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Research Output 1997 2019

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Article
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., 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
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
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
9 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

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

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

Research output: Contribution to journalArticle

Proteomics
proteomics
Dogs
Peptides
Phylogeny
16 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
13 Citations (Scopus)
Open Access
Idiopathic Pulmonary Fibrosis
Calcium-Binding Proteins
Mesenchymal Stromal Cells
Fibrosis
Myofibroblasts
3 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
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
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
11 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
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
14 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
88 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
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
49 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
27 Citations (Scopus)

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

Reed, J. R., Stone, M. D., Beadnell, T. C., Ryu, Y., Griffin, T. J. & Schwertfeger, K., Sep 24 2012, In : PLoS One. 7, 9, e45877.

Research output: Contribution to journalArticle

Receptor, Fibroblast Growth Factor, Type 1
Macrophages
mammary neoplasms (animal)
Tumors
macrophages
18 Citations (Scopus)

Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures

de Jong, E. & Griffin, T. J., Oct 5 2012, In : Journal of Proteome Research. 11, 10, p. 5059-5064 6 p.

Research output: Contribution to journalArticle

Firearms
Chromatography
Complex Mixtures
Static Electricity
Hydrophobic and Hydrophilic Interactions
41 Citations (Scopus)

Protein carbonylation and adipocyte mitochondrial function

Curtis, J. M., Hahn, W. S., Stone, M. D., Inda, J. J., Droullard, D. J., Kuzmicic, J. P., Donoghue, M. A., Long, E. K., Armien, A. G., Lavandero, S., Arriaga, E., Griffin, T. J. & Bernlohr, D. A., Sep 21 2012, In : Journal of Biological Chemistry. 287, 39, p. 32967-32980 14 p.

Research output: Contribution to journalArticle

Protein Carbonylation
Carbonylation
Adipocytes
Phosphate Transport Proteins
NADH Dehydrogenase
10 Citations (Scopus)

Scaling up multi-touch selection and querying: Interfaces and applications for combining mobile multi-touch input with large-scale visualization displays

Keefe, D. F., Gupta, A., Feldman, D., Carlis, J. V., Krehbiel Keefe, S. & Griffin, T. J., Oct 1 2012, In : International Journal of Human Computer Studies. 70, 10, p. 703-713 11 p.

Research output: Contribution to journalArticle

scaling
visualization
Visualization
Display devices
Biochemistry
48 Citations (Scopus)

SH3BP4 Is a Negative Regulator of Amino Acid-Rag GTPase-mTORC1 Signaling

Kim, Y-M., Stone, M., Hwang, T. H., Kim, Y. G., Dunlevy, J. R., Griffin, T. J. & Kim, D-H., Jun 29 2012, In : Molecular Cell. 46, 6, p. 833-846 14 p.

Research output: Contribution to journalArticle

src Homology Domains
Guanosine
Carrier Proteins
Amino Acids
Autophagy
13 Citations (Scopus)

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

Jagtap, P., Bandhakavi, S., Higgins, L., Mcgowan, T., Sa, R., Stone, M. D., Chilton, J., Arriaga, E. A., Seymour, S. L. & Griffin, T. J., Jun 1 2012, In : Proteomics. 12, 11, p. 1726-1730 5 p.

Research output: Contribution to journalArticle

Workflow
Pipelines
Saliva
Peptides
Processing
2011
11 Citations (Scopus)
Mouth Neoplasms
Biomarkers
Exudates and Transudates
Tumor Biomarkers
Proteomics
33 Citations (Scopus)

Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva

Bandhakavi, S., Van Riper, S. K., Tawfik, P. N., Stone, M. D., Haddad, T., Rhodus, N. L., Carlis, J. V. & Griffin, T. J., Mar 4 2011, In : Journal of Proteome Research. 10, 3, p. 1052-1061 10 p.

Research output: Contribution to journalArticle

Pulse time modulation
Saliva
Libraries
Workflow
Proteins
32 Citations (Scopus)

Large-scale phosphoproteomics analysis of whole saliva reveals a distinct phosphorylation pattern

Stone, M. D., Chen, X., McGowan, T., Bandhakavi, S., Cheng, B., Rhodus, N. L. & Griffin, T. J., Apr 1 2011, In : Journal of Proteome Research. 10, 4, p. 1728-1736 9 p.

Research output: Contribution to journalArticle

Phosphorylation
Phosphoproteins
Saliva
Salivary Proteins and Peptides
Phosphotransferases
30 Citations (Scopus)

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

de Jong, E., Van Riper, S. K., Koopmeiners, J., Carlis, J. V. & Griffin, T. J., Nov 20 2011, In : Clinica Chimica Acta. 412, 23-24, p. 2284-2288 5 p.

Research output: Contribution to journalArticle

Biomarkers
Saliva
Freezing
Peptides
Nutritional Status
2010
48 Citations (Scopus)
Microbiota
Tandem Mass Spectrometry
Metagenomics
Peptides
Archaea
8 Citations (Scopus)

Global assessment of protein turnover in recombinant antibody producing myeloma cells

Yee, J. C., Jacob, N. M., Jayapal, K. P., Kok, Y. J., Philp, R., Griffin, T. J. & Hu, W. S., Aug 1 2010, In : Journal of Biotechnology. 148, 4, p. 182-193 12 p.

Research output: Contribution to journalArticle

Antibody-Producing Cells
Antibodies
Proteins
Half-Life
Arginine