 14, 11, p. 4792-4804 13 p.

Research output: Contribution to journalArticle

Hibernation
Galaxies
Sciuridae
Proteomics
Proteins
32 Citations (Scopus)

Metaproteomic analysis using the Galaxy framework

Jagtap, P. D., Blakely, A., Murray, K., Stewart, S., Kooren, J., Johnson, J. E., Rhodus, N. L., Rudney, J. D. & Griffin, T. J., Oct 1 2015, In : Proteomics. 15, 20, p. 3553-3565 13 p.

Research output: Contribution to journalArticle

Galaxies
Workflow
Proteins
Blueprints
Protein Databases
3 Citations (Scopus)

Microbiomes - Embracing complexity

Jagtap, P., Griffin, T. & Armengaud, J., Oct 1 2015, In : Proteomics. 15, 20, p. 3405-3406 2 p.

Research output: Contribution to journalEditorial

Gene expression
Proteomics
16 Citations (Scopus)

MRNA 3′-UTR shortening is a molecular signature of mTORC1 activation

Chang, J. W., Zhang, W., Yeh, H. S., De Jong, E. P., Jun, S., Kim, K. H., Bae, S. S., Beckman, K., Hwang, T. H., Kim, K. S., Kim, D. H., Griffin, T. J., Kuang, R. & Yong, J., Jun 15 2015, In : Nature communications. 6, 7218.

Research output: Contribution to journalArticle

3' Untranslated Regions
Sirolimus
Chemical activation
signatures
activation
48 Citations (Scopus)

Multi-omic data analysis using Galaxy

Boekel, J., Chilton, J. M., Cooke, I. R., Horvatovich, P. L., Jagtap, P. D., Käll, L., Lehtiö, J., Lukasse, P., Moerland, P. D. & Griffin, T. J., Jan 1 2015, In : Nature biotechnology. 33, 2, p. 137-139 3 p.

Research output: Contribution to journalLetter

Galaxies
Proteomics
7 Citations (Scopus)

Salivary proteomics in bisphosphonate-related osteonecrosis of the jaw

Thumbigere-Math, V., Michalowicz, B. S., de Jong, E. P., Griffin, T. J., Basi, D. L., Hughes, P. J., Tsai, M. L., Swenson, K. K., Rockwell, L. & Gopalakrishnan, R., Jan 1 2015, In : Oral Diseases. 21, 1, p. 46-56 11 p.

Research output: Contribution to journalArticle

Bisphosphonate-Associated Osteonecrosis of the Jaw
Proteomics
Desmoplakins
Metalloproteases
Saliva

The human saliva proteome: Overview and emerging methods for characterization

Griffin, T. J., Jan 1 2015, Advances in Global Health Through Sensing Technologies 2015. Southern, S. O., Gartner, C., Stallings, J. D. & Rodriguez-Chavez, I. R. (eds.). SPIE, Vol. 9490. 949003

Research output: Chapter in Book/Report/Conference proceedingConference contribution

proteome
saliva
Proteome
emerging
proteins
12 Citations (Scopus)

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

Barnidge, D. R., Krick, T. P., Griffin, T. J. & Murray, D. L., Nov 15 2015, In : Rapid Communications in Mass Spectrometry. 29, 21, p. 2057-2060 4 p.

Research output: Contribution to journalArticle

Immunoglobulin Light Chains
Ionization
Mass spectrometry
Desorption
Electrophoresis
2014
5 Citations (Scopus)
Cytology
Papanicolaou Test
Feasibility Studies
Proteomics
Mass spectrometry
48 Citations (Scopus)

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

Jagtap, P. D., Johnson, J. E., Onsongo, G., Sadler, F. W., Murray, K., Wang, Y., Shenykman, G. M., Bandhakavi, S., Smith, L. M. & Griffin, T. J., Dec 5 2014, In : Journal of Proteome Research. 13, 12, p. 5898-5908 11 p.

Research output: Contribution to journalArticle

Galaxies
Workflow
Software
Proteomics
Peptides

Human saliva proteome: An overview

Griffin, T. J., Jan 1 2014, Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring IV. SPIE, Vol. 9112. 91120B

Research output: Chapter in Book/Report/Conference proceedingConference contribution

proteome
saliva
Proteome
proteins
Proteins
4 Citations (Scopus)

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

Van Riper, S. K., de Jong, E., Higgins, L., Carlis, J. V. & Griffin, T. J., Mar 7 2014, In : Journal of Proteome Research. 13, 3, p. 1281-1292 12 p.

Research output: Contribution to journalArticle

Labels
Workflow
High Pressure Liquid Chromatography
Molecules
Proteins
15 Citations (Scopus)

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

Yang, Y., Rhodus, N. L., Ondrey, F. G., Wuertz, B. R. K., Chen, X., Zhu, Y. & Griffin, T. J., Apr 18 2014, In : PloS one. 9, 4, e95389.

Research output: Contribution to journalArticle

Secretory Leukocyte Peptidase Inhibitor
Biopsy
Mouth Neoplasms
Brushes
Tumor Biomarkers
43 Citations (Scopus)

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

Sheynkman, G. M., Johnson, J. E., Jagtap, P. D., Shortreed, M. R., Onsongo, G., Frey, B. L., Griffin, T. J. & Smith, L. M., Jan 1 2014, In : BMC Genomics. 15, 1, 703.

Research output: Contribution to journalArticle

Galaxies
Proteomics
Mass Spectrometry
RNA
Workflow
2013
90 Citations (Scopus)

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

Jagtap, P. D., Goslinga, J., Kooren, J. A., Mcgowan, T., Wroblewski, M. S., Seymour, S. L. & Griffin, T. J., Apr 1 2013, In : Proteomics. 13, 8, p. 1352-1357 6 p.

Research output: Contribution to journalArticle

Databases
Peptides
Proteogenomics
Proteomics
Proteins
19 Citations (Scopus)

Mass spectrometry-based proteomics: Basic principles and emerging technologies and directions

Van Riper, S. K., de Jong, E., Carlis, J. V. & Griffin, T. J., Jan 1 2013, Radiation Proteomics: The Effects of Ionizing and Non-Ionizing Radiation on Cells and Tissues. Springer New York LLC, p. 1-35 35 p. (Advances in Experimental Medicine and Biology; vol. 990).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteomics
Mass spectrometry
Mass Spectrometry
Technology
Biological radiation effects

Mass spectrometry-based proteomics: basic principles and emerging technologies and directions.

Van Riper, S. K., de Jong, E. P., Carlis, J. V. & Griffin, T. J., Jun 20 2013, In : Advances in Experimental Medicine and Biology. 990, p. 1-35 35 p.

Research output: Contribution to journalReview article

Proteomics
Mass spectrometry
Mass Spectrometry
Technology
Biological radiation effects

The proteome of human saliva

Griffin, T. J., Aug 12 2013, Sensing Technologies for Global Health, Military Medicine, and Environmental Monitoring III. Vol. 8723. 87230A

Research output: Chapter in Book/Report/Conference proceedingConference contribution

proteome
saliva
Proteome
Proteins
Protein
2012
18 Citations (Scopus)

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

Yoder, A. R., Robinson, J. W., Dickey, D. M., Andersland, J., Rose, B. A., Stone, M. D., Griffin, T. J. & Potter, L. R., May 9 2012, In : PLoS One. 7, 5, e36747.

Research output: Contribution to journalArticle

guanylate cyclase
Phosphorylation
Guanylate Cyclase
phosphorylation
glutamates
50 Citations (Scopus)

Deep metaproteomic analysis of human salivary supernatant

Jagtap, P. D., Mcgowan, T., Bandhakavi, S., Tu, Z. J., Seymour, S., Griffin, T. J. & Rudney, J. D., Apr 1 2012, In : Proteomics. 12, 7, p. 992-1001 10 p.

Research output: Contribution to journalArticle

Proteome
Peptides
Proteins
Mouth Diseases
Selenomonas