Published in Bioinformatics on February 04, 2009
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J (2011) 2.38
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Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC Res Notes (2010) 0.88
An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies. BMC Genomics (2012) 0.87
Characterisation of genome-wide PLZF/RARA target genes. PLoS One (2011) 0.86
Sequence analysis of chromatin immunoprecipitation data for transcription factors. Methods Mol Biol (2010) 0.81
Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res (2015) 0.80
Integrated and Functional Genomics Analysis Validates the Relevance of the Nuclear Variant ErbB380kDa in Prostate Cancer Progression. PLoS One (2016) 0.75
Optofluidic UV-Vis spectrophotometer for online monitoring of photocatalytic reactions. Sci Rep (2016) 0.75
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
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Genome-wide location and function of DNA binding proteins. Science (2000) 31.25
Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90
Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics (2002) 20.59
Rosetta error model for gene expression analysis. Bioinformatics (2006) 4.67
Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics (2007) 2.50
ChIP-chip: data, model, and analysis. Biometrics (2007) 2.27
Normalization and experimental design for ChIP-chip data. BMC Bioinformatics (2007) 2.08
Computational epigenetics. Bioinformatics (2007) 1.92
GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol (2004) 15.61
Identification, activation, and selective in vivo ablation of mouse NK cells via NKp46. Proc Natl Acad Sci U S A (2007) 3.60
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics (2006) 3.50
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol Cell (2005) 3.15
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell (2013) 3.14
RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res (2011) 2.82
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol (2011) 2.79
Both integrated and differential regulation of components of the IL-2/IL-2 receptor system. Cytokine Growth Factor Rev (2006) 2.71
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J (2011) 2.38
Regulation of TCRbeta gene assembly by a promoter/enhancer holocomplex. Immunity (2006) 2.23
Immunoreceptor tyrosine-based inhibition motifs: a quest in the past and future. Immunol Rev (2008) 2.05
Genome-wide RNA polymerase II: not genes only! Trends Biochem Sci (2008) 2.02
Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet (2012) 1.98
Characterization of lysine 56 of histone H3 as an acetylation site in Saccharomyces cerevisiae. J Biol Chem (2005) 1.95
Essential function for SWI-SNF chromatin-remodeling complexes in the promoter-directed assembly of Tcrb genes. Nat Immunol (2007) 1.94
Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol (2011) 1.85
Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol (2012) 1.80
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res (2011) 1.79
The speed of change: towards a discontinuity theory of immunity? Nat Rev Immunol (2013) 1.72
Natural killer cells: from CD3(-)NKp46(+) to post-genomics meta-analyses. Curr Opin Immunol (2007) 1.65
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res (2012) 1.65
Bromodomain-dependent stage-specific male genome programming by Brdt. EMBO J (2012) 1.64
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst Biol (2009) 1.63
TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS One (2008) 1.60
A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Res (2010) 1.58
Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. EMBO J (2012) 1.55
Uncleaved TFIIA is a substrate for taspase 1 and active in transcription. Mol Cell Biol (2006) 1.51
Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS Comput Biol (2010) 1.49
TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRα gene expression. Cancer Cell (2012) 1.36
Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data. Nucleic Acids Res (2013) 1.33
Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol Cell (2002) 1.31
miR-9 controls the timing of neurogenesis through the direct inhibition of antagonistic factors. Dev Cell (2012) 1.29
Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev (2013) 1.24
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol (2013) 1.20
Diversity and plasticity of Th cell types predicted from regulatory network modelling. PLoS Comput Biol (2010) 1.17
Logical modelling of gene regulatory networks with GINsim. Methods Mol Biol (2012) 1.15
Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. J Theor Biol (2003) 1.15
Functional organisation of Escherichia coli transcriptional regulatory network. J Mol Biol (2008) 1.14
Metagenome annotation using a distributed grid of undergraduate students. PLoS Biol (2008) 1.14
The Ccr4-NOT deadenylase subunits CNOT7 and CNOT8 have overlapping roles and modulate cell proliferation. Mol Biol Cell (2009) 1.14
Dynamical modeling of syncytial mitotic cycles in Drosophila embryos. Mol Syst Biol (2007) 1.14
Differential responses of immune cells to type I interferon contribute to host resistance to viral infection. Cell Host Microbe (2012) 1.12
Sp1 transcriptional activity is up-regulated by phosphatase 2A in dividing T lymphocytes. J Biol Chem (2002) 1.09
Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLoS Comput Biol (2013) 1.09
ZEB-1, a repressor of the semaphorin 3F tumor suppressor gene in lung cancer cells. Neoplasia (2009) 1.09
Paramecium bursaria chlorella virus 1 proteome reveals novel architectural and regulatory features of a giant virus. J Virol (2012) 1.07
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc (2012) 1.07
Coronin-1A links cytoskeleton dynamics to TCR alpha beta-induced cell signaling. PLoS One (2008) 1.07
Coronin-1 expression in T lymphocytes: insights into protein function during T cell development and activation. Int Immunol (2004) 1.05
Divergent transcription is associated with promoters of transcriptional regulators. BMC Genomics (2013) 1.03
The lymphoid lineage-specific actin-uncapping protein Rltpr is essential for costimulation via CD28 and the development of regulatory T cells. Nat Immunol (2013) 1.00
Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module. Int J Dev Biol (2008) 0.99
Modular logical modelling of the budding yeast cell cycle. Mol Biosyst (2009) 0.98
Membrane-cytoskeleton interactions during the formation of the immunological synapse and subsequent T-cell activation. Immunol Rev (2002) 0.95
Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity. Transcription (2011) 0.94
Logical modelling of cell cycle control in eukaryotes: a comparative study. Mol Biosyst (2009) 0.94
A negative feedback regulatory loop associates the tyrosine kinase receptor ERBB2 and the transcription factor GATA4 in breast cancer cells. Mol Cancer Res (2009) 0.93
Wdr12, a mouse gene encoding a novel WD-Repeat Protein with a notchless-like amino-terminal domain. Genomics (2002) 0.93
In vivo reinsertion of excised episomes by the V(D)J recombinase: a potential threat to genomic stability. PLoS Biol (2007) 0.92
Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc. Genetics (2006) 0.91
Increased chromatin association of Sp1 in interphase cells by PP2A-mediated dephosphorylations. J Mol Biol (2006) 0.91
Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. Bioinformatics (2008) 0.89
Regulation of V(D)J recombination. Curr Opin Immunol (2006) 0.89
Active STAT5 regulates T-bet and eomesodermin expression in CD8 T cells and imprints a T-bet-dependent Tc1 program with repressed IL-6/TGF-β1 signaling. J Immunol (2013) 0.89
A defective NF-kappa B/RelB pathway in autoimmune-prone New Zealand black mice is associated with inefficient expansion of thymocyte and dendritic cells. J Immunol (2002) 0.88
Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.88
Restriction of transgene expression to the B-lymphoid progeny of human lentivirally transduced CD34+ cells. Mol Ther (2004) 0.88
Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC Res Notes (2010) 0.88
Assessing the role of the T cell receptor beta gene enhancer in regulating coding joint formation during V(D)J recombination. J Biol Chem (2003) 0.87