Published in BMC Bioinformatics on June 04, 2008
A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Res (2013) 1.18
De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput Biol (2011) 1.11
P-value-based regulatory motif discovery using positional weight matrices. Genome Res (2012) 1.09
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Res (2012) 0.97
On the value of intra-motif dependencies of human insulator protein CTCF. PLoS One (2014) 0.92
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data. BMC Bioinformatics (2015) 0.92
Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis. BMC Bioinformatics (2010) 0.85
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data. Bioinformatics (2011) 0.84
In silico identification of short nucleotide sequences associated with gene expression of pollen development in rice. Plant Cell Physiol (2008) 0.84
PairMotif+: a fast and effective algorithm for de novo motif discovery in DNA sequences. Int J Biol Sci (2013) 0.83
MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data. Nucleic Acids Res (2012) 0.83
DISCOVER: a feature-based discriminative method for motif search in complex genomes. Bioinformatics (2009) 0.81
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. BMC Bioinformatics (2013) 0.79
POWRS: position-sensitive motif discovery. PLoS One (2012) 0.78
MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biol (2009) 0.76
Unsupervised statistical discovery of spaced motifs in prokaryotic genomes. BMC Genomics (2017) 0.75
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. BMC Bioinformatics (2016) 0.75
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. BMC Bioinformatics (2010) 0.75
Differences in local genomic context of bound and unbound motifs. Gene (2012) 0.75
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
A greedy algorithm for aligning DNA sequences. J Comput Biol (2000) 47.89
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (1999) 14.36
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol (2000) 14.30
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol (2003) 7.72
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res (2004) 5.66
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res (2002) 4.29
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res (2001) 4.29
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics (2001) 4.29
High-resolution computational models of genome binding events. Nat Biotechnol (2006) 3.74
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res (2003) 3.71
Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res (2003) 3.53
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res (2006) 2.52
Finding functional sequence elements by multiple local alignment. Nucleic Acids Res (2004) 2.37
Clustering of DNA sequences in human promoters. Genome Res (2004) 2.30
Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res (2004) 1.69
Predicting transcription factor binding sites using local over-representation and comparative genomics. BMC Bioinformatics (2006) 1.50
Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet Genome Res (2005) 1.44
Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. J Comput Biol (2004) 1.40
Analysis of computational approaches for motif discovery. Algorithms Mol Biol (2006) 1.34
The identification of complete domains within protein sequences using accurate E-values for semi-global alignment. Nucleic Acids Res (2007) 1.24
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics (2005) 1.17
Combining frequency and positional information to predict transcription factor binding sites. Bioinformatics (2001) 1.16
Adding sequence context to a Markov background model improves the identification of regulatory elements. Bioinformatics (2006) 0.87
Lambda's switch: lessons from a module swap. Curr Biol (2006) 0.87
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A (2012) 10.22
Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol (2004) 2.78
Origin and evolution of human microRNAs from transposable elements. Genetics (2007) 2.39
Finding functional sequence elements by multiple local alignment. Nucleic Acids Res (2004) 2.37
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res (2002) 2.30
Evolutionary significance of gene expression divergence. Gene (2004) 2.04
Extrapolating from sequence--the 2009 H1N1 'swine' influenza virus. Nat Biotechnol (2009) 1.96
CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol (2012) 1.84
Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. Bioinformatics (2010) 1.73
Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res (2004) 1.69
Global similarity and local divergence in human and mouse gene co-expression networks. BMC Evol Biol (2006) 1.32
The identification of complete domains within protein sequences using accurate E-values for semi-global alignment. Nucleic Acids Res (2007) 1.24
Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements. Mol Cell Biol (2005) 1.18
Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol (2007) 1.17
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics (2005) 1.17
Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J Bacteriol (2012) 1.16
The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction. BMC Genomics (2012) 1.09
The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment. Nucleic Acids Res (2005) 1.07
The whole alignment and nothing but the alignment: the problem of spurious alignment flanks. Nucleic Acids Res (2008) 1.04
Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. Mob DNA (2010) 1.04
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics (2008) 1.02
Genome sequence of the Mycobacterium colombiense type strain, CECT 3035. J Bacteriol (2011) 0.98
Repetitive DNA elements, nucleosome binding and human gene expression. Gene (2009) 0.96
HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells. Mol Cell Biol (2013) 0.95
ESTIMATING THE GUMBEL SCALE PARAMETER FOR LOCAL ALIGNMENT OF RANDOM SEQUENCES BY IMPORTANCE SAMPLING WITH STOPPING TIMES. Ann Stat (2009) 0.95
Identification of immunity related genes to study the Physalis peruviana--Fusarium oxysporum pathosystem. PLoS One (2013) 0.94
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. Nucleic Acids Res (2008) 0.92
Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana. PLoS One (2011) 0.91
Expression patterns of protein kinases correlate with gene architecture and evolutionary rates. PLoS One (2008) 0.88
Prediction of transposable element derived enhancers using chromatin modification profiles. PLoS One (2011) 0.88
Adding sequence context to a Markov background model improves the identification of regulatory elements. Bioinformatics (2006) 0.87
Benchmarking computational tools for polymorphic transposable element detection. Brief Bioinform (2016) 0.85
Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome. Nucleic Acids Res (2010) 0.85
A c-Myc regulatory subnetwork from human transposable element sequences. Mol Biosyst (2009) 0.85
Identification of cis-regulatory elements in gene co-expression networks using A-GLAM. Methods Mol Biol (2009) 0.85
New finite-size correction for local alignment score distributions. BMC Res Notes (2012) 0.84
The correlation error and finite-size correction in an ungapped sequence alignment. Bioinformatics (2002) 0.83
Virulence and immune response induced by Mycobacterium avium complex strains in a model of progressive pulmonary tuberculosis and subcutaneous infection in BALB/c mice. Infect Immun (2013) 0.83
Effect of the transposable element environment of human genes on gene length and expression. Genome Biol Evol (2011) 0.82
Coalescent: an open-source and scalable framework for exact calculations in coalescent theory. BMC Bioinformatics (2012) 0.82
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements. BMC Bioinformatics (2006) 0.80
Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae. PLoS One (2011) 0.79
In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex. BMC Struct Biol (2012) 0.79
Objective method for estimating asymptotic parameters, with an application to sequence alignment. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.78
Polymorphism of the Pv200L fragment of merozoite surface protein-1 of Plasmodium vivax in clinical isolates from the Pacific coast of Colombia. Am J Trop Med Hyg (2011) 0.77
NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. BMC Genomics (2013) 0.76
Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera. PLoS One (2013) 0.76
Transcriptional regulation of N-acetylglutamate synthase. PLoS One (2012) 0.76
The practical evaluation of DNA barcode efficacy. Methods Mol Biol (2012) 0.76
Differences in local genomic context of bound and unbound motifs. Gene (2012) 0.75
Competitive inhibition of heparinase by persulfonated glycosaminoglycans: a tool to detect heparin contamination. Anal Chem (2011) 0.75
Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75
Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses. BMC Res Notes (2013) 0.75
Promoter analysis: gene regulatory motif identification with A-GLAM. Methods Mol Biol (2009) 0.75
This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction. Int J Bioinform Res Appl (2014) 0.75