Published in BMC Genomics on January 18, 2007
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19
DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res (2007) 3.18
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 3.02
Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res (2008) 2.52
Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res (2007) 1.79
Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes. RNA (2010) 1.40
Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol (2010) 1.40
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol (2009) 1.32
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. BMC Syst Biol (2013) 1.30
Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res (2010) 1.18
Transcriptional regulation of mammalian miRNA genes. Genomics (2010) 1.16
Genomic analysis of immune response against Vibrio cholerae hemolysin in Caenorhabditis elegans. PLoS One (2012) 0.88
Genomic analysis of stress response against arsenic in Caenorhabditis elegans. PLoS One (2013) 0.83
Seeing elegance in gene regulatory networks of the worm. Curr Opin Genet Dev (2011) 0.80
Transcriptional regulation of gene expression in C. elegans. WormBook (2013) 0.79
Fast, sensitive discovery of conserved genome-wide motifs. J Comput Biol (2012) 0.78
TFinDit: transcription factor-DNA interaction data depository. BMC Bioinformatics (2012) 0.78
C. elegans PAT-9 is a nuclear zinc finger protein critical for the assembly of muscle attachments. Cell Biosci (2012) 0.76
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PLoS Comput Biol (2014) 0.76
Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge. BioData Min (2015) 0.75
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
A protein interaction map of Drosophila melanogaster. Science (2003) 20.06
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res (2006) 4.32
A gene-centered C. elegans protein-DNA interaction network. Cell (2006) 3.84
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol (2005) 3.24
A gateway-compatible yeast one-hybrid system. Genome Res (2004) 3.23
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics (2006) 2.93
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res (2006) 2.50
Constructing transcriptional regulatory networks. Genes Dev (2005) 2.50
Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res (2007) 1.79
WorfDB: the Caenorhabditis elegans ORFeome Database. Nucleic Acids Res (2003) 1.65
Gateway-compatible yeast one-hybrid screens. CSH Protoc (2006) 1.18
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature (2004) 13.27
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet (2003) 7.25
BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3. Nature (2003) 4.79
Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet (2003) 4.09
A gene-centered C. elegans protein-DNA interaction network. Cell (2006) 3.84
Combined functional genomic maps of the C. elegans DNA damage response. Science (2002) 3.74
A first version of the Caenorhabditis elegans Promoterome. Genome Res (2004) 3.29
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol (2005) 3.24
A gateway-compatible yeast one-hybrid system. Genome Res (2004) 3.23
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev (2008) 3.19
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 3.02
Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res (2008) 2.52
Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol (2002) 2.47
Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protoc (2008) 1.89
Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics (2007) 1.83
Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res (2007) 1.79
The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays (2009) 1.72
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res (2011) 1.62
MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans. Development (2002) 1.57
Diet-induced developmental acceleration independent of TOR and insulin in C. elegans. Cell (2013) 1.51
A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol (2011) 1.49
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat Methods (2007) 1.49
C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mech Ageing Dev (2006) 1.44
The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev (2008) 1.42
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat Methods (2011) 1.41
Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol (2010) 1.40
Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell (2004) 1.40
High-throughput expression of C. elegans proteins. Genome Res (2004) 1.32
Using networks to measure similarity between genes: association index selection. Nat Methods (2013) 1.30
Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA. J Mol Biol (2004) 1.29
C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metab (2005) 1.28
Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Mol Cell (2013) 1.21
Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet (2011) 1.20
Gateway-compatible yeast one-hybrid screens. CSH Protoc (2006) 1.18
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res (2011) 1.15
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods (2011) 1.12
Enhanced Y1H assays for Arabidopsis. Nat Methods (2011) 1.10
Functional cdc25C dual-specificity phosphatase is required for S-phase entry in human cells. Mol Biol Cell (2003) 1.08
Complex expression dynamics and robustness in C. elegans insulin networks. Genome Res (2013) 1.06
The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res (2009) 1.01
Gene-centered regulatory networks. Brief Funct Genomics (2009) 0.98
Transcription factor functionality and transcription regulatory networks. Mol Biosyst (2008) 0.96
Integrated version of reverse two-hybrid system for the postproteomic era. Methods Enzymol (2002) 0.95
lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein. Genetics (2005) 0.90
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda) (2013) 0.85
Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res (2013) 0.84
Gene-centered yeast one-hybrid assays. Methods Mol Biol (2012) 0.81
RNA Interference in Caenorhabditis elegans. Curr Protoc Mol Biol (2015) 0.79
Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6. BMC Dev Biol (2014) 0.77
Genomics in 2011: challenges and opportunities. Genome Biol (2011) 0.75
A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans. Gene (2011) 0.75
Getting an edge on human disease. Mol Syst Biol (2009) 0.75
Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits. Cell (2014) 0.75