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Kinetics

  • 1.
    Zhang Y, Rózsa M, Liang Y, Bushey D, Wei Z, Zheng J, Reep D, Broussard G, Tsang A, Tsegaye G, Narayan S, Obara C, Lim J-X, Patel R, Zhang R, Ahrens M, Turner G, Wang S, Korff W, Schreiter E, Svoboda K, Hasseman J, Kolb I, Looger L. Fast and sensitive GCaMP calcium indicators for imaging neural populations. Nature. 2023;615(7954):884–891. PMCID: PMC10060165
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    Hu M, Dinh H, Shen Y, Suthers P, Foster C, Call C, Ye X, Pratas J, Fatma Z, Zhao H, Rabinowitz J, Maranas C. Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. Metab Eng. 2023;76:1–17. PMID: 36603705
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    Shimobayashi S, Ronceray P, Sanders D, Haataja M, Brangwynne C. Nucleation landscape of biomolecular condensates. Nature. 2021;599(7885):503–506. PMID: 34552246
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  • 1.
    Balo A, Caruso A, Tao L, Tantillo D, Seyedsayamdost M, Britt D. Trapping a cross-linked lysine-tryptophan radical in the catalytic cycle of the radical SAM enzyme SuiB. Proc Natl Acad Sci U S A. 2021;118(21). PMCID: PMC8166192
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    Lovelett R, Zhao E, Lalwani M, Toettcher J, Kevrekidis I, Avalos J. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol. 2021;10(2):219–227. PMID: 33492138
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    Ringel A, Drijvers J, Baker G, Catozzi A, García-Cañaveras J, Gassaway B, Miller B, Juneja V, Nguyen T, Joshi S, Yao C-H, Yoon H, Sage P, LaFleur M, Trombley J, Jacobson C, Maliga Z, Gygi S, Sorger P, Rabinowitz J, Sharpe A, Haigis M. Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity. Cell. 2020;183(7):1848–1866.e26. PMCID: PMC8064125
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    Ravindran P, Wilson M, Jena S, Toettcher J. Engineering combinatorial and dynamic decoders using synthetic immediate-early genes. Commun Biol. 2020;3(1):436. PMCID: PMC7426417
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  • 1.
    Ge E, Jani K, Diehl K, Müller M, Muir T. Nucleation and Propagation of Heterochromatin by the Histone Methyltransferase PRC2: Geometric Constraints and Impact of the Regulatory Subunit JARID2. J Am Chem Soc. 2019;141(38):15029–15039. PMCID: PMC6941475
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  • 1.
    Wojcik F, Dann G, Beh L, Debelouchina G, Hofmann R, Muir T. Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. Nat Commun. 2018;9(1):1394. PMCID: PMC5895630
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  • 1.
    Miller R, Shi Y, Lu W, Pirman D, Jatkar A, Blatnik M, Wu H, Cárdenas C, Wan M, Foskett K, Park J, Zhang Y, Holland W, Rabinowitz J, Birnbaum M. Targeting hepatic glutaminase activity to ameliorate hyperglycemia. Nat Med. 2018;24(4):518–524. PMCID: PMC6089616
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  • 1.
    Lee J, Sutterlin H, Wzorek J, Mandler M, Hagan C, Grabowicz M, Tomasek D, May M, Hart E, Silhavy T, Kahne D. Substrate binding to BamD triggers a conformational change in BamA to control membrane insertion. Proc Natl Acad Sci U S A. 2018;115(10):2359–2364. PMCID: PMC5877925
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  • 1.
    Donnelly A, Murphy G, Digianantonio K, Hecht M. A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nat Chem Biol. 2018;14(3):253–255. PMID: 29334382
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  • 1.
    Deng D, Sun P, Yan C, Ke M, Jiang X, Xiong L, Ren W, Hirata K, Yamamoto M, Fan S, Yan N. Molecular basis of ligand recognition and transport by glucose transporters. Nature. 2015;526(7573):391–6. PMID: 26176916
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  • 1.
    Oppenheimer N, Stone H. Effect of Hydrodynamic Interactions on Reaction Rates in Membranes. Biophys J. 2017;113(2):440–447. PMCID: PMC5529315
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  • 1.
    Zong C, Wu M, Qin J, Link J. Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch. J Am Chem Soc. 2017;139(30):10403–10409. PMCID: PMC5576865
    Reference Link
  • 1.
    Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, Damle M, Fang B, Wang C, Qian J, Lie N, Lanzillotta C, Rabinowitz J, Sun Z. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol. 2018;471:22–32. PMCID: PMC5702591
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  • 1.
    Habrian C, Chandrasekhara A, Shahrvini B, Hua B, Lee J, Jesinghaus R, Barry R, Gitai Z, Kollman J, Baldwin E. Inhibition of Escherichia coli CTP Synthetase by NADH and Other Nicotinamides and Their Mutual Interactions with CTP and GTP. Biochemistry. 2016;55(39):5554–5565. PMCID: PMC5584805
    Reference Link
  • 1.
    Allen C, Chen M, Trick A, Le D, Ferguson A, Link J. Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3. ACS Chem Biol. 2016;11(11):3043–3051. PMCID: PMC5148663
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  • 1.
    Rahimi M, Regan D, Arroyo M, Subramaniam A, Stone H, Staykova M. Shape Transformations of Lipid Bilayers Following Rapid Cholesterol Uptake. Biophys J. 2016;111(12):2651–2657. PMCID: PMC5192696
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  • 1.
    Hackett S, Zanotelli V, Xu W, Goya J, Park J, Perlman D, Gibney P, Botstein D, Storey J, Rabinowitz J. Systems-level analysis of mechanisms regulating yeast metabolic flux. Science. 2016;354(6311). PMCID: PMC5414049
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  • 1.
    Shin Y, Berry J, Pannucci N, Haataja M, Toettcher J, Brangwynne C. Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. Cell. 2017;168(1-2):159–171.e14. PMCID: PMC5562165
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  • 1.
    Paluch E, Nelson C, Biais N, Fabry B, Moeller J, Pruitt B, Wollnik C, Kudryasheva G, Rehfeldt F, Federle W. Mechanotransduction: use the force(s). BMC Biol. 2015;13:47. PMCID: PMC4491211
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  • 1.
    Adolfsen K, Brynildsen M. A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli. PLoS Comput Biol. 2015;11(11):e1004562. PMCID: PMC4636272
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    Berezhkovskii A, Shvartsman S. Dynamics of gradient formation by intracellular shuttling. J Chem Phys. 2015;143(7):074116. PMCID: PMC5562396
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  • 1.
    Mattingly H, Chen J, Arur S, Shvartsman S. A Transport Model for Estimating the Time Course of ERK Activation in the C. elegans Germline. Biophys J. 2015;109(11):2436–45. PMCID: PMC4675862
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  • 1.
    Noorbakhsh J, Schwab D, Sgro A, Gregor T, Mehta P. Modeling oscillations and spiral waves in Dictyostelium populations. Phys Rev E Stat Nonlin Soft Matter Phys. 2015;91(6):062711. PMCID: PMC5142844
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  • 1.
    Carey J, Lindman S, Bauer M, Linse S. Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci. 2007;16(11):2317–33. PMCID: PMC2211703
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  • 1.
    Lim B, Dsilva C, Levario T, Lu H, Schüpbach T, Kevrekidis I, Shvartsman S. Dynamics of Inductive ERK Signaling in the Drosophila Embryo. Curr Biol. 2015;25(13):1784–90. PMCID: PMC4675133
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  • 1.
    Di Talia S, Wieschaus E. Simple biochemical pathways far from steady state can provide switchlike and integrated responses. Biophys J. 2014;107(3):L1-L4. PMCID: PMC4129562
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  • 1.
    Segev R, Schneidman E, Goodhouse J, Berry M. Role of eye movements in the retinal code for a size discrimination task. J Neurophysiol. 2007;98(3):1380–91. PMID: 17625063
    Reference Link
  • 1.
    Hallenbeck P, Vimr E, Yu F, Bassler B, Troy F. Purification and properties of a bacteriophage-induced endo-N-acetylneuraminidase specific for poly-alpha-2,8-sialosyl carbohydrate units. J Biol Chem. 1987;262(8):3553–61. PMID: 3546309
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  • 1.
    Bassler B, Yu C, Lee Y, Roseman S. Chitin utilization by marine bacteria. Degradation and catabolism of chitin oligosaccharides by Vibrio furnissii. J Biol Chem. 1991;266(36):24276–86. PMID: 1761533
    Reference Link
  • 1.
    Yu C, Bassler B, Roseman S. Chemotaxis of the marine bacterium Vibrio furnissii to sugars. A potential mechanism for initiating the chitin catabolic cascade. J Biol Chem. 1993;268(13):9405–9. PMID: 8486635
    Reference Link
  • 1.
    Zhao G, Wan W, Mansouri S, Alfaro J, Bassler B, Cornell K, Zhou Z. Chemical synthesis of S-ribosyl-L-homocysteine and activity assay as a LuxS substrate. Bioorg Med Chem Lett. 2003;13(22):3897–900. PMID: 14592470
    Reference Link
  • 1.
    Hammer B, Bassler B. Distinct sensory pathways in Vibrio cholerae El Tor and classical biotypes modulate cyclic dimeric GMP levels to control biofilm formation. J Bacteriol. 2009;191(1):169–77. PMCID: PMC2612459
    Reference Link
  • 1.
    Wei Y, Perez L, Ng W-L, Semmelhack M, Bassler B. Mechanism of Vibrio cholerae autoinducer-1 biosynthesis. ACS Chem Biol. 2011;6(4):356–65. PMCID: PMC3077805
    Reference Link

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