Published in Genetics on September 09, 2014
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. Nucleic Acids Res (2016) 0.88
Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nat Genet (2016) 0.84
Spec-seq: determining protein-DNA-binding specificity by sequencing. Brief Funct Genomics (2014) 0.80
Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops. J Biol Chem (2015) 0.77
A quantitative understanding of lac repressor's binding specificity and flexibility. Quant Biol (2015) 0.75
Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq. Nucleic Acids Res (2016) 0.75
Inherent limitations of probabilistic models for protein-DNA binding specificity. PLoS Comput Biol (2017) 0.75
Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol (1961) 65.10
DNA binding sites: representation and discovery. Bioinformatics (2000) 16.01
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res (2013) 6.12
DNA-binding specificities of human transcription factors. Cell (2013) 5.14
A systems approach to measuring the binding energy landscapes of transcription factors. Science (2007) 5.06
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci (1998) 5.00
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science (2004) 4.92
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83
A perfectly symmetric lac operator binds the lac repressor very tightly. Proc Natl Acad Sci U S A (1983) 4.24
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell (2008) 3.96
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics (2006) 3.67
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res (2010) 3.46
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell (2011) 3.40
On the specificity of DNA-protein interactions. Proc Natl Acad Sci U S A (1986) 3.11
Dual DNA binding specificity of ADD1/SREBP1 controlled by a single amino acid in the basic helix-loop-helix domain. Mol Cell Biol (1995) 3.10
Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res (1986) 3.02
Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A (2006) 2.97
Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc Natl Acad Sci U S A (1989) 2.76
Inferring binding energies from selected binding sites. PLoS Comput Biol (2009) 2.66
Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc Natl Acad Sci U S A (1989) 2.61
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol (2011) 2.60
Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol (2011) 2.58
The lac repressor. C R Biol (2005) 2.57
Determining the specificity of protein-DNA interactions. Nat Rev Genet (2010) 2.38
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol (2005) 2.28
The lac repressor displays facilitated diffusion in living cells. Science (2012) 2.24
How lac repressor recognizes lac operator. Proc Natl Acad Sci U S A (1978) 2.15
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep (2013) 2.03
Thermodynamic origins of specificity in the lac repressor-operator interaction. Adaptability in the recognition of mutant operator sites. J Mol Biol (1985) 2.00
Quantitative specificity of the Mnt repressor. J Mol Biol (1997) 1.91
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res (2009) 1.88
Mutant lac repressors with new specificities hint at rules for protein--DNA recognition. EMBO J (1990) 1.77
Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution. Structure (1998) 1.71
Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site. J Mol Biol (1997) 1.63
Improved models for transcription factor binding site identification using nonindependent interactions. Genetics (2012) 1.61
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics (2013) 1.61
The next generation of transcription factor binding site prediction. PLoS Comput Biol (2013) 1.55
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol (2011) 1.40
Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J (2002) 1.37
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinformatics (2005) 1.31
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. Nucleic Acids Res (2005) 1.27
lac repressor mutants with double or triple exchanges in the recognition helix bind specifically to lac operator variants with multiple exchanges. EMBO J (1989) 1.18
Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the Lac repressor system. Chem Rev (2004) 1.15
Crystallographic analysis of Lac repressor bound to natural operator O1. J Mol Biol (2001) 1.13
Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation. Nat Genet (2014) 1.12
Deciphering the Sox-Oct partner code by quantitative cooperativity measurements. Nucleic Acids Res (2012) 1.11
Base substitution mutants of the lac operator: in vivo and in vitro affinities for lac repressor. Gene (1986) 1.08
Macromolecular binding equilibria in the lac repressor system: studies using high-pressure fluorescence spectroscopy. Biochemistry (1990) 1.07
Hinge-helix formation and DNA bending in various lac repressor-operator complexes. EMBO J (1999) 1.03
The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. J Mol Biol (1999) 1.02
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res (2014) 1.02
Putting numbers on the network connections. Bioessays (2007) 1.02
Towards evolving a better repressor. Protein Eng Des Sel (2009) 0.99
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data. Nucleic Acids Res (2014) 0.99
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res (2011) 0.97
Engineered disulfide linking the hinge regions within lactose repressor dimer increases operator affinity, decreases sequence selectivity, and alters allostery. Biochemistry (2001) 0.93
Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor. Nucleic Acids Res (2004) 0.92
Specificity of the Mnt protein. Independent effects of mutations at different positions in the operator. J Mol Biol (1993) 0.90
Specificity of the Mnt protein determined by binding to randomized operators. Proc Natl Acad Sci U S A (1991) 0.88
Symmetric lac operator derivatives: effects of half-operator sequence and spacing on repressor affinity. Gene (1990) 0.86
Functional rules for lac repressor-operator associations and implications for protein-DNA interactions. Protein Sci (2010) 0.84
Weak operator binding enhances simulated lac repressor-mediated DNA looping. Biopolymers (2013) 0.83
Theoretical and experimental dissection of DNA loop-mediated repression. Phys Rev Lett (2013) 0.82
Quantitative DNA sequencing to determine the relative protein-DNA binding constants to multiple DNA sequences. Anal Biochem (1994) 0.82
Assessing the effects of symmetry on motif discovery and modeling. PLoS One (2011) 0.77
Combinatorial Cis-regulation in Saccharomyces Species. G3 (Bethesda) (2016) 0.79
Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops. J Biol Chem (2015) 0.77
Inherent limitations of probabilistic models for protein-DNA binding specificity. PLoS Comput Biol (2017) 0.75