Research Output

2018

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

65 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

Suppression of RGSz1 function optimizes the actions of opioid analgesics by mechanisms that involve the Wnt/β-catenin pathway

Gaspari, S., Purushothaman, I., Cogliani, V., Sakloth, F., Neve, R. L., Howland, D., Ring, R. H., Ross, E. M., Shen, L. & Zachariou, V., Feb 27 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 9, p. E2085-E2094

Research output: Contribution to journalArticle

7 Scopus citations

Transmembrane Protease TMPRSS11B Promotes Lung Cancer Growth by Enhancing Lactate Export and Glycolytic Metabolism

Updegraff, B. L., Zhou, X., Guo, Y., Padanad, M. S., Chen, P. H., Yang, C., Sudderth, J., Rodriguez-Tirado, C., Girard, L., Minna, J. D., Mishra, P., DeBerardinis, R. J. & O'Donnell-Mendell, K. A., Jan 1 2018, (Accepted/In press) In : Cell Reports.

Research output: Contribution to journalArticle

5 Scopus citations

Who's In and Who's Out—Compositional Control of Biomolecular Condensates

Ditlev, J. A., Case, L. B. & Rosen, M. K., Jan 1 2018, (Accepted/In press) In : Journal of Molecular Biology.

Research output: Contribution to journalArticle

43 Scopus citations
2017

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Xiao, L., Diao, J., Greene, DA., Wang, J. & Luo, R., Jul 11 2017, In : Journal of Chemical Theory and Computation. 13, 7, p. 3398-3412 15 p.

Research output: Contribution to journalArticle

9 Scopus citations

A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration- resistant prostate cancer

Prostate Cancer DREAM Challenge Community, Jan 1 2017, In : JCO Clinical Cancer Informatics. 2017, 1, p. 1-15 15 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Allosteric Modulation of Grb2 Recruitment to the Intrinsically Disordered Scaffold Protein, LAT, by Remote Site Phosphorylation

Huang, W. Y. C., Ditlev, J. A., Chiang, H. K., Rosen, M. K. & Groves, J. T., Dec 13 2017, In : Journal of the American Chemical Society. 139, 49, p. 18009-18015 7 p.

Research output: Contribution to journalArticle

5 Scopus citations

An evolution-based strategy for engineering allosteric regulation

Pincus, D., Resnekov, O. & Reynolds, K. A., Apr 28 2017, In : Physical Biology. 14, 2, 025002.

Research output: Contribution to journalArticle

8 Scopus citations

Biomolecular condensates: organizers of cellular biochemistry

Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K., Feb 22 2017, (Accepted/In press) In : Nature Reviews Molecular Cell Biology.

Research output: Contribution to journalArticle

715 Scopus citations

Cell biology: ATP controls the crowd

Rice, A. M. & Rosen, M. K., May 19 2017, In : Science. 356, 6339, p. 701-702 2 p.

Research output: Contribution to journalShort survey

17 Scopus citations

Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily

Narayanan, C., Gagné, D., Reynolds, K. A. & Doucet, N., Dec 1 2017, In : Scientific reports. 7, 1, 3207.

Research output: Contribution to journalArticle

10 Scopus citations

Deconstruction of the ras switching cycle through saturation mutagenesis

Bandaru, P., Shah, N. H., Bhattacharyya, M., Barton, J. P., Kondo, Y., Cofsky, J. C., Gee, C. L., Chakraborty, A. K., Kortemme, T., Ranganathan, R. & Kuriyan, J., Jul 7 2017, In : eLife. 6, e27810.

Research output: Contribution to journalArticle

20 Scopus citations

Epithelial Patterning, Morphogenesis, and Evolution: Drosophila Eggshell as a Model

Osterfield, M., Berg, C. A. & Shvartsman, S. Y., May 22 2017, In : Developmental Cell. 41, 4, p. 337-348 12 p.

Research output: Contribution to journalReview article

Open Access
10 Scopus citations

Expression of SREBP-1c requires SREBP-2-mediated generation of a sterol ligand for LXR in livers of mice

Rong, S., Cortés, V. A., Rashid, S., Anderson, N. N., McDonald, J. G., Liang, G., Moon, Y. A., Hammer, R. E. & Horton, J. D., Feb 28 2017, In : eLife. 6, e25015.

Research output: Contribution to journalArticle

38 Scopus citations

Fighting against evolution of antibiotic resistance by utilizing evolvable antimicrobial drugs

Cansizoglu, M. F. & Toprak, E., May 11 2017, (Accepted/In press) In : Current Genetics. p. 1-4 4 p.

Research output: Contribution to journalArticle

13 Scopus citations

Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance

Abdizadeh, H., Tamer, Y. T., Acar, O., Toprak, E., Atilgan, A. R. & Atilgan, C., 2017, In : Physical Chemistry Chemical Physics. 19, 18, p. 11416-11428 13 p.

Research output: Contribution to journalArticle

8 Scopus citations

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

Harmon, T. S., Holehouse, A. S., Rosen, M. K. & Pappu, R. V., Nov 1 2017, In : eLife. 6, e30294.

Research output: Contribution to journalArticle

101 Scopus citations

Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs

Lin, Y., Currie, S. L. & Rosen, M. K., Nov 17 2017, In : Journal of Biological Chemistry. 292, 46, p. 19110-19120 11 p.

Research output: Contribution to journalArticle

74 Scopus citations

Leveraging symmetry to predict self-assembly of multiple polymers

Lin, M. M., Sep 1 2017, In : Chemical Physics Letters. 683, p. 347-351 5 p.

Research output: Contribution to journalArticle

1 Scopus citations

LRP1 integrates murine macrophage cholesterol homeostasis and inflammatory responses in atherosclerosis

Xian, X., Ding, Y., Dieckmann, M., Zhou, L., Plattner, F., Liu, M., Parks, J. S., Hammer, R. E., Boucher, P., Tsai, S. & Herz, J., Nov 16 2017, In : eLife. 6, e29292.

Research output: Contribution to journalArticle

17 Scopus citations

Measurement of cortical elasticity in Drosophila melanogaster embryos using ferrofluids

Doubrovinski, K., Swan, M., Polyakov, O. & Wieschaus, E. F., Jan 31 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 5, p. 1051-1056 6 p.

Research output: Contribution to journalArticle

27 Scopus citations

Modeling renal cell carcinoma in mice: Bap1 and Pbrm1 inactivation drive tumor grade

Gu, Y. F., Cohn, S., Christie, A., McKenzie, T., Wolff, N., Do, Q. N., Madhuranthakam, A. J., Pedrosa, I., Wang, T., Dey, A., Busslinger, M., Xie, X-J., Hammer, R. E., McKay, R. M., Kapur, P. & Brugarolas, J. B., 2017, In : Cancer Discovery. 7, 8, p. 900-917 18 p.

Research output: Contribution to journalArticle

39 Scopus citations

Mutation effects predicted from sequence co-variation

Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C. & Marks, D. S., Feb 1 2017, In : Nature Biotechnology. 35, 2, p. 128-135 8 p.

Research output: Contribution to journalArticle

118 Scopus citations

On the Race to Starvation: How Do Bacteria Survive High Doses of Antibiotics?

Tamer, Y. T. & Toprak, E., Jan 1 2017, In : Molecular Cell. 68, 6, p. 1134-1146.e6

Research output: Contribution to journalShort survey

2 Scopus citations

OPA1 Isoforms in the Hierarchical Organization of Mitochondrial Functions

Del Dotto, V., Mishra, P., Vidoni, S., Fogazza, M., Maresca, A., Caporali, L., McCaffery, J. M., Cappelletti, M., Baruffini, E., Lenaers, G., Chan, D., Rugolo, M., Carelli, V. & Zanna, C., Jun 20 2017, In : Cell Reports. 19, 12, p. 2557-2571 15 p.

Research output: Contribution to journalArticle

51 Scopus citations

Peroxisomal protein PEX13 functions in selective autophagy

Lee, M. Y., Sumpter, R., Zou, Z., Sirasanagandla, S., Wei, Y., Mishra, P., Rosewich, H., Crane, D. I. & Levine, B., Jan 1 2017, In : EMBO Reports. 18, 1, p. 48-60 13 p.

Research output: Contribution to journalArticle

19 Scopus citations

Prohibitin 2 Is an Inner Mitochondrial Membrane Mitophagy Receptor

Wei, Y., Chiang, W. C., Sumpter, R., Mishra, P. & Levine, B., Jan 12 2017, In : Cell. 168, 1-2, p. 224-238.e10

Research output: Contribution to journalArticle

195 Scopus citations

Rac1 GTPase activates the WAVE regulatory complex through two distinct binding sites

Chen, B., Chou, H. T., Brautigam, C. A., Xing, W., Yang, S., Henry, L., Doolittle, L. K., Walz, T. & Rosen, M. K., Sep 26 2017, In : eLife. 6, e29795.

Research output: Contribution to journalArticle

29 Scopus citations

Reconstitution of TCR signaling using supported lipid bilayers

Su, X., Ditlev, J. A., Rosen, M. K. & Vale, R. D., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 65-76 12 p. (Methods in Molecular Biology; vol. 1584).

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Scopus citations

The binding of activated Gq to phospholipase C- exhibits anomalous affinity

Navaratnarajah, P., Gershenson, A. & Ross, E. M., Oct 6 2017, In : Journal of Biological Chemistry. 292, 40, p. 16787-16801 15 p.

Research output: Contribution to journalArticle

3 Scopus citations

The glutamate/cystine xCT antiporter antagonizes glutamine metabolism and reduces nutrient flexibility

Shin, C. S., Mishra, P., Watrous, J. D., Carelli, V., D'Aurelio, M., Jain, M. & Chan, D. C., Jan 1 2017, In : Nature communications. 8, 15074.

Research output: Contribution to journalArticle

48 Scopus citations

The human leukocyte antigen (HLA)-B27 peptidome in vivo, in spondyloarthritis-susceptible HLA-B27 transgenic rats and the effect of Erap1 deletion

Barnea, E., Kadosh, D. M., Haimovich, Y., Satumtira, N., Dorris, M. L., Nguyen, M. T., Hammer, R. E., Tran, T. M., Colbert, R. A., Taurog, J. D. & Admon, A., Apr 2017, In : Molecular and Cellular Proteomics. 16, 4, p. 642-662 21 p.

Research output: Contribution to journalArticle

25 Scopus citations

The interplay of ethics, animal welfare, and IACUC oversight on the reproducibility of animal studies

Pritt, S. L. & Hammer, R. E., Apr 1 2017, In : Comparative Medicine. 67, 2, p. 101-105 5 p.

Research output: Contribution to journalReview article

6 Scopus citations

The where, what, and when of membrane protein degradation in neurons

Jin, E. J., Kiral, F. R. & Hiesinger, P. R., 2017, (Accepted/In press) In : Developmental Neurobiology.

Research output: Contribution to journalArticle

12 Scopus citations

Valosin-containing protein (VCP/p97) inhibitors relieve mitofusin-dependent mitochondrial defects due to VCP disease mutants

Zhang, T., Mishra, P., Hay, B. A., Chan, D. & Guo, M., Mar 21 2017, In : eLife. 6, e17834.

Research output: Contribution to journalArticle

22 Scopus citations

Wiring visual systems: common and divergent mechanisms and principles

Kolodkin, A. L. & Hiesinger, P. R., Feb 1 2017, In : Current Opinion in Neurobiology. 42, p. 128-135 8 p.

Research output: Contribution to journalReview article

11 Scopus citations
2016

Actin is an evolutionarily-conserved damage-associated molecular pattern that signals tissue injury in Drosophila melanogaster

Srinivasan, N., Gordon, O., Ahrens, S., Franz, A., Deddouche, S., Chakravarty, P., Phillips, D., Yunus, A. A., Rosen, M. K., Valente, R. S., Teixeira, L., Thompson, B., Dionne, M. S., Wood, W. & Reis e Sousa, C., Nov 22 2016, In : eLife. 5, NOVEMBER2016, e19662.

Research output: Contribution to journalArticle

23 Scopus citations

All You Need Is Mentorship

Weinberg, R. A., Schuldiner, M., Wu, H., Stevens, B., Nielsen, J., Hiesinger, P. R. & Hassan, B. A., Mar 10 2016, In : Cell. 164, 6, p. 1092-1093 2 p.

Research output: Contribution to journalArticle

Amino acids regulate mTORC1 by an obligate two-step mechanism

Dyachok, J., Earnest, S., Iturraran, E. N., Cobb, M. H. & Ross, E. M., Oct 21 2016, In : Journal of Biological Chemistry. 291, 43, p. 22414-22426 13 p.

Research output: Contribution to journalArticle

18 Scopus citations

An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor

Shah, N. H., Wang, Q., Yan, Q., Karandur, D., Kadlecek, T. A., Fallahee, I. R., Russ, W. P., Ranganathan, R., Weiss, A. & Kuriyan, J., Oct 4 2016, In : eLife. 5, OCTOBER2016, e20105.

Research output: Contribution to journalArticle

30 Scopus citations

A protocol for functional assessment of whole-protein saturation mutagenesis libraries utilizing high-throughput sequencing

Stiffler, M. A., Subramanian, S. K., Salinas, V. H. & Ranganathan, R., Jul 3 2016, In : Journal of Visualized Experiments. 2016, 113, e54119.

Research output: Contribution to journalArticle

3 Scopus citations

Compositional Control of Phase-Separated Cellular Bodies

Banani, S. F., Rice, A. M., Peeples, W. B., Lin, Y., Jain, S., Parker, R. & Rosen, M. K., Jul 28 2016, In : Cell. 166, 3, p. 651-663 13 p.

Research output: Contribution to journalArticle

225 Scopus citations

Correction to Fat2 acts through the WAVE regulatory complex to drive collective cell migration during tissue rotation, [Journal of Cell Biology, 212, 5, (2016), 591-603] DOI:10.1083/jcb.201508081

Squarr, A. J., Brinkmann, K., Chen, B., Steinbacher, T., Ebnet, K., Rosen, M. K. & Bogdan, S., Mar 28 2016, In : Journal of Cell Biology. 212, 7, 1 p.

Research output: Contribution to journalComment/debate

Crystal structure of the human sterol transporter ABCG5/ABCG8

Lee, J. Y., Kinch, L. N., Borek, D. M., Wang, J., Wang, J., Urbatsch, I. L., Xie, X. S., Grishin, N. V., Cohen, J. C., Otwinowski, Z., Hobbs, H. H. & Rosenbaum, D. M., May 4 2016, In : Nature. 533, 7604, p. 561-564 4 p.

Research output: Contribution to journalArticle

112 Scopus citations

Data publication with the structural biology data grid supports live analysis

Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. I. & 50 others, Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., Fromme, J. C., Garcia, K. C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. J. B., Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M. & Sliz, P., Mar 7 2016, In : Nature communications. 7, 10882.

Research output: Contribution to journalArticle

64 Scopus citations

Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore

Wray, R., Iscla, I., Gao, Y., Li, H., Wang, J. & Blount, P., Jun 9 2016, In : PLoS Biology. 14, 6, e1002473.

Research output: Contribution to journalArticle

9 Scopus citations

Electric-field-stimulated protein mechanics

Hekstra, D. R., White, K. I., Socolich, M. A., Henning, R. W., Šrajer, V. & Ranganathan, R., Dec 15 2016, In : Nature. 540, 7633, p. 400-405 6 p.

Research output: Contribution to journalArticle

58 Scopus citations

Erratum: Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells (Nature Communications (2016) 7 (11641) DOI: 10.1038/ncomms11641)

Okumus, B., Landgraf, D., Lai, G. C., Bakshi, S., Arias-Castro, J. C., Yildiz, S., Huh, D., Fernandez-Lopez, R., Peterson, C. N., Toprak, E., El Karoui, M. & Paulsson, J., Jun 24 2016, In : Nature Communications. 7, 12130.

Research output: Contribution to journalComment/debate

Erratum to: Methyl labeling and TROSY NMR spectroscopy of proteins expressed in the eukaryote Pichia pastoris

Clark, L., Zahm, J. A., Ali, R., Kukula, M., Bian, L., Patrie, S. M., Gardner, K. H., Rosen, M. K. & Rosenbaum, D. M., Feb 19 2016, (Accepted/In press) In : Journal of Biomolecular NMR. p. 1 1 p.

Research output: Contribution to journalArticle