Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes

Nine new Pristionchus (Nematoda: Diplogastridae) species from China

(2021) NATSUMI KANZAKI et al.   ZOOTAXA

Screening for CRISPR/Cas9-induced mutations using a co-injection marker in the nematode Pristionchus pacificus

(2020) Ken-ichi Nakayama et al.   DEVELOPMENT GENES AND EVOLUTION

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

(2020) Ralf J. Sommer   GENETICS

Bacterial vitamin B12 production enhances nematode predatory behavior

(2020) Nermin Akduman et al.   ISME Journal

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

Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans

(2020) Milou WM Meeuse et al.   Molecular Systems Biology

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

(2020) Marina Athanasouli et al.   BMC GENOMICS

Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition in Pristionchus Nematodes

(2020) Ziduan Han et al.   GENETICS

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

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

New Gene Origin and Deep Taxon Phylogenomics: Opportunities and Challenges

(2019) Christian Rödelsperger et al.   TRENDS IN GENETICS

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

(2019) Christian Rödelsperger et al.   Scientific Reports

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

(2018) Bogdan Sieriebriennikov et al.   Cell Reports

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

(2018) Christian Rödelsperger et al.   CURRENT BIOLOGY

Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation

(2018) Michael S Werner et al.   GENOME RESEARCH

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

(2018) Neel Prabh et al.   GENOME RESEARCH

Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis

(2017) Marissa Macchietto et al.   Genome Biology and Evolution

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

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

(2017) Christian Rödelsperger et al.   Cell Reports

Environmental influence on Pristionchus pacificus mouth form through different culture methods

(2017) Michael S. Werner et al.   Scientific Reports

MetaCycle: an integrated R package to evaluate periodicity in large scale data

(2016) Gang Wu et al.   BIOINFORMATICS

Large-scale diversification without genetic isolation in nematode symbionts of figs

(2016) V. Susoy et al.   Science Advances

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

(2015) Praveen Baskaran et al.   BMC EVOLUTIONARY BIOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Rapid diversification associated with a macroevolutionary pulse of developmental plasticity

(2015) Vladislav Susoy et al.   eLife

Gene inactivation using the CRISPR/Cas9 system in the nematode Pristionchus pacificus

(2014) Hanh Witte et al.   DEVELOPMENT GENES AND EVOLUTION

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

(2014) Christian Rödelsperger et al.   GENETICS

Extensive Oscillatory Gene Expression during C. elegans Larval Development

(2014) Gert-Jan Hendriks et al.   MOLECULAR CELL

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

A Developmental Switch Coupled to the Evolution of Plasticity Acts through a Sulfatase

(2013) Erik J. Ragsdale et al.   CELL

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

(2013) Dong hyun Kim et al.   NATURE GENETICS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Antagonism of LIN-17/Frizzled and LIN-18/Ryk in Nematode Vulva Induction Reveals Evolutionary Alterations in Core Developmental Pathways

(2011) Xiaoyue Wang et al.   PLOS BIOLOGY

Co-option of the hormone-signalling module dafachronic acid–DAF-12 in nematode evolution

(2010) Gilberto Bento et al.   NATURE

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

(2008) Christoph Dieterich et al.   NATURE GENETICS