Published in Nucleic Acids Res on October 21, 2010
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res (2011) 6.59
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet (2012) 2.94
Enhancer loops appear stable during development and are associated with paused polymerase. Nature (2014) 2.36
Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature (2014) 1.82
A common set of DNA regulatory elements shapes Drosophila appendages. Dev Cell (2013) 1.79
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev (2012) 1.53
Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PLoS One (2015) 1.40
A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Rep (2012) 1.39
GRID-seq reveals the global RNA-chromatin interactome. Nat Biotechnol (2017) 1.38
RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev (2011) 1.38
Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet (2013) 1.38
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinformatics (2013) 1.34
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. BMC Syst Biol (2013) 1.30
Global view of enhancer-promoter interactome in human cells. Proc Natl Acad Sci U S A (2014) 1.26
Automated protein-DNA interaction screening of Drosophila regulatory elements. Nat Methods (2011) 1.21
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet (2013) 1.17
The Drosophila anatomy ontology. J Biomed Semantics (2013) 1.16
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis. PLoS Genet (2012) 1.10
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. BMC Bioinformatics (2011) 1.10
P-value-based regulatory motif discovery using positional weight matrices. Genome Res (2012) 1.09
Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development (2012) 1.05
Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nat Methods (2013) 1.00
Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Mol Syst Biol (2012) 0.99
Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster. PLoS Genet (2015) 0.99
Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet (2015) 0.95
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition. Elife (2014) 0.93
The role of Dichaete in transcriptional regulation during Drosophila embryonic development. BMC Genomics (2013) 0.91
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Res (2015) 0.91
SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete. Genome Biol (2014) 0.89
pubmed2ensembl: a resource for mining the biological literature on genes. PLoS One (2011) 0.89
Resources for functional genomics studies in Drosophila melanogaster. Genetics (2014) 0.88
Drosophila functional elements are embedded in structurally constrained sequences. PLoS Genet (2013) 0.87
Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila. BMC Genomics (2015) 0.87
TRRUST: a reference database of human transcriptional regulatory interactions. Sci Rep (2015) 0.87
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucleic Acids Res (2011) 0.87
Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. Chaos (2013) 0.86
A locus in Drosophila sechellia affecting tolerance of a host plant toxin. Genetics (2013) 0.86
Genome Surveyor 2.0: cis-regulatory analysis in Drosophila. Nucleic Acids Res (2011) 0.85
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res (2013) 0.85
cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. BMC Syst Biol (2014) 0.85
Messenger RNA is a functional component of a chromatin insulator complex. EMBO Rep (2013) 0.84
Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data. Front Genet (2013) 0.84
Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. Nucleic Acids Res (2015) 0.84
Regulation of gene expression in the genomic context. Comput Struct Biotechnol J (2014) 0.83
Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression. Comput Struct Biotechnol J (2014) 0.83
Quantitative modeling of a gene's expression from its intergenic sequence. PLoS Comput Biol (2014) 0.83
Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks. Microarrays (Basel) (2015) 0.83
Identifying transcriptional cis-regulatory modules in animal genomes. Wiley Interdiscip Rev Dev Biol (2014) 0.82
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Res (2013) 0.82
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res (2015) 0.82
Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules. BMC Genomics (2011) 0.81
Flanking sequence context-dependent transcription factor binding in early Drosophila development. BMC Bioinformatics (2013) 0.80
Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements. Genes Dev (2017) 0.79
Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs. PLoS One (2013) 0.79
Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. Genome Biol Evol (2014) 0.79
Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. Curr Genomics (2013) 0.79
The impact of trans-regulation on the evolutionary rates of metazoan proteins. Nucleic Acids Res (2013) 0.78
A statistical thin-tail test of predicting regulatory regions in the Drosophila genome. Theor Biol Med Model (2013) 0.78
Cross-species Conservation of context-specific networks. BMC Syst Biol (2016) 0.78
The Capacity to Act in Trans Varies Among Drosophila Enhancers. Genetics (2016) 0.77
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. BMC Genomics (2014) 0.77
Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes. PLoS One (2016) 0.77
Integrating the interactome and the transcriptome of Drosophila. BMC Bioinformatics (2014) 0.76
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PLoS Comput Biol (2014) 0.76
MEPD: medaka expression pattern database, genes and more. Nucleic Acids Res (2015) 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
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics (2015) 0.75
Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. Dev Biol (2015) 0.75
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. F1000Res (2015) 0.75
SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules. PLoS One (2016) 0.75
Redeployment of a conserved gene regulatory network during Aedes aegypti development. Dev Biol (2016) 0.75
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. Nucleic Acids Res (2016) 0.75
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. Nat Commun (2016) 0.75
Regulation of transcription factors on sexual dimorphism of fig wasps. Sci Rep (2015) 0.75
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PLoS One (2016) 0.75
Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression. BMC Evol Biol (2017) 0.75
Maps of context-dependent putative regulatory regions and genomic signal interactions. Nucleic Acids Res (2016) 0.75
TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos. J Vis Exp (2015) 0.75
Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. PLoS One (2017) 0.75
Perspectives on Gene Regulatory Network Evolution. Trends Genet (2017) 0.75
Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster. PeerJ (2017) 0.75
Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. Elife (2017) 0.75
Creating cell type-specific mutants by enhancer mutagenesis. Genes Dev (2017) 0.75
The human genome browser at UCSC. Genome Res (2002) 168.23
The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 38.24
Ensembl 2009. Nucleic Acids Res (2008) 25.38
FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res (2008) 12.15
Unlocking the secrets of the genome. Nature (2009) 11.80
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics (2004) 4.37
Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res (2007) 2.44
REDfly: a Regulatory Element Database for Drosophila. Bioinformatics (2005) 2.13
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res (2007) 1.99
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol (2005) 8.32
The Drosophila melanogaster Genetic Reference Panel. Nature (2012) 7.94
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res (2007) 3.80
LINNAEUS: a species name identification system for biomedical literature. BMC Bioinformatics (2010) 3.51
Functional evolution of a cis-regulatory module. PLoS Biol (2005) 3.21
Gene expression divergence recapitulates the developmental hourglass model. Nature (2010) 3.20
Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol (2005) 2.47
REDfly: a Regulatory Element Database for Drosophila. Bioinformatics (2005) 2.13
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res (2007) 1.99
Text mining for biology--the way forward: opinions from leading scientists. Genome Biol (2008) 1.91
Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics (2011) 1.91
Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol (2007) 1.89
The GNAT library for local and remote gene mention normalization. Bioinformatics (2011) 1.75
Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Mol Biol Evol (2003) 1.75
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics (2004) 1.62
An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. PLoS Genet (2006) 1.51
Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol (2006) 1.46
Reciprocal regulatory interactions between the Notch and Ras signaling pathways in the Drosophila embryonic mesoderm. Dev Biol (2002) 1.45
Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS One (2012) 1.40
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biol (2007) 1.38
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster. PLoS Genet (2012) 1.37
Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol (2009) 1.36
Purifying selection maintains highly conserved noncoding sequences in Drosophila. Mol Biol Evol (2007) 1.36
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. BMC Bioinformatics (2010) 1.34
A combinatorial code for pattern formation in Drosophila oogenesis. Dev Cell (2008) 1.33
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol (2008) 1.29
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics (2012) 1.29
Text-mining assisted regulatory annotation. Genome Biol (2008) 1.26
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Dev Cell (2009) 1.20
Drosophila melanogaster: a case study of a model genomic sequence and its consequences. Genome Res (2005) 1.15
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics (2006) 1.14
High mutation rates in human and ape pseudoautosomal genes. Gene (2003) 1.08
Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Res (2008) 1.08
The evolution of tRNA genes in Drosophila. Genome Biol Evol (2010) 1.06
Quantifying the life-history response to increased male exposure in female Drosophila melanogaster. Evolution (2010) 1.06
Preferential induction of apoptotic cell death in melanoma cells as compared with normal keratinocytes using a non-thermal plasma torch. Cancer Biol Ther (2012) 1.05
Evolutionary systems biology of amino acid biosynthetic cost in yeast. PLoS One (2010) 1.03
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol (2005) 1.00
CEACAM3: an innate immune receptor directed against human-restricted bacterial pathogens. Int J Med Microbiol (2008) 0.97
Vector-dependent gene expression driven by insulated P-element reporter vectors. Fly (Austin) (2007) 0.96
An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis. PLoS Genet (2012) 0.93
Proteome-wide analyses of human hepatocytes during differentiation and dedifferentiation. Hepatology (2013) 0.91
Evolutionary genomics of transposable elements in Saccharomyces cerevisiae. PLoS One (2012) 0.91
Assigning roles to protein mentions: the case of transcription factors. J Biomed Inform (2009) 0.89
pubmed2ensembl: a resource for mining the biological literature on genes. PLoS One (2011) 0.89
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucleic Acids Res (2011) 0.87
(Re)modeling the transcriptional enhancer. Nat Genet (2006) 0.86
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. BMC Genomics (2009) 0.84
Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland. BMC Mol Biol (2010) 0.84
A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome. Mol Biol Evol (2011) 0.83
A wholly defined Agilent microarray spike-in dataset. Bioinformatics (2011) 0.82
A dominant negative Cx43 mutant differentially affects tumorigenic and invasive properties in human metastatic melanoma cells. J Cell Physiol (2013) 0.82
Identifying transcriptional cis-regulatory modules in animal genomes. Wiley Interdiscip Rev Dev Biol (2014) 0.82
An age-of-allele test of neutrality for transposable element insertions. Genetics (2013) 0.80
Drosophila polymorphism database (DPDB): a portal for nucleotide polymorphism in Drosophila. Fly (Austin) (2007) 0.80
Identification of receptor-tyrosine-kinase-signaling target genes reveals receptor-specific activities and pathway branchpoints during Drosophila development. Genetics (2009) 0.76
The path to good aseptic guidance. PDA J Pharm Sci Technol (2004) 0.75