Published in Nucleic Acids Res on April 22, 2007
Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol Endocrinol (2011) 1.25
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res (2011) 1.09
Position-dependent motif characterization using non-negative matrix factorization. Bioinformatics (2008) 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
Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Res (2011) 0.96
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nucleic Acids Res (2009) 0.96
MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics (2007) 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
Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res (2011) 0.90
Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Res (2008) 0.88
Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genet (2013) 0.88
Modeling tissue-specific structural patterns in human and mouse promoters. Nucleic Acids Res (2009) 0.86
Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS One (2012) 0.85
Multivariate Hawkes process models of the occurrence of regulatory elements. BMC Bioinformatics (2010) 0.85
Cell-specific effects of variants of the 68-base pair tandem repeat on prodynorphin gene promoter activity. Addict Biol (2010) 0.84
Manduca sexta moricin promoter elements can increase promoter activities of Drosophila melanogaster antimicrobial peptide genes. Insect Biochem Mol Biol (2011) 0.83
Patterns and evolution of ACGT repeat cis-element landscape across four plant genomes. BMC Genomics (2013) 0.81
Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS One (2008) 0.81
Distance and helical phase dependence of synergistic transcription activation in cis-regulatory module. PLoS One (2012) 0.80
Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution. Genome Biol Evol (2010) 0.79
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. BMC Bioinformatics (2013) 0.79
Abundance, arrangement, and function of sequence motifs in the chicken promoters. BMC Genomics (2014) 0.79
Identification and characterization of an hnRNP E1 translational silencing motif. Nucleic Acids Res (2016) 0.78
Evolutionary Footprints of Short Tandem Repeats in Avian Promoters. Sci Rep (2016) 0.78
A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors. Nucleic Acids Res (2016) 0.78
Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition. PLoS One (2015) 0.76
Balancing selection maintains polymorphisms at neurogenetic loci in field experiments. Proc Natl Acad Sci U S A (2017) 0.76
SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules. PLoS One (2016) 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
Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis. Mol Genet Genomics (2011) 0.75
Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes. Genome Biol Evol (2017) 0.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res (1996) 13.50
Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31
Predicting gene expression from sequence. Cell (2004) 8.12
Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet (2001) 7.74
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Computational analysis of core promoters in the Drosophila genome. Genome Biol (2002) 5.60
Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol (2005) 5.19
Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev (2001) 4.54
The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev (1997) 4.25
CpG islands and genes. Curr Opin Genet Dev (1995) 3.83
Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell (2004) 3.82
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res (2004) 3.73
Megabase deletions of gene deserts result in viable mice. Nature (2004) 2.68
Immunity regulatory DNAs share common organizational features in Drosophila. Mol Cell (2004) 2.58
The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev (2004) 2.30
Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics (2003) 2.06
Identification of transcription factor binding sites in the human genome sequence. Mamm Genome (2002) 2.00
Pax-5 (BSAP) recruits Ets proto-oncogene family proteins to form functional ternary complexes on a B-cell-specific promoter. Genes Dev (1996) 1.98
Decoding human regulatory circuits. Genome Res (2004) 1.70
Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. Bioinformatics (2004) 1.66
Predicting transcription factor synergism. Nucleic Acids Res (2002) 1.66
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res (2004) 1.45
Constraints on spacing between transcription factor binding sites in a simple adenovirus promoter. Genes Dev (1988) 1.44
The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med (2002) 1.36
Perspectives on the RNA polymerase II core promoter. Biochem Soc Trans (2006) 1.20
Gene-Ontology analysis reveals association of tissue-specific 5' CpG-island genes with development and embryogenesis. Hum Mol Genet (2004) 1.16
Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes. Trends Genet (2005) 1.13
Structural requirements of the glucocorticoid and retinoic acid response units in the phosphoenolpyruvate carboxykinase gene promoter. Mol Endocrinol (1998) 1.11
A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun (2006) 1.11
Sequence and spacing of TATA box elements are critical for accurate initiation from the beta-phaseolin promoter. J Biol Chem (2003) 0.98
ACBP--a PPAR and SREBP modulated housekeeping gene. Mol Cell Biochem (2006) 0.91
Transcriptional regulation of protein complexes and biological pathways. Mamm Genome (2003) 0.90
Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics (2006) 0.86
Two distinct classes of CCAAT box elements that bind nuclear factor-Y/alpha-actinin-4: potential role in human CYP1A1 regulation. Toxicol Appl Pharmacol (2004) 0.85
Unique distance- and DNA-turn-dependent interactions in the human protein C gene promoter confer submaximal transcriptional activity. Biochem J (1999) 0.81
A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet (2007) 22.96
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol (2005) 3.98
Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog (2006) 3.67
Selection of target sites for mobile DNA integration in the human genome. PLoS Comput Biol (2006) 3.21
Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet (2012) 2.26
Transcriptional genomics associates FOX transcription factors with human heart failure. Circulation (2006) 2.00
Identification of transcription factor binding sites in the human genome sequence. Mamm Genome (2002) 2.00
GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res (2011) 1.87
Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus. Physiol Genomics (2012) 1.64
Gene coexpression network topology of cardiac development, hypertrophy, and failure. Circ Cardiovasc Genet (2010) 1.46
GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. Development (2007) 1.39
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biol (2009) 1.38
Hopx and Hdac2 interact to modulate Gata4 acetylation and embryonic cardiac myocyte proliferation. Dev Cell (2010) 1.38
Gene profiling of human adipose tissue during evoked inflammation in vivo. Diabetes (2009) 1.34
Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development. Development (2008) 1.32
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep (2011) 1.25
Functional analysis of Hes-1 in preadipocytes. Mol Endocrinol (2005) 1.21
Young proteins experience more variable selection pressures than old proteins. Genome Res (2010) 1.19
GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. Nucleic Acids Res (2013) 1.18
Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis. Genome Biol (2012) 1.16
Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus. Learn Mem (2006) 1.14
Regulation of lung endoderm progenitor cell behavior by miR302/367. Development (2011) 1.14
Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans. PLoS One (2010) 1.13
Susceptibility to myocardial ischemia reperfusion injury at early stage of type 1 diabetes in rats. Cardiovasc Diabetol (2013) 1.13
A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun (2006) 1.11
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res (2011) 1.09
Predictive models for protein crystallization. Methods (2004) 1.08
Why transcription factor binding sites are ten nucleotides long. Genetics (2012) 1.07
N-Acetylcysteine and allopurinol up-regulated the Jak/STAT3 and PI3K/Akt pathways via adiponectin and attenuated myocardial postischemic injury in diabetes. Free Radic Biol Med (2013) 1.07
Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies. J Biotechnol (2011) 1.05
Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biol (2007) 1.05
Lung cancer tumorigenicity and drug resistance are maintained through ALDH(hi)CD44(hi) tumor initiating cells. Oncotarget (2013) 1.00
Genome-wide analysis of natural selection on human cis-elements. PLoS One (2008) 1.00
Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PLoS One (2008) 0.99
Lumbar disc degeneration is linked to a carbohydrate sulfotransferase 3 variant. J Clin Invest (2013) 0.98
Hyperglycemia-induced protein kinase C β2 activation induces diastolic cardiac dysfunction in diabetic rats by impairing caveolin-3 expression and Akt/eNOS signaling. Diabetes (2013) 0.98
Recurring genomic breaks in independent lineages support genomic fragility. BMC Evol Biol (2006) 0.96
Sex and age dimorphism of myocardial gene expression in nonischemic human heart failure. Circ Cardiovasc Genet (2008) 0.96
An SNP selection strategy identified IL-22 associating with susceptibility to tuberculosis in Chinese. Sci Rep (2011) 0.95
MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics (2007) 0.94
Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. Circ Cardiovasc Genet (2009) 0.94
PU.1 can recruit BCL6 to DNA to repress gene expression in germinal center B cells. Mol Cell Biol (2009) 0.94
Improved cell survival and paracrine capacity of human embryonic stem cell-derived mesenchymal stem cells promote therapeutic potential for pulmonary arterial hypertension. Cell Transplant (2012) 0.94
YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus. EMBO J (2013) 0.94
Resistin gene variation is associated with systemic inflammation but not plasma adipokine levels, metabolic syndrome or coronary atherosclerosis in nondiabetic Caucasians. Clin Endocrinol (Oxf) (2008) 0.93
Intrinsically disordered proteins and conformational noise: implications in cancer. Cell Cycle (2012) 0.92
Mouse ribosomal RNA genes contain multiple differentially regulated variants. PLoS One (2008) 0.92
Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Mol Biol Evol (2011) 0.92
CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids Res (2013) 0.92
FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. Bioinformatics (2010) 0.91
Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. Genome Biol (2009) 0.90
dbPSHP: a database of recent positive selection across human populations. Nucleic Acids Res (2013) 0.90
Determinants of expression variability. Nucleic Acids Res (2014) 0.89
Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology (2007) 0.88
Genetic variant representation, annotation and prioritization in the post-GWAS era. Cell Res (2012) 0.88
Epigenomic and RNA structural correlates of polyadenylation. RNA Biol (2011) 0.87
Correlated evolution of transcription factors and their binding sites. Bioinformatics (2011) 0.87
Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. BMC Cancer (2013) 0.87
Vitamin D inhibits COX-2 expression and inflammatory response by targeting thioesterase superfamily member 4. J Biol Chem (2014) 0.87
A functional single-nucleotide polymorphism in the promoter of the gene encoding interleukin 6 is associated with susceptibility to tuberculosis. J Infect Dis (2012) 0.87
A fast and accurate SNP detection algorithm for next-generation sequencing data. Nat Commun (2012) 0.86
Generalizations of Markov model to characterize biological sequences. BMC Bioinformatics (2005) 0.86
Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics (2006) 0.86
Extraventricular neurocytoma in pediatric populations: A case report and review of the literature. Oncol Lett (2013) 0.86
Modeling and analysis of the emergency department at University of Kentucky Chandler Hospital using simulations. J Emerg Nurs (2009) 0.85
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. Nucleic Acids Res (2009) 0.85
Acacetin causes a frequency- and use-dependent blockade of hKv1.5 channels by binding to the S6 domain. J Mol Cell Cardiol (2011) 0.85
Widespread evidence of viral miRNAs targeting host pathways. BMC Bioinformatics (2013) 0.85
EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics (2011) 0.84
Basonuclin regulates a subset of ribosomal RNA genes in HaCaT cells. PLoS One (2007) 0.84
Patterns of sequence conservation in presynaptic neural genes. Genome Biol (2006) 0.84
Three independent determinants of protein evolutionary rate. J Mol Evol (2013) 0.83
PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res (2008) 0.83
TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance. Nucleic Acids Res (2007) 0.82
Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. Brief Bioinform (2014) 0.82
Regulating the regulators: modulators of transcription factor activity. Methods Mol Biol (2010) 0.82
Pituitary tumorous hyperplasia due to primary hypothyroidism. Acta Neurochir (Wien) (2012) 0.82
Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PLoS One (2008) 0.81
A note on efficient computation of haplotypes via perfect phylogeny. J Comput Biol (2004) 0.81
A tutorial of the poisson random field model in population genetics. Adv Bioinformatics (2008) 0.81
Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5, and EOMES in human hepatocellular carcinoma. Genome Biol (2014) 0.80
Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. Nucleic Acids Res (2013) 0.80
Pial arteriovenous fistula with giant venous varix and dilation of vein of Galen, treated with surgical clipping. Acta Neurochir (Wien) (2013) 0.80
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis. Nucleic Acids Res (2011) 0.80
Inference of gene-phenotype associations via protein-protein interaction and orthology. PLoS One (2013) 0.79
DDGni: dynamic delay gene-network inference from high-temporal data using gapped local alignment. Bioinformatics (2013) 0.79
Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature. Development (2012) 0.79
Identification of FAM96B as a novel prelamin A binding partner. Biochem Biophys Res Commun (2013) 0.78
Improved tagmentation-based whole-genome bisulfite sequencing for input DNA from less than 100 mammalian cells. Epigenomics (2015) 0.78
Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. BMC Genomics (2013) 0.77
A novel neural response algorithm for protein function prediction. BMC Syst Biol (2012) 0.77
Correlated evolution of positions within mammalian cis elements. PLoS One (2013) 0.76
wKGGSeq: A Comprehensive Strategy-Based and Disease-Targeted Online Framework to Facilitate Exome Sequencing Studies of Inherited Disorders. Hum Mutat (2015) 0.76
NdPASA: a pairwise sequence alignment server for distantly related proteins. Bioinformatics (2005) 0.76
Epigenomic model of cardiac enhancers with application to genome wide association studies. Pac Symp Biocomput (2013) 0.76
Functional divergence of gene duplicates - a domain-centric view. BMC Evol Biol (2012) 0.75
Histidine-rich proteins in prokaryotes: metal homeostasis and environmental habitat-related occurrence. Metallomics (2013) 0.75
Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1. BMC Evol Biol (2011) 0.75
ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data. Mol Cell Proteomics (2013) 0.75