A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans

One century away from home: how the red swamp crayfish took over the world

(2020) Francisco J. Oficialdegui et al.   REVIEWS IN FISH BIOLOGY AND FISHERIES

A high-resolution summary of Cambrian to Early Triassic marine invertebrate biodiversity

(2020) Jun-xuan Fan et al.   SCIENCE

Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)

(2020) Boping Tang et al.   GigaScience

Research advances in the genomics and applications for molecular breeding of aquaculture animals

(2020) Xinxin You et al.   AQUACULTURE

Chitinase involved in immune regulation by mediated the toll pathway of crustacea Procambarus clarkii

(2020) Min Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

(2019) Xiaojun Zhang et al.   Nature Communications

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

(2019) Liyi Zhang et al.   Nature Communications

Evolution and diversity of transposable elements in fish genomes

(2019) Feng Shao et al.   Scientific Reports

OUP accepted manuscript

(2018)   BIOINFORMATICS

Clonal genome evolution and rapid invasive spread of the marbled crayfish

(2018) Julian Gutekunst et al.   Nature Ecology & Evolution

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

(2018) Gui-Cai Xu et al.   GigaScience

A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome

(2017) James G Baldwin-Brown et al.   Genome Biology and Evolution

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

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

(2016) Vagheesh Narasimhan et al.   BIOINFORMATICS

Spontaneous Mutation Accumulation inDaphnia pulexin Selection-Free vs. Competitive Environments

(2016) Jullien M. Flynn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Molecular characterization and expression analysis of five chitinases associated with molting in the Chinese mitten crab, Eriocheir sinensis

(2015) Xuguang Li et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

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

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

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

An assessment of life-history studies for USA and Canadian crayfishes: identifying biases and knowledge gaps to improve conservation and management

(2013) Michael J. Moore et al.   Freshwater Science

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY