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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Vancomycin
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.
Thermodynamics
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.
Structure-Activity Relationship
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Stress, Mechanical
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.
Stochastic Processes
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.
Sequence Analysis, RNA
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Sensitivity and Specificity
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
RNA, Messenger
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
Reproducibility of Results
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Receptors, Formyl Peptide
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.
Proteins
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
Protein Structure, Secondary
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
Protein Folding
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
Protein Biosynthesis
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
Probability
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
Principal Component Analysis
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
Pliability
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
Phase Transition
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.
Peptidoglycan
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.
Peptides
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.
Nucleic Acid Conformation
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Motion
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
Monte Carlo Method
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.
Molecular Sequence Data
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.
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Molecular Conformation
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.
Models, Statistical
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Models, Molecular
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
Models, Chemical
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
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.
Models, Biological
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.
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.
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.
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.
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., 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.
Models, Anatomic
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.
Membrane Proteins
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.
Membrane Fluidity
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.
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.
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.
Lipid Metabolism
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.
Lipid Bilayers
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.
Gram-Negative Bacteria
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.
Genes, Bacterial
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
Gene Expression
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
Escherichia coli Proteins
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.
Escherichia coli
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.
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.
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.
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.
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.
Elasticity
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.
Databases, Protein
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., “Flexibility of beta-sheets: principal component analysis of database protein structures.”, Proteins, vol. 55, no. 1, pp. 91-8, 2004.
Cross-Linking Reagents
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.
Computer Simulation
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.
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.
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.
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.
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Cell Wall
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.
Cell Size
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.
Cell Membrane
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.
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.
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.
Cell Enlargement
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.
Caulobacter crescentus
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.
Cardiolipins
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.
Biophysics
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.
Base Sequence
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Base Composition
R. Mukhopadhyay, Emberly, E., Tang, C., and Wingreen, N. S., “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.
Bacillus subtilis
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., “Exponential sensitivity of noise-driven switching in genetic networks.”, Phys Biol, vol. 5, no. 2, p. 026005, 2008.
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.
Anti-Bacterial Agents
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.
Algorithms
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.