Published in Genes Dev on December 01, 2002
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
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
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics (2007) 2.55
Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev (2002) 2.52
Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res (2003) 2.50
Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res (2006) 2.26
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res (2007) 2.22
Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol (2004) 2.12
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res (2003) 1.90
Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci U S A (2005) 1.81
A competitive transcription factor binding mechanism determines the timing of late cell cycle-dependent gene expression. Mol Cell (2010) 1.74
Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol (2009) 1.73
GeneRank: using search engine technology for the analysis of microarray experiments. BMC Bioinformatics (2005) 1.71
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.65
Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics (2011) 1.65
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res (2006) 1.62
Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell (2012) 1.61
Yeast homolog of a cancer-testis antigen defines a new transcription complex. EMBO J (2006) 1.58
Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell (2006) 1.55
Design optimization methods for genomic DNA tiling arrays. Genome Res (2005) 1.53
High functional overlap between MluI cell-cycle box binding factor and Swi4/6 cell-cycle box binding factor in the G1/S transcriptional program in Saccharomyces cerevisiae. Genetics (2005) 1.51
Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev (2009) 1.43
Dynamics of Cdk1 substrate specificity during the cell cycle. Mol Cell (2011) 1.42
Widespread misinterpretable ChIP-seq bias in yeast. PLoS One (2013) 1.36
High-resolution timing of cell cycle-regulated gene expression. Proc Natl Acad Sci U S A (2007) 1.35
Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biol (2006) 1.33
G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol (2003) 1.27
H2A.Z functions to regulate progression through the cell cycle. Mol Cell Biol (2006) 1.27
Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol (2009) 1.27
SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell (2013) 1.25
Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs. BMC Bioinformatics (2004) 1.25
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci U S A (2010) 1.24
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. BMC Genomics (2008) 1.19
Clb6/Cdc28 and Cdc14 regulate phosphorylation status and cellular localization of Swi6. Mol Cell Biol (2004) 1.18
Linking DNA replication checkpoint to MBF cell-cycle transcription reveals a distinct class of G1/S genes. EMBO J (2012) 1.16
Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response. Cell Cycle (2012) 1.16
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics (2007) 1.16
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res (2009) 1.15
The forkhead transcription factor Fkh2 regulates the cell division cycle of Schizosaccharomyces pombe. Eukaryot Cell (2004) 1.15
Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc Natl Acad Sci U S A (2006) 1.10
Systems biology from a yeast omics perspective. FEBS Lett (2009) 1.08
The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback. PLoS Genet (2009) 1.05
A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res (2005) 1.04
Topology and control of the cell-cycle-regulated transcriptional circuitry. Genetics (2014) 1.03
Embryonic fibroblasts from mice lacking Tgif were defective in cell cycling. Mol Cell Biol (2006) 1.01
Exploiting combinatorial cultivation conditions to infer transcriptional regulation. BMC Genomics (2007) 1.00
The predicted G-protein-coupled receptor GPR-1 is required for female sexual development in the multicellular fungus Neurospora crassa. Eukaryot Cell (2006) 1.00
Essential global role of CDC14 in DNA synthesis revealed by chromosome underreplication unrecognized by checkpoints in cdc14 mutants. Proc Natl Acad Sci U S A (2009) 0.98
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. BMC Bioinformatics (2007) 0.97
The role of the Yap5 transcription factor in remodeling gene expression in response to Fe bioavailability. PLoS One (2012) 0.96
Mapping functional transcription factor networks from gene expression data. Genome Res (2013) 0.94
Quantitative proteomic analysis of chromatin reveals that Ctf18 acts in the DNA replication checkpoint. Mol Cell Proteomics (2011) 0.94
Spc24 and Stu2 promote spindle integrity when DNA replication is stalled. Mol Biol Cell (2007) 0.92
Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol (2010) 0.92
Physical Module Networks: an integrative approach for reconstructing transcription regulation. Bioinformatics (2011) 0.92
Regulation of a transcription factor network by Cdk1 coordinates late cell cycle gene expression. EMBO J (2014) 0.92
Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J (2004) 0.90
Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal? Trends Genet (2008) 0.90
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. Genome Biol (2007) 0.88
A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data. Nucleic Acids Res (2005) 0.88
Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol (2006) 0.87
Extracting expression modules from perturbational gene expression compendia. BMC Syst Biol (2008) 0.86
Yeast proteomics and protein microarrays. J Proteomics (2010) 0.86
A temperature-sensitive dcw1 mutant of Saccharomyces cerevisiae is cell cycle arrested with small buds which have aberrant cell walls. Eukaryot Cell (2004) 0.86
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. BMC Bioinformatics (2010) 0.85
G1/S transcription factor orthologues Swi4p and Swi6p are important but not essential for cell proliferation and influence hyphal development in the fungal pathogen Candida albicans. Eukaryot Cell (2011) 0.84
Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res (2010) 0.84
A sticky situation: untangling the transcriptional network controlling biofilm development in Candida albicans. Transcription (2012) 0.84
HIDEN: Hierarchical decomposition of regulatory networks. BMC Bioinformatics (2012) 0.83
Transcriptional regulation and the diversification of metabolism in wine yeast strains. Genetics (2011) 0.82
The forkhead transcription factor Hcm1 promotes mitochondrial biogenesis and stress resistance in yeast. J Biol Chem (2010) 0.82
Hcm1 integrates signals from Cdk1 and calcineurin to control cell proliferation. Mol Biol Cell (2015) 0.80
Recovering genetic regulatory networks from chromatin immunoprecipitation and steady-state microarray data. EURASIP J Bioinform Syst Biol (2008) 0.79
An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. Genome Biol (2015) 0.79
Robustness of transcriptional regulatory program influences gene expression variability. BMC Genomics (2009) 0.79
Functional Analysis and Characterization of Differential Coexpression Networks. Sci Rep (2015) 0.79
Identification of anaphase promoting complex substrates in S. cerevisiae. PLoS One (2012) 0.79
Identification of Transcription Factor-DNA Interactions In Vivo. Subcell Biochem (2011) 0.78
Transcriptomic analysis of cobalt stress in the marine yeast Debaryomyces hansenii. FEMS Yeast Res (2015) 0.78
Classifying transcription factor targets and discovering relevant biological features. Biol Direct (2008) 0.78
ELM1 is required for multidrug resistance in Saccharomyces cerevisiae. Genetics (2006) 0.78
Regulatory network structure as a dominant determinant of transcription factor evolutionary rate. PLoS Comput Biol (2012) 0.78
SBF transcription factor complex positively regulates UV mutagenesis in Saccharomyces cerevisiae. Biochem Biophys Res Commun (2009) 0.77
Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. Nucleic Acids Res (2016) 0.77
Cell cycle regulators interact with pathways that modulate microtubule stability in Saccharomyces cerevisiae. Eukaryot Cell (2011) 0.76
Deconvolution of chromatin immunoprecipitation-microarray (ChIP-chip) analysis of MBF occupancies reveals the temporal recruitment of Rep2 at the MBF target genes. Eukaryot Cell (2010) 0.76
The WTM genes in budding yeast amplify expression of the stress-inducible gene RNR3. Genetics (2006) 0.76
Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet (2015) 0.75
Saccharomyces cerevisiae FLO1 Gene Demonstrates Genetic Linkage to Increased Fermentation Rate at Low Temperatures. G3 (Bethesda) (2017) 0.75
Characterization of binding sites of eukaryotic transcription factors. Genomics Proteomics Bioinformatics (2006) 0.75
The Late S-Phase Transcription Factor Hcm1 Is Regulated through Phosphorylation by the Cell Wall Integrity Checkpoint. Mol Cell Biol (2016) 0.75
Set2 Methyltransferase Facilitates DNA Replication and Promotes Genotoxic Stress Responses through MBF-Dependent Transcription. Cell Rep (2017) 0.75
Reconciling conflicting models for global control of cell-cycle transcription. Cell Cycle (2017) 0.75
Transformation of intact yeast cells treated with alkali cations. J Bacteriol (1983) 100.26
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) 21.55
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
The B-type cyclin kinase inhibitor p40SIC1 controls the G1 to S transition in S. cerevisiae. Cell (1994) 11.08
Serial regulation of transcriptional regulators in the yeast cell cycle. Cell (2001) 7.99
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell (2001) 6.39
A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science (1993) 6.37
Use of polymerase chain reaction epitope tagging for protein tagging in Saccharomyces cerevisiae. Yeast (1995) 5.22
Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins. Cell (1993) 4.75
The role of SWI4 and SWI6 in the activity of G1 cyclins in yeast. Cell (1991) 4.53
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature (2000) 4.52
Transcriptional activation of CLN1, CLN2, and a putative new G1 cyclin (HCS26) by SWI4, a positive regulator of G1-specific transcription. Cell (1991) 4.44
Phosphorylation of Sic1p by G1 Cdk required for its degradation and entry into S phase. Science (1997) 4.18
Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol (2000) 4.15
Cdc53 targets phosphorylated G1 cyclins for degradation by the ubiquitin proteolytic pathway. Cell (1996) 4.06
Roles and regulation of Cln-Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J (1995) 3.89
Coordinated regulation of gene expression by the cell cycle transcription factor Swi4 and the protein kinase C MAP kinase pathway for yeast cell integrity. EMBO J (1996) 3.45
ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol (2002) 3.32
SWI6 protein is required for transcription of the periodically expressed DNA synthesis genes in budding yeast. Nature (1992) 3.32
Identification of a DNA binding factor involved in cell-cycle control of the yeast HO gene. Cell (1989) 3.18
The yeast SWI4 protein contains a motif present in developmental regulators and is part of a complex involved in cell-cycle-dependent transcription. Nature (1989) 3.02
A screen for genes required for meiosis and spore formation based on whole-genome expression. Curr Biol (2001) 2.98
Ubiquitination of the G1 cyclin Cln2p by a Cdc34p-dependent pathway. EMBO J (1995) 2.82
A central role for SWI6 in modulating cell cycle Start-specific transcription in yeast. Nature (1992) 2.79
G1 cyclin turnover and nutrient uptake are controlled by a common pathway in yeast. Genes Dev (1995) 2.77
Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature (2000) 2.74
Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle. Genes Dev (2002) 2.52
SBF cell cycle regulator as a target of the yeast PKC-MAP kinase pathway. Science (1997) 2.47
Signalling in the yeasts: an informational cascade with links to the filamentous fungi. Microbiol Mol Biol Rev (1998) 2.45
Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr Biol (2000) 2.31
Role of Swi4 in cell cycle regulation of CLN2 expression. Mol Cell Biol (1994) 2.30
A multipurpose transposon system for analyzing protein production, localization, and function in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (1997) 2.21
Anatomy of a transcription factor important for the start of the cell cycle in Saccharomyces cerevisiae. Nature (1992) 2.21
The forkhead protein Fkh2 is a component of the yeast cell cycle transcription factor SFF. EMBO J (2000) 1.95
Cell cycle-specific expression of the SWI4 transcription factor is required for the cell cycle regulation of HO transcription. Genes Dev (1991) 1.83
Sok2 regulates yeast pseudohyphal differentiation via a transcription factor cascade that regulates cell-cell adhesion. Mol Cell Biol (2000) 1.57
MAPK specificity in the yeast pheromone response independent of transcriptional activation. Curr Biol (2001) 1.50
A dosage-dependent suppressor of a temperature-sensitive calmodulin mutant encodes a protein related to the fork head family of DNA-binding proteins. Mol Cell Biol (1993) 1.50
Unfolding of microarray data. J Comput Biol (2001) 1.45
Binding to the yeast SwI4,6-dependent cell cycle box, CACGAAA, is cell cycle regulated in vivo. Nucleic Acids Res (1996) 1.28
Regulation of the yeast DNA replication genes through the Mlu I cell cycle box is dependent on SWI6. Proc Natl Acad Sci U S A (1992) 1.25
The GCR1 requirement for yeast glycolytic gene expression is suppressed by dominant mutations in the SGC1 gene, which encodes a novel basic-helix-loop-helix protein. Mol Cell Biol (1995) 1.10
The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes the calmodulin-binding protein in the yeast spindle pole body. Biochim Biophys Acta (1998) 1.09
The E-box DNA binding protein Sgc1p suppresses the gcr2 mutation, which is involved in transcriptional activation of glycolytic genes in Saccharomyces cerevisiae. FEBS Lett (1999) 0.97
SWI6 is a regulatory subunit of two different cell cycle START-dependent transcription factors in Saccharomyces cerevisiae. J Cell Sci Suppl (1992) 0.96
In vitro binding to the leucine tRNA gene identifies a novel yeast homeobox gene. Chromosoma (1993) 0.92
POG1, a novel yeast gene, promotes recovery from pheromone arrest via the G1 cyclin CLN2. Genetics (1999) 0.91
YHP1 encodes a new homeoprotein that binds to the IME1 promoter in Saccharomyces cerevisiae. Yeast (2000) 0.87
Mutational and hyperexpression-induced disruption of bipolar budding in yeast. Microbiology (2000) 0.83
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Unlocking the secrets of the genome. Nature (2009) 11.80
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Variation in transcription factor binding among humans. Science (2010) 9.33
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
HTRA1 promoter polymorphism in wet age-related macular degeneration. Science (2006) 7.12
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol (2010) 5.98
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
DNA-binding specificities of human transcription factors. Cell (2013) 5.14
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
What is a gene, post-ENCODE? History and updated definition. Genome Res (2007) 4.96
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A (2006) 4.84
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res (2007) 4.59
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol (2009) 4.18
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
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
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
An integrated approach for finding overlooked genes in yeast. Nat Biotechnol (2002) 3.88
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res (2012) 3.83
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell (2009) 3.69
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res (2012) 3.61
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res (2010) 3.46
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41