Research Output

A mesoscopic description of contractile cytoskeletal meshworks

Doubrovinski, K., Polyakov, O. & Kaschube, M., Oct 1 2010, In : European Physical Journal E. 33, 2, p. 105-110 6 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

A modified soft docking method for proteins and peptides

Wang, J. M., Chen, L. R., Jing, F. & Xu, X. J., Dec 1 1997, In : Chinese Chemical Letters. 8, 7, p. 615-618 4 p.

Research output: Contribution to journalArticle

1 Scopus citations

A molecular pathway for light-dependent photoreceptor apoptosis in Drosophila

Kiselev, A., Socolich, M., Vinós, J., Hardy, R. W., Zuker, C. S. & Ranganathan, R., Jan 1 2000, In : Neuron. 28, 1, p. 139-152 14 p.

Research output: Contribution to journalArticle

Open Access
197 Scopus citations

A mutant human proinsulin is secreted from islets of Langerhans in increased amounts via an unregulated pathway

Carroll, R. J., Hammer, R. E., Chan, S. J., Swift, H. H., Rubenstein, A. H. & Steiner, D. F., Jan 1 1988, In : Proceedings of the National Academy of Sciences of the United States of America. 85, 23, p. 8943-8947 5 p.

Research output: Contribution to journalArticle

Open Access
109 Scopus citations
76 Scopus citations

An acetate switch regulates stress erythropoiesis

Xu, M., Nagati, J. S., Xie, J., Li, J., Walters, H., Moon, Y. A., Gerard, R. D., Huang, C-L., Comerford, S. A., Hammer, R. E., Horton, J. D., Chen, R. & Garcia, J. A., Sep 1 2014, In : Nature medicine. 20, 9, p. 1018-1026 9 p.

Research output: Contribution to journalArticle

35 Scopus citations

An Algorithm to Automate Yeast Segmentation and Tracking

Doncic, A., Eser, U., Atay, O. & Skotheim, J. M., Mar 8 2013, In : PloS one. 8, 3, e57970.

Research output: Contribution to journalArticle

29 Scopus citations

Analysis of full and partial agonists binding to β2- adrenergic receptor suggests a role of transmembrane helix v in agonist-specific conformational changes

Katritch, V., Reynolds, K. A., Cherezov, V., Hanson, M. A., Roth, C. B., Yeager, M. & Abagyan, R., Jul 1 2009, In : Journal of Molecular Recognition. 22, 4, p. 307-318 12 p.

Research output: Contribution to journalArticle

94 Scopus citations

Analysis of genomic regions involved in regulation of the rabbit surfactant protein A gene in transgenic mice

Alcorn, J. L., Hammer, R. E., Graves, K. R., Smith, M. E., Maika, S. D., Michael, L. F., Gao, E., Wang, Y. & Mendelson, C. R., Aug 1 1999, In : American Journal of Physiology - Lung Cellular and Molecular Physiology. 277, 2 21-2, p. L349-L361

Research output: Contribution to journalArticle

26 Scopus citations

Analysis of SCAMP1 function in secretory vesicle exocytosis by means of gene targeting in mice

Fernández-Chacón, R., De Toledo, G. A., Hammer, R. E. & Südhof, T. C., Nov 12 1999, In : Journal of Biological Chemistry. 274, 46, p. 32551-32554 4 p.

Research output: Contribution to journalArticle

45 Scopus citations

An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis

Wang, W., Lim, W. A., Jakalian, A., Wang, J., Wang, J., Luo, R., Bayly, C. I. & Kollman, P. A., Oct 8 2001, In : Journal of the American Chemical Society. 123, 17, p. 3986-3994 9 p.

Research output: Contribution to journalArticle

121 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

An endocrine-specific element is an integral component of an exocrine-specific pancreatic enhancer

Kruse, F., Rose, S. D., Swift, G. H., Hammer, R. E. & MacDonald, R. J., Jan 1 1993, In : Genes and Development. 7, 5, p. 774-786 13 p.

Research output: Contribution to journalArticle

Open Access
35 Scopus citations

A neuroligin-3 mutation implicated in autism increases inhibitory synaptic transmission in mice

Tabuchi, K., Blundell, J., Etherton, M. R., Hammer, R. E., Liu, X., Powell, C. M. & Südhof, T. C., Oct 5 2007, In : Science. 318, 5847, p. 71-76 6 p.

Research output: Contribution to journalArticle

621 Scopus citations

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

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

A new MHC locus that influences class I peptide presentation

Simmons, W. A., Roopenian, D. C., Summerfield, S. G., Jones, R. C., Galocha, B., Christianson, G. J., Maika, S. D., Zhou, M., Gaskell, S. J., Bordoli, R. S., Ploegh, H. L., Slaughter, C. A., Lindahl, K. F., Hammer, R. E. & Taurog, J. D., Nov 1997, In : Immunity. 7, 5, p. 641-651 11 p.

Research output: Contribution to journalArticle

11 Scopus citations

A new MHC locus that influences class I peptide presentation.

Taurog, J. D., Lindahl, K. F., Hammer, R. E., Slaughter, C. A., Maika, S. D., Zhou, M., Roopenian, D. C., Christianson, G. J., Gaskell, S. J., Jones, R. C., Bordoli, R., Ploegh, H. L., Galocha, B. & Summerfield, S. G., Oct 1999, In : Immunity. 11, 4, 1 p.

Research output: Contribution to journalComment/debate

Open Access

A new test of computational protein design: Predicting posttranslational modification specificity for the enzyme SMYD2

Reynolds, K. A., Jan 6 2015, In : Structure. 23, 1, p. 11-12 2 p.

Research output: Contribution to journalShort survey

A new transgenic mouse model of chronic hyperglycemia

Schaefer, E. M., Viard, V., Morin, J., Ferré, P., Pénicaud, L., Ramos, P., Maika, S. D., Ellis, L. & Hammer, R. E., Jan 1 1994, In : Diabetes. 43, 1, p. 143-153 11 p.

Research output: Contribution to journalArticle

10 Scopus citations

An interdomain sector mediating allostery in Hsp70 molecular chaperones

Smock, R. G., Rivoire, O., Russ, W. P., Swain, J. F., Leibler, S., Ranganathan, R. & Gierasch, L. M., Oct 6 2010, In : Molecular Systems Biology. 6, 414.

Research output: Contribution to journalArticle

90 Scopus citations

An object-oriented library for computational protein design

Chowdry, A. B., Reynolds, K. A., Hanes, M. S., Voorhies, M., Pokala, N. & Handel, T. M., Nov 15 2007, In : Journal of Computational Chemistry. 28, 14, p. 2378-2388 11 p.

Research output: Contribution to journalArticle

30 Scopus citations

A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods

Novinec, M., Korenč, M., Caflisch, A., Ranganathan, R., Lenarčič, B. & Baici, A., 2014, In : Nature communications. 5, 1 p., 3287.

Research output: Contribution to journalArticle

43 Scopus citations

A novel electron transfer mechanism suggested by crystallographic studies of mitochondrial cytochrome bc1 complex

Xia, D., Kim, H., Yu, C. A., Yu, L., Kachurin, A., Zhang, L. & Deisenhofer, J., Dec 1 1998, In : Biochemistry and Cell Biology. 76, 5, p. 673-679 7 p.

Research output: Contribution to journalArticle

11 Scopus citations

A novel mechanism of actin filament processive capping by formin: Solution of the rotation paradox

Shemesh, T., Otomo, T., Rosen, M. K., Bershadsky, A. D. & Kozlov, M. M., Sep 12 2005, In : Journal of Cell Biology. 170, 6, p. 889-893 5 p.

Research output: Contribution to journalArticle

42 Scopus citations

APC2 cullin protein and APC11 RING protein comprise the minimal ubiquitin ligase module of the anaphase-promoting complex

Tang, Z., Li, B., Bharadwaj, R., Zhu, H., Özkan, E., Hakala, K., Deisenhofer, J. & Yu, H., 2001, In : Molecular biology of the cell. 12, 12, p. 3839-3851 13 p.

Research output: Contribution to journalArticle

136 Scopus citations

A phospho-switch controls the dynamic association of synapsins with synaptic vesicles

Hosaka, M., Hammer, R. E. & Südhof, T. C., Oct 1999, In : Neuron. 24, 2, p. 377-387 11 p.

Research output: Contribution to journalArticle

200 Scopus citations

Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation

He, B., Doubrovinski, K., Polyakov, O. & Wieschaus, E., Jan 1 2014, In : Nature. 508, 7496, p. 392-396 5 p.

Research output: Contribution to journalArticle

109 Scopus citations

A plausible model for the digital response of p53 to DNA damage

Ma, L., Wagner, J., Rice, J. J., Hu, W., Levine, A. J. & Stolovitzky, G. A., Oct 4 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 40, p. 14266-14271 6 p.

Research output: Contribution to journalArticle

240 Scopus citations

Apo(a) Expression in Transgenic Mice

Hobbs, H. H., Chiesa, G., Gaw, A., Lawn, R., Maika, S. D., Koschinsky, M. & Hammer, R. E., Apr 1994, In : Annals of the New York Academy of Sciences. 714, 1, p. 231-236 6 p.

Research output: Contribution to journalArticle

ApoE Receptor 2 Controls Neuronal Survival in the Adult Brain

Beffert, U., Nematollah Farsian, F., Masiulis, I., Hammer, R. E., Yoon, S. O., Giehl, K. M. & Herz, J., Dec 19 2006, In : Current Biology. 16, 24, p. 2446-2452 7 p.

Research output: Contribution to journalArticle

56 Scopus citations

A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations

Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J. & Kollman, P., Dec 1 2003, In : Journal of Computational Chemistry. 24, 16, p. 1999-2012 14 p.

Research output: Contribution to journalArticle

3193 Scopus citations

A potential SH3 domain-binding site in the Crk SH2 domain

Anafi, M., Rosen, M. K., Gish, G. D., Kay, L. E. & Pawson, T., Sep 16 1996, In : Journal of Biological Chemistry. 271, 35, p. 21365-21374 10 p.

Research output: Contribution to journalArticle

47 Scopus citations

APP interacts with LRP4 and agrin to coordinate the development of the neuromuscular junction in mice

Choi, H. Y., Liu, Y., Tennert, C., Sugiura, Y., Karakatsani, A., Kröger, S., Johnson, E. B., Hammer, R. E., Lin, W. & Herz, J., Aug 20 2013, In : eLife. 2013, 2, e00220.

Research output: Contribution to journalArticle

32 Scopus citations
9 Scopus citations
62 Scopus citations

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient

Wang, J. & Hou, T., Dec 1 2011, In : Journal of Computational Chemistry. 32, 16, p. 3505-3519 15 p.

Research output: Contribution to journalArticle

64 Scopus citations
34 Scopus citations

Applications of genetic algorithms on the structure - Activity relationship analysis of some cinnamamides

Hou, T. J., Wang, J. M., Liao, N. & Xu, X. J., Jan 1 1999, In : Journal of Chemical Information and Computer Sciences. 39, 5, p. 775-781 7 p.

Research output: Contribution to journalArticle

68 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 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

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

Aqueous solubility prediction based on weighted atom type counts and solvent accessible surface areas

Wang, J., Hou, T. & Xu, X., Mar 23 2009, In : Journal of Chemical Information and Modeling. 49, 3, p. 571-581 11 p.

Research output: Contribution to journalArticle

44 Scopus citations

A rapid whole-mount staining procedure for nuclei of mammalian embryos

Pursel, V. G., Wall, R. J., Rexroad, C. E., Hammer, R. E. & Brinster, R. L., Dec 1985, In : Theriogenology. 24, 6, p. 687-691 5 p.

Research output: Contribution to journalArticle

147 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

8 Scopus citations

A role for Mints in transmitter release: Mint 1 knockout mice exhibit impaired GABAergic synaptic transmission

Ho, A., Morishita, W., Hammer, R. E., Malenka, R. C. & Südhof, T. C., Feb 4 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 3, p. 1409-1414 6 p.

Research output: Contribution to journalArticle

73 Scopus citations

Arp2/3 complex is bound and activated by two WASP proteins

Padrick, S. B., Doolittle, L. K., Brautigam, C. A., King, D. S. & Rosen, M. K., Aug 16 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 33, p. E472-E479

Research output: Contribution to journalArticle

112 Scopus citations

Arp2/3-independent assembly of actin by Vibrio type III effector VopL

Liverman, A. D. B., Cheng, H. C., Trosky, J. E., Leung, D. W., Yarbrough, M. L., Burdette, D. L., Rosen, M. K. & Orth, K., Oct 23 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 43, p. 17117-17122 6 p.

Research output: Contribution to journalArticle

114 Scopus citations

Arrestin binding determines the rate of inactivation of the G protein-coupled receptor rhodopsin in vivo

Ranganathan, R. & Stevens, C. F., Jun 16 1995, In : Cell. 81, 6, p. 841-848 8 p.

Research output: Contribution to journalArticle

45 Scopus citations