Published in Nucleic Acids Res on May 11, 1982
Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res (1984) 21.53
Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res (1985) 9.17
Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Res (1984) 6.08
ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res (2003) 5.12
Compilation and analysis of DNA sequences associated with apparent streptomycete promoters. Nucleic Acids Res (1992) 4.95
Delila system tools. Nucleic Acids Res (1984) 4.84
A computer algorithm for testing potential prokaryotic terminators. Nucleic Acids Res (1984) 4.73
Portable microcomputer software for nucleotide sequence analysis. Nucleic Acids Res (1982) 4.72
The current status and portability of our sequence handling software. Nucleic Acids Res (1986) 4.54
Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc Natl Acad Sci U S A (1990) 4.45
Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01
Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res (1983) 3.81
Structure and mapping of antigenic domains of protein antigen b, a 38,000-molecular-weight protein of Mycobacterium tuberculosis. Infect Immun (1989) 3.43
Gene sequence and predicted amino acid sequence of the motA protein, a membrane-associated protein required for flagellar rotation in Escherichia coli. J Bacteriol (1984) 3.41
Nitrogen fixation specific regulatory genes of Klebsiella pneumoniae and Rhizobium meliloti share homology with the general nitrogen regulatory gene ntrC of K. pneumoniae. Nucleic Acids Res (1985) 3.38
DNA sequence of mip, a Legionella pneumophila gene associated with macrophage infectivity. Infect Immun (1989) 3.29
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol (2004) 3.15
Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res (1986) 3.02
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A biophysical approach to transcription factor binding site discovery. Genome Res (2003) 2.62
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res (2005) 2.58
Machine learning and its applications to biology. PLoS Comput Biol (2007) 2.57
Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol (2006) 2.53
The complete nucleotide sequence of the gene coding for diphtheria toxin in the corynephage omega (tox+) genome. Nucleic Acids Res (1983) 2.51
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
DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
Tandem translation starts in the cheA locus of Escherichia coli. J Bacteriol (1991) 1.97
A survey of motif discovery methods in an integrated framework. Biol Direct (2006) 1.94
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Rhizobium meliloti fixGHI sequence predicts involvement of a specific cation pump in symbiotic nitrogen fixation. J Bacteriol (1989) 1.87
Sequence analysis and transcriptional regulation of the Escherichia coli grpE gene, encoding a heat shock protein. Nucleic Acids Res (1988) 1.87
Nucleotide sequence encoding the flavoprotein and hydrophobic subunits of the succinate dehydrogenase of Escherichia coli. Biochem J (1984) 1.78
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. Genome Res (2006) 1.78
Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA replication. EMBO J (1984) 1.75
The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription. J Bacteriol (1988) 1.73
Nucleotide sequence of the small double-stranded RNA segment of bacteriophage phi 6: novel mechanism of natural translational control. J Virol (1986) 1.72
Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res (1997) 1.69
Nucleotide sequence of the transcription unit containing the aroL and aroM genes from Escherichia coli K-12. J Bacteriol (1986) 1.66
Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res (1994) 1.63
Improved models for transcription factor binding site identification using nonindependent interactions. Genetics (2012) 1.61
Signal search analysis: a new method to localize and characterize functionally important DNA sequences. Nucleic Acids Res (1984) 1.60
Probabilistic inference of transcription factor binding from multiple data sources. PLoS One (2008) 1.58
Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A (2012) 1.55
Neural network optimization for E. coli promoter prediction. Nucleic Acids Res (1991) 1.54
Nucleotide sequence of the structural gene for dUTPase of Escherichia coli K-12. EMBO J (1983) 1.53
The complete nucleotide sequence of the adenylate cyclase gene of Escherichia coli. Nucleic Acids Res (1984) 1.53
Structural and transcriptional evidence for related thrS and infC expression. Proc Natl Acad Sci U S A (1983) 1.51
Modeling the specificity of protein-DNA interactions. Quant Biol (2013) 1.50
Structural and functional relationships between fumarase and aspartase. Nucleotide sequences of the fumarase (fumC) and aspartase (aspA) genes of Escherichia coli K12. Biochem J (1986) 1.50
Characterization of a two-gene locus from Bartonella bacilliformis associated with the ability to invade human erythrocytes. Infect Immun (1995) 1.49
MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics (2009) 1.49
Genes 55, alpha gt, 47 and 46 of bacteriophage T4: the genomic organization as deduced by sequence analysis. EMBO J (1985) 1.46
Protein classification artificial neural system. Protein Sci (1992) 1.43
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics (2009) 1.42
A systematic, large-scale comparison of transcription factor binding site models. BMC Genomics (2016) 1.39
Evolution of biological information. Nucleic Acids Res (2000) 1.37
Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions. FEBS Lett (2007) 1.37
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning. Genome Biol (2017) 1.37
Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless. Genome Res (2006) 1.32
The complete nucleotide sequence of bacteriophage HP1 DNA. Nucleic Acids Res (1996) 1.32
Peptidyl-tRNA hydrolase is involved in lambda inhibition of host protein synthesis. EMBO J (1991) 1.31
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res (2014) 1.31
Molecular characterization of the 98-kilodalton iron-regulated outer membrane protein of Neisseria meningitidis. Infect Immun (1993) 1.29
Identification and utilization of arbitrary correlations in models of recombination signal sequences. Genome Biol (2002) 1.29
The asiA gene of bacteriophage T4 codes for the anti-sigma 70 protein. J Bacteriol (1993) 1.28
Sequence and cloning of bacteriophage T4 gene 63 encoding RNA ligase and tail fibre attachment activities. EMBO J (1984) 1.27
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
Escherichia coli translational initiation factor IF3: a unique case of translational regulation. Proc Natl Acad Sci U S A (1984) 1.25
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res (2005) 1.22
Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks. Mol Biol Cell (2002) 1.20
The bacteriophage T4 regA gene: primary sequence of a translational repressor. Nucleic Acids Res (1984) 1.19
A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Res (2013) 1.18
Complete nucleotide sequence of the fumarase gene fumA, of Escherichia coli. Nucleic Acids Res (1984) 1.18
Nucleotide sequence of the genome of Pf3, an IncP-1 plasmid-specific filamentous bacteriophage of Pseudomonas aeruginosa. J Virol (1985) 1.16
Prediction of splice junctions in mRNA sequences. Nucleic Acids Res (1985) 1.14
Nucleotide sequence analysis of the cat gene of Proteus mirabilis: comparison with the type I (Tn9) cat gene. J Bacteriol (1985) 1.14
Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants. Genome Res (2013) 1.14
An efficient Shine-Dalgarno sequence but not translation is necessary for lacZ mRNA stability in Escherichia coli. J Bacteriol (1994) 1.12
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol (2008) 1.12
Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12. J Bacteriol (1989) 1.12
In vivo gene expression directed by synthetic promoter constructions restricted to the -10 and -35 consensus hexamers of E. coli. Nucleic Acids Res (1989) 1.12
Maximally efficient modeling of DNA sequence motifs at all levels of complexity. Genetics (2011) 1.10
Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics (2012) 1.09
Murein-metabolizing enzymes from Escherichia coli: sequence analysis and controlled overexpression of the slt gene, which encodes the soluble lytic transglycosylase. J Bacteriol (1991) 1.09
Search for basonuclin target genes. Biochem Biophys Res Commun (2006) 1.07
Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling. J Exp Med (2003) 1.06
Interactions of Sox10 and Egr2 in myelin gene regulation. Neuron Glia Biol (2007) 1.04
Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput Biol (2013) 1.04
Cloning, genetic analysis, and nucleotide sequence of a determinant coding for a 19-kilodalton peptidoglycan-associated protein (Ppl) of Legionella pneumophila. Infect Immun (1991) 1.04
Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984. Nomenclature Committee of the International Union of Biochemistry (NC-IUB). Proc Natl Acad Sci U S A (1986) 1.04
Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic Acids Res (2007) 1.02
Computational identification and functional validation of regulatory motifs in cartilage-expressed genes. Genome Res (2007) 1.01
Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev (2014) 1.01
A general procedure for locating and analyzing protein-binding sequence motifs in nucleic acids. Proc Natl Acad Sci U S A (1998) 0.98
Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res (2009) 0.98
Self-organized neural maps of human protein sequences. Protein Sci (1994) 0.95
Translational initiation in prokaryotes. Annu Rev Microbiol (1981) 18.46
Autoregulation and function of a repressor in bacteriophage lambda. Science (1976) 6.83
The nucleotide sequence of tufB and four nearby tRNA structural genes of Escherichia coli. Gene (1980) 5.66
The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res (1981) 5.52
A role for mRNA secondary structure in the control of translation initiation. Nature (1982) 5.01
Nucleotide sequence from the genetic left end of bacteriophage T7 DNA to the beginning of gene 4. J Mol Biol (1981) 4.56
The nucleotide sequence of the cloned tufA gene of Escherichia coli. Gene (1980) 4.17
The genome of bacteriophage T4. Bacteriol Rev (1976) 3.74
Nucleotide sequence of the lexA gene of E. coli. Cell (1981) 3.61
Nucleotide sequence of the lexA gene of Escherichia coli K-12. Nucleic Acids Res (1981) 2.75
Nucleotide sequence coding for the respiratory NADH dehydrogenase of Escherichia coli. UUG initiation codon. Eur J Biochem (1981) 2.73
Nucleotide sequence of the gene for ribosomal protein S20 and its flanking regions. J Biol Chem (1981) 2.41
Temperature-sensitive mutation in the initiation codon of the rIIB gene of bacteriophage T4. Proc Natl Acad Sci U S A (1979) 2.18
Protein cleavage during virus assembly: a novel specificity of assembly dependent cleavage in bacteriophage T4. Proc Natl Acad Sci U S A (1976) 1.55
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science (1990) 35.96
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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
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
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A consensus sequence for binding of Lrp to DNA. J Bacteriol (1995) 1.88
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Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res (1994) 1.63
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Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol (1996) 1.61
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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
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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
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