Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics

Ubiquitous Selfish Toxin-Antidote Elements in Caenorhabditis Species

(2021) Eyal Ben-David et al.   CURRENT BIOLOGY

Selfing is the safest sex for Caenorhabditis tropicalis

(2021) Luke M Noble et al.   eLife

The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes

(2021) Christian Rödelsperger   BMC GENOMICS

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis

(2021) Mehmet Dayi et al.   Scientific Reports

Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans

(2021) Daehan Lee et al.   Nature Ecology & Evolution

The Genome of Caenorhabditis bovis

(2020) Lewis Stevens et al.   CURRENT BIOLOGY

Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization

(2020) Anastasia A. Teterina et al.   GENETICS

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

Recompleting the Caenorhabditis elegans genome

(2019) Jun Yoshimura et al.   GENOME RESEARCH

Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans

(2019) Chuna Kim et al.   GENOME RESEARCH

Reproductive transitions in plants and animals: selfing syndrome, sexual selection, and speciation

(2019) Asher D. Cutter   NEW PHYTOLOGIST

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations

(2019) Tim A Crombie et al.   eLife

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni

(2018) Xiaoliang Ren et al.   NUCLEIC ACIDS RESEARCH

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins

(2018) Da Yin et al.   SCIENCE

Biology and genome of a newly discovered sibling species of Caenorhabditis elegans

(2018) Natsumi Kanzaki et al.   Nature Communications

MinION-based long-read sequencing and assembly extends theCaenorhabditis elegansreference genome

(2017) John R. Tyson et al.   GENOME RESEARCH

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 the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

(2017) Céline Ferrari et al.   BMC ECOLOGY

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

(2016) Daniel E. Cook et al.   GENETICS

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

(2016) Daniel E. Cook et al.   GENETICS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

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

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

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

Full-genome evolutionary histories of selfing, splitting, and selection inCaenorhabditis

(2015) Cristel G. Thomas et al.   GENOME RESEARCH

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

A Streamlined System for Species Diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with Name Designations for 15 Distinct Biological Species

(2014) Marie-Anne Félix 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

A Variant in the Neuropeptide Receptor npr-1 is a Major Determinant of Caenorhabditis elegans Growth and Physiology

(2014) Erik C. Andersen et al.   PLoS Genetics

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

(2013) Marie-Anne Félix et al.   BMC EVOLUTIONARY BIOLOGY

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae

(2012) Marie-Anne Félix et al.   BMC BIOLOGY

A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits

(2011) Karin C Kiontke et al.   BMC EVOLUTIONARY BIOLOGY

Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination

(2011) Joseph A. Ross et al.   PLoS Genetics

Gap5—editing the billion fragment sequence assembly

(2010) James K. Bonfield et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Recombinational Landscape and Population Genomics of Caenorhabditis elegans

(2009) Matthew V. Rockman et al.   PLoS Genetics

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Breeding Designs for Recombinant Inbred Advanced Intercross Lines

(2008) Matthew V. Rockman et al.   GENETICS

Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing

(2008) A. D. Cutter et al.   GENETICS

Oscheius tipulae, a widespread hermaphroditic soil nematode, displays a higher genetic diversity and geographical structure than Caenorhabditis elegans

(2008) DOROTHÉE BAÏLLE et al.   MOLECULAR ECOLOGY

Widespread Genetic Incompatibility in C. Elegans Maintained by Balancing Selection

(2008) H. S. Seidel et al.   SCIENCE