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Binding Sites

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  • Skoge, Monica L, Robert G Endres, and Ned S Wingreen. (2006) 2006. “Receptor-Receptor Coupling in Bacterial Chemotaxis: Evidence for Strongly Coupled Clusters.”. Biophys J 90 (12): 4317-26.
    Reference Link
  • Persikov, Anton, V, and Mona Singh. (2011) 2011. “An Expanded Binding Model for Cys2His2 Zinc Finger Protein-DNA Interfaces.”. Phys Biol 8 (3): 035010.
    Reference Link
  • Chi, An, Curtis Huttenhower, Lewis Y Geer, Joshua J Coon, John E P Syka, Dina L Bai, Jeffrey Shabanowitz, Daniel J Burke, Olga G Troyanskaya, and Donald F Hunt. (2007) 2007. “Analysis of Phosphorylation Sites on Proteins from Saccharomyces Cerevisiae by Electron Transfer Dissociation (ETD) Mass Spectrometry.”. Proc Natl Acad Sci U S A 104 (7): 2193-8.
    Reference Link
  • Papatsenko, Dmitri, and Michael Levine. (2005) 2005. “Quantitative Analysis of Binding Motifs Mediating Diverse Spatial Readouts of the Dorsal Gradient in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 102 (14): 4966-71.
    Reference Link
  • Zartman, Jeremiah J, and Stanislav Y Shvartsman. (2007) 2007. “Enhancer Organization: Transistor With a Twist or Something in a Different Vein?”. Curr Biol 17 (24).
    Reference Link
  • Bennett, Bryson D, Elizabeth H Kimball, Melissa Gao, Robin Osterhout, Stephen J Van Dien, and Joshua D Rabinowitz. (2009) 2009. “Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia Coli.”. Nat Chem Biol 5 (8): 593-9.
    Reference Link
  • Ng, Wai-Leung, Yunzhou Wei, Lark J Perez, Jianping Cong, Tao Long, Matthew Koch, Martin F Semmelhack, Ned S Wingreen, and Bonnie L Bassler. (2010) 2010. “Probing Bacterial Transmembrane Histidine Kinase Receptor-Ligand Interactions With Natural and Synthetic Molecules.”. Proc Natl Acad Sci U S A 107 (12): 5575-80.
    Reference Link
  • Ndifon, Wilfred, Ned S Wingreen, and Simon A Levin. (2009) 2009. “Differential Neutralization Efficiency of Hemagglutinin Epitopes, Antibody Interference, and the Design of Influenza Vaccines.”. Proc Natl Acad Sci U S A 106 (21): 8701-6.
    Reference Link
  • Farley, Emma K, Katrina M Olson, Wei Zhang, Alexander J Brandt, Daniel S Rokhsar, and Michael S Levine. (2015) 2015. “Suboptimization of Developmental Enhancers.”. Science 350 (6258): 325-8.
    Reference Link
  • Capra, John A, Roman A Laskowski, Janet M Thornton, Mona Singh, and Thomas A Funkhouser. (2009) 2009. “Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.”. PLoS Comput Biol 5 (12): e1000585.
    Reference Link
  • Persikov, Anton, V, Elizabeth F Rowland, Benjamin L Oakes, Mona Singh, and Marcus B Noyes. (2014) 2014. “Deep Sequencing of Large Library Selections Allows Computational Discovery of Diverse Sets of Zinc Fingers That Bind Common Targets.”. Nucleic Acids Res 42 (3): 1497-508.
    Reference Link
  • Kobren, Shilpa Nadimpalli, and Mona Singh. (2019) 2019. “Systematic Domain-Based Aggregation of Protein Structures Highlights DNA-, RNA- and Other Ligand-Binding Positions.”. Nucleic Acids Res 47 (2): 582-93. doi:10.1093/nar/gky1224.
    Reference Link
  • McIsaac, Scott, Allegra A Petti, Harmen J Bussemaker, and David Botstein. (2012) 2012. “Perturbation-Based Analysis and Modeling of Combinatorial Regulation in the Yeast Sulfur Assimilation Pathway.”. Mol Biol Cell 23 (15): 2993-3007.
    Reference Link
  • Markstein, Michele, and Michael Levine. (2002) 2002. “Decoding Cis-Regulatory DNAs in the Drosophila Genome.”. Curr Opin Genet Dev 12 (5): 601-6.
    Reference Link
  • Munro, Daniel, Dario Ghersi, and Mona Singh. (2018) 2018. “Two Critical Positions in Zinc Finger Domains Are Heavily Mutated in Three Human Cancer Types.”. PLoS Comput Biol 14 (6): e1006290. doi:10.1371/journal.pcbi.1006290.
    Reference Link
  • Kulkarni, Rahul, V, Kerwyn Casey Huang, Morten Kloster, and Ned S Wingreen. (2004) 2004. “Pattern Formation Within Escherichia Coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules.”. Phys Rev Lett 93 (22): 228103.
    Reference Link
  • Persikov, Anton, V, and Mona Singh. (2014) 2014. “De Novo Prediction of DNA-Binding Specificities for Cys2His2 Zinc Finger Proteins.”. Nucleic Acids Res 42 (1): 97-108.
    Reference Link
  • Wetzel, Joshua L, and Mona Singh. (2020) 2020. “Sharing DNA-Binding Information across Structurally Similar Proteins Enables Accurate Specificity Determination.”. Nucleic Acids Res 48 (2): e9. doi:10.1093/nar/gkz1087.
    Reference Link
  • Papatsenko, Dmitri, Yury Goltsev, and Michael Levine. (2009) 2009. “Organization of Developmental Enhancers in the Drosophila Embryo.”. Nucleic Acids Res 37 (17): 5665-77.
    Reference Link
  • Nibu, Yutaka, Kate Senger, and Michael Levine. (2003) 2003. “CtBP-Independent Repression in the Drosophila Embryo.”. Mol Cell Biol 23 (11): 3990-9.
    Reference Link
  • Stathopoulos, Angelike, and Michael Levine. (2005) 2005. “Localized Repressors Delineate the Neurogenic Ectoderm in the Early Drosophila Embryo.”. Dev Biol 280 (2): 482-93.
    Reference Link
  • Bialek, William, and Sima Setayeshgar. (2008) 2008. “Cooperativity, Sensitivity, and Noise in Biochemical Signaling.”. Phys Rev Lett 100 (25): 258101.
    Reference Link
  • Endres, Robert G, and Ned S Wingreen. (2006) 2006. “Weight Matrices for Protein-DNA Binding Sites from a Single Co-Crystal Structure.”. Phys Rev E Stat Nonlin Soft Matter Phys 73 (6 Pt 1): 061921.
    Reference Link
  • Ghersi, Dario, and Mona Singh. (2014) 2014. “Interaction-Based Discovery of Functionally Important Genes in Cancers.”. Nucleic Acids Res 42 (3): e18.
    Reference Link
  • Cande, Jessica Doran, Yury Goltsev, and Michael S Levine. (2009) 2009. “Conservation of Enhancer Location in Divergent Insects.”. Proc Natl Acad Sci U S A 106 (34): 14414-9.
    Reference Link
  • Pompeani, Audra J, Joseph J Irgon, Michael F Berger, Martha L Bulyk, Ned S Wingreen, and Bonnie L Bassler. (2008) 2008. “The Vibrio Harveyi Master Quorum-Sensing Regulator, LuxR, a TetR-Type Protein Is Both an Activator and a Repressor: DNA Recognition and Binding Specificity at Target Promoters.”. Mol Microbiol 70 (1): 76-88.
    Reference Link
  • Wang, Wei, Michael Cherry, Yigal Nochomovitz, Emmitt Jolly, David Botstein, and Hao Li. (2005) 2005. “Inference of Combinatorial Regulation in Yeast Transcriptional Networks: A Case Study of Sporulation.”. Proc Natl Acad Sci U S A 102 (6): 1998-2003.
    Reference Link
  • Broedersz, Chase P, Xindan Wang, Yigal Meir, Joseph J Loparo, David Z Rudner, and Ned S Wingreen. (2014) 2014. “Condensation and Localization of the Partitioning Protein ParB on the Bacterial Chromosome.”. Proc Natl Acad Sci U S A 111 (24): 8809-14.
    Reference Link
  • Kelly, Robert C, Megan E Bolitho, Douglas A Higgins, Wenyun Lu, Wai-Leung Ng, Philip D Jeffrey, Joshua D Rabinowitz, Martin F Semmelhack, Frederick M Hughson, and Bonnie L Bassler. (2009) 2009. “The Vibrio Cholerae Quorum-Sensing Autoinducer CAI-1: Analysis of the Biosynthetic Enzyme CqsA.”. Nat Chem Biol 5 (12): 891-5.
    Reference Link
  • Senger, Kate, Grant W Armstrong, William J Rowell, Jennifer M Kwan, Michele Markstein, and Michael Levine. (2004) 2004. “Immunity Regulatory DNAs Share Common Organizational Features in Drosophila.”. Mol Cell 13 (1): 19-32.
    Reference Link
  • Osada, Robert, Elena Zaslavsky, and Mona Singh. (2004) 2004. “Comparative Analysis of Methods for Representing and Searching for Transcription Factor Binding Sites.”. Bioinformatics 20 (18): 3516-25.
    Reference Link
  • Endres, Robert G, Thomas C Schulthess, and Ned S Wingreen. (2004) 2004. “Toward an Atomistic Model for Predicting Transcription-Factor Binding Sites.”. Proteins 57 (2): 262-8.
    Reference Link
  • Yoshimoto, Hiroyuki, Kirstie Saltsman, Audrey P Gasch, Hong Xia Li, Nobuo Ogawa, David Botstein, Patrick O Brown, and Martha S Cyert. (2002) 2002. “Genome-Wide Analysis of Gene Expression Regulated by the Calcineurin Crz1p Signaling Pathway in Saccharomyces Cerevisiae.”. J Biol Chem 277 (34): 31079-88.
    Reference Link
  • Hark, A T, and S M Tilghman. (1998) 1998. “Chromatin Conformation of the H19 Epigenetic Mark.”. Hum Mol Genet 7 (12): 1979-85.
    Reference Link
  • Click, Eleanor S, Tim Stearns, and David Botstein. (2002) 2002. “Systematic Structure-Function Analysis of the Small GTPase Arf1 in Yeast.”. Mol Biol Cell 13 (5): 1652-64.
    Reference Link
  • Markstein, Michele, Peter Markstein, Vicky Markstein, and Michael S Levine. (2002) 2002. “Genome-Wide Analysis of Clustered Dorsal Binding Sites Identifies Putative Target Genes in the Drosophila Embryo.”. Proc Natl Acad Sci U S A 99 (2): 763-8.
    Reference Link
  • Jiang, Peng, and Mona Singh. (2014) 2014. “CCAT: Combinatorial Code Analysis Tool for Transcriptional Regulation.”. Nucleic Acids Res 42 (5): 2833-47.
    Reference Link
  • McIsaac, Scott, Benjamin L Oakes, Xin Wang, Krysta A Dummit, David Botstein, and Marcus B Noyes. (2013) 2013. “Synthetic Gene Expression Perturbation Systems With Rapid, Tunable, Single-Gene Specificity in Yeast.”. Nucleic Acids Res 41 (4): e57.
    Reference Link
  • Bowman, Aaron B, John M Levorse, Robert S Ingram, and Shirley M Tilghman. (2003) 2003. “Functional Characterization of a Testis-Specific DNA Binding Activity at the H19 Igf2 Imprinting Control Region.”. Mol Cell Biol 23 (22): 8345-51.
    Reference Link
  • Troyanskaya, Olga G, Kara Dolinski, Art B Owen, Russ B Altman, and David Botstein. (2003) 2003. “A Bayesian Framework for Combining Heterogeneous Data Sources for Gene Function Prediction (in Saccharomyces cerevisiae).”. Proc Natl Acad Sci U S A 100 (14): 8348-53.
    Reference Link
  • McIsaac, Scott, Patrick A Gibney, Sunil S Chandran, Kirsten R Benjamin, and David Botstein. (2014) 2014. “Synthetic Biology Tools for Programming Gene Expression Without Nutritional Perturbations in Saccharomyces Cerevisiae.”. Nucleic Acids Res 42 (6): e48.
    Reference Link
  • Katz, David J, Michael A Beer, John M Levorse, and Shirley M Tilghman. (2005) 2005. “Functional Characterization of a Novel Ku70 80 Pause Site at the H19 Igf2 Imprinting Control Region.”. Mol Cell Biol 25 (10): 3855-63.
    Reference Link
  • Shaevitz, Joshua W, Elio A Abbondanzieri, Robert Landick, and Steven M Block. (2003) 2003. “Backtracking by Single RNA Polymerase Molecules Observed at Near-Base-Pair Resolution.”. Nature 426 (6967): 684-7.
    Reference Link
  • Hong, Joung-Woo, David A Hendrix, and Michael S Levine. (2008) 2008. “Shadow Enhancers As a Source of Evolutionary Novelty.”. Science 321 (5894): 1314.
    Reference Link
  • Berman, Benjamin P, Yutaka Nibu, Barret D Pfeiffer, Pavel Tomancak, Susan E Celniker, Michael Levine, Gerald M Rubin, and Michael B Eisen. (2002) 2002. “Exploiting Transcription Factor Binding Site Clustering to Identify Cis-Regulatory Modules Involved in Pattern Formation in the Drosophila Genome.”. Proc Natl Acad Sci U S A 99 (2): 757-62.
    Reference Link
  • Klein, Daryl E, Valerie M Nappi, Gregory T Reeves, Stanislav Y Shvartsman, and Mark A Lemmon. (2004) 2004. “Argos Inhibits Epidermal Growth Factor Receptor Signalling by Ligand Sequestration.”. Nature 430 (7003): 1040-4.
    Reference Link

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