Research Output

2020

Novel MscL agonists that allow multiple antibiotics cytoplasmic access activate the channel through a common binding site

Wray, R., Wang, J., Iscla, I. & Blount, P., Jan 1 2020, In : PloS one. 15, 1, e0228153.

Research output: Contribution to journalArticle

Open Access

Strategies for Engineering and Rewiring Kinase Regulation

McCormick, J. W., Pincus, D., Resnekov, O. & Reynolds, K. A., Mar 2020, In : Trends in biochemical sciences. 45, 3, p. 259-271 13 p.

Research output: Contribution to journalReview article

Target discovery of selective non-small-cell lung cancer toxins reveals inhibitors of mitochondrial complex i

Madhusudhan, N., Hu, B., Mishra, P., Calva-Moreno, J. F., Patel, K., Boriack, R., Ready, J. M. & Nijhawan, D., Jan 17 2020, In : ACS chemical biology. 15, 1, p. 158-170 13 p.

Research output: Contribution to journalArticle

TLR9 and beclin 1 crosstalk regulates muscle AMPK activation in exercise

Liu, Y., Nguyen, P. T., Wang, X., Zhao, Y., Meacham, C. E., Zou, Z., Bordieanu, B., Johanns, M., Vertommen, D., Wijshake, T., May, H., Xiao, G., Shoji-Kawata, S., Rider, M. H., Morrison, S. J., Mishra, P. & Levine, B., Feb 27 2020, In : Nature. 578, 7796, p. 605-609 5 p.

Research output: Contribution to journalArticle

2 Scopus citations

α-ketobutyrate links alterations in cystine metabolism to glucose oxidation in mtDNA mutant cells

Lesner, N. P., Gokhale, A. S., Kota, K., DeBerardinis, R. J. & Mishra, P., Jul 2020, In : Metabolic Engineering. 60, p. 157-167 11 p.

Research output: Contribution to journalArticle

Open Access
2019

A composition-dependent molecular clutch between T cell signaling condensates and actin

Ditlev, J. A., Vega, A. R., Köster, D. V., Su, X., Tani, T., Lakoduk, A. M., Vale, R. D., Mayor, S., Jaqaman, K. & Rosen, M. K., Jul 3 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

A fully-automated, robust, and versatile algorithm for long-term budding yeast segmentation and tracking

Ezgi Wood, N. & Doncic, A., Mar 1 2019, In : PloS one. 14, 3, e0206395.

Research output: Contribution to journalArticle

Open Access

A substitution mutation in a conserved domain of mammalian acetate-dependent acetyl CoA synthetase 2 results in destabilized protein and impaired HIF-2 signaling

Nagati, J. S., Xu, M., Garcia, T., Comerford, S. A., Hammer, R. E. & Garcia, J. A., Jan 1 2019, In : PloS one. 14, 11, e0225105.

Research output: Contribution to journalArticle

Open Access

A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism

Schober, A. F., Mathis, A. D., Ingle, C., Park, J. O., Chen, L., Rabinowitz, J. D., Junier, I., Rivoire, O. & Reynolds, K. A., Jun 11 2019, In : Cell Reports. 27, 11, p. 3359-3370.e7

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Blockade of MCU-Mediated Ca 2+ Uptake Perturbs Lipid Metabolism via PP4-Dependent AMPK Dephosphorylation

Tomar, D., Jaña, F., Dong, Z., Quinn, W. J., Jadiya, P., Breves, S. L., Daw, C. C., Srikantan, S., Shanmughapriya, S., Nemani, N., Carvalho, E., Tripathi, A., Worth, A. M., Zhang, X., Razmpour, R., Seelam, A., Rhode, S., Mehta, A. V., Murray, M., Slade, D. & 12 others, Ramirez, S. H., Mishra, P., Gerhard, G. S., Caplan, J., Norton, L., Sharma, K., Rajan, S., Balciunas, D., Wijesinghe, D. S., Ahima, R. S., Baur, J. A. & Madesh, M., Mar 26 2019, In : Cell Reports. 26, 13, p. 3709-3725.e7

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
1 Scopus citations

High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection

Tamer, Y. T., Gaszek, I. K., Abdizadeh, H., Batur, T. A., Reynolds, K. A., Atilgan, A. R., Atilgan, C. & Toprak, E., Jan 1 2019, In : Molecular biology and evolution. 36, 7, p. 1533-1550 18 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Improved strategy for isoleucine 1H/13C methyl labeling in Pichia pastoris

Ali, R., Clark, L. D., Zahm, J. A., Lemoff, A., Ramesh, K., Rosenbaum, D. M. & Rosen, M. K., Dec 1 2019, In : Journal of biomolecular NMR. 73, 12, p. 687-697 11 p.

Research output: Contribution to journalArticle

Open Access

Insight of Captagon Abuse by Chemogenomics Knowledgebase-guided Systems Pharmacology Target Mapping Analyses

Wu, N., Feng, Z., He, X., Kwon, W., Wang, J. & Xie, X. Q., Dec 1 2019, In : Scientific reports. 9, 1, 2268.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Metallothionein-human gh fusion genes stimulate growth of mice

Palmiter, R. D., Norstedt, G., Gelinas, R. E., Hammer, R. E. & Brinster, R. L., Jan 1 2019, Biotechnology and Biological Frontiers. Taylor and Francis, p. 468-479 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

MiR-26 suppresses adipocyte progenitor differentiation and fat production by targeting Fbxl19

Acharya, A., Berry, D. C., Zhang, H., Jiang, Y., Jones, B. T., Hammer, R. E., Graff, J. M. & Mendell, J. T., Oct 1 2019, In : Genes and Development. 33, 19-20, p. 1367-1380 14 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Modulation of mutant krasG12D-driven lung tumorigenesis in vivo by gain or loss of PCDH7 function

Zhou, X., Padanad, M. S., Evers, B. M., Smith, B., Novaresi, N., Suresh, S., Richardson, J. A., Stein, E., Zhu, J., Hammer, R. E. & O'Donnell, K. A., Feb 1 2019, In : Molecular Cancer Research. 17, 2, p. 594-603 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

MYC promotes tryptophan uptake and metabolism by the kynurenine pathway in colon cancer

Venkateswaran, N., Lafita-Navarro, M. C., Hao, Y. H., Kilgore, J. A., Perez-Castro, L., Braverman, J., Borenstein-Auerbach, N., Kim, M., Lesner, N. P., Mishra, P., Brabletz, T., Shay, J. W., DeBerardinis, R. J., Williams, N. S., Yilmaz, O. H. & Conacci-Sorrell, M., Sep 1 2019, In : Genes and Development. 33, 17-18, p. 1236-1251 16 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

New application of: In silico methods in identifying mechanisms of action and key components of anti-cancer herbal formulation YIV-906 (PHY906)

Liu, S., He, X., Man, V. H., Ji, B., Liu, J. & Wang, J., Jan 1 2019, In : Physical Chemistry Chemical Physics. 21, 42, p. 23501-23513 13 p.

Research output: Contribution to journalArticle

Non-antibiotic Small-Molecule Regulation of DHFR-Based Destabilizing Domains In Vivo

Peng, H., Chau, V. Q., Phetsang, W., Sebastian, R. M., Stone, M. R. L., Datta, S., Renwick, M., Tamer, Y. T., Toprak, E., Koh, A., Blaskovich, M. A. T. & Hulleman, J. D., Dec 13 2019, In : Molecular Therapy - Methods and Clinical Development. 15, p. 27-39 13 p.

Research output: Contribution to journalArticle

Open Access

Novel compounds that specifically bind and modulate MscL: insights into channel gating mechanisms

Wray, R., Iscla, I., Kovacs, Z., Wang, J. & Blount, P., Mar 1 2019, In : FASEB Journal. 33, 3, p. 3180-3189 10 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Organization of Chromatin by Intrinsic and Regulated Phase Separation

Gibson, B. A., Doolittle, L. K., Schneider, M. W. G., Jensen, L. E., Gamarra, N., Henry, L., Gerlich, D. W., Redding, S. & Rosen, M. K., Oct 3 2019, In : Cell. 179, 2, p. 470-484.e21

Research output: Contribution to journalArticle

30 Scopus citations

Phosphorylation of nephrin induces phase separated domains that move through actomyosin contraction

Kim, S., Kalappurakkal, J. M., Mayor, S. & Rosen, M. K., Nov 15 2019, In : Molecular biology of the cell. 30, 24, p. 2996-3012 17 p.

Research output: Contribution to journalArticle

Open Access

PUMILIO hyperactivity drives premature aging of norad-deficient mice

Kopp, F., Elguindy, M. M., Yalvac, M. E., Zhang, H., Chen, B., Gillett, F. A., Lee, S., Sivakumar, S., Yu, H., Xie, Y., Mishra, P., Sahenk, Z. & Mendell, J. T., Feb 2019, In : eLife. 8, e42650.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations

Pyruvate-Carboxylase-Mediated Anaplerosis Promotes Antioxidant Capacity by Sustaining TCA Cycle and Redox Metabolism in Liver

Cappel, D. A., Deja, S., Duarte, J. A. G., Kucejova, B., Iñigo, M., Fletcher, J. A., Fu, X., Berglund, E. D., Liu, T., Elmquist, J. K., Hammer, S., Mishra, P., Browning, J. D. & Burgess, S. C., Jun 4 2019, In : Cell Metabolism. 29, 6, p. 1291-1305.e8

Research output: Contribution to journalArticle

7 Scopus citations

Rapid ultrasensitive detection platform for antimicrobial susceptibility testing

Cansizoglu, M. F., Tamer, Y. T., Farid, M., Koh, A. & Toprak, E., May 1 2019, In : PLoS biology. 17, 5, p. e3000291

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Regulating G protein-coupled receptors by topological inversion

Denard, B., Han, S., Kim, J. Y., Ross, E. M. & Ye, J., Mar 2019, In : eLife. 8, e40234.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Regulation of Transmembrane Signaling by Phase Separation

Case, L. B., Ditlev, J. A. & Rosen, M. K., May 6 2019, In : Annual Review of Biophysics. 48, p. 465-494 30 p.

Research output: Contribution to journalReview article

12 Scopus citations

Stoichiometry controls activity of phase-separated clusters of actin signaling proteins

Case, L. B., Zhang, X., Ditlev, J. A. & Rosen, M. K., Mar 8 2019, In : Science (New York, N.Y.). 363, 6431, p. 1093-1097 5 p.

Research output: Contribution to journalArticle

25 Scopus citations

Tau local structure shields an amyloid-forming motif and controls aggregation propensity

Chen, D., Drombosky, K. W., Hou, Z., Sari, L., Kashmer, O. M., Ryder, B. D., Perez, V. A., Woodard, D. N. R., Lin, M. M., Diamond, M. I. & Joachimiak, L. A., Dec 1 2019, In : Nature communications. 10, 1, 2493.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

The Circadian Protein Nocturnin Regulates Metabolic Adaptation in Brown Adipose Tissue

Onder, Y., Laothamatas, I., Berto, S., Sewart, K., Kilaru, G., Bordieanu, B., Stubblefield, J. J., Konopka, G., Mishra, P. & Green, C. B., Sep 27 2019, In : iScience. 19, p. 83-92 10 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The ubiquitin ligase UBE3B, disrupted in intellectual disability and absent speech, regulates metabolic pathways by targeting BCKDK

Cheon, S., Kaur, K., Nijem, N., Tuncay, I. O., Kumar, P., Dean, M., Juusola, J., Guillen-Sacoto, M. J., Bedoukian, E., Ierardi-Curto, L., Kaplan, P., Bradley Schaefer, G., Mishra, P. & Chahrour, M., Feb 26 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 9, p. 3662-3667 6 p.

Research output: Contribution to journalArticle

3 Scopus citations
2018

An evolutionary hotspot defines functional differences between CRYPTOCHROMES

Rosensweig, C., Reynolds, K. A., Gao, P., Laothamatas, I., Shan, Y., Ranganathan, R., Takahashi, J. S. & Green, C. B., Dec 1 2018, In : Nature Communications. 9, 1, 1138.

Research output: Contribution to journalArticle

17 Scopus citations

A Precise Cdk Activity Threshold Determines Passage through the Restriction Point

Schwarz, C., Johnson, A., Kõivomägi, M., Zatulovskiy, E., Kravitz, C. J., Doncic, A. & Skotheim, J. M., Jan 18 2018, In : Molecular Cell. 69, 2, p. 253-264.e5

Research output: Contribution to journalArticle

15 Scopus citations

A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast

Moretto, F., Wood, N. E., Kelly, G., Doncic, A. & Van Werven, F. J., Dec 1 2018, In : Nature Communications. 9, 1, 780.

Research output: Contribution to journalArticle

6 Scopus citations

A simplified mechanism for anisotropic constriction in Drosophila mesoderm

Doubrovinski, K., Tchoufag, J. & Mandadapu, K., Dec 10 2018, In : Development (Cambridge, England). 145, 24

Research output: Contribution to journalArticle

1 Scopus citations

Breaking down cellulose fibrils with a mid-infrared laser

Domin, D., Man, V. H., Van-Oanh, N. T., Wang, J., Kawasaki, T., Derreumaux, P. & Nguyen, P. H., Oct 1 2018, In : Cellulose. 25, 10, p. 5553-5568 16 p.

Research output: Contribution to journalArticle

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

Shang, J., Hu, B., Wang, J., Zhu, F., Kang, Y., Li, D., Sun, H., Kong, D. X. & Hou, T., Jun 25 2018, In : Journal of Chemical Information and Modeling. 58, 6, p. 1182-1193 12 p.

Research output: Contribution to journalArticle

13 Scopus citations

Coevolution-based inference of amino acid interactions underlying protein function

Salinas, V. H. & Ranganathan, R., Jul 19 2018, In : eLife. 7, e34300.

Research output: Contribution to journalArticle

20 Scopus citations

Computational systems pharmacology analysis of cannabidiol: a combination of chemogenomics-knowledgebase network analysis and integrated in silico modeling and simulation

Bian, Y. M., He, X. B., Jing, Y. K., Wang, L. R., Wang, J. M. & Xie, X. Q., Jan 1 2018, (Accepted/In press) In : Acta Pharmacologica Sinica.

Research output: Contribution to journalArticle

7 Scopus citations

Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA

Suno, R., Kimura, K. T., Nakane, T., Yamashita, K., Wang, J., Fujiwara, T., Yamanaka, Y., Im, D., Horita, S., Tsujimoto, H., Tawaramoto, M. S., Hirokawa, T., Nango, E., Tono, K., Kameshima, T., Hatsui, T., Joti, Y., Yabashi, M., Shimamoto, K., Yamamoto, M. & 4 others, Rosenbaum, D. M., Iwata, S., Shimamura, T. & Kobayashi, T., Jan 2 2018, In : Structure. 26, 1, p. 7-19.e5

Research output: Contribution to journalArticle

21 Scopus citations

Engineering allosteric regulation in protein kinases

Pincus, D., Pandey, J. P., Feder, Z. A., Creixell, P., Resnekov, O. & Reynolds, K. A., Nov 6 2018, In : Science Signaling. 11, 555, eaar3250.

Research output: Contribution to journalArticle

6 Scopus citations

Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity

Creixell, P., Pandey, J. P., Palmeri, A., Bhattacharyya, M., Creixell, M., Ranganathan, R., Pincus, D. & Yaffe, M. B., Oct 24 2018, In : Cell Systems. 7, 4, p. 371-383.e4

Research output: Contribution to journalArticle

7 Scopus citations

Integration of Multiple Metabolic Signals Determines Cell Fate Prior to Commitment

Argüello-Miranda, O., Liu, Y., Wood, N. E., Kositangool, P. & Doncic, A., Sep 6 2018, In : Molecular Cell. 71, 5, p. 733-744.e11

Research output: Contribution to journalArticle

5 Scopus citations

Interplay between ChREBP and SREBP-1c coordinates postprandial glycolysis and lipogenesis in livers of mice

Linden, A. G., Li, S., Choi, H. Y., Fang, F., Fukasawa, M., Uyeda, K., Hammer, R. E., Horton, J. D., Engelking, L. & Liang, G., Jan 1 2018, In : Journal of Lipid Research. 59, 3, p. 475-487 13 p.

Research output: Contribution to journalArticle

30 Scopus citations

Intrinsically Disordered Regions Can Contribute Promiscuous Interactions to RNP Granule Assembly

Protter, D. S. W., Rao, B. S., Van Treeck, B., Lin, Y., Mizoue, L., Rosen, M. K. & Parker, R., Feb 6 2018, In : Cell Reports. 22, 6, p. 1401-1412 12 p.

Research output: Contribution to journalArticle

63 Scopus citations

Loss of Dis3l2 partially phenocopies perlman syndrome in mice and results in upregulation of Igf2 in nephron progenitor cells

Hunter, R. W., Liu, Y., Manjunath, H., Acharya, A., Jones, B. T., Zhang, H., Chen, B., Ramalingam, H., Hammer, R. E., Xie, Y., Richardson, J. A., Rakheja, D., Carroll, T. J. & Mendell, J. T., Jul 1 2018, In : Genes and Development. 32, 13-14, p. 903-908 6 p.

Research output: Contribution to journalArticle

10 Scopus citations

MIRO-1 Determines Mitochondrial Shape Transition upon GPCR Activation and Ca2+ Stress

Nemani, N., Carvalho, E., Tomar, D., Dong, Z., Ketschek, A., Breves, S. L., Jaña, F., Worth, A. M., Heffler, J., Palaniappan, P., Tripathi, A., Subbiah, R., Riitano, M. F., Seelam, A., Manfred, T., Itoh, K., Meng, S., Sesaki, H., Craigen, W. J., Rajan, S. & 9 others, Shanmughapriya, S., Caplan, J., Prosser, B. L., Gill, D. L., Stathopulos, P. B., Gallo, G., Chan, D. C., Mishra, P. & Madesh, M., Apr 24 2018, In : Cell Reports. 23, 4, p. 1005-1019 15 p.

Research output: Contribution to journalArticle

15 Scopus citations

Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites

Yoshizawa, T., Ali, R., Jiou, J., Fung, H. Y. J., Burke, K. A., Kim, S. J., Lin, Y., Peeples, W. B., Saltzberg, D., Soniat, M., Baumhardt, J. M., Oldenbourg, R., Sali, A., Fawzi, N. L., Rosen, M. K. & Chook, Y. M., Jan 1 2018, (Accepted/In press) In : Cell.

Research output: Contribution to journalArticle

55 Scopus citations

Putting Evolution to Work

Ranganathan, R., Nov 29 2018, In : Cell. 175, 6, p. 1449-1451 3 p.

Research output: Contribution to journalShort survey

1 Scopus citations