Published in Nucleic Acids Res on July 07, 2007
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res (2008) 2.00
A reexamination of information theory-based methods for DNA-binding site identification. BMC Bioinformatics (2009) 1.12
Why transcription factor binding sites are ten nucleotides long. Genetics (2012) 1.07
70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence. Nucleic Acids Res (2010) 1.06
The genome organization of Thermotoga maritima reflects its lifestyle. PLoS Genet (2013) 1.00
The fitness landscapes of cis-acting binding sites in different promoter and environmental contexts. PLoS Genet (2010) 0.98
Discovery of novel tumor suppressor p53 response elements using information theory. Nucleic Acids Res (2008) 0.98
A brief review of molecular information theory. Nano Commun Netw (2010) 0.91
Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain. PLoS Genet (2012) 0.86
Genome-wide analysis of the salmonella Fis regulon and its regulatory mechanism on pathogenicity islands. PLoS One (2013) 0.83
Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. PLoS One (2007) 0.83
Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res (2009) 0.82
TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites. EURASIP J Bioinform Syst Biol (2010) 0.81
Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization. PLoS Comput Biol (2013) 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
Downregulation of the Escherichia coli guaB promoter by FIS. Microbiology (2008) 0.79
High-throughput mapping of protein occupancy identifies functional elements without the restriction of a candidate factor approach. Nucleic Acids Res (2010) 0.78
Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74
Information content of binding sites on nucleotide sequences. J Mol Biol (1986) 30.48
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol (1987) 17.53
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res (1982) 9.99
Information content of individual genetic sequences. J Theor Biol (1997) 5.62
Improving biosensor analysis. J Mol Recognit (2000) 4.83
Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol (1992) 3.39
Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. Biotechniques (2004) 2.35
Identifying target sites for cooperatively binding factors. Bioinformatics (2001) 2.31
Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA. Methods Enzymol (1991) 2.18
CLAMP: a biosensor kinetic data analysis program. Trends Biochem Sci (1998) 2.12
Information analysis of human splice site mutations. Hum Mutat (1998) 2.08
The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding. Proc Natl Acad Sci U S A (1991) 1.93
Anatomy of Escherichia coli ribosome binding sites. J Mol Biol (2001) 1.90
Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res (2004) 1.87
Kinetic studies on Cro repressor-operator DNA interaction. J Mol Biol (1987) 1.85
Reading of DNA sequence logos: prediction of major groove binding by information theory. Methods Enzymol (1996) 1.77
Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts. J Mol Biol (1996) 1.74
Selection of DNA binding sites by regulatory proteins. Trends Biochem Sci (1988) 1.73
Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res (1997) 1.69
Information analysis of Fis binding sites. Nucleic Acids Res (1997) 1.66
Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res (1994) 1.63
Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J Mol Biol (2002) 1.60
Neural network models for promoter recognition. J Biomol Struct Dyn (1989) 1.55
Quantitative prediction of NF-kappa B DNA-protein interactions. Proc Natl Acad Sci U S A (2002) 1.54
Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J Mol Biol (2000) 1.49
Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res (2006) 1.47
Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res (2002) 1.46
Real-time DNA binding measurements of the ETS1 recombinant oncoproteins reveal significant kinetic differences between the p42 and p51 isoforms. Protein Sci (1994) 1.44
Evolution of biological information. Nucleic Acids Res (2000) 1.37
Genome organisation and chromatin structure in Escherichia coli. Biochimie (2001) 1.37
DNA-binding properties of the Hin recombinase. J Biol Chem (1989) 1.31
Theory of molecular machines. II. Energy dissipation from molecular machines. J Theor Biol (1991) 1.28
Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIAcore technology. J Mol Recognit (2000) 1.18
FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli. Biochim Biophys Acta (1990) 1.18
Multiple homeostatic mechanisms in the control of P1 plasmid replication. Proc Natl Acad Sci U S A (2005) 1.15
DNA supercoiling and transcription in Escherichia coli: The FIS connection. Biochimie (2001) 1.13
Equilibrium analysis of high affinity interactions using BIACORE. Anal Biochem (1998) 1.13
Survey of the year 2005 commercial optical biosensor literature. J Mol Recognit (2006) 1.04
The promoter of the tgt/sec operon in Escherichia coli is preceded by an upstream activation sequence that contains a high affinity FIS binding site. Nucleic Acids Res (1992) 1.02
Molecular flip-flops formed by overlapping Fis sites. Nucleic Acids Res (2003) 0.92
The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping. Nucleic Acids Res (2001) 0.92
The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis. Mol Microbiol (1996) 0.88
Mechanism of DNA binding by the ADR1 zinc finger transcription factor as determined by SPR. J Mol Biol (2003) 0.87
Subunit exchange and the role of dimer flexibility in DNA binding by the Fis protein. Biochemistry (2002) 0.87
Identification of new Fis binding sites by DNA scission with Fis-1,10-phenanthroline-copper(I) chimeras. Biochemistry (1996) 0.86
Promoter strength prediction based on occurrence frequencies of consensus patterns. J Theor Biol (1994) 0.85
The Fis protein: it's not just for DNA inversion anymore. Mol Microbiol (1993) 0.85
Proteomic and biochemical analysis of purified human immunodeficiency virus type 1 produced from infected monocyte-derived macrophages. J Virol (2006) 3.59
Broadly cross-reactive HIV-1-neutralizing human monoclonal Fab selected for binding to gp120-CD4-CCR5 complexes. Proc Natl Acad Sci U S A (2002) 3.08
Echinomycin, a small-molecule inhibitor of hypoxia-inducible factor-1 DNA-binding activity. Cancer Res (2005) 2.49
Anatomy of Escherichia coli sigma70 promoters. Nucleic Acids Res (2006) 2.25
Small membrane proteins found by comparative genomics and ribosome binding site models. Mol Microbiol (2008) 1.84
Induction of prolonged survival of CD4+ T lymphocytes by intermittent IL-2 therapy in HIV-infected patients. J Clin Invest (2005) 1.82
Identification and characterization of a new cross-reactive human immunodeficiency virus type 1-neutralizing human monoclonal antibody. J Virol (2004) 1.80
Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proc Natl Acad Sci U S A (2007) 1.76
Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res (2007) 1.67
Heparin-regulated release of growth factors in vitro and angiogenic response in vivo to implanted hyaluronan hydrogels containing VEGF and bFGF. Biomaterials (2006) 1.58
Increased efficacy of HIV-1 neutralization by antibodies at low CCR5 surface concentration. Biochem Biophys Res Commun (2006) 1.58
The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function. Nucleic Acids Res (2002) 1.58
Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins. Nucleic Acids Res (2006) 1.47
Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res (2006) 1.47
Xeroderma pigmentosum-variant patients from America, Europe, and Asia. J Invest Dermatol (2008) 1.46
Characterization of the B cell epitopes associated with a truncated form of Pseudomonas exotoxin (PE38) used to make immunotoxins for the treatment of cancer patients. J Immunol (2006) 1.42
Assembly properties of human immunodeficiency virus type 1 Gag-leucine zipper chimeras: implications for retrovirus assembly. J Virol (2008) 1.39
Two essential splice lariat branchpoint sequences in one intron in a xeroderma pigmentosum DNA repair gene: mutations result in reduced XPC mRNA levels that correlate with cancer risk. Hum Mol Genet (2003) 1.34
Selection of a novel gp41-specific HIV-1 neutralizing human antibody by competitive antigen panning. J Immunol Methods (2006) 1.19
Practical application of bioinformatics by the multidisciplinary VIZIER consortium. Antiviral Res (2010) 1.17
Cell type-specific, topoisomerase II-dependent inhibition of hypoxia-inducible factor-1alpha protein accumulation by NSC 644221. Clin Cancer Res (2007) 1.17
Functional role of Alix in HIV-1 replication. Virology (2009) 1.16
Novel high-throughput electrochemiluminescent assay for identification of human tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors and characterization of furamidine (NSC 305831) as an inhibitor of Tdp1. Nucleic Acids Res (2007) 1.16
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. Nucleic Acids Res (2006) 1.15
A high-throughput fluorescence-anisotropy screen that identifies small molecule inhibitors of the DNA binding of B-ZIP transcription factors. Anal Biochem (2005) 1.09
A novel high-affinity human monoclonal antibody to mesothelin. Int J Cancer (2011) 1.06
Application of azide-alkyne cycloaddition 'click chemistry' for the synthesis of Grb2 SH2 domain-binding macrocycles. Bioorg Med Chem Lett (2006) 1.06
Dual growth factor-induced angiogenesis in vivo using hyaluronan hydrogel implants. Biomaterials (2005) 1.05
Molecular characterization of feline immunodeficiency virus budding. J Virol (2007) 1.04
Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry. Proteomics (2004) 1.00
The DNA binding and 3'-end preferential activity of human tyrosyl-DNA phosphodiesterase. Nucleic Acids Res (2010) 1.00
Multiple interactions across the surface of the gp120 core structure determine the global neutralization resistance phenotype of human immunodeficiency virus type 1. J Virol (2003) 0.98
Comparative analyses of a small molecule/enzyme interaction by multiple users of Biacore technology. Anal Biochem (2004) 0.98
Discovery of novel tumor suppressor p53 response elements using information theory. Nucleic Acids Res (2008) 0.98
Gastric cancer-specific protein profile identified using endoscopic biopsy samples via MALDI mass spectrometry. J Proteome Res (2010) 0.98
Discovery of small-molecule human immunodeficiency virus type 1 entry inhibitors that target the gp120-binding domain of CD4. J Virol (2005) 0.96
Protected aminooxyprolines for expedited library synthesis: application to Tsg101-directed proline-oxime containing peptides. Bioorg Med Chem Lett (2007) 0.96
Effect of gelatin on heparin regulation of cytokine release from hyaluronan-based hydrogels. Drug Deliv (2008) 0.96
Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases. Nucleic Acids Res (2005) 0.95
Identification of HIV-1 nucleocapsid protein: nucleic acid antagonists with cellular anti-HIV activity. Biochem Biophys Res Commun (2002) 0.95
Evaluation of macrocyclic Grb2 SH2 domain-binding peptide mimetics prepared by ring-closing metathesis of C-terminal allylglycines with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic. Bioorg Med Chem (2005) 0.94
Identification of conserved vault RNA expression elements and a non-expressed mouse vault RNA gene. Gene (2003) 0.93
Energy cost of infection burden: an approach to understanding the dynamics of host-pathogen interactions. J Theor Biol (2005) 0.92
Molecular flip-flops formed by overlapping Fis sites. Nucleic Acids Res (2003) 0.92
A high-throughput screen for identification of molecular mimics of Smac/DIABLO utilizing a fluorescence polarization assay. Anal Biochem (2003) 0.91
SAR by oxime-containing peptide libraries: application to Tsg101 ligand optimization. Chembiochem (2008) 0.90
4-Pregnen-21-ol-3,20-dione-21-(4-bromobenzenesulfonate) (NSC 88915) and related novel steroid derivatives as tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors. J Med Chem (2009) 0.89
Role of Ets/Id proteins for telomerase regulation in human cancer cells. Exp Mol Pathol (2003) 0.89
Ring-closing metathesis of C-terminal allylglycine residues with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic as an approach to novel Grb2 SH2 domain-binding macrocycles. Chembiochem (2005) 0.89
Quantitative assessment of islets of Langerhans encapsulated in alginate. Tissue Eng Part C Methods (2011) 0.89
Single DNA molecule stretching measures the activity of chemicals that target the HIV-1 nucleocapsid protein. Anal Biochem (2006) 0.88
Synthesis and biological evaluation of the first dual tyrosyl-DNA phosphodiesterase I (Tdp1)-topoisomerase I (Top1) inhibitors. J Med Chem (2012) 0.87
Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands. Nucleic Acids Res (2006) 0.85
Oxime-based linker libraries as a general approach for the rapid generation and screening of multidentate inhibitors. Nat Protoc (2012) 0.85
A novel mechanism for inhibition of HIV-1 reverse transcriptase. Bioorg Chem (2002) 0.85
Synthesis and biological evaluation of indenoisoquinolines that inhibit both tyrosyl-DNA phosphodiesterase I (Tdp1) and topoisomerase I (Top1). J Med Chem (2012) 0.84
Conserved structures exposed in HIV-1 envelope glycoproteins stabilized by flexible linkers as potent entry inhibitors and potential immunogens. Biochemistry (2002) 0.83
Elucidation of New Binding Interactions with the Tumor Susceptibility Gene 101 (Tsg101) Protein Using Modified HIV-1 Gag-p6 Derived Peptide Ligands. ACS Med Chem Lett (2011) 0.83
The octapeptidic end of the C-terminal tail of histone H2A is cleaved off in cells exposed to carcinogenic nickel(II). Chem Res Toxicol (2003) 0.82
A very early induction of major vault protein accompanied by increased drug resistance in U-937 cells. Int J Cancer (2002) 0.82
Quantitative cortical synapse proteomics of a transgenic migraine mouse model with mutated Ca(V)2.1 calcium channels. Proteomics (2010) 0.82
Synthesis of a C-terminally biotinylated macrocyclic peptide mimetic exhibiting high Grb2 SH2 domain-binding affinity. Bioorg Med Chem (2005) 0.82
Perfusion effects and hydrodynamics. Adv Biochem Eng Biotechnol (2007) 0.82
Macrocyclization in the design of non-phosphorus-containing Grb2 SH2 domain-binding ligands. J Med Chem (2004) 0.82
Synthesis of a 5-methylindolyl-containing macrocycle that displays ultrapotent Grb2 SH2 domain-binding affinity. J Med Chem (2004) 0.82
Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction. Chem Biodivers (2005) 0.81
Design and synthesis of conformationally constrained Grb2 SH2 domain binding peptides employing alpha-methylphenylalanyl based phosphotyrosyl mimetics. J Med Chem (2005) 0.81
Enrichment of low-molecular-weight proteins from biofluids for biomarker discovery. Expert Rev Proteomics (2005) 0.80
A novel macrocyclic tetrapeptide mimetic that exhibits low-picomolar Grb2 SH2 domain-binding affinity. Biochem Biophys Res Commun (2003) 0.80
Retinoic acid-induced downmodulation of telomerase activity in human cancer cells. Exp Mol Pathol (2005) 0.80
Enhanced Transport Capabilities via Nanotechnologies: Impacting Bioefficacy, Controlled Release Strategies, and Novel Chaperones. J Drug Deliv (2011) 0.79
Measuring the binding stoichiometry of HIV-1 Gag to very-low-density oligonucleotide surfaces using surface plasmon resonance spectroscopy. J Biomol Tech (2007) 0.79
Selectivity and mechanism of action of a growth factor receptor-bound protein 2 SRC homology 2 domain binding antagonist. J Med Chem (2008) 0.79