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

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A
J. Akiko Heck, Gresham, D., Botstein, D., and Alani, E., “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.
R. G. Endres and Wingreen, N. S., “Accuracy of direct gradient sensing by cell-surface receptors.”, Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
R. G. Endres and Wingreen, N. S., “Accuracy of direct gradient sensing by single cells.”, Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., “Achieving optimal growth through product feedback inhibition in metabolism.”, PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “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.
D. Swanson and Wingreen, N. S., “Active biopolymers confer fast reorganization kinetics.”, Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi.”, Mol Syst Biol, vol. 7, p. 491, 2011.
P. Mehta and Gregor, T., “Approaching the molecular origins of collective dynamics in oscillating cell populations.”, Curr Opin Genet Dev, vol. 20, no. 6, pp. 574-80, 2010.
B
N. Wingreen and Botstein, D., “Back to the future: education for systems-level biologists.”, Nat Rev Mol Cell Biol, vol. 7, no. 11, pp. 829-32, 2006.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., “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.
L. Qiao, Nachbar, R. B., Kevrekidis, I. G., and Shvartsman, S. Y., “Bistability and oscillations in the Huang-Ferrell model of MAPK signaling.”, PLoS Comput Biol, vol. 3, no. 9, pp. 1819-26, 2007.
L. Christiaen, Stolfi, A., and Levine, M., “BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.”, Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
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Q. Bao, Lu, W., Rabinowitz, J. D., and Shi, Y., “Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1.”, Mol Cell, vol. 25, no. 2, pp. 181-92, 2007.
K. D. Irvine and Wieschaus, E., “Cell intercalation during Drosophila germband extension and its regulation by pair-rule segmentation genes.”, Development, vol. 120, no. 4, pp. 827-41, 1994.
K. Casey Huang, Mukhopadhyay, R., Wen, B., Gitai, Z., and Wingreen, N. S., “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.
J. E. Keymer, Endres, R. G., Skoge, M., Meir, Y., and Wingreen, N. S., “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.
C. H. Hansen, Endres, R. G., and Wingreen, N. S., “Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation.”, PLoS Comput Biol, vol. 4, no. 1, p. e1, 2008.
R. G. Endres, Falke, J. J., and Wingreen, N. S., “Chemotaxis receptor complexes: from signaling to assembly.”, PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
M. E. Kavousanakis, Kanodia, J. S., Kim, Y., Kevrekidis, I. G., and Shvartsman, S. Y., “A compartmental model for the bicoid gradient.”, Dev Biol, vol. 345, no. 1, pp. 12-7, 2010.
G. T. Reeves, Kalifa, R., Klein, D. E., Lemmon, M. A., and Shvartsman, S. Y., “Computational analysis of EGFR inhibition by Argos.”, Dev Biol, vol. 284, no. 2, pp. 523-35, 2005.
S. H Wiley, Shvartsman, S. Y., and Lauffenburger, D. A., “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
N. S. Wingreen and Levin, S. A., “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
W. Bialek and Setayeshgar, S., “Cooperativity, sensitivity, and noise in biochemical signaling.”, Phys Rev Lett, vol. 100, no. 25, p. 258101, 2008.
M. J. Brauer, Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., and Botstein, D., “Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.”, Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
R. Mukhopadhyay and Wingreen, N. S., “Curvature and shape determination of growing bacteria.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 6 Pt 1, p. 062901, 2009.
K. Casey Huang, Mukhopadhyay, R., and Wingreen, N. S., “A curvature-mediated mechanism for localization of lipids to bacterial poles.”, PLoS Comput Biol, vol. 2, no. 11, p. e151, 2006.
D
J. Yuan and Rabinowitz, J. D., “Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition.”, J Am Chem Soc, vol. 129, no. 30, pp. 9294-5, 2007.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “Dimensionality and dynamics in the behavior of C. elegans.”, PLoS Comput Biol, vol. 4, no. 4, p. e1000028, 2008.
Y. Deng, Sun, M., and Shaevitz, J. W., “Direct measurement of cell wall stress stiffening and turgor pressure in live bacterial cells.”, Phys Rev Lett, vol. 107, no. 15, p. 158101, 2011.
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M., “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
M. A. Hibbs, Myers, C. L., Huttenhower, C., Hess, D. C., Li, K., Caudy, A. A., and Troyanskaya, O. G., “Directing experimental biology: a case study in mitochondrial biogenesis.”, PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
S. Thutupalli, Sun, M., Bunyak, F., Palaniappan, K., and Shaevitz, J. W., “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.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Discrete models of autocrine cell communication in epithelial layers.”, Biophys J, vol. 84, no. 6, pp. 3624-35, 2003.
J. D. Rabinowitz, Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X. - J., Li, G., and Rabitz, H., “Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase.”, Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
M. Piazza, Feng, X. - J., Rabinowitz, J. D., and Rabitz, H., “Diverse metabolic model parameters generate similar methionine cycle dynamics.”, J Theor Biol, vol. 251, no. 4, pp. 628-39, 2008.
S. R McIsaac, Huang, K. Casey, Sengupta, A., and Wingreen, N. S., “Does the potential for chaos constrain the embryonic cell-cycle oscillator?”, PLoS Comput Biol, vol. 7, no. 7, p. e1002109, 2011.
C. D. van Raamsdonk and Tilghman, S. M., “Dosage requirement and allelic expression of PAX6 during lens placode formation.”, Development, vol. 127, no. 24, pp. 5439-48, 2000.
N. Yakoby, Lembong, J., Schüpbach, T., and Shvartsman, S. Y., “Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.”, Development, vol. 135, no. 2, pp. 343-51, 2008.
D. Papatsenko and Levine, M. S., “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.
L. S. Cheung, Simakov, D. S. A., Fuchs, A., Pyrowolakis, G., and Shvartsman, S. Y., “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.
M. Skoge, Meir, Y., and Wingreen, N. S., “Dynamics of cooperativity in chemical sensing among cell-surface receptors.”, Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., “Dynamics of maternal morphogen gradients in Drosophila.”, Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
C. H. Hansen, Sourjik, V., and Wingreen, N. S., “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.
S. P. Gross, Welte, M. A., Block, S. M., and Wieschaus, E. F., “Dynein-mediated cargo transport in vivo. A switch controls travel distance.”, J Cell Biol, vol. 148, no. 5, pp. 945-56, 2000.
E
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., “Efficient multiple object tracking using mutually repulsive active membranes.”, PLoS One, vol. 8, no. 6, p. e65769, 2013.
D. S. A. Simakov, Cheung, L. S., Pismen, L. M., and Shvartsman, S. Y., “EGFR-dependent network interactions that pattern Drosophila eggshell appendages.”, Development, vol. 139, no. 15, pp. 2814-20, 2012.
G. J. Stephens, de Mesquita, M. Bueno, Ryu, W. S., and Bialek, W., “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.
J. J. Zartman and Shvartsman, S. Y., “Enhancer organization: transistor with a twist or something in a different vein?”, Curr Biol, vol. 17, no. 24, pp. R1048-50, 2007.
A. S. Futran, A Link, J., Seger, R., and Shvartsman, S. Y., “ERK as a model for systems biology of enzyme kinetics in cells.”, Curr Biol, vol. 23, no. 21, pp. R972-9, 2013.
T. Mignot, Shaevitz, J. W., Hartzell, P. L., and Zusman, D. R., “Evidence that focal adhesion complexes power bacterial gliding motility.”, Science, vol. 315, no. 5813, pp. 853-6, 2007.
R. M. Cooper, Wingreen, N. S., and Cox, E. C., “An excitable cortex and memory model successfully predicts new pseudopod dynamics.”, PLoS One, vol. 7, no. 3, p. e33528, 2012.
A. V. Persikov and Singh, M., “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
S. S. Jeffrey, Fero, M. J., Børresen-Dale, A. - L., and Botstein, D., “Expression array technology in the diagnosis and treatment of breast cancer.”, Mol Interv, vol. 2, no. 2, pp. 101-9, 2002.
F
R. E. Dawes-Hoang, Parmar, K. M., Christiansen, A. E., Phelps, C. B., Brand, A. H., and Wieschaus, E. F., “folded gastrulation, cell shape change and the control of myosin localization.”, Development, vol. 132, no. 18, pp. 4165-78, 2005.
A. M. Berezhkovskii, Sample, C., and Shvartsman, S. Y., “Formation of morphogen gradients: local accumulation time.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 83, no. 5 Pt 1, p. 051906, 2011.
S. C. Little, Tkačik, G., Kneeland, T. B., Wieschaus, E. F., and Gregor, T., “The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA.”, PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
G. J. Stephens, Johnson-Kerner, B., Bialek, W., and Ryu, W. S., “From modes to movement in the behavior of Caenorhabditis elegans.”, PLoS One, vol. 5, no. 11, p. e13914, 2010.
C. Y. Park, Wong, A. K., Greene, C. S., Rowland, J., Guan, Y., Bongo, L. A., Burdine, R. D., and Troyanskaya, O. G., “Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.”, PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
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A. M. Berezhkovskii and Shvartsman, S. Y., “On the GFP-based analysis of dynamic concentration profiles.”, Biophys J, vol. 106, no. 3, pp. L13-5, 2014.
J. Fan, Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., and Rabinowitz, J. D., “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.
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
H
M. J. Brauer, Saldanha, A. J., Dolinski, K., and Botstein, D., “Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.”, Mol Biol Cell, vol. 16, no. 5, pp. 2503-17, 2005.
E. Emberly and Wingreen, N. S., “Hourglass model for a protein-based circadian oscillator.”, Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
A. M. Berezhkovskii, Sample, C., and Shvartsman, S. Y., “How long does it take to establish a morphogen gradient?”, Biophys J, vol. 99, no. 8, pp. L59-61, 2010.
I
G. Tkačik, Callan, C. G., and Bialek, W., “Information capacity of genetic regulatory elements.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 78, no. 1 Pt 1, p. 011910, 2008.
O. G. Troyanskaya, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
J
T. Lecuit and Wieschaus, E., “Junctions as organizing centers in epithelial cells? A fly perspective.”, Traffic, vol. 3, no. 2, pp. 92-7, 2002.
K
A. R. Ureta, Endres, R. G., Wingreen, N. S., and Silhavy, T. J., “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.
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M. I. Monine, Berezhkovskii, A. M., Joslin, E. J., H Wiley, S., Lauffenburger, D. A., and Shvartsman, S. Y., “Ligand accumulation in autocrine cell cultures.”, Biophys J, vol. 88, no. 4, pp. 2384-90, 2005.
T. Mora and Wingreen, N. S., “Limits of sensing temporal concentration changes by single cells.”, Phys Rev Lett, vol. 104, no. 24, p. 248101, 2010.
R. Mukhopadhyay, Huang, K. Casey, and Wingreen, N. S., “Lipid localization in bacterial cells through curvature-mediated microphase separation.”, Biophys J, vol. 95, no. 3, pp. 1034-49, 2008.
J. W. Shaevitz and Fletcher, D. A., “Load fluctuations drive actin network growth.”, Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
P. V. Gordon, Muratov, C. B., and Shvartsman, S. Y., “Local accumulation times for source, diffusion, and degradation models in two and three dimensions.”, J Chem Phys, vol. 138, no. 10, p. 104121, 2013.
P. V. Gordon, Sample, C., Berezhkovskii, A. M., Muratov, C. B., and Shvartsman, S. Y., “Local kinetics of morphogen gradients.”, Proc Natl Acad Sci U S A, vol. 108, no. 15, pp. 6157-62, 2011.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Long-range signal transmission in autocrine relays.”, Biophys J, vol. 84, no. 2 Pt 1, pp. 883-96, 2003.
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S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., “MAPK signaling in equations and embryos.”, Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
R. G. Endres and Wingreen, N. S., “Maximum likelihood and the single receptor.”, Phys Rev Lett, vol. 103, no. 15, p. 158101, 2009.
K. E. Daly, Huang, K. Casey, Wingreen, N. S., and Mukhopadhyay, R., “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.
S. J. Silverman, Petti, A. A., Slavov, N., Parsons, L., Briehof, R., Thiberge, S. Y., Zenklusen, D., Gandhi, S. J., Larson, D. R., Singer, R. H., and Botstein, D., “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.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
S. Y. Shvartsman, Muratov, C. B., and Lauffenburger, D. A., “Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis.”, Development, vol. 129, no. 11, pp. 2577-89, 2002.
M. Coppey, Berezhkovskii, A. M., Kim, Y., Boettiger, A. N., and Shvartsman, S. Y., “Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein.”, Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
P. B. Kidd and Wingreen, N. S., “Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism.”, Phys Biol, vol. 7, no. 1, p. 016006, 2010.
T. Mora, Yu, H., and Wingreen, N. S., “Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.”, Phys Rev Lett, vol. 103, no. 24, p. 248102, 2009.
O. Grimm, Coppey, M., and Wieschaus, E., “Modelling the Bicoid gradient.”, Development, vol. 137, no. 14, pp. 2253-64, 2010.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., “The molecular origins of chiral growth in walled cells.”, Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., “Morphogenesis at criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
M. Sun, Wartel, M., Cascales, E., Shaevitz, J. W., and Mignot, T., “Motor-driven intracellular transport powers bacterial gliding motility.”, Proc Natl Acad Sci U S A, vol. 108, no. 18, pp. 7559-64, 2011.
N. Ouzounov, Nguyen, J. P., Bratton, B. P., Jacobowitz, D., Gitai, Z., and Shaevitz, J. W., “MreB Orientation Correlates with Cell Diameter in Escherichia coli.”, Biophys J, vol. 111, no. 5, pp. 1035-43, 2016.
M. Nofal, Zhang, K., Han, S., and Rabinowitz, J. D., “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.
C. Sample and Shvartsman, S. Y., “Multiscale modeling of diffusion in the early Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 2010.
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F. Markowetz, Kostka, D., Troyanskaya, O. G., and Spang, R., “Nested effects models for high-dimensional phenotyping screens.”, Bioinformatics, vol. 23, no. 13, pp. i305-12, 2007.
D. Bruce Borenstein, Meir, Y., Shaevitz, J. W., and Wingreen, N. S., “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.
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T. Gregor, Fujimoto, K., Masaki, N., and Sawai, S., “The onset of collective behavior in social amoebae.”, Science, vol. 328, no. 5981, pp. 1021-5, 2010.
E. Banks, Nabieva, E., Chazelle, B., and Singh, M., “Organization of physical interactomes as uncovered by network schemas.”, PLoS Comput Biol, vol. 4, no. 10, p. e1000203, 2008.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., “Overview of the Alliance for Cellular Signaling.”, Nature, vol. 420, no. 6916, pp. 703-6, 2002.
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J. J. Zartman, Cheung, L. S., Niepielko, M. G., Bonini, C., Haley, B., Yakoby, N., and Shvartsman, S. Y., “Pattern formation by a moving morphogen source.”, Phys Biol, vol. 8, no. 4, p. 045003, 2011.
J. Lembong, Yakoby, N., and Shvartsman, S. Y., “Pattern formation by dynamically interacting network motifs.”, Proc Natl Acad Sci U S A, vol. 106, no. 9, pp. 3213-8, 2009.
J. S. Kanodia, Liang, H. - L., Kim, Y., Lim, B., Zhan, M., Lu, H., Rushlow, C. A., and Shvartsman, S. Y., “Pattern formation by graded and uniform signals in the early Drosophila embryo.”, Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
R. V. Kulkarni, Huang, K. Casey, Kloster, M., and Wingreen, N. S., “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
M. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., “Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.”, Cell, vol. 153, no. 5, pp. 976-87, 2013.
A. M. Berezhkovskii and Shvartsman, S. Y., “Physical interpretation of mean local accumulation time of morphogen gradient formation.”, J Chem Phys, vol. 135, no. 15, p. 154115, 2011.
W. Bialek and Setayeshgar, S., “Physical limits to biochemical signaling.”, Proc Natl Acad Sci U S A, vol. 102, no. 29, pp. 10040-5, 2005.
J. O. Dubuis, Tkačik, G., Wieschaus, E. F., Gregor, T., and Bialek, W., “Positional information, in bits.”, Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
R. G. Endres and Wingreen, N. S., “Precise adaptation in bacterial chemotaxis through "assistance neighborhoods".”, Proc Natl Acad Sci U S A, vol. 103, no. 35, pp. 13040-4, 2006.
B. Houchmandzadeh, Wieschaus, E., and Leibler, S., “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.
Y. Meir, Jakovljevic, V., Oleksiuk, O., Sourjik, V., and Wingreen, N. S., “Precision and kinetics of adaptation in bacterial chemotaxis.”, Biophys J, vol. 99, no. 9, pp. 2766-74, 2010.
E. M. Airoldi, Huttenhower, C., Gresham, D., Lu, C., Caudy, A. A., Dunham, M. J., Broach, J. R., Botstein, D., and Troyanskaya, O. G., “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
A. V. Persikov, Osada, R., and Singh, M., “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
T. Gregor, Tank, D. W., Wieschaus, E. F., and Bialek, W., “Probing the limits to positional information.”, Cell, vol. 130, no. 1, pp. 153-64, 2007.
M. Costa, Wilson, E. T., and Wieschaus, E., “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.
O. G. Troyanskaya, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
Q
L. A. Goentoro, Reeves, G. T., Kowal, C. P., Martinelli, L., Schüpbach, T., and Shvartsman, S. Y., “Quantifying the Gurken morphogen gradient in Drosophila oogenesis.”, Dev Cell, vol. 11, no. 2, pp. 263-72, 2006.
G. T. Reeves, Muratov, C. B., Schüpbach, T., and Shvartsman, S. Y., “Quantitative models of developmental pattern formation.”, Dev Cell, vol. 11, no. 3, pp. 289-300, 2006.
C. M. Waters, Lu, W., Rabinowitz, J. D., and Bassler, B. L., “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.
R
M. L. Skoge, Endres, R. G., and Wingreen, N. S., “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”, Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
L. Vastag, Jorgensen, P., Peshkin, L., Wei, R., Rabinowitz, J. D., and Kirschner, M. W., “Remodeling of the metabolome during early frog development.”, PLoS One, vol. 6, no. 2, p. e16881, 2011.
E. Wieschaus and Sweeton, D., “Requirements for X-linked zygotic gene activity during cellularization of early Drosophila embryos.”, Development, vol. 104, no. 3, pp. 483-93, 1988.
V. Sourjik and Wingreen, N. S., “Responding to chemical gradients: bacterial chemotaxis.”, Curr Opin Cell Biol, vol. 24, no. 2, pp. 262-8, 2012.
N. S. Tolwinski and Wieschaus, E., “Rethinking WNT signaling.”, Trends Genet, vol. 20, no. 4, pp. 177-81, 2004.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, “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.
D. L. Nikolić, Boettiger, A. N., Bar-Sagi, D., Carbeck, J. D., and Shvartsman, S. Y., “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.
G. Tkačik, Gregor, T., and Bialek, W., “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, “RTK signaling modulates the Dorsal gradient.”, Development, vol. 139, no. 16, pp. 3032-9, 2012.
S
D. Greenfield, McEvoy, A. L., Shroff, H., Crooks, G. E., Wingreen, N. S., Betzig, E., and Liphardt, J., “Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy.”, PLoS Biol, vol. 7, no. 6, p. e1000137, 2009.
H. Wang, Wingreen, N. S., and Mukhopadhyay, R., “Self-organized periodicity of protein clusters in growing bacteria.”, Phys Rev Lett, vol. 101, no. 21, p. 218101, 2008.
C. B. Muratov, Gordon, P. V., and Shvartsman, S. Y., “Self-similar dynamics of morphogen gradients.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 84, no. 4 Pt 1, p. 041916, 2011.
S. Y. Shvartsman, “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.
C. B. Muratov and Shvartsman, S. Y., “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
C. Jang, Hui, S., Lu, W., Cowan, A. J., Morscher, R. J., Lee, G., Liu, W., Tesz, G. J., Birnbaum, M. J., and Rabinowitz, J. D., “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
D. H. Lenz, Mok, K. C., Lilley, B. N., Kulkarni, R. V., Wingreen, N. S., and Bassler, B. L., “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.
J. Lembong, Yakoby, N., and Shvartsman, S. Y., “Spatial regulation of BMP signaling by patterned receptor expression.”, Tissue Eng Part A, vol. 14, no. 9, pp. 1469-77, 2008.
T. Gregor, Wieschaus, E. F., McGregor, A. P., Bialek, W., and Tank, D. W., “Stability and nuclear dynamics of the bicoid morphogen gradient.”, Cell, vol. 130, no. 1, pp. 141-52, 2007.
J. W. Shaevitz, Block, S. M., and Schnitzer, M. J., “Statistical kinetics of macromolecular dynamics.”, Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Silvestri, E., Viale, M., and Walczak, A. M., “Statistical mechanics for natural flocks of birds.”, Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 2012.
T. Mora, Yu, H., Sowa, Y., and Wingreen, N. S., “Steps in the bacterial flagellar motor.”, PLoS Comput Biol, vol. 5, no. 10, p. e1000540, 2009.
L. Batsilas, Berezhkovskii, A. M., and Shvartsman, S. Y., “Stochastic model of autocrine and paracrine signals in cell culture assays.”, Biophys J, vol. 85, no. 6, pp. 3659-65, 2003.
P. Liu, Kevrekidis, I. G., and Shvartsman, S. Y., “Substrate-dependent control of ERK phosphorylation can lead to oscillations.”, Biophys J, vol. 101, no. 11, pp. 2572-81, 2011.
Y. Kim, Paroush, Z. 'ev, Nairz, K., Hafen, E., Jiménez, G., and Shvartsman, S. Y., “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
J. A. Drocco, Wieschaus, E. F., and Tank, D. W., “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
Y. Guan, Dunham, M., Caudy, A., and Troyanskaya, O., “Systematic planning of genome-scale experiments in poorly studied species.”, PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
D. Amador-Noguez, Feng, X. - J., Fan, J., Roquet, N., Rabitz, H., and Rabinowitz, J. D., “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.
J. Munger, Bennett, B. D., Parikh, A., Feng, X. - J., McArdle, J., Rabitz, H. A., Shenk, T., and Rabinowitz, J. D., “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
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., “T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”, PLoS Biol, vol. 1, no. 2, p. E53, 2003.
M. Coppey, Berezhkovskii, A. M., Sealfon, S. C., and Shvartsman, S. Y., “Time and length scales of autocrine signals in three dimensions.”, Biophys J, vol. 93, no. 6, pp. 1917-22, 2007.
Y. Guan, Gorenshteyn, D., Burmeister, M., Wong, A. K., Schimenti, J. C., Handel, M. Ann, Bult, C. J., Hibbs, M. A., and Troyanskaya, O. G., “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Transitions in the model of epithelial patterning.”, Dev Dyn, vol. 226, no. 1, pp. 155-9, 2003.
V
R. G. Endres, Oleksiuk, O., Hansen, C. H., Meir, Y., Sourjik, V., and Wingreen, N. S., “Variable sizes of Escherichia coli chemoreceptor signaling teams.”, Mol Syst Biol, vol. 4, p. 211, 2008.
Y
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.