High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

(2021) Peng Qin et al.   CELL

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

(2021) Zhikun Wu et al.   Nature Communications

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

A Graph-Based Pan-Genome Guides Biological Discovery

(2020) Yongfu Tao et al.   Molecular Plant

The Number of Larval Molts Is Controlled by Hox in Caterpillars

(2020) Takaaki Daimon et al.   CURRENT BIOLOGY

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

High-quality genome assembly of the silkworm, Bombyx mori

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

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

(2019) Mahul Chakraborty et al.   Nature Communications

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

(2019) Agnieszka A. Golicz et al.   TRENDS IN GENETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

The evolutionary road from wild moth to domestic silkworm

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

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Structure analysis of the spinneret from Bombyx mori and its influence on silk qualities

(2018) Nangkuo Guo et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

The pangenome of an agronomically important crop plant Brassica oleracea

(2016) Agnieszka A. Golicz et al.   Nature Communications

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Unique transposon landscapes are pervasive acrossDrosophila melanogastergenomes

(2015) Reazur Rahman et al.   NUCLEIC ACIDS RESEARCH

Aspartate Decarboxylase is Required for a Normal Pupa Pigmentation Pattern in the Silkworm, Bombyx mori

(2015) Fangyin Dai et al.   Scientific Reports

A novel laminin β gene BmLanB1-w regulates wing-specific cell adhesion in silkworm, Bombyx mori

(2015) Xiaoling Tong et al.   Scientific Reports

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

(2014) Yuki Naito et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Copy number variations among silkworms

(2014) Qian Zhao et al.   BMC GENOMICS

Positional cloning of the sex-linked giant egg (Ge) locus in the silkworm,Bombyx mori

(2014) T. Fujii et al.   INSECT MOLECULAR BIOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation

(2013) Emmanuel F Mongodin et al.   BMC GENOMICS

Periodic Wnt1 expression in response to ecdysteroid generates twin-spot markings on caterpillars

(2013) Junichi Yamaguchi et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Electroporation-mediated somatic transgenesis for rapid functional analysis in insects

(2012) T. Ando et al.   DEVELOPMENT

CD36 homolog divergence is responsible for the selectivity of carotenoid species migration to the silk gland of the silkwormBombyx mori

(2012) Takashi Sakudoh et al.   JOURNAL OF LIPID RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Identification and characterization of the fusion transcript, composed of the apterous homolog and a putative protein phosphatase gene, generated by 1.5-Mb interstitial deletion in the vestigial (Vg) mutant of Bombyx mori

(2011) T. Fujii et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

Repression of tyrosine hydroxylase is responsible for the sex-linked chocolate mutation of the silkworm, Bombyx mori

(2010) C. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Yellow-e Determines the Color Pattern of Larval Head and Tail Spots of the SilkwormBombyx mori

(2009) Katsuhiko Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2009) Q. Xia et al.   SCIENCE

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The genome of a lepidopteran model insect, the silkworm Bombyx mori

(2008) The International Silkworm Genome   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY