List of Faculty Publications
Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua
, “Designability of alpha-helical proteins.”, Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
, “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”, Proteins, vol. 49, no. 3, pp. 403-12, 2002.
, “Emergence of highly designable protein-backbone conformations in an off-lattice model.”, Proteins, vol. 47, no. 4, pp. 506-12, 2002.
, “Identifying proteins of high designability via surface-exposure patterns.”, Proteins, vol. 47, no. 3, pp. 295-304, 2002.
, “Kondo model for the "0.7 anomaly" in transport through a quantum point contact.”, Phys Rev Lett, vol. 89, no. 19, p. 196802, 2002.
, “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”, Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
, “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
, “Local moment formation in quantum point contacts.”, Phys Rev Lett, vol. 90, no. 2, p. 026804, 2003.
, “Scaling of mutational effects in models for pleiotropy.”, Genetics, vol. 164, no. 3, pp. 1221-8, 2003.
, “Statistical mechanics of RNA folding: importance of alphabet size.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 68, no. 4 Pt 1, p. 041904, 2003.
, “Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.”, EMBO J, vol. 22, no. 4, pp. 870-81, 2003.
, “Fast accurate evaluation of protein solvent exposure.”, Proteins, vol. 57, no. 3, pp. 565-76, 2004.
, “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
, “Min-protein oscillations in round bacteria.”, Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
, “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
, “Physics. Quantum many-body effects in a single-electron transistor.”, Science, vol. 304, no. 5675, pp. 1258-9, 2004.
, “The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.”, Cell, vol. 118, no. 1, pp. 69-82, 2004.
, “Toward an atomistic model for predicting transcription-factor binding sites.”, Proteins, vol. 57, no. 2, pp. 262-8, 2004.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “Chemosensing in Escherichia coli: two regimes of two-state receptors.”, Proc Natl Acad Sci U S A, vol. 103, no. 6, pp. 1786-91, 2006.
, “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
, “A curvature-mediated mechanism for localization of lipids to bacterial poles.”, PLoS Comput Biol, vol. 2, no. 11, p. e151, 2006.
, “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
, “Precise adaptation in bacterial chemotaxis through "assistance neighborhoods".”, Proc Natl Acad Sci U S A, vol. 103, no. 35, pp. 13040-4, 2006.
, “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”, Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
, “Weight matrices for protein-DNA binding sites from a single co-crystal structure.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 73, no. 6 Pt 1, p. 061921, 2006.
, “Chemotaxis receptor complexes: from signaling to assembly.”, PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
, “Evolution, interactions, and biological networks.”, PLoS Biol, vol. 5, no. 1, p. e11, 2007.
, “Growth-induced instability in metabolic networks.”, Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
, “Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water.”, Proc Natl Acad Sci U S A, vol. 104, no. 8, pp. 2626-30, 2007.
, “Kinetic analysis of the assembly of the outer membrane protein LamB in Escherichia coli mutants each lacking a secretion or targeting factor in a different cellular compartment.”, J Bacteriol, vol. 189, no. 2, pp. 446-54, 2007.
, “Turning to the cold.”, Nat Cell Biol, vol. 9, no. 9, pp. 1029-31, 2007.
, “Accuracy of direct gradient sensing by single cells.”, Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
, “Cell shape and cell-wall organization in Gram-negative bacteria.”, Proc Natl Acad Sci U S A, vol. 105, no. 49, pp. 19282-7, 2008.
, “Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation.”, PLoS Comput Biol, vol. 4, no. 1, p. e1, 2008.
, “Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.”, Cell, vol. 134, no. 3, pp. 461-73, 2008.
, “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
, “An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.”, J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
, “Lipid localization in bacterial cells through curvature-mediated microphase separation.”, Biophys J, vol. 95, no. 3, pp. 1034-49, 2008.
, “PSICIC: noise and asymmetry in bacterial division revealed by computational image analysis at sub-pixel resolution.”, PLoS Comput Biol, vol. 4, no. 11, p. e1000233, 2008.
, “A quantitative comparison of sRNA-based and protein-based gene regulation.”, Mol Syst Biol, vol. 4, p. 221, 2008.
, “Self-organized periodicity of protein clusters in growing bacteria.”, Phys Rev Lett, vol. 101, no. 21, p. 218101, 2008.
, “Variable sizes of Escherichia coli chemoreceptor signaling teams.”, Mol Syst Biol, vol. 4, p. 211, 2008.
, “The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.”, Mol Microbiol, vol. 70, no. 1, pp. 76-88, 2008.
, “Accuracy of direct gradient sensing by cell-surface receptors.”, Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
, “Curvature and shape determination of growing bacteria.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 6 Pt 1, p. 062901, 2009.
, “Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines.”, Proc Natl Acad Sci U S A, vol. 106, no. 21, pp. 8701-6, 2009.
, “Information processing and signal integration in bacterial quorum sensing.”, Mol Syst Biol, vol. 5, p. 325, 2009.
, “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
, “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
, “Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.”, Phys Rev Lett, vol. 103, no. 24, p. 248102, 2009.
, “Quantifying the integration of quorum-sensing signals with single-cell resolution.”, PLoS Biol, vol. 7, no. 3, p. e68, 2009.
, “Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy.”, PLoS Biol, vol. 7, no. 6, p. e1000137, 2009.
, “Steps in the bacterial flagellar motor.”, PLoS Comput Biol, vol. 5, no. 10, p. e1000540, 2009.
, “Achieving optimal growth through product feedback inhibition in metabolism.”, PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
, “Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis.”, EMBO J, vol. 29, no. 20, pp. 3484-95, 2010.
, “A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli.”, Proc Natl Acad Sci U S A, vol. 107, no. 40, pp. 17170-5, 2010.
, “Evaluating gene expression dynamics using pairwise RNA FISH data.”, PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
, “How can vaccines against influenza and other viral diseases be made more effective?”, PLoS Biol, vol. 8, no. 12, p. e1000571, 2010.
, “In vivo residue-specific histone methylation dynamics.”, J Biol Chem, vol. 285, no. 5, pp. 3341-50, 2010.
, “Limits of sensing temporal concentration changes by single cells.”, Phys Rev Lett, vol. 104, no. 24, p. 248101, 2010.
, “Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.”, Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
, “Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism.”, Phys Biol, vol. 7, no. 1, p. 016006, 2010.
, “Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response.”, Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
, “Precision and kinetics of adaptation in bacterial chemotaxis.”, Biophys J, vol. 99, no. 9, pp. 2766-74, 2010.
, “Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules.”, Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5575-80, 2010.
, “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
, “Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi.”, Mol Syst Biol, vol. 7, p. 491, 2011.
, “The bacterial actin MreB rotates, and rotation depends on cell-wall assembly.”, Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
, “Does the potential for chaos constrain the embryonic cell-cycle oscillator?”, PLoS Comput Biol, vol. 7, no. 7, p. e1002109, 2011.
, “Dynamics of cooperativity in chemical sensing among cell-surface receptors.”, Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
, “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
, “Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 4 Pt 1, p. 041922, 2011.
, “Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria.”, Mol Microbiol, vol. 81, no. 2, pp. 340-53, 2011.
, “Non-genetic individuality in Escherichia coli motor switching.”, Phys Biol, vol. 8, no. 2, p. 024001, 2011.
, “Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”, Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
, “Thermal robustness of signaling in bacterial chemotaxis.”, Cell, vol. 145, no. 2, pp. 312-21, 2011.
, “α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition.”, Nat Chem Biol, vol. 7, no. 12, pp. 894-901, 2011.
, “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”, PLoS One, vol. 7, no. 3, p. e33528, 2012.
, “Responding to chemical gradients: bacterial chemotaxis.”, Curr Opin Cell Biol, vol. 24, no. 2, pp. 262-8, 2012.
, “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”, Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
, “Chemical sensing by nonequilibrium cooperative receptors.”, Phys Rev Lett, vol. 110, no. 24, p. 248102, 2013.
, “Chemical Sensing by Nonequilibrium Cooperative Receptors.”, Phys Rev Lett, vol. 110, no. 24, 2013.
, “Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model.”, PLoS One, vol. 8, no. 5, p. e63304, 2013.
, “Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis.”, Genetics, vol. 195, no. 2, pp. 443-55, 2013.
, “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
, “Enzyme clustering accelerates processing of intermediates through metabolic channeling.”, Nat Biotechnol, vol. 32, no. 10, pp. 1011-8, 2014.
, “Imprecision of adaptation in Escherichia coli chemotaxis.”, PLoS One, vol. 9, no. 1, p. e84904, 2014.
, “Large-scale filament formation inhibits the activity of CTP synthetase.”, Elife, vol. 3, p. e03638, 2014.
, “The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices.”, PLoS Comput Biol, vol. 10, no. 12, p. e1003932, 2014.
, “Solutions to the public goods dilemma in bacterial biofilms.”, Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
, “Working together at the interface of physics and biology.”, Phys Biol, vol. 11, no. 5, p. 053010, 2014.
, “Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.”, ISME J, vol. 9, no. 1, pp. 68-80, 2015.
, “Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.”, Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.