Kim, Yoosik, Ze’ev Paroush, Knud Nairz, Ernst Hafen, Gerardo Jiménez, and Stanislav Y Shvartsman. (2011) 2011. “Substrate-Dependent Control of MAPK Phosphorylation in Vivo.”. Mol Syst Biol 7: 467. Reference Link
Nikolić, Djordje L, Alistair N Boettiger, Dafna Bar-Sagi, Jeffrey D Carbeck, and Stanislav Y Shvartsman. (2006) 2006. “Role of Boundary Conditions in an Experimental Model of Epithelial Wound Healing.”. Am J Physiol Cell Physiol 291 (1). Reference Link
Meir, Yigal, Vladimir Jakovljevic, Olga Oleksiuk, Victor Sourjik, and Ned S Wingreen. (2010) 2010. “Precision and Kinetics of Adaptation in Bacterial Chemotaxis.”. Biophys J 99 (9): 2766-74. Reference Link
Sample, Christine, and Stanislav Y Shvartsman. (2010) 2010. “Multiscale Modeling of Diffusion in the Early Drosophila Embryo.”. Proc Natl Acad Sci U S A 107 (22): 10092-6. Reference Link
Gordon, Peter, V, Cyrill B Muratov, and Stanislav Y Shvartsman. (2013) 2013. “Local Accumulation Times for Source, Diffusion, and Degradation Models in Two and Three Dimensions.”. J Chem Phys 138 (10): 104121. Reference Link
Stephens, Greg J, Bethany Johnson-Kerner, William Bialek, and William S Ryu. 2010. “From Modes to Movement in the Behavior of Caenorhabditis Elegans.”. PLoS One 5 (11): e13914. Reference Link
Skoge, Monica, Yigal Meir, and Ned S Wingreen. (2011) 2011. “Dynamics of Cooperativity in Chemical Sensing Among Cell-Surface Receptors.”. Phys Rev Lett 107 (17): 178101. Reference Link
Harbison, Susan T, Mary Anna Carbone, Julien Ayroles, Eric A Stone, Richard F Lyman, and Trudy F C Mackay. (2009) 2009. “Co-Regulated Transcriptional Networks Contribute to Natural Genetic Variation in Drosophila Sleep.”. Nat Genet 41 (3): 371-5. Reference Link
Wingreen, Ned, and David Botstein. (2006) 2006. “Back to the Future: Education for Systems-Level Biologists.”. Nat Rev Mol Cell Biol 7 (11): 829-32. Reference Link
Liu, Ping, Ioannis G Kevrekidis, and Stanislav Y Shvartsman. (2011) 2011. “Substrate-Dependent Control of ERK Phosphorylation Can Lead to Oscillations.”. Biophys J 101 (11): 2572-81. Reference Link
Ursell, Tristan S, Jeffrey Nguyen, Russell D Monds, Alexandre Colavin, Gabriel Billings, Nikolay Ouzounov, Zemer Gitai, Joshua W Shaevitz, and Kerwyn Casey Huang. (2014) 2014. “Rod-Like Bacterial Shape Is Maintained by Feedback Between Cell Curvature and Cytoskeletal Localization.”. Proc Natl Acad Sci U S A 111 (11). Reference Link
Houchmandzadeh, B, E Wieschaus, and S Leibler. (2005) 2005. “Precise Domain Specification in the Developing Drosophila Embryo.”. Phys Rev E Stat Nonlin Soft Matter Phys 72 (6 Pt 1): 061920. Reference Link
Sun, Mingzhai, Morgane Wartel, Eric Cascales, Joshua W Shaevitz, and Tâm Mignot. (2011) 2011. “Motor-Driven Intracellular Transport Powers Bacterial Gliding Motility.”. Proc Natl Acad Sci U S A 108 (18): 7559-64. Reference Link
Shaevitz, Joshua W, and Daniel A Fletcher. (2007) 2007. “Load Fluctuations Drive Actin Network Growth.”. Proc Natl Acad Sci U S A 104 (40): 15688-92. Reference Link
Little, Shawn C, Gašper Tkačik, Thomas B Kneeland, Eric F Wieschaus, and Thomas Gregor. (2011) 2011. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized MRNA.”. PLoS Biol 9 (3): e1000596. Reference Link
Cheung, Lily S, David S A Simakov, Alisa Fuchs, George Pyrowolakis, and Stanislav Y Shvartsman. (2013) 2013. “Dynamic Model for the Coordination of Two Enhancers of Broad by EGFR Signaling.”. Proc Natl Acad Sci U S A 110 (44): 17939-44. Reference Link
Brauer, Matthew J, Curtis Huttenhower, Edoardo M Airoldi, Rachel Rosenstein, John C Matese, David Gresham, Viktor M Boer, Olga G Troyanskaya, and David Botstein. (2008) 2008. “Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast.”. Mol Biol Cell 19 (1): 352-67. Reference Link
Mehta, Pankaj, and Thomas Gregor. (2010) 2010. “Approaching the Molecular Origins of Collective Dynamics in Oscillating Cell Populations.”. Curr Opin Genet Dev 20 (6): 574-80. Reference Link
Batsilas, Lazaros, Alexander M Berezhkovskii, and Stanislav Y Shvartsman. (2003) 2003. “Stochastic Model of Autocrine and Paracrine Signals in Cell Culture Assays.”. Biophys J 85 (6): 3659-65. Reference Link
Leffler, Ellen M, Kevin Bullaughey, Daniel R Matute, Wynn K Meyer, Laure Ségurel, Aarti Venkat, Peter Andolfatto, and Molly Przeworski. 2012. “Revisiting an Old Riddle: What Determines Genetic Diversity Levels Within Species?”. PLoS Biol 10 (9): e1001388. Reference Link
Endres, Robert G, and Ned S Wingreen. (2006) 2006. “Precise Adaptation in Bacterial Chemotaxis through ‘assistance neighborhoods’.”. Proc Natl Acad Sci U S A 103 (35): 13040-4. Reference Link
Krotov, Dmitry, Julien Dubuis, Thomas Gregor, and William Bialek. (2014) 2014. “Morphogenesis at Criticality.”. Proc Natl Acad Sci U S A 111 (10): 3683-8. Reference Link
Mukhopadhyay, Ranjan, Kerwyn Casey Huang, and Ned S Wingreen. (2008) 2008. “Lipid Localization in Bacterial Cells through Curvature-Mediated Microphase Separation.”. Biophys J 95 (3): 1034-49. Reference Link
Berezhkovskii, Alexander M, Christine Sample, and Stanislav Y Shvartsman. (2011) 2011. “Formation of Morphogen Gradients: Local Accumulation Time.”. Phys Rev E Stat Nonlin Soft Matter Phys 83 (5 Pt 1): 051906. Reference Link
Papatsenko, Dmitri, and Michael S Levine. (2008) 2008. “Dual Regulation by the Hunchback Gradient in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 105 (8): 2901-6. Reference Link
Bialek, William, and Sima Setayeshgar. (2008) 2008. “Cooperativity, Sensitivity, and Noise in Biochemical Signaling.”. Phys Rev Lett 100 (25): 258101. Reference Link
Teng, Shu-Wen, Jessica N Schaffer, Kimberly C Tu, Pankaj Mehta, Wenyun Lu, N P Ong, Bonnie L Bassler, and Ned S Wingreen. (2011) 2011. “Active Regulation of Receptor Ratios Controls Integration of Quorum-Sensing Signals in Vibrio Harveyi.”. Mol Syst Biol 7: 491. Reference Link
Mora, Thierry, Howard Yu, Yoshiyuki Sowa, and Ned S Wingreen. (2009) 2009. “Steps in the Bacterial Flagellar Motor.”. PLoS Comput Biol 5 (10): e1000540. Reference Link
Tolwinski, Nicholas S, and Eric Wieschaus. (2004) 2004. “Rethinking WNT Signaling.”. Trends Genet 20 (4): 177-81. Reference Link
Dubuis, Julien, Gašper Tkačik, Eric F Wieschaus, Thomas Gregor, and William Bialek. (2013) 2013. “Positional Information, in Bits.”. Proc Natl Acad Sci U S A 110 (41): 16301-8. Reference Link
Huang, Kerwyn Casey, David W Ehrhardt, and Joshua W Shaevitz. (2012) 2012. “The Molecular Origins of Chiral Growth in Walled Cells.”. Curr Opin Microbiol 15 (6): 707-14. Reference Link
Mora, Thierry, and Ned S Wingreen. (2010) 2010. “Limits of Sensing Temporal Concentration Changes by Single Cells.”. Phys Rev Lett 104 (24): 248101. Reference Link
Dawes-Hoang, Rachel E, Kush M Parmar, Audrey E Christiansen, Chris B Phelps, Andrea H Brand, and Eric F Wieschaus. (2005) 2005. “Folded Gastrulation, Cell Shape Change and the Control of Myosin Localization.”. Development 132 (18): 4165-78. Reference Link
Yakoby, Nir, Jessica Lembong, Trudi Schüpbach, and Stanislav Y Shvartsman. (2008) 2008. “Drosophila Eggshell Is Patterned by Sequential Action of Feedforward and Feedback Loops.”. Development 135 (2): 343-51. Reference Link
Wingreen, Ned S, and Simon A Levin. (2006) 2006. “Cooperation Among Microorganisms.”. PLoS Biol 4 (9): e299. Reference Link
Swanson, Douglas, and Ned S Wingreen. (2011) 2011. “Active Biopolymers Confer Fast Reorganization Kinetics.”. Phys Rev Lett 107 (21): 218103. Reference Link
Bialek, William, Andrea Cavagna, Irene Giardina, Thierry Mora, Edmondo Silvestri, Massimiliano Viale, and Aleksandra M Walczak. (2012) 2012. “Statistical Mechanics for Natural Flocks of Birds.”. Proc Natl Acad Sci U S A 109 (13): 4786-91. Reference Link
Sourjik, Victor, and Ned S Wingreen. (2012) 2012. “Responding to Chemical Gradients: Bacterial Chemotaxis.”. Curr Opin Cell Biol 24 (2): 262-8. Reference Link
Bialek, William, and Sima Setayeshgar. (2005) 2005. “Physical Limits to Biochemical Signaling.”. Proc Natl Acad Sci U S A 102 (29): 10040-5. Reference Link
Grimm, Oliver, Mathieu Coppey, and Eric Wieschaus. (2010) 2010. “Modelling the Bicoid Gradient.”. Development 137 (14): 2253-64. Reference Link
Monine, Michael I, Alexander M Berezhkovskii, Elizabeth J Joslin, Steven Wiley, Douglas A Lauffenburger, and Stanislav Y Shvartsman. (2005) 2005. “Ligand Accumulation in Autocrine Cell Cultures.”. Biophys J 88 (4): 2384-90. Reference Link
Jeffrey, Stefanie S, Michael J Fero, Anne-Lise Børresen-Dale, and David Botstein. (2002) 2002. “Expression Array Technology in the Diagnosis and Treatment of Breast Cancer.”. Mol Interv 2 (2): 101-9. Reference Link
van Raamsdonk, C D, and S M Tilghman. (2000) 2000. “Dosage Requirement and Allelic Expression of PAX6 During Lens Placode Formation.”. Development 127 (24): 5439-48. Reference Link
Wiley, Steven, Stanislav Y Shvartsman, and Douglas A Lauffenburger. (2003) 2003. “Computational Modeling of the EGF-Receptor System: A Paradigm for Systems Biology.”. Trends Cell Biol 13 (1): 43-50. Reference Link
Wang, Siyuan, Hugo Arellano-Santoyo, Peter A Combs, and Joshua W Shaevitz. (2010) 2010. “Actin-Like Cytoskeleton Filaments Contribute to Cell Mechanics in Bacteria.”. Proc Natl Acad Sci U S A 107 (20): 9182-5. Reference Link
Shaevitz, Joshua W, Steven M Block, and Mark J Schnitzer. (2005) 2005. “Statistical Kinetics of Macromolecular Dynamics.”. Biophys J 89 (4): 2277-85. Reference Link
Wieschaus, E, and D Sweeton. (1988) 1988. “Requirements for X-Linked Zygotic Gene Activity During Cellularization of Early Drosophila Embryos.”. Development 104 (3): 483-93. Reference Link
Berezhkovskii, Alexander M, and Stanislav Y Shvartsman. (2011) 2011. “Physical Interpretation of Mean Local Accumulation Time of Morphogen Gradient Formation.”. J Chem Phys 135 (15): 154115. Reference Link
Mora, Thierry, Howard Yu, and Ned S Wingreen. (2009) 2009. “Modeling Torque Versus Speed, Shot Noise, and Rotational Diffusion of the Bacterial Flagellar Motor.”. Phys Rev Lett 103 (24): 248102. Reference Link
Ureta, Alejandro R, Robert G Endres, Ned S Wingreen, and Thomas J Silhavy. (2007) 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 189 (2): 446-54. Reference Link