Published in BMC Bioinformatics on October 28, 2004
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
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Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res (2005) 4.28
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58
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Universal patterns of purifying selection at noncoding positions in bacteria. Genome Res (2007) 1.11
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Variable structure motifs for transcription factor binding sites. BMC Genomics (2010) 0.95
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. BMC Bioinformatics (2006) 0.95
Modeling an evolutionary conserved circadian cis-element. PLoS Comput Biol (2008) 0.93
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Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. BMC Bioinformatics (2007) 0.91
Systematic identification of conserved motif modules in the human genome. BMC Genomics (2010) 0.91
Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs. BMC Bioinformatics (2006) 0.91
Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol (2009) 0.90
GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima. BMC Bioinformatics (2006) 0.90
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation. BMC Genomics (2009) 0.89
CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. PLoS Comput Biol (2008) 0.87
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Erasing errors due to alignment ambiguity when estimating positive selection. Mol Biol Evol (2014) 0.84
Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics. Plant Physiol (2012) 0.84
BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences. BMC Bioinformatics (2006) 0.83
CoMoDis: composite motif discovery in mammalian genomes. Nucleic Acids Res (2006) 0.83
A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs. BMC Bioinformatics (2012) 0.81
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Phylogeny based discovery of regulatory elements. BMC Bioinformatics (2006) 0.81
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Integration of known transcription factor binding site information and gene expression data to advance from co-expression to co-regulation. Genomics Proteomics Bioinformatics (2007) 0.80
MotifClick: prediction of cis-regulatory binding sites via merging cliques. BMC Bioinformatics (2011) 0.80
New insights into the genetic regulation of Plasmodium falciparum obtained by Bayesian modeling. Gene Regul Syst Bio (2007) 0.80
Cell interactions and patterned intercalations shape and link epithelial tubes in C. elegans. PLoS Genet (2013) 0.79
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The effect of orthology and coregulation on detecting regulatory motifs. PLoS One (2010) 0.78
MTAP: the motif tool assessment platform. BMC Bioinformatics (2008) 0.78
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Inference of transcriptional regulation using gene expression data from the bovine and human genomes. BMC Genomics (2007) 0.78
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Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. J Exp Bot (2016) 0.75
Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies. BMC Bioinformatics (2017) 0.75
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Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res (2001) 4.22
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics (2002) 3.61
Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res (2003) 3.53
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res (2004) 2.84
Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res (2000) 2.80
Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. Pac Symp Biocomput (2004) 2.17
Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics (2003) 2.06
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Res (2002) 1.87
Motif discovery in heterogeneous sequence data. Pac Symp Biocomput (2004) 1.60
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Mol Microbiol (2003) 5.68
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet (2009) 4.72
Finding motifs using random projections. J Comput Biol (2002) 4.61
Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell (2007) 4.58
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol (2005) 4.48
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Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res (2007) 3.59
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Genome-wide orchestration of cardiac functions by the orphan nuclear receptors ERRalpha and gamma. Cell Metab (2007) 3.00
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A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res (2009) 2.55
Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (2004) 2.50
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PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res (2006) 2.27
Evolutionarily conserved sequence elements that positively regulate IFN-gamma expression in T cells. Proc Natl Acad Sci U S A (2004) 2.21
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The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68
Discovery of regulatory elements in vertebrates through comparative genomics. Nat Biotechnol (2005) 1.65
A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol (2007) 1.53
Measuring the accuracy of genome-size multiple alignments. Genome Biol (2007) 1.50
BH3-ligand regulates access of MCL-1 to its E3 ligase. FEBS Lett (2005) 1.49
A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet (2013) 1.37
The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res (2010) 1.36
Exact and heuristic algorithms for the Indel Maximum Likelihood Problem. J Comput Biol (2007) 1.35
Analysis of computational approaches for motif discovery. Algorithms Mol Biol (2006) 1.34
High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods (2009) 1.24
The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol Cell Proteomics (2010) 1.23
On the inference of parsimonious indel evolutionary scenarios. J Bioinform Comput Biol (2006) 1.14
Seeder: discriminative seeding DNA motif discovery. Bioinformatics (2008) 1.10
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A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics (2012) 1.03
Modeling contaminants in AP-MS/MS experiments. J Proteome Res (2010) 1.03
MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. Nucleic Acids Res (2006) 1.03
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Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol (2010) 0.99
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases. PLoS Comput Biol (2009) 0.99
Identification of the Treponema pallidum subsp. pallidum TP0092 (RpoE) regulon and its implications for pathogen persistence in the host and syphilis pathogenesis. J Bacteriol (2012) 0.99
Detecting non-coding selective pressure in coding regions. BMC Evol Biol (2007) 0.98
Long-range regulation is a major driving force in maintaining genome integrity. BMC Evol Biol (2009) 0.94
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Computing chromosome conformation. Methods Mol Biol (2010) 0.90
Hox in motion: tracking HoxA cluster conformation during differentiation. Nucleic Acids Res (2013) 0.90
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PLoS One (2011) 0.90
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Predicting direct protein interactions from affinity purification mass spectrometry data. Algorithms Mol Biol (2010) 0.86
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Following the 'tracks': Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin, Dynamin, and the homeobox protein Mirror. Dev Biol (2013) 0.85
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics (2008) 0.85
Detection of locally over-represented GO terms in protein-protein interaction networks. J Comput Biol (2010) 0.85
Genome-wide mouse mutagenesis reveals CD45-mediated T cell function as critical in protective immunity to HSV-1. PLoS Pathog (2013) 0.84
Nuclear import of RNA polymerase II is coupled with nucleocytoplasmic shuttling of the RNA polymerase II-associated protein 2. Nucleic Acids Res (2013) 0.84
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Classifying leukemia types with chromatin conformation data. Genome Biol (2014) 0.83
TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum ssp. pallidum. Mol Microbiol (2009) 0.83
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Mapping association between long-range cis-regulatory regions and their target genes using synteny. J Comput Biol (2011) 0.77
Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics (2011) 0.77
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