Research output per year
Research output per year
- 1 - 50 out of 222 results
Search results
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2021
Landscape of drug-resistance mutations in kinase regulatory hotspots
Kim, P., Li, H., Wang, J. & Zhao, Z., May 1 2021, In: Briefings in Bioinformatics. 22, 3, bbaa108.Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
2019
A fully-automated, robust, and versatile algorithm for long-term budding yeast segmentation and tracking
Ezgi Wood, N. & Doncic, A., Mar 2019, In: PloS one. 14, 3, e0206395.Research output: Contribution to journal › Article › peer-review
Open Access17 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 journal › Article › peer-review
Open Access32 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 journal › Article › peer-review
Open Access20 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 journal › Article › peer-review
Open Access61 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.e5Research output: Contribution to journal › Article › peer-review
Open Access57 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 journal › Article › peer-review
Open Access31 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 journal › Article › peer-review
Open Access3 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 journal › Article › peer-review
Open Access11 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 journal › Article › peer-review
45 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 journal › Article › peer-review
Open Access75 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, Jan 2 2018, In: Structure. 26, 1, p. 7-19.e5Research output: Contribution to journal › Article › peer-review
Open Access45 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 journal › Article › peer-review
17 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.e4Research output: Contribution to journal › Article › peer-review
Open Access15 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.e11Research output: Contribution to journal › Article › peer-review
Open Access25 Scopus citations -
Putting Evolution to Work
Ranganathan, R., Nov 29 2018, In: Cell. 175, 6, p. 1449-1451 3 p.Research output: Contribution to journal › Short survey › peer-review
Open Access4 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 journal › Article › peer-review
Open Access18 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, 2017, In: JCO Clinical Cancer Informatics. 2017, 1, p. 1-15 15 p.Research output: Contribution to journal › Article › peer-review
Open Access14 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 journal › Article › peer-review
Open Access11 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 journal › Article › peer-review
Open Access19 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 journal › Article › peer-review
Open Access61 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 journal › Article › peer-review
19 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 journal › Article › peer-review
19 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 journal › Article › peer-review
1 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 journal › Article › peer-review
Open Access70 Scopus citations -
On the Race to Starvation: How Do Bacteria Survive High Doses of Antibiotics?
Tamer, Y. T. & Toprak, E., 2017, In: Molecular cell. 68, 6, p. 1019-1021 3 p.Research output: Contribution to journal › Short survey › peer-review
Open Access4 Scopus citations -
2016
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 journal › Article › peer-review
Open Access67 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 journal › Article › peer-review
5 Scopus citations -
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 journal › Article › peer-review
Open Access218 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 journal › Article › peer-review
Open Access31 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 journal › Article › peer-review
133 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 journal › Comment/debate › peer-review
Open Access2 Scopus citations -
Evolution-Based Functional Decomposition of Proteins
Rivoire, O., Reynolds, K. A. & Ranganathan, R., Jun 2016, In: PLoS Computational Biology. 12, 6, e1004817.Research output: Contribution to journal › Article › peer-review
Open Access90 Scopus citations -
High-resolution crystal structure of the human CB1 cannabinoid receptor
Shao, Z., Yin, J., Chapman, K., Grzemska, M., Clark, L., Wang, J. & Rosenbaum, D. M., Dec 22 2016, In: Nature. 540, 7634, p. 602-606 5 p.Research output: Contribution to journal › Article › peer-review
295 Scopus citations -
In Silico Chemogenomics Knowledgebase and Computational System Neuropharmacology Approach for Cannabinoid Drug Research
Xie, X. Q., Wang, L., Wang, J., Xie, Z., Yang, P. & Ouyang, Q., Jan 1 2016, Neuropathology of Drug Addictions and Substance Misuse Volume 3: General Processes and Mechanisms, Prescription Medications, Caffeine and Areca, Polydrug Misuse, Emerging Addictions and Non-Drug Addictions. Elsevier, Vol. 3. p. 183-195 13 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter
3 Scopus citations -
Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells
Okumus, B., Landgraf, D., Lai, G. C., Bakhsi, S., Arias-Castro, J. C., Yildiz, S., Huh, D., Fernandez-Lopez, R., Peterson, C. N., Toprak, E., El Karoui, M. & Paulsson, J., May 18 2016, In: Nature communications. 7, 11641.Research output: Contribution to journal › Article › peer-review
Open Access38 Scopus citations -
Origins of Allostery and Evolvability in Proteins: A Case Study
Raman, A. S., White, K. I. & Ranganathan, R., Jul 14 2016, In: Cell. 166, 2, p. 468-480 13 p.Research output: Contribution to journal › Article › peer-review
Open Access95 Scopus citations -
Sequence-Specific Targeting of Bacterial Resistance Genes Increases Antibiotic Efficacy
Ayhan, D. H., Tamer, Y. T., Akbar, M., Bailey, S. M., Wong, M., Daly, S. M., Greenberg, D. E. & Toprak, E., Sep 15 2016, In: PLoS biology. 14, 9, e1002552.Research output: Contribution to journal › Article › peer-review
Open Access59 Scopus citations -
Switch-like Transitions Insulate Network Motifs to Modularize Biological Networks
Atay, O., Doncic, A. & Skotheim, J. M., Aug 24 2016, In: Cell Systems. 3, 2, p. 121-132 12 p.Research output: Contribution to journal › Article › peer-review
Open Access18 Scopus citations -
The Context-Dependence of Mutations: A Linkage of Formalisms
Poelwijk, F. J., Krishna, V. & Ranganathan, R., Jun 2016, In: PLoS Computational Biology. 12, 6, e1004771.Research output: Contribution to journal › Article › peer-review
Open Access54 Scopus citations -
Timing Correlations in Proteins Predict Functional Modules and Dynamic Allostery
Lin, M. M., May 4 2016, In: Journal of the American Chemical Society. 138, 15, p. 5036-5043 8 p.Research output: Contribution to journal › Article › peer-review
12 Scopus citations -
2015
Advances in computationally modeling human oral bioavailability
Wang, J. & Hou, T., Jun 23 2015, In: Advanced Drug Delivery Reviews. 86, p. 11-16 6 p.Research output: Contribution to journal › Review article › peer-review
Open Access34 Scopus citations -
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 journal › Short survey › peer-review
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Compartmentalization of a bistable switch enables memory to cross a feedback-driven transition
Doncic, A., Atay, O., Valk, E., Grande, A., Bush, A., Vasen, G., Colman-Lerner, A., Loog, M. & Skotheim, J. M., Mar 15 2015, In: Cell. 160, 6, p. 1182-1195 14 p.Research output: Contribution to journal › Article › peer-review
Open Access33 Scopus citations -
Cooperativity leads to temporally-correlated fluctuations in the bacteriophage lambda genetic switch
Shenker, J. Q. & Lin, M. M., Apr 8 2015, In: Frontiers in Plant Science. 6, APR, 214.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes
Palmer, A. C., Toprak, E., Baym, M., Kim, S., Veres, A., Bershtein, S. & Kishony, R., Jun 10 2015, In: Nature communications. 6, 7385.Research output: Contribution to journal › Article › peer-review
99 Scopus citations -
Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase
Stiffler, M. A., Hekstra, D. R. & Ranganathan, R., Feb 26 2015, In: Cell. 160, 5, p. 882-892 11 p.Research output: Contribution to journal › Article › peer-review
171 Scopus citations -
Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance
Chevereau, G., Dravecká, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E. & Bollenbach, T., Nov 18 2015, In: PLoS biology. 13, 11, e1002299.Research output: Contribution to journal › Article › peer-review
Open Access70 Scopus citations -
The application of in silico drug-likeness predictions in pharmaceutical research
Tian, S., Wang, J., Li, Y., Li, D., Xu, L. & Hou, T., Jun 23 2015, In: Advanced Drug Delivery Reviews. 86, p. 2-10 9 p.Research output: Contribution to journal › Review article › peer-review
311 Scopus citations -
2014
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, p. 3287 1 p., 3287.Research output: Contribution to journal › Article › peer-review
Open Access66 Scopus citations