Published in J Mol Biol on April 05, 1986
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res (2003) 52.26
Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74
Predicting deleterious amino acid substitutions. Genome Res (2001) 28.95
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A (1994) 18.46
RNA sequence analysis using covariance models. Nucleic Acids Res (1994) 14.60
Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci U S A (1989) 14.45
Accounting for human polymorphisms predicted to affect protein function. Genome Res (2002) 14.10
Multiple alignment using simulated annealing: branch point definition in human mRNA splicing. Nucleic Acids Res (1992) 12.08
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res (1998) 6.95
Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07
Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic Acids Res (1989) 5.22
A predictive model for regulatory sequences directing liver-specific transcription. Genome Res (2001) 5.16
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res (2002) 5.04
Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol Rev (1996) 4.93
Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res (1992) 4.93
Information content of Caenorhabditis elegans splice site sequences varies with intron length. Nucleic Acids Res (1990) 4.58
Predicting gene regulatory elements in silico on a genomic scale. Genome Res (1998) 4.52
Conserved and variable functions of the sigmaE stress response in related genomes. PLoS Biol (2006) 4.46
Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc Natl Acad Sci U S A (1990) 4.45
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev (2005) 3.78
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. Nucleic Acids Res (2001) 3.77
Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat (2011) 3.75
Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res (2004) 3.53
Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res (1990) 3.46
DNA sequences at immunoglobulin switch region recombination sites. Nucleic Acids Res (1993) 3.18
Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids. Nucleic Acids Res (1993) 3.06
Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res (1993) 2.94
Domain enhanced lookup time accelerated BLAST. Biol Direct (2012) 2.87
PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res (2003) 2.81
The initiation of translation in E. coli: apparent base pairing between the 16srRNA and downstream sequences of the mRNA. Nucleic Acids Res (1990) 2.81
Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res (2000) 2.80
Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci (1994) 2.54
Rapid construction of empirical RNA fitness landscapes. Science (2010) 2.52
Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1. Nucleic Acids Res (1991) 2.48
Training back-propagation neural networks to define and detect DNA-binding sites. Nucleic Acids Res (1991) 2.47
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Determining the specificity of protein-DNA interactions. Nat Rev Genet (2010) 2.38
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics (2009) 2.35
Evolution of biological complexity. Proc Natl Acad Sci U S A (2000) 2.32
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res (2009) 2.27
Anatomy of Escherichia coli sigma70 promoters. Nucleic Acids Res (2006) 2.25
Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes Dev (2003) 2.23
Informational complexity and functional activity of RNA structures. J Am Chem Soc (2004) 2.19
Functional analysis of transcription factor binding sites in human promoters. Genome Biol (2012) 2.12
Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genomics (2004) 2.04
Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol (2007) 2.04
Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet (2013) 2.03
Overlapping codes within protein-coding sequences. Genome Res (2010) 2.02
Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct Integr Genomics (2003) 1.98
Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics (1995) 1.98
Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet (2009) 1.95
Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res (2004) 1.94
Mechanism for iron-regulated transcription of the Escherichia coli cir gene: metal-dependent binding of fur protein to the promoters. J Bacteriol (1989) 1.93
A consensus sequence for cleavage by vertebrate DNA topoisomerase II. Nucleic Acids Res (1988) 1.93
Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis. Proc Natl Acad Sci U S A (1998) 1.90
The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Res (2006) 1.89
rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift. J Bacteriol (1994) 1.88
Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res (2006) 1.88
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biol (2006) 1.87
Prediction of Saccharomyces cerevisiae replication origins. Genome Biol (2004) 1.81
Bacteriophage T4 regA protein binds to mRNAs and prevents translation initiation. Proc Natl Acad Sci U S A (1987) 1.79
Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol (2004) 1.78
The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. BMC Syst Biol (2010) 1.75
MethTools--a toolbox to visualize and analyze DNA methylation data. Nucleic Acids Res (2000) 1.74
Comparative analysis of FUR regulons in gamma-proteobacteria. Nucleic Acids Res (2001) 1.70
The downstream box: an efficient and independent translation initiation signal in Escherichia coli. EMBO J (1996) 1.70
Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res (1997) 1.69
Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res (2007) 1.67
From "simple" DNA-protein interactions to the macromolecular machines of gene expression. Annu Rev Biophys Biomol Struct (2007) 1.67
Information analysis of Fis binding sites. Nucleic Acids Res (1997) 1.66
PARSESNP: A tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res (2003) 1.63
Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res (1994) 1.63
Tn10 insertion specificity is strongly dependent upon sequences immediately adjacent to the target-site consensus sequence. Proc Natl Acad Sci U S A (1992) 1.62
Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res (2010) 1.59
A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J (2011) 1.59
RhlR expression in Pseudomonas aeruginosa is modulated by the Pseudomonas quinolone signal via PhoB-dependent and -independent pathways. J Bacteriol (2006) 1.59
Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein. J Bacteriol (2005) 1.57
Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA (2002) 1.55
The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol (2010) 1.54
Demand theory of gene regulation. II. Quantitative application to the lactose and maltose operons of Escherichia coli. Genetics (1998) 1.53
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinformatics (2007) 1.52
Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471-1480 in 16S ribosomal RNA affects expression of glnS. Nucleic Acids Res (1991) 1.51
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Coevolution of a homing endonuclease and its host target sequence. J Mol Biol (2007) 1.49
Construction and analysis of a profile library characterizing groups of structurally known proteins. Protein Sci (1996) 1.47
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics (2006) 1.44
Identification and characterization of E.coli ribosomal binding sites by free energy computation. Nucleic Acids Res (1993) 1.42
Statistical significance of cis-regulatory modules. BMC Bioinformatics (2007) 1.41
Sequence features that drive human promoter function and tissue specificity. Genome Res (2010) 1.40
The initiation codon affects ribosome binding and translational efficiency in Escherichia coli of cI mRNA with or without the 5' untranslated leader. J Bacteriol (2001) 1.39
Specificity landscapes of DNA binding molecules elucidate biological function. Proc Natl Acad Sci U S A (2010) 1.39
Coding limits on the number of transcription factors. BMC Genomics (2006) 1.38
Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci (1997) 1.38
Evolution of biological information. Nucleic Acids Res (2000) 1.37
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science (1990) 35.96
Translational initiation in prokaryotes. Annu Rev Microbiol (1981) 18.46
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
Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci (1990) 6.16
Extension inhibition analysis of translation initiation complexes. Methods Enzymol (1988) 5.58
Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci (1997) 5.51
Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J Mol Biol (1992) 5.38
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
rII cistrons of bacteriophage T4. DNA sequence around the intercistronic divide and positions of genetic landmarks. J Mol Biol (1981) 4.76
Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection. Cell (1994) 4.24
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
OxyR and SoxRS regulation of fur. J Bacteriol (1999) 3.71
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
Translation of the UGA triplet in vitro by tryptophan transfer RNA's. J Mol Biol (1971) 3.52
RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci U S A (1992) 3.46
The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms. Nucleic Acids Res (2001) 3.45
Determination of the amount of homology required for recombination in bacteriophage T4. Cell (1982) 3.35
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
Selection of the initiator tRNA by Escherichia coli initiation factors. Genes Dev (1989) 2.92
Aptamers as therapeutic and diagnostic agents. J Biotechnol (2000) 2.89
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
Mater, a maternal effect gene required for early embryonic development in mice. Nat Genet (2000) 2.73
SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J Mol Biol (1991) 2.64
A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA. Proc Natl Acad Sci U S A (1976) 2.59
Modeling regulatory networks with weight matrices. Pac Symp Biocomput (1999) 2.52
lacZ translation initiation mutations. J Mol Biol (1984) 2.51
Translational regulation of expression of the bacteriophage T4 lysozyme gene. Nucleic Acids Res (1986) 2.45
A comparative genomics approach to prediction of new members of regulons. Genome Res (2001) 2.37
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
High affinity ligands from in vitro selection: complex targets. Proc Natl Acad Sci U S A (1998) 2.30
Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J Mol Biol (1992) 2.29
Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res (2001) 2.12
Information analysis of human splice site mutations. Hum Mutat (1998) 2.08
Systematic review of randomised controlled trials of sildenafil (Viagra) in the treatment of male erectile dysfunction. Br J Gen Pract (2001) 2.07
No evidence for early decrease in blood oxygenation in rat whisker cortex in response to functional activation. Neuroimage (2001) 2.07
Direct transfer of transforming growth factor beta 1 gene into arteries stimulates fibrocellular hyperplasia. Proc Natl Acad Sci U S A (1993) 2.03
Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. J Mol Biol (1992) 2.00
Autogenous translational repression of bacteriophage T4 gene 32 expression in vitro. J Mol Biol (1978) 1.99
Quantitative specificity of the Mnt repressor. J Mol Biol (1997) 1.91
The effectiveness of the levonorgestrel-releasing intrauterine system in menorrhagia: a systematic review. BJOG (2001) 1.91
Anatomy of Escherichia coli ribosome binding sites. J Mol Biol (2001) 1.90
A consensus sequence for binding of Lrp to DNA. J Bacteriol (1995) 1.88
Dual translational initiation sites control function of the lambda S gene. EMBO J (1989) 1.87
Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3. Genes Dev (1990) 1.81
Bacteriophage T4 regA protein binds to mRNAs and prevents translation initiation. Proc Natl Acad Sci U S A (1987) 1.79
Identification of protein coding regions in genomic DNA. J Mol Biol (1995) 1.77
Inhibition of RNA polymerase by streptolydigin. Nat New Biol (1971) 1.76
Regulation of gene 32 expression during bacteriophage T4 infection of Escherichia coli. J Biol Chem (1976) 1.71
Computation-directed identification of OxyR DNA binding sites in Escherichia coli. J Bacteriol (2001) 1.68
Translational reinitiation in the rIIB cistron of bacteriophage T4. J Mol Biol (1981) 1.67
Transcriptional activation of bacteriophage T4 middle promoters by the motA protein. J Mol Biol (1988) 1.67
An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics (1998) 1.66
Outcome data from the LEAP (Live, Eat and Play) trial: a randomized controlled trial of a primary care intervention for childhood overweight/mild obesity. Int J Obes (Lond) (2006) 1.66
Information analysis of Fis binding sites. Nucleic Acids Res (1997) 1.66
Translational, autogenous regulation of gene 32 expression during bacteriophage T4 infection. J Biol Chem (1976) 1.64
Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res (1994) 1.63
Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function. Proc Natl Acad Sci U S A (1981) 1.63
Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol (1996) 1.61
Influence of mRNA determinants on translation initiation in Escherichia coli. J Mol Biol (1991) 1.61
Overproduction of bacteriophage Q beta maturation (A2) protein leads to cell lysis. Cell (1983) 1.60
The phage T4 nrdB intron: a deletion mutant of a version found in the wild. Genes Dev (1991) 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
The bacteriophage T4 dexA gene: sequence and analysis of a gene conditionally required for DNA replication. Mol Gen Genet (1987) 1.54
Analysis in vivo of translational mutants of the rIIB cistron of bacteriophage T4. J Mol Biol (1981) 1.54
Detection of Escherichia coli ribosome binding at translation initiation sites in the absence of tRNA. J Mol Biol (1991) 1.52
High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites. Biochemistry (1995) 1.50
Libraries for genomic SELEX. Nucleic Acids Res (1997) 1.48
Autogenous translational operator recognized by bacteriophage T4 DNA polymerase. J Mol Biol (1990) 1.48
Mutations affecting translation of the bacteriophage T4 rIIB gene cloned in Escherichia coli. Mol Gen Genet (1987) 1.45
The Rex system of bacteriophage lambda: tolerance and altruistic cell death. Genes Dev (1992) 1.44