Research Output

2014

Biochemical reconstitution of the WAVE regulatory complex

Chen, B., Padrick, S. B., Henry, L. & Rosen, M. K., Jan 1 2014, Reconstituting the Cytoskeleton. Academic Press Inc., p. 55-72 18 p. (Methods in Enzymology; vol. 540).

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations

Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging

Sapir, A., Tsur, A., Koorman, T., Ching, K., Mishra, P., Bardenheier, A., Podolsky, L., Bening-Abu-Shach, U., Boxem, M., Chou, T. F., Broday, L. & Sternberg, P. W., Sep 16 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 37, p. E3880-E3889

Research output: Contribution to journalArticle

26 Scopus citations

Differential splicing and glycosylation of Apoer2 alters synaptic plasticity and fear learning

Wasser, C. R., Masiulis, I., Durakoglugil, M. S., Lane-Donovan, C., Xian, X., Beffert, U., Agarwala, A., Hammer, R. E. & Herz, J., Nov 25 2014, In : Science Signaling. 7, 353, ra113.

Research output: Contribution to journalArticle

21 Scopus citations

Dominance of misfolded intermediates in the dynamics of α-helix folding

Lin, M. M., Shorokhov, D. & Zewail, A. H., Oct 7 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 40, p. 14424-14429 6 p.

Research output: Contribution to journalArticle

13 Scopus citations

Ena/VASP proteins cooperate with the WAVE complex to regulate the actin cytoskeleton

Chen, X. J., Squarr, A. J., Stephan, R., Chen, B., Higgins, T. E., Barry, D. J., Martin, M. C., Rosen, M. K., Bogdan, S. & Way, M., Sep 8 2014, In : Developmental Cell. 30, 5, p. 569-584 16 p.

Research output: Contribution to journalArticle

45 Scopus citations

Erratum: Proteolytic cleavage of Opa1 stimulates mitochondrial inner membrane fusion and couples fusion to oxidative phosphorylation (Cell Metabolism (2014) 19 (630-641))

Mishra, P., Carelli, V., Manfredi, G. & Chan, D. C., May 6 2014, In : Cell Metabolism. 19, 5, 1 p.

Research output: Contribution to journalComment/debate

1 Scopus citations

Erratum: Retromer Binding to FAM21 and the WASH Complex Is Perturbed by the Parkinson Disease-Linked VPS35(D620N) Mutation (Current Biology (2014) 24 (1670-1676))

McGough, I. J., Steinberg, F., Jia, D., Barbuti, P. A., McMillan, K. J., Heesom, K. J., Whone, A. L., Caldwell, M. A., Billadeau, D. D., Rosen, M. K. & Cullen, P. J., Jul 21 2014, In : Current Biology. 24, 14, 1 p.

Research output: Contribution to journalComment/debate

7 Scopus citations

Finding a common path: Predicting gene function using inferred evolutionary trees

Reynolds, K. A., Jul 14 2014, In : Developmental Cell. 30, 1, p. 4-5 2 p.

Research output: Contribution to journalShort survey

Fluidic and microfluidic tools for quantitative systems biology

Okumus, B., Yildiz, S. & Toprak, E., Feb 1 2014, In : Current Opinion in Biotechnology. 25, p. 30-38 9 p.

Research output: Contribution to journalReview article

15 Scopus citations

Lin28b is sufficient to drive liver cancer and necessary for its maintenance in murine models

Nguyen, L. H., Robinton, D. A., Seligson, M. T., Wu, L., Li, L., Rakheja, D., Comerford, S. A., Ramezani, S., Sun, X., Parikh, M. S., Yang, E. H., Powers, J. T., Shinoda, G., Shah, S. P., Hammer, R. E., Daley, G. Q. & Zhu, H., Aug 11 2014, In : Cancer Cell. 26, 2, p. 248-261 14 p.

Research output: Contribution to journalArticle

99 Scopus citations

Local F-actin network links synapse formation and axon branching

Chia, P. H., Chen, B., Li, P., Rosen, M. K. & Shen, K., Jan 27 2014, In : Cell. 156, 1-2, p. 208-220 13 p.

Research output: Contribution to journalArticle

64 Scopus citations

Mitochondrial dynamics and inheritance during cell division, development and disease

Mishra, P. & Chan, D. C., Jan 1 2014, In : Nature Reviews Molecular Cell Biology. 15, 10, p. 634-646 13 p.

Research output: Contribution to journalReview article

383 Scopus citations

MORT: A powerful foundational library for computational biology and CADD

Zhang, Q., Zhang, W., Li, Y., Wang, J., Zhang, J. & Hou, T., Jun 27 2014, In : Journal of Cheminformatics. 6, 1, 36.

Research output: Contribution to journalArticle

3 Scopus citations

Phase transitions of multivalent proteins can promote clustering of membrane receptors

Banjade, S. & Rosen, M. K., 2014, In : eLife. 3

Research output: Contribution to journalArticle

144 Scopus citations

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

Sun, H., Li, Y., Tian, S., Wang, J. & Hou, T., Jul 2014, In : PLoS Computational Biology. 10, 7, e1003729.

Research output: Contribution to journalArticle

70 Scopus citations

Proteolytic cleavage of Opa1 stimulates mitochondrial inner membrane fusion and couples fusion to oxidative phosphorylation

Mishra, P., Carelli, V., Manfredi, G. & Chan, D. C., Apr 1 2014, In : Cell Metabolism. 19, 4, p. 630-641 12 p.

Research output: Contribution to journalArticle

174 Scopus citations

Retromer binding to FAM21 and the WASH complex is perturbed by the Parkinson disease-linked VPS35(D620N) mutation

McGough, I. J., Steinberg, F., Jia, D., Barbuti, P. A., McMillan, K. J., Heesom, K. J., Whone, A. L., Caldwell, M. A., Billadeau, D. D., Rosen, M. K. & Cullen, P. J., Jul 21 2014, In : Current Biology. 24, 14, p. 1670-1676 7 p.

Research output: Contribution to journalArticle

87 Scopus citations

Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution

Oz, T., Guvenek, A., Yildiz, S., Karaboga, E., Tamer, Y. T., Mumcuyan, N., Ozan, V. B., Senturk, G. H., Cokol, M., Yeh, P. & Toprak, E., Sep 2014, In : Molecular biology and evolution. 31, 9, p. 2387-2401 15 p.

Research output: Contribution to journalArticle

99 Scopus citations

Systems-level characterization of the kernel mechanism of the cyanobacterial circadian oscillator

Ma, L. & Ranganathan, R., Mar 1 2014, In : BioSystems. 117, 1, p. 30-39 10 p.

Research output: Contribution to journalArticle

The haemophilus ducreyi lspa1 protein inhibits phagocytosis by using a new mechanism involving Activation of C-terminal src kinase

Dodd, D. A., Worth, R. G., Rosen, M. K., Grinstein, S., van Oers, N. S. C. & Hansen, E. J., May 20 2014, In : mBio. 5, 3

Research output: Contribution to journalArticle

7 Scopus citations

The WAVE regulatory complex links diverse receptors to the actin cytoskeleton

Chen, B., Brinkmann, K., Chen, Z., Pak, C. W., Liao, Y., Shi, S., Henry, L., Grishin, N. V., Bogdan, S. & Rosen, M. K., Jan 27 2014, In : Cell. 156, 1-2, p. 195-207 13 p.

Research output: Contribution to journalArticle

129 Scopus citations

Vascular and parenchymal amyloid pathology in an Alzheimer disease knock-in mouse model: Interplay with cerebral blood flow

Li, H., Guo, Q., Inoue, T., Polito, V. A., Tabuchi, K., Hammer, R. E., Pautler, R. G., Taffet, G. E. & Zheng, H., Aug 9 2014, In : Molecular Neurodegeneration. 9, 1, 28.

Research output: Contribution to journalArticle

43 Scopus citations
2013

Accelerated conformational entropy calculations using graphic processing units

Zhang, Q., Wang, J., Guerrero, G. D., Cecilia, J. M., García, J. M., Li, Y., Pérez-Sánchez, H. & Hou, T., Aug 26 2013, In : Journal of Chemical Information and Modeling. 53, 8, p. 2057-2064 8 p.

Research output: Contribution to journalArticle

6 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

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

Assessing the performance of MM/PBSA and MM/GBSA methods. 3. the impact of force fields and ligand charge models

Xu, L., Sun, H., Li, Y., Wang, J. & Hou, T., Jul 18 2013, In : Journal of Physical Chemistry B. 117, 28, p. 8408-8421 14 p.

Research output: Contribution to journalArticle

270 Scopus citations

Building a morbidostat: An automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition

Toprak, E., Veres, A., Yildiz, S., Pedraza, J. M., Chait, R., Paulsson, J. & Kishony, R., Feb 2013, In : Nature Protocols. 8, 3, p. 555-567 13 p.

Research output: Contribution to journalArticle

59 Scopus citations
21 Scopus citations

Environmental Dependence of Genetic Constraint

de Vos, M. G. J., Poelwijk, F. J., Battich, N., Ndika, J. D. T. & Tans, S. J., Jun 1 2013, In : PLoS genetics. 9, 6, e1003580.

Research output: Contribution to journalArticle

32 Scopus citations

Evolution-based design of proteins

Reynolds, K. A., Russ, W. P., Socolich, M. & Ranganathan, R., 2013, Methods in Protein Design. Academic Press Inc., p. 213-235 23 p. (Methods in Enzymology; vol. 523).

Research output: Chapter in Book/Report/Conference proceedingChapter

23 Scopus citations

Feedforward Regulation Ensures Stability and Rapid Reversibility of a Cellular State

Doncic, A. & Skotheim, J. M., Jun 27 2013, In : Molecular cell. 50, 6, p. 856-868 13 p.

Research output: Contribution to journalArticle

39 Scopus citations

Mammalian phospholipase C

Kadamur, G. & Ross, E. M., Feb 10 2013, In : Annual review of physiology. 75, p. 127-154 28 p.

Research output: Contribution to journalReview article

188 Scopus citations

Measurement and analysis of in vitro actin polymerization

Doolittle, L. K., Rosen, M. K. & Padrick, S. B., 2013, Methods in Molecular Biology. Humana Press Inc., Vol. 1046. p. 273-293 21 p. (Methods in Molecular Biology; vol. 1046).

Research output: Chapter in Book/Report/Conference proceedingChapter

28 Scopus citations

Modeling compound-target interaction network of traditional chinese medicines for type II diabetes mellitus: Insight for polypharmacology and drug design

Tian, S., Li, Y., Li, D., Xu, X., Wang, J., Zhang, Q. & Hou, T., Jul 22 2013, In : Journal of Chemical Information and Modeling. 53, 7, p. 1787-1803 17 p.

Research output: Contribution to journalArticle

30 Scopus citations

Modeling heterogeneous responsiveness of intrinsic apoptosis pathway

Ooi, H. K. & Ma, L., Jul 23 2013, In : BMC Systems Biology. 7, 65.

Research output: Contribution to journalArticle

13 Scopus citations

Optimality in evolution: New insights from synthetic biology

de Vos, M. G. J., Poelwijk, F. J. & Tans, S. J., Aug 1 2013, In : Current Opinion in Biotechnology. 24, 4, p. 797-802 6 p.

Research output: Contribution to journalReview article

9 Scopus citations

Pathogenesis of autosomal dominant hereditary spastic paraplegia (SPG6) revealed by a rat model.

Watanabe, F., Arnold, W. D., Hammer, R. E., Ghodsizadeh, O., Moti, H., Schumer, M., Hashmi, A., Hernandez, A., Sneh, A., Sahenk, Z. & Kisanuki, Y. Y., Nov 2013, In : Journal of neuropathology and experimental neurology. 72, 11, p. 1016-1028 13 p.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations

Purification of Arp2/3 complex from saccharomyces cerevisiae

Doolittle, L. K., Rosen, M. K. & Padrick, S. B., 2013, Methods in Molecular Biology. Humana Press Inc., Vol. 1046. p. 251-271 21 p. (Methods in Molecular Biology; vol. 1046).

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations

Purification of native Arp2/3 complex from bovine thymus

Doolittle, L. K., Rosen, M. K. & Padrick, S. B., 2013, Methods in Molecular Biology. Humana Press Inc., Vol. 1046. p. 231-250 20 p. (Methods in Molecular Biology; vol. 1046).

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations

Regulation of WASH-dependent actin polymerization and protein trafficking by ubiquitination

Hao, Y. H., Doyle, J. M., Ramanathan, S., Gomez, T. S., Jia, D., Xu, M., Chen, Z. J., Billadeau, D. D., Rosen, M. K. & Potts, P. R., Feb 28 2013, In : Cell. 152, 5, p. 1051-1064 14 p.

Research output: Contribution to journalArticle

104 Scopus citations

The bacterial effector VopL organizes actin into filament-like structures

Zahm, J. A., Padrick, S. B., Chen, Z., Pak, C. W., Yunus, A. A., Henry, L., Tomchick, D. R., Chen, Z. & Rosen, M. K., Oct 10 2013, In : Cell. 155, 2, p. 423-434 12 p.

Research output: Contribution to journalArticle

26 Scopus citations

Three-color single molecule imaging shows WASP detachment from Arp2/3 complex triggers actin filament branch formation

Smith, B. A., Padrick, S. B., Doolittle, L. K., Daugherty-Clarke, K., Corrêa, I. R., Xu, M. Q., Goode, B. L., Rosen, M. K. & Gelles, J., Sep 3 2013, In : eLife. 2013, 2, e01008.

Research output: Contribution to journalArticle

57 Scopus citations
2012

Activation Biosensor for G Protein-Coupled Receptors: A FRET-Based m1 Muscarinic Activation Sensor That Regulates Gq

Chang, S. & Ross, E. M., Sep 20 2012, In : PloS one. 7, 9, e45651.

Research output: Contribution to journalArticle

11 Scopus citations

ADMET evaluation in drug discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A comprehensive database of pharmacokinetic and toxic properties for drugs

Cao, D., Wang, J., Zhou, R., Li, Y., Yu, H. & Hou, T., May 25 2012, In : Journal of Chemical Information and Modeling. 52, 5, p. 1132-1137 6 p.

Research output: Contribution to journalArticle

36 Scopus citations

ADMET evaluation in drug discovery. 12. Development of binary classification models for prediction of hERG potassium channel blockage

Wang, S., Li, Y., Wang, J., Chen, L., Zhang, L., Yu, H. & Hou, T., Apr 2 2012, In : Molecular Pharmaceutics. 9, 4, p. 996-1010 15 p.

Research output: Contribution to journalArticle

93 Scopus citations

Autoimmune epididymoorchitis is essential to the pathogenesis of male-specific spondylarthritis in HLA-B27-transgenic rats

Taurog, J. D., Rival, C., Van Duivenvoorde, L. M., Satumtira, N., Dorris, M. L., Sun, M., Shelton, J. M., Richardson, J. A., Hamra, F. K., Hammer, R. E. & Tung, K. S. K., Aug 1 2012, In : Arthritis and rheumatism. 64, 8, p. 2518-2528 11 p.

Research output: Contribution to journalArticle

24 Scopus citations
6 Scopus citations

Develop and test a solvent accessible surface area-based model in conformational entropy calculations

Wang, J. & Hou, T., May 25 2012, In : Journal of Chemical Information and Modeling. 52, 5, p. 1199-1212 14 p.

Research output: Contribution to journalArticle

39 Scopus citations

Development of polarizable models for molecular mechanical calculations. 3. polarizable water models conforming to thole polarization screening schemes

Wang, J., Cieplak, P., Cai, Q., Hsieh, M. J., Wang, J., Duan, Y. & Luo, R., Jul 19 2012, In : Journal of Physical Chemistry B. 116, 28, p. 7999-8008 10 p.

Research output: Contribution to journalArticle

34 Scopus citations

Development of polarizable models for molecular mechanical calculations. 4. van der waals parametrization

Wang, J., Cieplak, P., Li, J., Cai, Q., Hsieh, M. J., Luo, R. & Duan, Y., Jun 21 2012, In : Journal of Physical Chemistry B. 116, 24, p. 7088-7101 14 p.

Research output: Contribution to journalArticle

29 Scopus citations