Transcriptional regulatory code of a eukaryotic genome.

A genomic code for nucleosome positioning. Nature (2006) 15.38

Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A (2006) 13.68

The DNA-encoded nucleosome organization of a eukaryotic genome. Nature (2008) 11.41

An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics (2006) 11.13

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol (2006) 8.38

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93

The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J (2005) 7.10

Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07

Wisdom of crowds for robust gene network inference. Nat Methods (2012) 6.91

Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol (2005) 6.37

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell (2011) 6.29

Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol (2008) 6.09

Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol (2008) 5.88

Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature (2007) 5.81

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol (2008) 5.71

Protein networks in disease. Genome Res (2008) 5.65

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol (2006) 5.57

Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol (2005) 5.38

Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell (2005) 5.36

Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol (2008) 5.36

High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res (2009) 5.11

Histone deacetylase inhibitors enhance memory and synaptic plasticity via CREB:CBP-dependent transcriptional activation. J Neurosci (2007) 5.02

STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92

A universal framework for regulatory element discovery across all genomes and data types. Mol Cell (2007) 4.50

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49

Gene-environment interaction in yeast gene expression. PLoS Biol (2008) 4.48

Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol (2005) 4.48

Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol (2007) 4.40

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol (2008) 4.34

Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol (2007) 4.31

Mechanisms that specify promoter nucleosome location and identity. Cell (2009) 4.14

ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80

Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins (2006) 3.78

Differential network biology. Mol Syst Biol (2012) 3.74

Direct isolation and identification of promoters in the human genome. Genome Res (2005) 3.68

Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A (2006) 3.68

Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res (2006) 3.67

Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science (2011) 3.67

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

A systems approach to mapping DNA damage response pathways. Science (2006) 3.55

The evolution of combinatorial gene regulation in fungi. PLoS Biol (2008) 3.53

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol (2005) 3.35

Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature (2008) 3.32

Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature (2008) 3.32

Learning a prior on regulatory potential from eQTL data. PLoS Genet (2009) 3.31

Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature (2008) 3.30

Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24

Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet (2005) 3.23

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22

Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol (2009) 3.20

A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19

CEAS: cis-regulatory element annotation system. Nucleic Acids Res (2006) 3.15

Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol (2006) 3.15

NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol (2008) 3.11

Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res (2008) 3.09

Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet (2006) 3.08

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet (2009) 3.06

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.06

A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev (2006) 3.05

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol (2008) 3.02

Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A (2006) 2.97

Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation. Mol Cell (2009) 2.91

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res (2009) 2.89

T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res (2005) 2.88

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A (2005) 2.84

Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet (2007) 2.77

Associating transcription factor-binding site motifs with target GO terms and target genes. Nucleic Acids Res (2008) 2.69

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol (2009) 2.67

Characterization of genome-wide p53-binding sites upon stress response. Nucleic Acids Res (2008) 2.67

Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet (2008) 2.67

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res (2006) 2.63

Transcriptional regulatory circuits: predicting numbers from alphabets. Science (2009) 2.61

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol (2011) 2.60

Dynamic properties of network motifs contribute to biological network organization. PLoS Biol (2005) 2.58

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57

A recently evolved transcriptional network controls biofilm development in Candida albicans. Cell (2012) 2.56

A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell (2011) 2.55

From DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet (2009) 2.54

The Ehrlich pathway for fusel alcohol production: a century of research on Saccharomyces cerevisiae metabolism. Appl Environ Microbiol (2008) 2.53

The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol (2010) 2.53

Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol (2006) 2.53

Systematic identification of functional orthologs based on protein network comparison. Genome Res (2006) 2.47

DBD: a transcription factor prediction database. Nucleic Acids Res (2006) 2.46

Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol (2008) 2.46

Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A (2006) 2.39

Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39

Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters. EMBO J (2006) 2.38

DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A (2006) 2.38

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol (2011) 2.37

Reconstructing dynamic regulatory maps. Mol Syst Biol (2007) 2.36

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics (2009) 2.35

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res (2008) 2.30

SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res (2006) 2.30

A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet (2008) 2.28

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics (2010) 2.24

Cancer systems biology: a network modeling perspective. Carcinogenesis (2009) 2.22

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol (1961) 65.10

Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52

Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74

Genome-wide location and function of DNA binding proteins. Science (2000) 31.25

TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res (2003) 29.26

Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55

Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) 16.49

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol (1998) 13.99

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet (2001) 13.05

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23

The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature (1999) 9.29

A short nucleotide sequence required for regulation of HIS4 by the general control system of yeast. Cell (1983) 8.31

The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res (1999) 7.59

The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol (1995) 7.31

SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics (1999) 6.79

TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J Comput Biol (1994) 6.62

Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics (2003) 5.99

Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev (2001) 4.91

The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80. Cell (1987) 4.49

Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell (2003) 4.12

Regulated degradation of the transcription factor Gcn4. EMBO J (1994) 3.64

FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res (2003) 2.82

Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome Res (2003) 2.54

The Saccharomyces cerevisiae DAL80 repressor protein binds to multiple copies of GATAA-containing sequences (URSGATA). J Bacteriol (1993) 2.36

Cooperative binding interactions required for function of the Ty1 sterile responsive element. Mol Cell Biol (1997) 2.12

Monitoring the Gcn4 protein-mediated response in the yeast Saccharomyces cerevisiae. J Biol Chem (1998) 2.07

Proline-independent binding of PUT3 transcriptional activator protein detected by footprinting in vivo. Mol Cell Biol (1991) 1.98

Detection of leucine-independent DNA site occupancy of the yeast Leu3p transcriptional activator in vivo. Mol Cell Biol (1995) 1.79

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59

The structure of haplotype blocks in the human genome. Science (2002) 50.88

A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80

Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52

Integrative genomics viewer. Nat Biotechnol (2011) 42.83

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48

Core transcriptional regulatory circuitry in human embryonic stem cells. Cell (2005) 34.93

The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60

Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29

Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83

Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16

Control of developmental regulators by Polycomb in human embryonic stem cells. Cell (2006) 28.21

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99

Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature (2006) 25.90

Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41

Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37

A chromatin landmark and transcription initiation at most promoters in human cells. Cell (2007) 23.41

Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04

High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97

ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72

Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00

A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66

ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61

International network of cancer genome projects. Nature (2010) 20.35

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96

Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83

A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell (2007) 18.35

The mammalian epigenome. Cell (2007) 18.13

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06

The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88

Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51

Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48

Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell (2008) 16.38

Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28

Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13

Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36

Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13

Genetic mapping in human disease. Science (2008) 15.12

Genome-wide map of nucleosome acetylation and methylation in yeast. Cell (2005) 15.08

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90

Mediator and cohesin connect gene expression and chromatin architecture. Nature (2010) 14.34

BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell (2011) 14.34

The genomic complexity of primary human prostate cancer. Nature (2011) 14.06

Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01

The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99

MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79

A landscape of driver mutations in melanoma. Cell (2012) 12.61

High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56

Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32

Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27

Control of pancreas and liver gene expression by HNF transcription factors. Science (2004) 12.05

Unlocking the secrets of the genome. Nature (2009) 11.80

Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell (2003) 11.78