Research Output

2020

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

Hubler, S. L., Kumar, P., Mehta, S., Easterly, C., Johnson, J. E., Jagtap, P. D. & Griffin, T. J., Jan 3 2020, In : Journal of Proteome Research. 19, 1, p. 161-173 13 p.

Research output: Contribution to journalArticle

The microenvironment matters: the secret life of intramuscular lipid droplets

Chow, L. S. & Mashek, D. G., Mar 1 2020, In : The Journal of Physiology. 598, 6, p. 1117-1118 2 p.

Research output: Contribution to journalArticle

The Underpinnings of PNPLA3-Mediated Fatty Liver Emerge

Shang, L. & Mashek, D. G., Jan 1 2020, In : Hepatology. 71, 1, p. 375-377 3 p.

Research output: Contribution to journalComment/debate

2 Scopus citations
2019

BRASSINOSTEROID-SIGNALING KINASE 3, a plasma membrane-associated scaffold protein involved in early brassinosteroid signaling

Ren, H., Willige, B. C., Jaillais, Y., Geng, S., Park, M., Gray, W. M. & Chory, J., Jan 1 2019, In : PLoS genetics. 15, 1, e1007904.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Corrigendum: Persistent upregulation of the β-Tubulin tubb6, linked to muscle regeneration, is a source of microtubule disorganization in dystrophic muscle (Human Molecular Genetics (2019) 28:7 (1117-1135) DOI: 10.1093/hmg/ddy418)

Randazzo, D., Khalique, U., Belanto, J. J., Kenea, A., Talsness, D. M., Olthoff, J. T., Tran, M. D., Zaal, K. J., Pak, K., Pinal-Fernandez, I., Mammen, A. L., Sackett, D., Ervasti, J. M. & Ralston, E., Jun 1 2019, In : Human molecular genetics. 28, 11, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Data Independent Acquisition in Practice: Foundations and Resources for Implementing DIA

Neely, B., Kirkpatrick, J., Midha, M., Stemmer, P., Martin, L. R., Wang, Y., Herring, L., Phinney, B., Shan, B., Chien, A. & Jagtap, P., Dec 1 2019, In : Journal of biomolecular techniques : JBT. 30, p. S46

Research output: Contribution to journalArticle

Distinct cancer-promoting stromal gene expression depending on lung function

Sandri, B. J., Masvidal, L., Murie, C., Bartish, M., Avdulov, S., Higgins, L. A., 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

2 Scopus citations

Distinct mechanical properties in homologous spectrin-like repeats of utrophin

Rajaganapathy, S., McCourt, J. L., Ghosal, S., Lindsay, A., McCourt, P. M., Lowe, D. A., Ervasti, J. M. & Salapaka, M. V., Dec 1 2019, In : Scientific reports. 9, 1, 5210.

Research output: Contribution to journalArticle

Open Access
Open Access

Dystrophinopathy-associated dysfunction of Krebs cycle metabolism

Lindsay, A., Chamberlain, C. M., Witthuhn, B. A., Lowe, D. A. & Ervasti, J. M., Jan 1 2019, In : Human molecular genetics. 28, 6, p. 942-951 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

GABARAPs and LC3s have opposite roles in regulating ULK1 for autophagy induction

Grunwald, D. S., Otto, N. M., Park, J. M., Song, D. & Kim, D. H., Jan 1 2019, (Accepted/In press) In : Autophagy. 16, 4, p. 600-614 15 p.

Research output: Contribution to journalArticle

4 Scopus citations

Isometric resistance training increases strength and alters histopathology of dystrophin-deficient mouse skeletal muscle

Lindsay, A., Larson, A. A., Verma, M., Ervasti, J. M. & Lowe, D. A., Feb 2019, In : Journal of applied physiology. 126, 2, p. 363-375 13 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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., Kumar, P., Hubler, S., Mesuere, B., Rudney, J., Griffin, T. J. & Jagtap, P. D., Jan 1 2019, In : Molecular and Cellular Proteomics. 18, 8, p. S82-S91

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Mitochondrial PE potentiates respiratory enzymes to amplify skeletal muscle aerobic capacity

Heden, T. D., Johnson, J. M., Ferrara, P. J., Eshima, H., Verkerke, A. R. P., Wentzler, E. J., Siripoksup, P., Narowski, T. M., Coleman, C. B., Lin, C. T., Ryan, T. E., Reidy, P. T., de Castro Brás, L. E., Karner, C. M., Burant, C. F., Alan Maschek, J., Cox, J. E., Mashek, D. G., Kardon, G., Boudina, S. & 7 others, Zeczycki, T. N., Rutter, J., Shaikh, S. R., Vance, J. E., Drummond, M. J., Darrell Neufer, P. & Funai, K., Sep 11 2019, In : Science advances. 5, 9, eaax8352.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control

Chang, J. W., Yeh, H. S., Park, M., Erber, L., Sun, J., Cheng, S., Bui, A. M., Fahmi, N. A., Nasti, R., Kuang, R., Chen, Y., Zhang, W. & Yong, J., Nov 4 2019, In : Nucleic acids research. 47, 19, p. 10373-10387 15 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Multiomic Profiling of Tyrosine Kinase Inhibitor-Resistant K562 Cells Suggests Metabolic Reprogramming to Promote Cell Survival

Noel, B. M., Ouellette, S. B., Marholz, L., Dickey, D., Navis, C., Yang, T. Y., Nguyen, V., Parker, S. J., Bernlohr, D., Sachs, Z. & Parker, L. L., Apr 5 2019, In : Journal of Proteome Research. 18, 4, p. 1842-1856 15 p.

Research output: Contribution to journalArticle

3 Scopus citations

Mutation of a Conserved Motif of PP2C.D Phosphatases Confers SAUR Immunity and Constitutive Activity

Wong, J. H., Spartz, A. K., Park, M., Du, M. & Gray, W. M., Sep 1 2019, In : Plant physiology. 181, 1, p. 353-366 14 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Persistent upregulation of the β-tubulin tubb6, linked to muscle regeneration, is a source of microtubule disorganization in dystrophic muscle

Randazzo, D., Khalique, U., Belanto, J. J., Kenea, A., Talsness, D. M., Olthoff, J. T., Tran, M. D., Zaal, K. J., Pak, K., Pinal-Fernandez, I., Mammen, A. L., Sackett, D., Ervasti, J. M. & Ralston, E., Jan 1 2019, In : Human molecular genetics. 28, 7, p. 1117-1135 19 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Prescription patterns of anti-diabetic medications and clinical outcomes in Asian patients with heart failure and diabetes mellitus

on behalf of the ASIAN-HF Investigators, May 2019, In : European Journal of Heart Failure. 21, 5, p. 685-688 4 p.

Research output: Contribution to journalLetter

2 Scopus citations

Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing

Saito, M. A., Bertrand, E. M., Duffy, M. E., Gaylord, D. A., Held, N. A., Hervey, W. J., Hettich, R. L., Jagtap, P. D., Janech, M. G., Kinkade, D. B., Leary, D. H., McIlvin, M. R., Moore, E. K., Morris, R. M., Neely, B. A., Nunn, B. L., Saunders, J. K., Shepherd, A. I., Symmonds, N. I. & Walsh, D. A., Apr 5 2019, In : Journal of Proteome Research. 18, 4, p. 1461-1476 16 p.

Research output: Contribution to journalReview article

3 Scopus citations

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

THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Enzymes

CGTP Collaborators, Dec 1 2019, In : British Journal of Pharmacology. 176, S1, p. S297-S396

Research output: Contribution to journalArticle

Open Access
41 Scopus citations

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., 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

3 Scopus citations

Transgenic substitution with Greater Amberjack Seriola dumerili fish insulin 2 in NOD mice reduces beta cell immunogenicity

Foo, K. S., Skowronski, A. A., Baum, D., Firdessa-Fite, R., Thams, S., Shang, L., Creusot, R. J., LeDuc, C. A., Egli, D. & Leibel, R. L., Dec 1 2019, In : Scientific reports. 9, 1, 4965.

Research output: Contribution to journalArticle

Open Access

Unconventional secretion of adipocyte fatty acid binding protein 4 is mediated by autophagic proteins in a sirtuin-1-dependent manner

Josephrajan, A., Hertzel, A. V., Bohm, E. K., McBurney, M. W., Imai, S. I., Mashek, D. G., Kim, D. H. & Bernlohr, D. A., Sep 1 2019, In : Diabetes. 68, 9, p. 1767-1777 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

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., Impens, F. & Martens, L., Feb 1 2019, In : Journal of Proteome Research. 18, 2, p. 728-731 4 p.

Research output: Contribution to journalArticle

3 Scopus citations

Variable cytoplasmic actin expression impacts the sensitivity of different dystrophin-deficient mdx skeletal muscles to eccentric contraction

Lindsay, A., Southern, W. M., McCourt, P. M., Larson, A. A., Hodges, J. S., Lowe, D. A. & Ervasti, J. M., Jul 2019, In : FEBS Journal. 286, 13, p. 2562-2576 15 p.

Research output: Contribution to journalArticle

2 Scopus citations
2018

An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response

Chang, J. W., Zhang, W., Yeh, H. S., Park, M., Yao, C., Shi, Y., Kuang, R. & Yong, J., Jul 6 2018, In : Nucleic acids research. 46, 12, p. 5996-6008 13 p.

Research output: Contribution to journalArticle

6 Scopus citations
Open Access
9 Scopus citations
Open Access
5 Scopus citations

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

1 Scopus citations

Community-Driven Data Analysis Training for Biology

Galaxy Training Network, Jun 27 2018, In : Cell Systems. 6, 6, p. 752-758.e1

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Comparative Metaproteomics to Study Environmental Changes

Matallana-Surget, S., Jagtap, P. D., Griffin, T. J., Beraud, M. & Wattiez, R., Jan 1 2018, Metagenomics: Perspectives, Methods, and Applications. Elsevier Inc., p. 327-363 37 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

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

Blank, C., Easterly, C., Gruening, B., Johnson, J., 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., Tanca, A., Griffin, T. J. & Jagtap, P. D., Mar 1 2018, In : Proteomes. 6, 1, 7.

Research output: Contribution to journalArticle

Open Access
13 Scopus citations

Dystrophin As a Molecular Shock Absorber

Le, S., Yu, M., Hovan, L., Zhao, Z., Ervasti, J. & Yan, J., Dec 26 2018, In : ACS nano. 12, 12, p. 12140-12148 9 p.

Research output: Contribution to journalArticle

6 Scopus citations

Essential nucleotide- and protein-dependent functions of Actb/β-actin

Patrinostro, X., Roy, P., Lindsay, A., Chamberlain, C. M., Sundby, L. J., Starker, C., Voytas, D. F., Ervasti, J. M. & Perrin, B. J., Jul 31 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 31, p. 7973-7978 6 p.

Research output: Contribution to journalArticle

Open Access
7 Scopus citations
Open Access
1 Scopus citations

Human hepatic stellate cell isolation and characterization

Shang, L., Hosseini, M., Liu, X., Kisseleva, T. & Brenner, D. A., Jan 1 2018, In : Journal of Gastroenterology. 53, 1, p. 6-17 12 p.

Research output: Contribution to journalReview article

Open Access
12 Scopus citations

Impaired muscle relaxation and mitochondrial fission associated with genetic ablation of cytoplasmic actin isoforms

O'Rourke, A. R., Lindsay, A., Tarpey, M. D., Yuen, S., McCourt, P., Nelson, D. M., Perrin, B. J., Thomas, D. D., Spangenburg, E. E., Lowe, D. A. & Ervasti, J. M., Feb 2018, In : FEBS Journal. 285, 3, p. 481-500 20 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations
Open Access

Integrative effects of dystrophin loss on metabolic function of the mdx mouse

Strakova, J., Kamdar, F., Kulhanek, D., Razzoli, M., Garry, D. J., Ervasti, J. M., Bartolomucci, A. & Townsend, D. W., Dec 1 2018, In : Scientific reports. 8, 1, 13624.

Research output: Contribution to journalArticle

Open Access

Loss of peroxiredoxin-2 exacerbates eccentric contraction-induced force loss in dystrophin-deficient muscle

Olthoff, J. T., Lindsay, A., Abo-Zahrah, R., Baltgalvis, K. A., Patrinostro, X., Belanto, J. J., Yu, D. Y., Perrin, B. J., Garry, D. J., Rodney, G. G., Lowe, D. A. & Ervasti, J. M., Dec 1 2018, In : Nature communications. 9, 1, 5104.

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

Mouse models of two missense mutations in actin-binding domain 1 of dystrophin associated with duchenne or becker muscular dystrophy

McCourt, J. L., Talsness, D. M., Lindsay, A., Arpke, R. W., Chatterton, P. D., Nelson, D. M., Chamberlain, C. M., Olthoff, J. T., Belanto, J. J., McCourt, P. M., Kyba, M., Lowe, D. A. & Ervasti, J. M., Feb 1 2018, In : Human molecular genetics. 27, 3, p. 451-462 12 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

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

4 Scopus citations

Neopterin/7,8-dihydroneopterin is elevated in Duchenne muscular dystrophy patients and protects mdx skeletal muscle function

Lindsay, A., Schmiechen, A., Chamberlain, C. M., Ervasti, J. M. & Lowe, D. A., Jul 1 2018, In : Experimental Physiology. 103, 7, p. 995-1009 15 p.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

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

2 Scopus citations