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

Phenotypic Plasticity: From Theory and Genetics to Current and Future Challenges

(2020) Ralf J. Sommer   GENETICS

Sex chromosome evolution in parasitic nematodes of humans

(2020) Jeremy M. Foster et al.   Nature Communications

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell

(2020) Bogdan Sieriebriennikov et al.   PLoS Genetics

Convergent evolution of small molecule pheromones in Pristionchus nematodes

(2020) Chuanfu Dong et al.   eLife

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

(2020) Marina Athanasouli et al.   BMC GENOMICS

Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution

(2020) Christian Rödelsperger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Polyphenism of a novel trait integrated rapidly evolving genes into ancestrally plastic networks

(2020) Sofia Casasa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis

(2019) Toni Beltran et al.   DEVELOPMENTAL CELL

Small peptide–mediated self-recognition prevents cannibalism in predatory nematodes

(2019) James W. Lightfoot et al.   SCIENCE

De Novo, Divergence, and Mixed Origin Contribute to the Emergence of Orphan Genes in Pristionchus Nematodes

(2019) Neel Prabh et al.   G3-Genes Genomes Genetics

Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

(2019) Ashleigh B. Smythe et al.   BMC EVOLUTIONARY BIOLOGY

Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus

(2019) Christian Rödelsperger et al.   Scientific Reports

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

(2018) Da Yin et al.   SCIENCE

A Developmental Switch Generating Phenotypic Plasticity Is Part of a Conserved Multi-gene Locus

(2018) Bogdan Sieriebriennikov et al.   Cell Reports

Improving the annotation of the Heterorhabditis bacteriophora genome

(2018) Florence McLean et al.   GigaScience

Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages

(2018) Christian Rödelsperger et al.   CURRENT BIOLOGY

Deep taxon sampling reveals the evolutionary dynamics of novel gene families in ​Pristionchus nematodes

(2018) Neel Prabh et al.   GENOME RESEARCH

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

(2018) Natsumi Kanzaki et al.   Nature Communications

Comparative genomics of the major parasitic worms

(2018)   NATURE GENETICS

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

WormBase ParaSite − a comprehensive resource for helminth genomics

(2017) Kevin L. Howe et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus

(2017) Christian Rödelsperger et al.   Cell Reports

Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option

(2016) Aude Gilabert et al.   BMC GENOMICS

Genomic Profiles of Diversification and Genotype–Phenotype Association in Island Nematode Lineages

(2016) Angela McGaughran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes

(2016) Scott T. Small et al.   MOLECULAR ECOLOGY

The genomic basis of parasitism in the Strongyloides clade of nematodes

(2016) Vicky L Hunt et al.   NATURE GENETICS

Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention

(2016) Samantha N. McNulty et al.   Scientific Reports

The genome of Onchocerca volvulus, agent of river blindness

(2016) James A. Cotton et al.   Nature Microbiology

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

The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families

(2015) Erich M Schwarz et al.   NATURE GENETICS

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

(2015) Melanie G. Mayer et al.   PLoS Genetics

Characterization of Genetic Diversity in the NematodePristionchus pacificusfrom Population-Scale Resequencing Data

(2014) Christian Rödelsperger et al.   GENETICS

Genome of the human hookworm Necator americanus

(2014) Yat T Tang et al.   NATURE GENETICS

The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

(2014) James A Cotton et al.   GENOME BIOLOGY

The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda

(2013) Philipp H Schiffer et al.   BMC GENOMICS

The Draft Genome and Transcriptome of Panagrellus redivivus Are Shaped by the Harsh Demands of a Free-Living Lifestyle

(2013) J. Srinivasan et al.   GENETICS

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

(2013) Christopher A Desjardins et al.   NATURE GENETICS

A Lover and a Fighter: The Genome Sequence of an Entomopathogenic Nematode Heterorhabditis bacteriophora

(2013) Xiaodong Bai et al.   PLoS One

Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells

(2012) Jianbin Wang et al.   DEVELOPMENTAL CELL

The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets

(2012) Christelle Godel et al.   FASEB JOURNAL

The draft genome of the parasitic nematode Trichinella spiralis

(2011) Makedonka Mitreva et al.   NATURE GENETICS

Improving animal phylogenies with genomic data

(2011) Maximilian J. Telford et al.   TRENDS IN GENETICS

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus

(2011) Taisei Kikuchi et al.   PLoS Pathogens

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

(2009) A. Barriere et al.   GENOME RESEARCH

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY

Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism

(2008) C. H. Opperman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA