SilkDB: a knowledgebase for silkworm biology and genomics

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at http://silkworm.genomics.org.cn.

• Publication year

  2004

• Venue

  Nucleic Acids Res.

• Publication date

  2004-12-17

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1093/nar/gki116PMID 15608225PMCID 540070
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource

  2004influential reference
• The genome sequence of silkworm, Bombyx mori.

  2004cited by this paper
• GenBank: update

  2004influential reference
• Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao.

  2004cited by this paper
• BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

  2004cited by this paper
• The construction of an EST database for Bombyx mori and its application

  2003cited by this paper
• The InterPro Database, 2003 brings increased coverage and new features

  2003cited by this paper
• A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

  2002cited by this paper
• A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)

  2002cited by this paper
• The Genome Sequence of the Malaria Mosquito Anopheles gambiae

  2002cited by this paper
• Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

  2002cited by this paper
• Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence

  2002cited by this paper
• RePS: a sequence assembler that masks exact repeats identified from the shotgun data.

  2002cited by this paper
• Molecular structure of a novel gypsy-Ty3-like retrotranspon, Kabuki and nested retrotransposable elements on the W chromosome of the silkworm

  2000cited by this paper
• Ab initio gene finding in Drosophila genomic DNA.

  2000cited by this paper
• The genome sequence of Drosophila melanogaster.

  2000cited by this paper
• Molecular structure of a novel gypsy-Ty3-like retrotransposon (Kabuki) and nested retrotransposable elements on the W chromosome of the silkworm Bombyx mori

  2000cited by this paper
• Genome sequence of the nematode C. elegans: a platform for investigating biology.

  1998cited by this paper
• Prediction of complete gene structures in human genomic DNA.

  1997cited by this paper
• Molecular Model Systems in the Lepidoptera

  1995cited by this paper
• The Bombyx mori genome: analysis by DNA reassociation kinetics

  1974cited by this paper

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• Integrating Multi-Omics, Bioinformatics and Genome Editing for Sustainable Sericulture

  2025cites this paper
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  2025cites this paper
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  2023cites this paper
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  2021cites this paper
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  2021cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
• DNA Sequencing and the Evolution of the “-Omics”

  2019cites this paper
• Insect genomes: progress and challenges

  2019cites this paper
• Developmental and transcriptomic features characterize defects of silk gland growth and silk production in silkworm naked pupa mutant.

  2019cites this paper
• SGID: a comprehensive and interactive database of the silkworm

  2019cites this paper
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  2019cites this paper
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  2019cites this paper
• SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm

  2019cites this paper
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  2019cites this paper
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  2019cites this paper
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  2019cites this paper
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  2019cites this paper
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  2018cites this paper
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  2018cites this paper
• MicroRNA Expression Analysis of Naked Silkworms.

  2018cites this paper
• Structural analysis of neutral glycosphingolipids from the silkworm Bombyx mori and the difference in ceramide composition between larvae and pupae

  2018cites this paper
• Global invasion history of the world’s most abundant pest butterfly: a citizen science population genomics study

  2018cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
• Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

  2017influential citation
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  2017cites this paper
• Silkworm (Bombyx mori) and its constituents: A fascinating insect in science and research

  2017cites this paper
• Comparative transcriptomes analysis of the wing disc between two silkworm strains with different size of wings

  2017cites this paper
• Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome

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  2017cites this paper
• Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

  2017cites this paper
• Evolutionary Genetics of Adaptation in Lepidoptera

  2016influential citation
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  2016cites this paper
• A comparison of virus genome sequences with their host silkworm, Bombyx mori.

  2016cites this paper
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  2016influential citation
• ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods

  2016cites this paper
• Comparative Transcriptome Analysis Reveals Different Silk Yields of Two Silkworm Strains

  2016cites this paper
• Cloning and analysis of DnaJ family members in the silkworm, Bombyx mori.

  2016cites this paper
• Chapter 6 Insect Regulatory Genomics

  2016cites this paper
• An Evaluation of Spatio-Temporal Changes in the Population Genomics of a Butterfly Hybrid Zone Over a Thirty Year Period of Climatic Change

  2016influential citation
• Genome-wide identification and analysis of JHBP-domain family members in the silkworm Bombyx mori

  2016cites this paper
• Cloning, expression and functional analysis of a delta 6-desaturase gene from the silkworm, Bombyx mori L.

  2016cites this paper
• Identification of C-type lectin-domain proteins (CTLDPs) in silkworm Bombyx mori.

  2015cites this paper
• Increased expression of CSP and CYP genes in adult silkworm females exposed to avermectins

  2015cites this paper
• Transcriptomic Analysis of the Anterior Silk Gland in the Domestic Silkworm (Bombyx mori) – Insight into the Mechanism of Silk Formation and Spinning

  2015cites this paper
• Insect Regulatory Genomics

  2015cites this paper
• A multi-objective optimization approach accurately resolves protein domain architectures

  2015cites this paper
• The Mulberry Silkworm--A New Source of Bioactive Proteins

  2015cites this paper
• Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes

  2015cites this paper
• Temporal expression profiling of novel Spodoptera litura nucleopolyhedrovirus-encoded microRNAs upon infection of Sf21 cells.

  2015cites this paper
• De novo transcriptome assembly and analysis of Sf21 cells using illumina paired end sequencing

  2015cites this paper
• Transcriptomic analysis of developmental features of Bombyx mori wing disc during metamorphosis

  2014cites this paper
• Molecular Evidence of RNA Editing in Bombyx Chemosensory Protein Family

  2014cites this paper
• MorusDB: a resource for mulberry genomics and genome biology

  2014cites this paper
• Crystal Structure of Bombyx mori Lipoprotein 6: Comparative Structural Analysis of the 30-kDa Lipoprotein Family

  2014influential citation
• Phylogenetic Analyses and Characterization of RNase X25 from Drosophila melanogaster Suggest a Conserved Housekeeping Role and Additional Functions for RNase T2 Enzymes in Protostomes

  2014cites this paper
• Within-population variability in a moth sex pheromone blend: genetic basis and behavioural consequences

  2014cites this paper
• CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models.

  2014cites this paper
• Expression Profile and Gene Age Jointly Shaped the Genome-Wide Distribution of Premature Termination Codons in a Drosophila melanogaster Population

  2014cites this paper
• Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum

  2013cites this paper
• Seri-bioinformatics: emerging trends and challenges in silkworm research

  2013cites this paper
• Construction of the ie1-Bacmid Expression System and Its Use to Express EGFP and BmAGO2 in BmN Cells

  2013cites this paper
• BmCREC Is an Endoplasmic Reticulum (ER) Resident Protein and Required for ER/Golgi Morphology*

  2013cites this paper
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  2013cites this paper
• Multiple ancient horizontal gene transfers and duplications in lepidopteran species

  2013cites this paper
• LepChorionDB, a database of Lepidopteran chorion proteins and a set of tools useful for the identification of chorion proteins in Lepidopteran proteomes.

  2013cites this paper
• Tudor domain containing 12 (TDRD12) is essential for secondary PIWI interacting RNA biogenesis in mice

  2013cites this paper
• Maize toxin degrades peritrophic matrix proteins and stimulates compensatory transcriptome responses in fall armyworm midgut.

  2013cites this paper
• Interactions between dsRNA and factors affecting the efficiency of RNAi in silkmoth (Bombyx mori)

  2013cites this paper
• Mutation of a vitelline membrane protein, BmEP80, is responsible for the silkworm "Ming" lethal egg mutant.

  2013cites this paper
• The impact of computer science in molecular medicine: enabling high-throughput research.

  2013cites this paper
• Linkage map of the peppered moth, Biston betularia (Lepidoptera, Geometridae): a model of industrial melanism

  2012cites this paper
• Genomic Analysis of Mitochondrial Carrier Genes in the Bombyx mori

  2012cites this paper
• The tau-like protein in silkworm (Bombyx mori) induces microtubule bundle formation.

  2012cites this paper
• Solexa sequencing based transcriptome analysis of Helicoverpa armigera larvae

  2012cites this paper
• SILKWORM LARVAL MIDGUT: A STRIKING EXAMPLE OF TISSUE REMODELING

  2012influential citation
• Expression and localization of silkworm adaptor protein complex-1 subunits, which were down-regulated post baculovirus infection

  2012cites this paper
• Identification of MicroRNAs in Helicoverpa armigera and Spodoptera litura Based on Deep Sequencing and Homology Analysis

  2012cites this paper
• Differential expression of the Bombyx mori diapause-termination timer gene Ea4 in diapause-inducing temperature and photoperiod.

  2012cites this paper
• Insect genomic resources : status , availability and future

  2012cites this paper
• Genome-Wide Identification and Immune Response Analysis of Serine Protease Inhibitor Genes in the Silkworm, Bombyx mori

  2012cites this paper
• A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits

  2011cites this paper
• Quantitative Trait Loci affecting the size of wing eyespots in a seasonally polyphenic butterfly 1

  2011influential citation
• Horizontal gene transfer in silkworm, Bombyx mori

  2011influential citation
• Comparative Genomics of the Odorant-Binding and Chemosensory Protein Gene Families across the Arthropoda: Origin and Evolutionary History of the Chemosensory System

  2011cites this paper
• Genetic analysis of the xenobiotic resistance‐associated ABC gene subfamilies of the Lepidoptera

  2011cites this paper
• Eukaryotic origin of a metabolic pathway in virus by horizontal gene transfer.

  2011cites this paper
• The Ubiquity of the Insulin Superfamily Across the Eukaryotes Detected Using a Bioinformatics Approach

  2011cites this paper