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
“Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
, “An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces.”, Phys Biol, vol. 8, no. 3, p. 035010, 2011.
, “Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria.”, Mol Microbiol, vol. 81, no. 2, pp. 340-53, 2011.
, “Riboneogenesis in yeast.”, Cell, vol. 145, no. 6, pp. 969-80, 2011.
, “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.
, “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.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
, “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”, Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
, “Gibbs sampling and helix-cap motifs.”, Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
, “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.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “Toward an atomistic model for predicting transcription-factor binding sites.”, Proteins, vol. 57, no. 2, pp. 262-8, 2004.
, “Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”, J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
, “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 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.
, “Designability of alpha-helical proteins.”, Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 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.
, “Systematic structure-function analysis of the small GTPase Arf1 in yeast.”, Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
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