Published in PLoS One on January 22, 2014
Varying levels of complexity in transcription factor binding motifs. Nucleic Acids Res (2015) 0.95
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data. BMC Bioinformatics (2015) 0.92
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. Front Genet (2016) 0.79
DiffLogo: a comparative visualization of sequence motifs. BMC Bioinformatics (2015) 0.77
InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites. Bioinformatics (2016) 0.75
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinformatics (2016) 0.75
CircularLogo: A lightweight web application to visualize intra-motif dependencies. BMC Bioinformatics (2017) 0.75
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science (1993) 36.84
Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74
Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res (1984) 21.53
GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell (2007) 16.66
MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res (2006) 15.32
Characterization of translational initiation sites in E. coli. Nucleic Acids Res (1982) 11.91
The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell (1999) 9.74
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38
Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet (2006) 7.18
CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet (2001) 6.80
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
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci U S A (2007) 4.91
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83
F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (2008) 4.77
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins (1990) 4.42
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics (2001) 4.29
An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics (2001) 3.71
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res (2001) 3.63
PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics (2004) 3.63
Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res (2003) 3.53
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol (2005) 3.35
Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol (1999) 3.20
The insulation of genes from external enhancers and silencing chromatin. Proc Natl Acad Sci U S A (2002) 2.60
Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol (2011) 2.58
A weight array method for splicing signal analysis. Comput Appl Biosci (1993) 2.50
Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res (2012) 2.45
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (2004) 2.29
A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep (2013) 1.92
Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science (2004) 1.88
Quantitative prediction of NF-kappa B DNA-protein interactions. Proc Natl Acad Sci U S A (2002) 1.54
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. BMC Bioinformatics (2007) 1.52
The Gibbs Centroid Sampler. Nucleic Acids Res (2007) 1.19
Finding short DNA motifs using permuted Markov models. J Comput Biol (2005) 1.13
De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput Biol (2011) 1.11
Non-additivity in protein-DNA binding. Bioinformatics (2005) 1.09
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. BMC Bioinformatics (2008) 1.08
PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. PLoS Comput Biol (2008) 0.95
Jury remains out on simple models of transcription factor specificity. Nat Biotechnol (2011) 0.92