Published in Genome Res on October 19, 2006
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Multiple non-collinear TF-map alignments of promoter regions. BMC Bioinformatics (2007) 0.86
Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas. BMC Bioinformatics (2011) 0.86
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Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae. BMC Plant Biol (2009) 0.83
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Res (2012) 0.83
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Prediction and experimental validation of novel STAT3 target genes in human cancer cells. PLoS One (2009) 0.83
Functional genomics as a tool in virus research. Indian J Microbiol (2008) 0.82
A fast weak motif-finding algorithm based on community detection in graphs. BMC Bioinformatics (2013) 0.82
Identifying novel transcriptional components controlling energy metabolism. Cell Metab (2011) 0.82
Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition. PLoS One (2011) 0.81
DISCOVER: a feature-based discriminative method for motif search in complex genomes. Bioinformatics (2009) 0.81
Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data. BMC Syst Biol (2008) 0.81
CompMoby: comparative MobyDick for detection of cis-regulatory motifs. BMC Bioinformatics (2008) 0.80
Emerging applications of read profiles towards the functional annotation of the genome. Front Genet (2015) 0.79
Exploring the effects of polymorphisms on cis-regulatory signal transduction response. Trends Mol Med (2012) 0.79
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery. PLoS One (2012) 0.79
A valid strategy for precise identifications of transcription factor binding sites in combinatorial regulation using bioinformatic and experimental approaches. Plant Methods (2013) 0.79
To understand the whole, you must know the parts: unraveling the roles of protein-DNA interactions in genome regulation. Analyst (2011) 0.79
Uncovering transcription factor modules using one- and three-dimensional analyses. J Biol Chem (2012) 0.78
Advanced methods for the analysis of chromatin-associated proteins. Physiol Genomics (2014) 0.78
Identification of transcription factor-DNA interactions using chromatin immunoprecipitation assays. Methods Mol Biol (2009) 0.78
Assessing the effects of symmetry on motif discovery and modeling. PLoS One (2011) 0.77
DiffLogo: a comparative visualization of sequence motifs. BMC Bioinformatics (2015) 0.77
In silico promoters: modelling of cis-regulatory context facilitates target predictio. J Cell Mol Med (2008) 0.76
Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation. Nucleic Acids Res (2008) 0.76
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. BMC Genomics (2012) 0.76
Correlated evolution of positions within mammalian cis elements. PLoS One (2013) 0.76
Synthesis of Arylazide- and Diazirine-Containing CrAsH-EDT2 Photoaffinity Probes. Arch Pharm (Weinheim) (2016) 0.75
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences. BMC Syst Biol (2012) 0.75
HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics (2016) 0.75
Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice. Front Plant Sci (2015) 0.75
The regulatory loop of COMP1 and HNF-4-miR-150-p27 in various signaling pathways. Oncol Lett (2014) 0.75
Chromosome-wide analysis of protein binding and modifications. Methods Mol Biol (2009) 0.75
Promoter analysis: gene regulatory motif identification with A-GLAM. Methods Mol Biol (2009) 0.75
Functional pathway mapping analysis for hypoxia-inducible factors. BMC Syst Biol (2011) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 30.22
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Assembling millions of short DNA sequences using SSAKE. Bioinformatics (2006) 18.71
The Genome sequence of the SARS-associated coronavirus. Science (2003) 16.68
Slider--maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics (2008) 14.04
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med (2010) 13.07
Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature (2011) 9.71
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
De novo transcriptome assembly with ABySS. Bioinformatics (2009) 8.38
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med (2011) 7.35
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res (2006) 6.75
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev (2002) 6.74
Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res (2006) 6.54
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics (2008) 6.53
T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells. Immunity (2004) 6.43
Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev (2004) 6.19
The new paradigm of flow cell sequencing. Genome Res (2008) 5.81
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74
The genetic landscape of high-risk neuroblastoma. Nat Genet (2013) 4.71
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A (2006) 4.18
Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature (2012) 4.13
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res (2008) 4.11
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A (2007) 4.00
Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell (2009) 3.96
Sequence biases in large scale gene expression profiling data. Nucleic Acids Res (2006) 3.83
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80
High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol (2004) 3.76
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet (2007) 3.75
Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods (2002) 3.37
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet (2006) 3.29
ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One (2010) 3.15
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods (2002) 2.99
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics (2006) 2.98
A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res (2007) 2.97
Comparison of sample preparation methods for ChIP-chip assays. Biotechniques (2006) 2.89
High quality SNP calling using Illumina data at shallow coverage. Bioinformatics (2010) 2.82
Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Res (2002) 2.78
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res (2009) 2.74
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res (2004) 2.72
Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J Biol Chem (2002) 2.68
Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. Mol Cell (2006) 2.48
Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Curr Biol (2003) 2.47
Hive plots--rational approach to visualizing networks. Brief Bioinform (2011) 2.46
A SAGE approach to discovery of genes involved in autophagic cell death. Curr Biol (2003) 2.40
A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A (2005) 2.35
Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques (2007) 2.28
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Res (2002) 2.27
Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses. Genomics (2005) 2.27
Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol (2011) 2.27
Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. N Engl J Med (2011) 2.25
Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene (2003) 2.22
The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol (2012) 2.19
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics (2013) 2.18
KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem (2011) 2.15
Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol (2003) 2.12
Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. J Clin Oncol (2006) 2.11
E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res (2008) 2.07
Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol (2010) 2.06
A physical map of the genome of Atlantic salmon, Salmo salar. Genomics (2005) 2.03
E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on lysine 9. J Biol Chem (2003) 2.02
The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol (2006) 2.00
Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Res (2004) 1.97
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res (2005) 1.93
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Res (2010) 1.90
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res (2005) 1.89
Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J Biol Chem (2007) 1.88
Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol (2013) 1.88
A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc Natl Acad Sci U S A (2010) 1.85
Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther (2003) 1.84
Sockeye: a 3D environment for comparative genomics. Genome Res (2004) 1.80
Bromodomain-containing protein 4 (BRD4) regulates RNA polymerase II serine 2 phosphorylation in human CD4+ T cells. J Biol Chem (2012) 1.76
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res (2006) 1.74
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res (2002) 1.72
Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers. Cancer Epidemiol Biomarkers Prev (2008) 1.72
Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem (2009) 1.71
Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res (2005) 1.71
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet (2013) 1.64
The identification of E2F1-specific target genes. Proc Natl Acad Sci U S A (2002) 1.63
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics (2010) 1.57
ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol (2008) 1.55