Published in BMC Genomics on October 17, 2007
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics (2008) 1.91
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep (2011) 1.25
A transcription factor affinity-based code for mammalian transcription initiation. Genome Res (2009) 1.23
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. BMC Genomics (2008) 1.15
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
Ensemble approach combining multiple methods improves human transcription start site prediction. BMC Genomics (2010) 0.81
Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network. PLoS One (2013) 0.79
Integrated Strategy Improves the Prediction Accuracy of miRNA in Large Dataset. PLoS One (2016) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
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Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 12.33
Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev (2001) 9.54
CpG islands as gene markers in the human genome. Genomics (1992) 7.45
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
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Data mining in bioinformatics using Weka. Bioinformatics (2004) 6.06
Computational identification of promoters and first exons in the human genome. Nat Genet (2001) 5.88
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Computational analysis of core promoters in the Drosophila genome. Genome Biol (2002) 5.60
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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
Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res (2005) 3.59
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Large-scale human promoter mapping using CpG islands. Nat Genet (2000) 3.02
Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach. J Mol Biol (2000) 2.88
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res (2006) 2.52
Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol (2000) 2.41
The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev (2004) 2.30
An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics (2004) 2.19
Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res (2007) 2.12
Promoter prediction analysis on the whole human genome. Nat Biotechnol (2004) 2.08
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol (2006) 2.02
Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics (2002) 1.85
Promoter prediction in the human genome. Bioinformatics (2001) 1.67
Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol (2005) 1.64
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res (2006) 1.55
PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res (2003) 1.41
The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med (2002) 1.36
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res (2007) 1.28
Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res (2003) 1.15
A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun (2006) 1.11
Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. Genome Res (2002) 1.09
Boosting with stumps for predicting transcription start sites. Genome Biol (2007) 1.08
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput Appl Biosci (1997) 0.91
Generalizations of Markov model to characterize biological sequences. BMC Bioinformatics (2005) 0.86
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
Personality, gender, and age in the language of social media: the open-vocabulary approach. PLoS One (2013) 2.14
Identification of transcription factor binding sites in the human genome sequence. Mamm Genome (2002) 2.00
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
Emerging trends in regenerative medicine: a scientometric analysis in CiteSpace. Expert Opin Biol Ther (2012) 1.41
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
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res (2007) 1.28
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
Basonuclin: a novel mammalian maternal-effect gene. Development (2006) 1.18
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
A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun (2006) 1.11
Using prior knowledge to improve genetic network reconstruction from microarray data. In Silico Biol (2004) 1.11
Automatic term list generation for entity tagging. Bioinformatics (2005) 1.10
Search for basonuclin target genes. Biochem Biophys Res Commun (2006) 1.07
Why transcription factor binding sites are ten nucleotides long. Genetics (2012) 1.07
Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biol (2007) 1.05
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
Basonuclin-null mutation impairs homeostasis and wound repair in mouse corneal epithelium. PLoS One (2007) 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
Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure. Circ Cardiovasc Genet (2009) 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
CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids Res (2013) 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
Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. Genome Biol (2009) 0.90
Estimation of ribosomal RNA transcription rate in situ. Biotechniques (2004) 0.90
Determinants of expression variability. Nucleic Acids Res (2014) 0.89
CoRAL: predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Res (2013) 0.88
Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology (2007) 0.88
Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. BMC Cancer (2013) 0.87
Epigenomic and RNA structural correlates of polyadenylation. RNA Biol (2011) 0.87
Gli proteins up-regulate the expression of basonuclin in Basal cell carcinoma. Cancer Res (2004) 0.87
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
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families. Nucleic Acids Res (2009) 0.85
Widespread evidence of viral miRNAs targeting host pathways. BMC Bioinformatics (2013) 0.85
The CRASSS plug-in for integrating annotation data with hierarchical clustering results. Bioinformatics (2004) 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
PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res (2008) 0.83
Three independent determinants of protein evolutionary rate. J Mol Evol (2013) 0.83
Regulating the regulators: modulators of transcription factor activity. Methods Mol Biol (2010) 0.82
TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance. Nucleic Acids Res (2007) 0.82
Mapping ribosomal RNA transcription activity in the mouse eye. Dev Dyn (2006) 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
The 2013 US Government Shutdown (#Shutdown) and health: an emerging role for social media. Am J Public Health (2014) 0.81
A tutorial of the poisson random field model in population genetics. Adv Bioinformatics (2008) 0.81
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis. Nucleic Acids Res (2011) 0.80
Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. Nucleic Acids Res (2013) 0.80
Myocardin-like protein 2 regulates TGFβ signaling in embryonic stem cells and the developing vasculature. Development (2012) 0.79
Molecular study of five Chinese patients with 46XX partial 17a-hydroxylase/17,20-lyase deficiency. Gynecol Endocrinol (2011) 0.78
Development of low-dose reproductive hormone therapies in China. Gynecol Endocrinol (2006) 0.78
Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. BMC Genomics (2013) 0.77
Correlated evolution of positions within mammalian cis elements. PLoS One (2013) 0.76
BNC1 is required for maintaining mouse spermatogenesis. Genesis (2012) 0.76
Epigenomic model of cardiac enhancers with application to genome wide association studies. Pac Symp Biocomput (2013) 0.76
PREDICTING INDIVIDUAL WELL-BEING THROUGH THE LANGUAGE OF SOCIAL MEDIA. Pac Symp Biocomput (2016) 0.75
Expression of variant ribosomal RNA genes in mouse oocytes and preimplantation embryos. Biol Reprod (2011) 0.75
Limitations of threshold-based brain oxygen monitoring for seizure detection. Neurocrit Care (2011) 0.75
Functional divergence of gene duplicates - a domain-centric view. BMC Evol Biol (2012) 0.75
Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1. BMC Evol Biol (2011) 0.75
Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75
Genotyping of a Chinese family with 46,XX and 46,XY 17-hydroxylase deficiency. Gynecol Endocrinol (2009) 0.75
Developmental expression of chicken FOXN1 and putative target genes during feather development. Int J Dev Biol (2014) 0.75
Extracting templates from radiology reports using sequence alignment. Int J Data Min Bioinform (2012) 0.75