Research Output

Filter
Article
2020

A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups

Mische, S. M., Fisher, N. C., Meyn, S. M., Church, K. S., Hegstad-Davies, R. L., Weis-Garcia, F., Adams, M., Ashton, J. M., Delventhal, K. M., Dragon, J. A., Holmes, L., Jagtap, P., Kubow, K. E., Mason, C. E., Palmblad, M., Searle, B. C., Turck, C. W. & Knudtson, K. L., Apr 1 2020, In : Journal of biomolecular techniques : JBT. 31, 1, p. 11-26 16 p.

Research output: Contribution to journalArticle

Open Access

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

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., Apr 2 2020, In : Autophagy. 16, 4, p. 600-614 15 p.

Research output: Contribution to journalArticle

1 Scopus citations

Hepatic PLIN5 signals via SIRT1 to promote autophagy and prevent inflammation during fasting

Zhang, E., Cui, W., Lopresti, M., Mashek, M. T., Najt, C. P., Hu, H. & Mashek, D. G., Jan 1 2020, In : Journal of lipid research. 61, 3, p. 338-350 13 p.

Research output: Contribution to journalArticle

Identification of Lineage-Specific Transcription Factors That Prevent Activation of Hepatic Stellate Cells and Promote Fibrosis Resolution

Liu, X., Xu, J., Rosenthal, S., Zhang, L. J., McCubbin, R., Meshgin, N., Shang, L., Koyama, Y., Ma, H. Y., Sharma, S., Heinz, S., Glass, C. K., Benner, C., Brenner, D. A. & Kisseleva, T., May 2020, In : Gastroenterology. 158, 6, p. 1728-1744.e14

Research output: Contribution to journalArticle

Open Access

Lipid droplet-associated kinase STK25 regulates peroxisomal activity and metabolic stress response in steatotic liver

Nerstedt, A., Kurhe, Y., Cansby, E., Caputo, M., Gao, L., Vorontsov, E., Ståhlman, M., Nuñez-Durán, E., Borén, J., Marschall, H. U., Mashek, D. G., Saunders, D. N., Sihlbom, C., Hoy, A. J. & Mahlapuu, M., Feb 1 2020, In : Journal of lipid research. 61, 2, p. 178-191 14 p.

Research output: Contribution to journalArticle

Lipophagy-derived fatty acids undergo extracellular efflux via lysosomal exocytosis

Cui, W., Sathyanarayan, A., Lopresti, M., Aghajan, M., Chen, C. & Mashek, D. G., Jan 1 2020, (Accepted/In press) In : Autophagy.

Research output: Contribution to journalArticle

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

Mcgowan, T., Johnson, J. E., Kumar, P., Sajulga, R., Mehta, S., Jagtap, P. D. & Griffin, T. J., Apr 6 2020, In : GigaScience. 9, 4, giaa025.

Research output: Contribution to journalArticle

Open Access

Stem Cell–Derived Cardiomyocytes and Beta-Adrenergic Receptor Blockade in Duchenne Muscular Dystrophy Cardiomyopathy

Kamdar, F., Das, S., Gong, W., Klaassen Kamdar, A., Meyers, T. A., Shah, P., Ervasti, J. M., Townsend, D. W., Kamp, T. J., Wu, J. C., Garry, M. G., Zhang, J. & Garry, D. J., Mar 17 2020, In : Journal of the American College of Cardiology. 75, 10, p. 1159-1174 16 p.

Research output: Contribution to journalArticle

1 Scopus citations

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

Open Access

Time-Restricted Eating Effects on Body Composition and Metabolic Measures in Humans who are Overweight: A Feasibility Study

Chow, L. S., Manoogian, E. N. C., Alvear, A., Fleischer, J. G., Thor, H., Dietsche, K., Wang, Q., Hodges, J. S., Esch, N., Malaeb, S., Harindhanavudhi, T., Nair, K. S., Panda, S. & Mashek, D. G., May 1 2020, In : Obesity. 28, 5, p. 860-869 10 p.

Research output: Contribution to journalArticle

1 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
9 Scopus citations

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

4 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
1 Scopus citations

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

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

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 2019, In : Plant physiology. 181, 1, p. 353-366 14 p.

Research output: Contribution to journalArticle

Open Access
3 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
4 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

1 Scopus citations

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
81 Scopus citations
4 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

2 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

4 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

Open Access
7 Scopus citations
Open Access
11 Scopus citations
6 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

Open Access
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
6 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
15 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
8 Scopus citations
Open Access
1 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
2 Scopus citations

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
8 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

Open Access
5 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

Open Access
2 Scopus citations

Regulation of the natriuretic peptide receptor 2 (Npr2) by phosphorylation of juxtamembrane serine and threonine residues is essential for bifurcation of sensory axons

Schmidt, H., Dickey, D. M., Dumoulin, A., Octave, M., Robinson, J. W., Kühn, R., Feil, R., Potter, L. R. & Rathjen, F. G., Nov 7 2018, In : Journal of Neuroscience. 38, 45, p. 9768-9780 13 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations