Published in Genome Res on August 01, 2002
The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res (2003) 15.27
Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2002) 8.89
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol (2002) 8.59
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2007) 6.27
Computational analysis of core promoters in the Drosophila genome. Genome Biol (2002) 5.60
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res (2007) 4.73
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics (2007) 4.62
A Drosophila full-length cDNA resource. Genome Biol (2002) 3.67
An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol (2003) 3.08
Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science (2007) 2.97
The construction of an EST database for Bombyx mori and its application. Proc Natl Acad Sci U S A (2003) 2.56
GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyosin to stretch and shape the Golgi to promote budding. Cell (2009) 2.54
Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol (2007) 2.54
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res (2006) 2.49
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res (2004) 2.47
Diversity and dynamics of the Drosophila transcriptome. Nature (2014) 2.47
An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell (2013) 2.36
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A (2003) 2.33
Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res (2010) 2.29
The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res (2010) 2.25
Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev (2003) 1.96
X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev (2006) 1.70
RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs. Nucleic Acids Res (2003) 1.61
Assessment of SAGE in transcript identification. Genome Res (2003) 1.52
Isolation of new polar granule components in Drosophila reveals P body and ER associated proteins. Mech Dev (2008) 1.48
A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A (2005) 1.46
RNA editing in Drosophila melanogaster: New targets and functional consequences. RNA (2006) 1.43
Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nat Struct Mol Biol (2009) 1.42
Single-cell mapping of neural and glial gene expression in the developing Drosophila CNS midline cells. Dev Biol (2006) 1.40
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol (2007) 1.39
Organelle-specific control of intracellular transport: distinctly targeted isoforms of the regulator Klar. Mol Biol Cell (2005) 1.37
cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics (2007) 1.35
MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res (2008) 1.33
HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. EMBO J (2007) 1.27
Duox, Flotillin-2, and Src42A are required to activate or delimit the spread of the transcriptional response to epidermal wounds in Drosophila. PLoS Genet (2011) 1.26
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Dev Cell (2009) 1.20
A Drosophila Smyd4 homologue is a muscle-specific transcriptional modulator involved in development. PLoS One (2008) 1.19
The kinesinlike protein Subito contributes to central spindle assembly and organization of the meiotic spindle in Drosophila oocytes. Mol Biol Cell (2005) 1.11
A genome-scale protein interaction profile of Drosophila p53 uncovers additional nodes of the human p53 network. Proc Natl Acad Sci U S A (2010) 1.11
Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). Nucleic Acids Res (2005) 1.11
Feedback from rhodopsin controls rhodopsin exclusion in Drosophila photoreceptors. Nature (2011) 1.10
Ordered partitioning reveals extended splice-site consensus information. Genome Res (2004) 1.09
Multiple transcription factor codes activate epidermal wound-response genes in Drosophila. Proc Natl Acad Sci U S A (2009) 1.08
Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila. BMC Plant Biol (2008) 1.08
Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep. Proc Natl Acad Sci U S A (2003) 1.07
Drosophila melanogaster Cad99C, the orthologue of human Usher cadherin PCDH15, regulates the length of microvilli. J Cell Biol (2005) 1.07
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinformatics (2009) 1.06
High-throughput gene discovery in the rat. Genome Res (2004) 1.02
Detecting novel low-abundant transcripts in Drosophila. RNA (2005) 1.02
Determination of gene expression patterns using high-throughput RNA in situ hybridization to whole-mount Drosophila embryos. Nat Protoc (2009) 1.01
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol (2005) 1.00
The C8ORF38 homologue Sicily is a cytosolic chaperone for a mitochondrial complex I subunit. J Cell Biol (2013) 1.00
Drosophila lipophorin receptors mediate the uptake of neutral lipids in oocytes and imaginal disc cells by an endocytosis-independent mechanism. PLoS Genet (2011) 0.97
Characterization of 954 bovine full-CDS cDNA sequences. BMC Genomics (2005) 0.96
Conserved genomic organisation of Group B Sox genes in insects. BMC Genet (2005) 0.96
Regulation of Drosophila vasa in vivo through paralogous cullin-RING E3 ligase specificity receptors. Mol Cell Biol (2010) 0.95
Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones. BMC Genomics (2007) 0.95
Extensive exon reshuffling over evolutionary time coupled to trans-splicing in Drosophila. Genome Res (2003) 0.94
Type II phosphatidylinositol 4-kinase regulates trafficking of secretory granule proteins in Drosophila. Development (2012) 0.93
Complex regulation and multiple developmental functions of misfire, the Drosophila melanogaster ferlin gene. BMC Dev Biol (2007) 0.93
Chromosome axis defects induce a checkpoint-mediated delay and interchromosomal effect on crossing over during Drosophila meiosis. PLoS Genet (2010) 0.93
Mitochondrial fusion but not fission regulates larval growth and synaptic development through steroid hormone production. Elife (2014) 0.92
Mixture modeling of transcript abundance classes in natural populations. Genome Biol (2007) 0.92
Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors. Development (2012) 0.92
Transcriptional control of steroid biosynthesis genes in the Drosophila prothoracic gland by ventral veins lacking and knirps. PLoS Genet (2014) 0.91
RanBPM regulates cell shape, arrangement, and capacity of the female germline stem cell niche in Drosophila melanogaster. J Cell Biol (2008) 0.90
Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons. Genome Res (2003) 0.90
Impressive expressions: developing a systematic database of gene-expression patterns in Drosophila embryogenesis. Genome Biol (2003) 0.90
Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury. BMC Genomics (2007) 0.88
In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila. G3 (Bethesda) (2014) 0.86
Identification of regulatory modules mediating specific expression of the roughest gene in Drosophila melanogaster. Dev Genes Evol (2004) 0.85
Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome. Nucleic Acids Res (2014) 0.84
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. BMC Genomics (2009) 0.84
Relational databases: a transparent framework for encouraging biology students to think informatically. Cell Biol Educ (2004) 0.83
Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein. Nat Commun (2011) 0.83
Whole mount RNA fluorescent in situ hybridization of Drosophila embryos. J Vis Exp (2013) 0.83
The 3of5 web application for complex and comprehensive pattern matching in protein sequences. BMC Bioinformatics (2006) 0.82
Control of tissue morphology by Fasciclin III-mediated intercellular adhesion. Development (2013) 0.81
Cooperative and antagonistic contributions of two heterochromatin proteins to transcriptional regulation of the Drosophila sex determination decision. PLoS Genet (2011) 0.81
Whole-genome analysis of muscle founder cells implicates the chromatin regulator Sin3A in muscle identity. Cell Rep (2014) 0.81
Identification of mushroom body miniature, a zinc-finger protein implicated in brain development of Drosophila. Proc Natl Acad Sci U S A (2004) 0.81
TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites. EURASIP J Bioinform Syst Biol (2010) 0.81
Class I myosins have overlapping and specialized functions in left-right asymmetric development in Drosophila. Genetics (2015) 0.80
A genome-wide analysis reveals that the Drosophila transcription factor Lola promotes axon growth in part by suppressing expression of the actin nucleation factor Spire. Neural Dev (2011) 0.80
Drosophila neuroligin 1 regulates synaptic growth and function in response to activity and phosphoinositide-3-kinase. Mol Cell Neurosci (2012) 0.79
Contrasting patterns of transposable element insertions in Drosophila heat-shock promoters. PLoS One (2009) 0.79
The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol (2015) 0.78
Feeding-Related Traits Are Affected by Dosage of the foraging Gene in Drosophila melanogaster. Genetics (2016) 0.77
Identification of receptor-tyrosine-kinase-signaling target genes reveals receptor-specific activities and pathway branchpoints during Drosophila development. Genetics (2009) 0.76
Expression and characterization of Drosophila signal peptide peptidase-like (sppL), a gene that encodes an intramembrane protease. PLoS One (2012) 0.76
Molecular evidence of RNA editing in Bombyx chemosensory protein family. PLoS One (2014) 0.76
The postsynaptic t-SNARE Syntaxin 4 controls traffic of Neuroligin 1 and Synaptotagmin 4 to regulate retrograde signaling. Elife (2016) 0.75
The Drosophila Hox gene Ultrabithorax acts both in muscles and motoneurons to orchestrate formation of specific neuromuscular connections. Development (2016) 0.75
The Drosophila MCPH1-B isoform is a substrate of the APCCdh1 E3 ubiquitin ligase complex. Biol Open (2014) 0.75
The wavy Mutation Maps to the Inositol 1,4,5-Trisphosphate 3-Kinase 2 (IP3K2) Gene of Drosophila and Interacts with IP3R to Affect Wing Development. G3 (Bethesda) (2015) 0.75
Spastic paraplegia-linked phospholipase PAPLA1 is necessary for development, reproduction, and energy metabolism in Drosophila. Sci Rep (2017) 0.75
Evaluation of vector-primed cDNA library production from microgram quantities of total RNA. Nucleic Acids Res (2004) 0.75
Taking Stock of the Drosophila Research Ecosystem. Genetics (2017) 0.75
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Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res (1998) 96.63
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Complementary DNA sequencing: expressed sequence tags and human genome project. Science (1991) 19.42
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Generation and analysis of 280,000 human expressed sequence tags. Genome Res (1996) 8.27
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A Drosophila complementary DNA resource. Science (2000) 4.98
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Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res (2000) 3.98
Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res (2000) 3.78
Identification of five new genes on the Y chromosome of Drosophila melanogaster. Proc Natl Acad Sci U S A (2001) 2.09
Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides. Proc Natl Acad Sci U S A (2000) 1.97
Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method. Biotechniques (2001) 1.94
Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Genomics (2001) 1.76
A biologist's view of the Drosophila genome annotation assessment project. Genome Res (2000) 1.60
Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries. Gene (2001) 1.53
An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library. Genome Res (2001) 1.50
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
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol (2002) 9.31
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2002) 8.89
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol (2002) 8.59
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A (2002) 8.56
The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics (2004) 8.40
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol (2002) 8.07
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J (2002) 7.70
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A (2008) 6.35
Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2007) 6.27
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Direct generation of functional dopaminergic neurons from mouse and human fibroblasts. Nature (2011) 6.21
Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev (2005) 5.78
Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet (2007) 5.75
A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell (2008) 5.63
Computational analysis of core promoters in the Drosophila genome. Genome Biol (2002) 5.60
High-throughput mapping of a dynamic signaling network in mammalian cells. Science (2005) 5.21
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol (2002) 5.09
CAGE: cap analysis of gene expression. Nat Methods (2006) 5.04
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res (2007) 4.73
A GAL4-driver line resource for Drosophila neurobiology. Cell Rep (2012) 4.67
The Toll and Imd pathways are the major regulators of the immune response in Drosophila. EMBO J (2002) 4.63
Refinement of tools for targeted gene expression in Drosophila. Genetics (2010) 4.53
Targeted mutagenesis by homologous recombination in D. melanogaster. Genes Dev (2002) 4.21
Tiny RNAs associated with transcription start sites in animals. Nat Genet (2009) 4.19
Somatic retrotransposition alters the genetic landscape of the human brain. Nature (2011) 4.16
Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res (2003) 4.01
A visual motion detection circuit suggested by Drosophila connectomics. Nature (2013) 3.94
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Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50
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Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol (2004) 3.36
Hidden layers of human small RNAs. BMC Genomics (2008) 3.31
A protein complex network of Drosophila melanogaster. Cell (2011) 3.31
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res (2003) 3.21
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19
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Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol (2002) 3.09
ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proc Natl Acad Sci U S A (2002) 3.09
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature (2012) 3.08
Small RNAs derived from snoRNAs. RNA (2009) 3.04