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2020

Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme

Thompson, S., Zhang, Y., Ingle, C., Reynolds, K. A. & Kortemme, T., Jul 23 2020, In : eLife. 9

Research output: Contribution to journalArticle

Open Access

An evolution-based model for designing chorismate mutase enzymes

Russ, W. P., Figliuzzi, M., Stocker, C., Barrat-Charlaix, P., Socolich, M., Kast, P., Hilvert, D., Monasson, R., Cocco, S., Weigt, M. & Ranganathan, R., Jul 24 2020, In : Science. 369, 6502, p. 440-445 6 p.

Research output: Contribution to journalArticle

A quantitative inventory of yeast P body proteins reveals principles of composition and specificity

Xing, W., Muhlrad, D., Parker, R. & Rosen, M. K., Jun 2020, In : eLife. 9, p. 1-63 63 p., e56525.

Research output: Contribution to journalArticle

Open Access

DAPLE protein inhibits nucleotide exchange on Gαs and Gαq via the same motif that activates Gαi

Marivin, A., Maziarz, M., Zhao, J., DiGiacomo, V., Calvo, I. O., Mann, E. A., Ear, J., Blanco-Canosa, J. B., Ross, E. M., Ghosh, P. & Garcia-Marcos, M., Feb 21 2020, In : Journal of Biological Chemistry. 295, 8, p. 2270-2284 15 p.

Research output: Contribution to journalArticle

Directional allosteric regulation of protein filament length

Jermyn, A. S., Cao, W., Elam, W. A., De La Cruz, E. M. & Lin, M. M., Mar 2020, In : Physical Review E. 101, 3, 032409.

Research output: Contribution to journalArticle

Dynamin regulates the dynamics and mechanical strength of the actin cytoskeleton as a multifilament actin-bundling protein

Zhang, R., Lee, D. M., Jimah, J. R., Gerassimov, N., Yang, C., Kim, S., Luvsanjav, D., Winkelman, J., Mettlen, M., Abrams, M. E., Kalia, R., Keene, P., Pandey, P., Ravaux, B., Kim, J. H., Ditlev, J. A., Zhang, G., Rosen, M. K., Frost, A., Alto, N. M. & 5 others, Gardel, M., Schmid, S. L., Svitkina, T. M., Hinshaw, J. E. & Chen, E. H., Jun 1 2020, In : Nature cell biology. 22, 6, p. 674-688 15 p.

Research output: Contribution to journalArticle

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

1 Scopus citations

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

4D electron microscopy of T cell activation

Lu, Y., Yoo, B. K., Ng, A. H. C., Kim, J., Yeom, S., Tang, J., Lin, M. M., Zewail, A. H. & Heath, J. R., Oct 29 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 44, p. 22014-22019 6 p.

Research output: Contribution to journalArticle

Open Access

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 2019, In : eLife. 8, e42695.

Research output: Contribution to journalArticle

Open Access
9 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
1 Scopus citations

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., Nov 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
3 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
6 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., Mar 1 2019, In : Acta Pharmacologica Sinica. 40, 3, p. 374-386 13 p.

Research output: Contribution to journalArticle

10 Scopus citations

Functional divergence caused by mutations in an energetic hotspot in ERK2

Taylor, C. A., Cormier, K. W., Keenan, S. E., Earnest, S., Stippec, S., Wichaidit, C., Juang, Y. C., Wang, J., Shvartsman, S. Y., Goldsmith, E. J. & Cobb, M. H., Jul 30 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 31, p. 15514-15523 10 p.

Research output: Contribution to journalArticle

Open Access
6 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., 2019, In : Molecular biology and evolution. 36, 7, p. 1533-1550 18 p.

Research output: Contribution to journalArticle

Open Access
5 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
1 Scopus citations

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

Learning the pattern of epistasis linking genotype and phenotype in a protein

Poelwijk, F. J., Socolich, M. & Ranganathan, R., Dec 1 2019, In : Nature communications. 10, 1, 4213.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

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
4 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 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
9 Scopus citations

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. Y., 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
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

50 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
11 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

12 Scopus citations

Rapid ultrasensitive detection platform for antimicrobial susceptibility testing

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

Research output: Contribution to journalArticle

Open Access
5 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

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

Case, L. B., Zhang, X., Ditlev, J. A. & Rosen, M. K., 2019, In : Science. 363, 6431, p. 1093-1097 5 p.

Research output: Contribution to journalArticle

35 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
9 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
3 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. H., 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

5 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

22 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

19 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

9 Scopus citations

A set of experimentally validated, mutually orthogonal primers for combinatorially specifying genetic components

Subramanian, S. K., Russ, W. P. & Ranganathan, R., Jun 6 2018, In : Synthetic Biology. 3, 1, ysx008.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

A simplified mechanism for anisotropic constriction in drosophila mesoderm

Doubrovinski, K., Tchoufag, J. & Mandadapu, K., Dec 15 2018, In : Development (Cambridge). 145, 24, dev167387.

Research output: Contribution to journalArticle

1 Scopus citations

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

15 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

23 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

23 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

8 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

6 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., 2018, In : Journal of lipid research. 59, 3, p. 475-487 13 p.

Research output: Contribution to journalArticle

39 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

73 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

12 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

19 Scopus citations