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
“Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
, “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.
, “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.”, Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
, “RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis.”, Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 2015.
, “Condensation and localization of the partitioning protein ParB on the bacterial chromosome.”, Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
, “Cell shape can mediate the spatial organization of the bacterial cytoskeleton.”, Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
, “ELAV mediates 3' UTR extension in the Drosophila nervous system.”, Genes Dev, vol. 26, no. 20, pp. 2259-64, 2012.
, “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
, “Dynamics of cooperativity in chemical sensing among cell-surface receptors.”, Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
, “Filament depolymerization can explain chromosome pulling during bacterial mitosis.”, PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.”, PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
, “Stalled Hox promoters as chromosomal boundaries.”, Genes Dev, vol. 23, no. 13, pp. 1505-9, 2009.
, “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.
, “The role of input noise in transcriptional regulation.”, PLoS One, vol. 3, no. 7, p. e2774, 2008.
, “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”, Proc Natl Acad Sci U S A, vol. 104, no. 7, pp. 2193-8, 2007.
, “Functional analysis of gene duplications in Saccharomyces cerevisiae.”, Genetics, vol. 175, no. 2, pp. 933-43, 2007.
, “Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters.”, Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
, “Weight matrices for protein-DNA binding sites from a single co-crystal structure.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 73, no. 6 Pt 1, p. 061921, 2006.
, “Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.”, Mol Cell Biol, vol. 25, no. 10, pp. 3855-63, 2005.
, “Argos inhibits epidermal growth factor receptor signalling by ligand sequestration.”, Nature, vol. 430, no. 7003, pp. 1040-4, 2004.
, “Comparative analysis of methods for representing and searching for transcription factor binding sites.”, Bioinformatics, vol. 20, no. 18, pp. 3516-25, 2004.
, “Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules.”, Phys Rev Lett, vol. 93, no. 22, p. 228103, 2004.
, “Predicting specificity in bZIP coiled-coil protein interactions.”, Genome Biol, vol. 5, no. 2, p. R11, 2004.
, “Rethinking WNT signaling.”, Trends Genet, vol. 20, no. 4, pp. 177-81, 2004.
, “Signal propagation and failure in discrete autocrine relays.”, Phys Rev Lett, vol. 93, no. 11, p. 118101, 2004.
, “Computational modeling of the EGF-receptor system: a paradigm for systems biology.”, Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
, “CtBP-independent repression in the Drosophila embryo.”, Mol Cell Biol, vol. 23, no. 11, pp. 3990-9, 2003.
, “Long-range signal transmission in autocrine relays.”, Biophys J, vol. 84, no. 2 Pt 1, pp. 883-96, 2003.
, “Probing the kinesin reaction cycle with a 2D optical force clamp.”, Proc Natl Acad Sci U S A, vol. 100, no. 5, pp. 2351-6, 2003.
, “Transitions in the model of epithelial patterning.”, Dev Dyn, vol. 226, no. 1, pp. 155-9, 2003.
, “CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus.”, Nature, vol. 405, no. 6785, pp. 486-9, 2000.
, “A Drosophila homolog of the tumor suppressor gene adenomatous polyposis coli down-regulates beta-catenin but its zygotic expression is not essential for the regulation of Armadillo.”, Proc Natl Acad Sci U S A, vol. 94, no. 1, pp. 242-7, 1997.
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