SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm

High-quality genome assembly of the silkworm, Bombyx mori

(2019) Munetaka Kawamoto et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Developmental and transcriptomic features characterize defects of silk gland growth and silk production in silkworm naked pupa mutant

(2019) Wenbo Hu et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Insect genomes: progress and challenges

(2019) Fei Li et al.   INSECT MOLECULAR BIOLOGY

Deep Insight into the Transcriptome of the Single Silk Gland of Bombyx mori

(2019) Run Shi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

(2019) Ling Xu et al.   NUCLEIC ACIDS RESEARCH

Improving Silkworm Genome Annotation Using a Proteogenomics Approach

(2019) Xiaogang Ye et al.   JOURNAL OF PROTEOME RESEARCH

OUP accepted manuscript

(2018)   BIOINFORMATICS

The evolutionary road from wild moth to domestic silkworm

(2018) Hui Xiang et al.   Nature Ecology & Evolution

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

(2017) Jamie Waese et al.   PLANT CELL

SilkPathDB: a comprehensive resource for the study of silkworm pathogens

(2017) Tian Li et al.   Database-The Journal of Biological Databases and Curation

BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori

(2016) Qiu-Zhong Zhou et al.   BMC BIOINFORMATICS

PIECE 2.0: an update for the plant gene structure comparison and evolution database

(2016) Yi Wang et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Ballgown bridges the gap between transcriptome assembly and expression analysis

(2015) Alyssa C Frazee et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

BmTEdb: a collective database of transposable elements in the silkworm genome

(2013) Hong-En Xu et al.   Database-The Journal of Biological Databases and Curation

PIECE: a database for plant gene structure comparison and evolution

(2012) Yi Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

KAIKObase: An integrated silkworm genome database and data mining tool

(2009) Michihiko Shimomura et al.   BMC GENOMICS

SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology

(2009) Jun Duan et al.   NUCLEIC ACIDS RESEARCH

Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)

(2009) Q. Xia et al.   SCIENCE

Microbiology in the post-genomic era

(2008) Duccio Medini et al.   NATURE REVIEWS MICROBIOLOGY