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
Filters: Keyword is Models, Biological [Clear All Filters]
“Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.”, Genetics, vol. 174, no. 1, pp. 519-23, 2006.
, “Accuracy of direct gradient sensing by cell-surface receptors.”, Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
, “Accuracy of direct gradient sensing by single cells.”, Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
, “Achieving optimal growth through product feedback inhibition in metabolism.”, PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
, “Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria.”, Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 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.
, “Approaching the molecular origins of collective dynamics in oscillating cell populations.”, Curr Opin Genet Dev, vol. 20, no. 6, pp. 574-80, 2010.
, “Back to the future: education for systems-level biologists.”, Nat Rev Mol Cell Biol, vol. 7, no. 11, pp. 829-32, 2006.
, “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.
, “Bistability and oscillations in the Huang-Ferrell model of MAPK signaling.”, PLoS Comput Biol, vol. 3, no. 9, pp. 1819-26, 2007.
, “BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.”, Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
, “Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1.”, Mol Cell, vol. 25, no. 2, pp. 181-92, 2007.
, “Cell intercalation during Drosophila germband extension and its regulation by pair-rule segmentation genes.”, Development, vol. 120, no. 4, pp. 827-41, 1994.
, “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.
, “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.
, “Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation.”, PLoS Comput Biol, vol. 4, no. 1, p. e1, 2008.
, “Chemotaxis receptor complexes: from signaling to assembly.”, PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
, “A compartmental model for the bicoid gradient.”, Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
, “Computational analysis of EGFR inhibition by Argos.”, Dev Biol, vol. 284, no. 2, pp. 523-35, 2005.
, “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
, “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
, “Cooperativity, sensitivity, and noise in biochemical signaling.”, Phys Rev Lett, vol. 100, no. 25, p. 258101, 2008.
, “Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.”, Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
, “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 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.
, “A curvature-mediated mechanism for localization of lipids to bacterial poles.”, PLoS Comput Biol, vol. 2, no. 11, p. e151, 2006.
, “Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition.”, J Am Chem Soc, vol. 129, no. 30, pp. 9294-5, 2007.
, “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
, “Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells.”, Phys Rev Lett, vol. 107, no. 15, p. 158101, 2011.
, “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
, “Directing experimental biology: a case study in mitochondrial biogenesis.”, PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
, “Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation.”, J R Soc Interface, vol. 12, no. 109, p. 20150049, 2015.
, “Discrete models of autocrine cell communication in epithelial layers.”, Biophys J, vol. 84, no. 6, pp. 3624-35, 2003.
, “Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase.”, Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
, “Diverse metabolic model parameters generate similar methionine cycle dynamics.”, J Theor Biol, vol. 251, no. 4, pp. 628-39, 2008.
, “Does the potential for chaos constrain the embryonic cell-cycle oscillator?”, PLoS Comput Biol, vol. 7, no. 7, p. e1002109, 2011.
, “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
, “Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.”, Development, vol. 135, no. 2, pp. 343-51, 2008.
, “Dual regulation by the Hunchback gradient in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 105, no. 8, pp. 2901-6, 2008.
, “Dynamic model for the coordination of two enhancers of broad by EGFR signaling.”, Proc Natl Acad Sci U S A, vol. 110, no. 44, pp. 17939-44, 2013.
, “Dynamics of cooperativity in chemical sensing among cell-surface receptors.”, Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
, “Dynamics of maternal morphogen gradients in Drosophila.”, Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
, “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.
, “Dynein-mediated cargo transport in vivo. A switch controls travel distance.”, J Cell Biol, vol. 148, no. 5, pp. 945-56, 2000.
, “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
, “EGFR-dependent network interactions that pattern Drosophila eggshell appendages.”, Development, vol. 139, no. 15, pp. 2814-20, 2012.
, “Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7286-9, 2011.
, “Enhancer organization: transistor with a twist or something in a different vein?”, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
, “ERK as a model for systems biology of enzyme kinetics in cells.”, Curr Biol, vol. 23, no. 21, pp. R972-9, 2013.
, “Evidence that focal adhesion complexes power bacterial gliding motility.”, Science, vol. 315, no. 5813, pp. 853-6, 2007.
, “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”, PLoS One, vol. 7, no. 3, p. e33528, 2012.
, “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
, “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
, “folded gastrulation, cell shape change and the control of myosin localization.”, Development, vol. 132, no. 18, pp. 4165-78, 2005.
, “Formation of morphogen gradients: local accumulation time.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 5 Pt 1, p. 051906, 2011.
, “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA.”, PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
, “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
, “Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.”, PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
, “On the GFP-based analysis of dynamic concentration profiles.”, Biophys J, vol. 106, no. 3, pp. L13-5, 2014.
, “Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia.”, Mol Syst Biol, vol. 9, p. 712, 2013.
, “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
, “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
, “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
, “How long does it take to establish a morphogen gradient?”, Biophys J, vol. 99, no. 8, pp. L59-61, 2010.
, “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
, “Junctions as organizing centers in epithelial cells? A fly perspective.”, Traffic, vol. 3, no. 2, pp. 92-7, 2002.
, “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.
, “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
, “Limits of sensing temporal concentration changes by single cells.”, Phys Rev Lett, vol. 104, no. 24, p. 248101, 2010.
, “Lipid localization in bacterial cells through curvature-mediated microphase separation.”, Biophys J, vol. 95, no. 3, pp. 1034-49, 2008.
, “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
, “Local accumulation times for source, diffusion, and degradation models in two and three dimensions.”, J Chem Phys, vol. 138, no. 10, p. 104121, 2013.
, “Local kinetics of morphogen gradients.”, Proc Natl Acad Sci U S A, vol. 108, no. 15, pp. 6157-62, 2011.
, “Long-range signal transmission in autocrine relays.”, Biophys J, vol. 84, no. 2 Pt 1, pp. 883-96, 2003.
, “MAPK signaling in equations and embryos.”, Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
, “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
, “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.
, “Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate.”, Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
, “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
, “Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.”, Development, vol. 129, no. 11, pp. 2577-89, 2002.
, “Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein.”, Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
, “Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism.”, Phys Biol, vol. 7, no. 1, p. 016006, 2010.
, “Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.”, Phys Rev Lett, vol. 103, no. 24, p. 248102, 2009.
, “Modelling the Bicoid gradient.”, Development, vol. 137, no. 14, pp. 2253-64, 2010.
, “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
, “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
, “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
, “MreB Orientation Correlates with Cell Diameter in Escherichia coli.”, Biophys J, vol. 111, no. 5, pp. 1035-43, 2016.
, “mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein.”, Mol Cell, vol. 67, no. 6, pp. 936-946.e5, 2017.
, “Multiscale modeling of diffusion in the early Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 2010.
, “Nested effects models for high-dimensional phenotyping screens.”, Bioinformatics, vol. 23, no. 13, pp. i305-12, 2007.
, “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.
, “The onset of collective behavior in social amoebae.”, Science, vol. 328, no. 5981, pp. 1021-5, 2010.
, “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
, “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
, “Pattern formation by a moving morphogen source.”, Phys Biol, vol. 8, no. 4, p. 045003, 2011.
, “Pattern formation by dynamically interacting network motifs.”, Proc Natl Acad Sci U S A, vol. 106, no. 9, pp. 3213-8, 2009.
, “Pattern formation by graded and uniform signals in the early Drosophila embryo.”, Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
, “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
, “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
, “Physical interpretation of mean local accumulation time of morphogen gradient formation.”, J Chem Phys, vol. 135, no. 15, p. 154115, 2011.
, “Physical limits to biochemical signaling.”, Proc Natl Acad Sci U S A, vol. 102, no. 29, pp. 10040-5, 2005.
, “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
, “Precise adaptation in bacterial chemotaxis through "assistance neighborhoods".”, Proc Natl Acad Sci U S A, vol. 103, no. 35, pp. 13040-4, 2006.
, “Precise domain specification in the developing Drosophila embryo.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 72, no. 6 Pt 1, p. 061920, 2005.
, “Precision and kinetics of adaptation in bacterial chemotaxis.”, Biophys J, vol. 99, no. 9, pp. 2766-74, 2010.
, “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
, “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
, “Probing the limits to positional information.”, Cell, vol. 130, no. 1, pp. 153-64, 2007.
, “A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation.”, Cell, vol. 76, no. 6, pp. 1075-89, 1994.
, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
, “Quantifying the Gurken morphogen gradient in Drosophila oogenesis.”, Dev Cell, vol. 11, no. 2, pp. 263-72, 2006.
, “Quantitative models of developmental pattern formation.”, Dev Cell, vol. 11, no. 3, pp. 289-300, 2006.
, “Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT.”, J Bacteriol, vol. 190, no. 7, pp. 2527-36, 2008.
, “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”, Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
, “Remodeling of the metabolome during early frog development.”, PLoS One, vol. 6, no. 2, p. e16881, 2011.
, “Requirements for X-linked zygotic gene activity during cellularization of early Drosophila embryos.”, Development, vol. 104, no. 3, pp. 483-93, 1988.
, “Responding to chemical gradients: bacterial chemotaxis.”, Curr Opin Cell Biol, vol. 24, no. 2, pp. 262-8, 2012.
, “Rethinking WNT signaling.”, Trends Genet, vol. 20, no. 4, pp. 177-81, 2004.
, “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
, “Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization.”, Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
, “Role of boundary conditions in an experimental model of epithelial wound healing.”, Am J Physiol Cell Physiol, vol. 291, no. 1, pp. C68-75, 2006.
, “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
, “Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy.”, PLoS Biol, vol. 7, no. 6, p. e1000137, 2009.
, “Self-organized periodicity of protein clusters in growing bacteria.”, Phys Rev Lett, vol. 101, no. 21, p. 218101, 2008.
, “Self-similar dynamics of morphogen gradients.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 84, no. 4 Pt 1, p. 041916, 2011.
, “Shooting from the hip: spatial control of signal release by intracellular waves.”, Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9087-9, 2002.
, “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
, “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
, “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.
, “Spatial regulation of BMP signaling by patterned receptor expression.”, Tissue Eng Part A, vol. 14, no. 9, pp. 1469-77, 2008.
, “Stability and nuclear dynamics of the bicoid morphogen gradient.”, Cell, vol. 130, no. 1, pp. 141-52, 2007.
, “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
, “Statistical mechanics for natural flocks of birds.”, Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 2012.
, “Steps in the bacterial flagellar motor.”, PLoS Comput Biol, vol. 5, no. 10, p. e1000540, 2009.
, “Stochastic model of autocrine and paracrine signals in cell culture assays.”, Biophys J, vol. 85, no. 6, pp. 3659-65, 2003.
, “Substrate-dependent control of ERK phosphorylation can lead to oscillations.”, Biophys J, vol. 101, no. 11, pp. 2572-81, 2011.
, “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
, “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
, “Systematic planning of genome-scale experiments in poorly studied species.”, PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
, “Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum.”, J Bacteriol, vol. 192, no. 17, pp. 4452-61, 2010.
, “Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy.”, Nat Biotechnol, vol. 26, no. 10, pp. 1179-86, 2008.
, “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
, “Time and length scales of autocrine signals in three dimensions.”, Biophys J, vol. 93, no. 6, pp. 1917-22, 2007.
, “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
, “Transitions in the model of epithelial patterning.”, Dev Dyn, vol. 226, no. 1, pp. 155-9, 2003.
, “Variable sizes of Escherichia coli chemoreceptor signaling teams.”, Mol Syst Biol, vol. 4, p. 211, 2008.
, “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
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