Published in J Mol Biol on August 15, 1997
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A (2002) 3.07
Inferring binding energies from selected binding sites. PLoS Comput Biol (2009) 2.66
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
Determining the specificity of protein-DNA interactions. Nat Rev Genet (2010) 2.38
Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol (2007) 2.04
Adaptive evolution of transcription factor binding sites. BMC Evol Biol (2004) 2.03
Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet (2009) 1.95
Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res (2006) 1.88
In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol (2007) 1.82
Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. Proc Natl Acad Sci U S A (2005) 1.68
From "simple" DNA-protein interactions to the macromolecular machines of gene expression. Annu Rev Biophys Biomol Struct (2007) 1.67
Sequence of the genome of Salmonella bacteriophage P22. J Bacteriol (2000) 1.56
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites. Proc Natl Acad Sci U S A (2008) 1.49
Transcriptional regulation by competing transcription factor modules. PLoS Comput Biol (2006) 1.47
Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res (2002) 1.46
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. Nucleic Acids Res (2005) 1.27
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc Natl Acad Sci U S A (2010) 1.23
From biophysics to evolutionary genetics: statistical aspects of gene regulation. BMC Bioinformatics (2007) 1.22
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Res (2007) 1.17
Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci U S A (2011) 1.11
Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinformatics (2007) 1.06
Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor. Nucleic Acids Res (2004) 0.92
Modeling the quantitative specificity of DNA-binding proteins from example binding sites. PLoS One (2009) 0.91
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. BMC Bioinformatics (2009) 0.89
A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery. Nucleic Acids Res (2008) 0.89
Evolutionary meandering of intermolecular interactions along the drift barrier. Proc Natl Acad Sci U S A (2014) 0.89
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucleic Acids Res (2002) 0.88
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Genetics (2014) 0.86
Formation of regulatory modules by local sequence duplication. PLoS Comput Biol (2011) 0.85
Splicing enhancement in the yeast rp51b intron. RNA (2000) 0.85
Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res (2013) 0.84
Percolation of the phd repressor-operator interface. J Bacteriol (2005) 0.82
Spec-seq: determining protein-DNA-binding specificity by sequencing. Brief Funct Genomics (2014) 0.80
From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters. BMC Mol Biol (2009) 0.79
Assessing the effects of symmetry on motif discovery and modeling. PLoS One (2011) 0.77
Dynamics of Transcription Factor Binding Site Evolution. PLoS Genet (2015) 0.77
Proteins searching for their target on DNA by one-dimensional diffusion: overcoming the "speed-stability" paradox. J Biol Phys (2013) 0.76
cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum. Eukaryot Cell (2006) 0.75
Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers. Nucleic Acids Res (2011) 0.75
A case study of the dynamics of in vitro DNA evolution under constant selection pressure. J Mol Evol (2008) 0.75
Information content of binding sites on nucleotide sequences. J Mol Biol (1986) 30.48
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (1999) 14.36
Characterization of translational initiation sites in E. coli. Nucleic Acids Res (1982) 11.91
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res (1982) 9.99
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation. Nucleic Acids Res (1982) 7.79
Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res (1992) 7.51
Quantifying residual HIV-1 replication in patients receiving combination antiretroviral therapy. N Engl J Med (1999) 7.07
Enhanced long-term potentiation and impaired learning in mice with mutant postsynaptic density-95 protein. Nature (1998) 6.29
Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci (1990) 6.16
An hPer2 phosphorylation site mutation in familial advanced sleep phase syndrome. Science (2001) 6.07
IL-17 stimulates the production and expression of proinflammatory cytokines, IL-beta and TNF-alpha, by human macrophages. J Immunol (1998) 5.79
Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci (1997) 5.51
BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control. Immunity (2000) 5.36
Structure of the bacteriophage phi29 DNA packaging motor. Nature (2000) 5.25
Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic Acids Res (1989) 5.22
Selection of optimal DNA oligos for gene expression arrays. Bioinformatics (2001) 5.19
Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res (1992) 4.93
Consensus patterns in DNA. Methods Enzymol (1990) 4.89
Delila system tools. Nucleic Acids Res (1984) 4.84
Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res (1997) 4.04
Information content and free energy in DNA--protein interactions. J Theor Biol (1998) 3.91
The Emerging Risk Factors Collaboration: analysis of individual data on lipid, inflammatory and other markers in over 1.1 million participants in 104 prospective studies of cardiovascular diseases. Eur J Epidemiol (2007) 3.81
ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput (2000) 3.66
Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry (1990) 3.64
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
Constitutive activation of Stat3 signaling abrogates apoptosis in squamous cell carcinogenesis in vivo. Proc Natl Acad Sci U S A (2000) 3.44
A putative exchange factor for Rho1 GTPase is required for initiation of cytokinesis in Drosophila. Genes Dev (1999) 3.25
Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Res (1993) 3.15
Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol Microbiol (1992) 3.10
Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res (1986) 3.02
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput Appl Biosci (1995) 2.83
Mortality attributable to cigarette smoking in China. JAMA (1997) 2.72
Modeling regulatory networks with weight matrices. Pac Symp Biocomput (1999) 2.52
lacZ translation initiation mutations. J Mol Biol (1984) 2.51
A comparative genomics approach to prediction of new members of regulons. Genome Res (2001) 2.37
Synthesis of epothilones A and B in solid and solution phase. Nature (1997) 2.35
Measuring recent thymic emigrants in blood of normal and HIV-1-infected individuals before and after effective therapy. J Exp Med (1999) 2.33
Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA. J Mol Biol (1988) 2.32
Identifying target sites for cooperatively binding factors. Bioinformatics (2001) 2.31
Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J Mol Biol (1992) 2.29
Mental-physical co-morbidity and its relationship with disability: results from the World Mental Health Surveys. Psychol Med (2008) 2.15
High interlaboratory reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry-based species identification of nonfermenting bacteria. J Clin Microbiol (2009) 2.13
A vascular endothelial growth factor antagonist is produced by the human placenta and released into the maternal circulation. Biol Reprod (1998) 2.12
Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res (2001) 2.12
Depression-anxiety relationships with chronic physical conditions: results from the World Mental Health Surveys. J Affect Disord (2007) 2.12
Uncoupling protein-3 is a mediator of thermogenesis regulated by thyroid hormone, beta3-adrenergic agonists, and leptin. J Biol Chem (1997) 2.06
NS5A, a nonstructural protein of hepatitis C virus, binds growth factor receptor-bound protein 2 adaptor protein in a Src homology 3 domain/ligand-dependent manner and perturbs mitogenic signaling. Proc Natl Acad Sci U S A (1999) 2.03
Transcriptional repression by the proto-oncogene BCL-6. Oncogene (1996) 1.94
Constitutive μ-opioid receptor activity leads to long-term endogenous analgesia and dependence. Science (2013) 1.91
A consensus sequence for binding of Lrp to DNA. J Bacteriol (1995) 1.88
Occupational exposure to bisphenol-A (BPA) and the risk of self-reported male sexual dysfunction. Hum Reprod (2009) 1.87
Deficiency in fatty acid synthase leads to premature cell death and dramatic alterations in plant morphology. Plant Cell (2000) 1.84
Identification of protein coding regions in genomic DNA. J Mol Biol (1995) 1.77
Structure determination of the head-tail connector of bacteriophage phi29. Acta Crystallogr D Biol Crystallogr (2001) 1.74
Detection of incidental colorectal tumours with 18F-labelled 2-fluoro-2-deoxyglucose positron emission tomography/computed tomography scans: results of a prospective study. Colorectal Dis (2011) 1.73
Quantum criticality and nodal superconductivity in the FeAs-based superconductor KFe2As2. Phys Rev Lett (2010) 1.68
An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics (1998) 1.66
P-element mutations affecting embryonic peripheral nervous system development in Drosophila melanogaster. Genetics (1995) 1.65
Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res (1994) 1.63
Field performance of transgenic elite commercial hybrid rice expressing bacillus thuringiensis delta-endotoxin. Nat Biotechnol (2000) 1.62
Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol (1996) 1.61
Pulse methylprednisolone treatment of idiopathic steroid-resistant nephrotic syndrome. Pediatr Nephrol (2001) 1.60
P-element insertion alleles of essential genes on the third chromosome of Drosophila melanogaster: mutations affecting embryonic PNS development. Genetics (1997) 1.60
atonal regulates neurite arborization but does not act as a proneural gene in the Drosophila brain. Neuron (2000) 1.58
CooA, a CO-sensing transcription factor from Rhodospirillum rubrum, is a CO-binding heme protein. Proc Natl Acad Sci U S A (1997) 1.57
Autoregulation of gene expression. Quantitative evaluation of the expression and function of the bacteriophage T4 gene 32 (single-stranded DNA binding) protein system. J Mol Biol (1982) 1.57
From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops. Proc Natl Acad Sci U S A (1997) 1.56
Characterization of the region encoding the CO-induced hydrogenase of Rhodospirillum rubrum. J Bacteriol (1996) 1.54
Prostaglandin E(2) regulates the level and stability of cyclooxygenase-2 mRNA through activation of p38 mitogen-activated protein kinase in interleukin-1 beta-treated human synovial fibroblasts. J Biol Chem (2001) 1.54
Syntaxin 1A interacts with multiple exocytic proteins to regulate neurotransmitter release in vivo. Neuron (1999) 1.52
Microglial activation and dopaminergic cell injury: an in vitro model relevant to Parkinson's disease. J Neurosci (2001) 1.52
The complete genome of Enterovirus 71 China strain. Sci China C Life Sci (2001) 1.50
Mutations affecting the development of the peripheral nervous system in Drosophila: a molecular screen for novel proteins. Genetics (2000) 1.49
Antizyme protects against abnormal accumulation and toxicity of polyamines in ornithine decarboxylase-overproducing cells. Proc Natl Acad Sci U S A (1994) 1.46
Association of perceived stigma and mood and anxiety disorders: results from the World Mental Health Surveys. Acta Psychiatr Scand (2008) 1.46
Factors influencing survival after AIDS: report from the Multicenter AIDS Cohort Study (MACS). J Acquir Immune Defic Syndr (1994) 1.43
Regulation of vascular endothelial growth factor expression by acidosis in human cancer cells. Oncogene (2001) 1.41
Deletion of the murine Duffy gene (Dfy) reveals that the Duffy receptor is functionally redundant. Mol Cell Biol (2000) 1.40
Bone marrow mesenchymal stem cell transplantation improves ovarian function and structure in rats with chemotherapy-induced ovarian damage. Cytotherapy (2008) 1.38
Impact of APOE in mild cognitive impairment. Neurology (2004) 1.37
Overexpression of protective antigen as a novel approach to enhance vaccine efficacy of Brucella abortus strain RB51. Infect Immun (2000) 1.32
Regulation of leptin promoter function by Sp1, C/EBP, and a novel factor. Endocrinology (1998) 1.30
Aldosterone and angiotensin II synergistically stimulate migration in vascular smooth muscle cells through c-Src-regulated redox-sensitive RhoA pathways. Arterioscler Thromb Vasc Biol (2008) 1.28
Production and characterization of monoclonal antibodies specific for the lipopolysaccharide of Escherichia coli O157. J Clin Microbiol (1997) 1.27
Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1. J Virol (2001) 1.27
The single-channel dose-response relation is consistently steep for rod cyclic nucleotide-gated channels: implications for the interpretation of macroscopic dose-response relations. Biochemistry (1999) 1.25
Species-specific in vitro pharmacological effects of the cannabinoid receptor 2 (CB2) selective ligand AM1241 and its resolved enantiomers. Br J Pharmacol (2007) 1.24
Regulation of BOB.1/OBF.1 stability by SIAH. EMBO J (2001) 1.23
Anti-malarial agent artesunate inhibits TNF-alpha-induced production of proinflammatory cytokines via inhibition of NF-kappaB and PI3 kinase/Akt signal pathway in human rheumatoid arthritis fibroblast-like synoviocytes. Rheumatology (Oxford) (2007) 1.23
Distribution of medical insurance in China. Soc Sci Med (1995) 1.23
Complementation of Brucella abortus RB51 with a functional wboA gene results in O-antigen synthesis and enhanced vaccine efficacy but no change in rough phenotype and attenuation. Infect Immun (2000) 1.22
Reduced Nurr1 expression increases the vulnerability of mesencephalic dopamine neurons to MPTP-induced injury. J Neurochem (1999) 1.21
Constant neurofibrillary changes in the neocortex in progressive supranuclear palsy. Basic differences with Alzheimer's disease and aging. Neurosci Lett (1990) 1.20
Isolation and complete nucleotide sequence of a Chinese Sindbis-like virus. J Gen Virol (2000) 1.19
Brucella abortus strain RB51 as a vector for heterologous protein expression and induction of specific Th1 type immune responses. Infect Immun (2000) 1.18
SAMIE: statistical algorithm for modeling interaction energies. Pac Symp Biocomput (2001) 1.17
A novel marker for assessment of liver matrix remodeling: an enzyme-linked immunosorbent assay (ELISA) detecting a MMP generated type I collagen neo-epitope (C1M). Biomarkers (2011) 1.16
N-methylpurine DNA glycosylase overexpression increases alkylation sensitivity by rapidly removing non-toxic 7-methylguanine adducts. Nucleic Acids Res (2005) 1.15
Determinants of childhood overweight and obesity in China. Br J Nutr (2007) 1.15
Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinformatics (2000) 1.14