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

Microevolution of Duplications and Deletions and Their Impact on Gene Expression in the Nematode Pristionchus pacificus

(2015) Praveen Baskaran et al.   PLoS One

Natural Variation in Dauer Pheromone Production and Sensing Supports Intraspecific Competition in Nematodes

(2014) Neelanjan Bose et al.   CURRENT BIOLOGY

BLIND ordering of large-scale transcriptomic developmental timecourses

(2014) L. Anavy et al.   DEVELOPMENT

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

(2014) Christian Rödelsperger et al.   GENETICS

A wax ester promotes collective host finding in the nematode Pristionchus pacificus

(2014) Sider Penkov et al.   Nature Chemical Biology

A novel method for cross-species gene expression analysis

(2013) Erik Kristiansson et al.   BMC BIOINFORMATICS

Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish

(2013) Liandong Yang et al.   BMC GENOMICS

System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes

(2013) Daniel J. Bumbarger et al.   CELL

Cryptic variation in vulva development by cis-regulatory evolution of a HAIRY-binding site

(2013) Simone Kienle et al.   Nature Communications

Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

(2012) Amit Sinha et al.   BMC GENOMICS

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

Expressional and functional variation of horizontally acquired cellulases in the nematode Pristionchus pacificus

(2012) Lisa N. Schuster et al.   GENE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

System Wide Analysis of the Evolution of Innate Immunity in the Nematode Model Species Caenorhabditis elegans and Pristionchus pacificus

(2012) Amit Sinha et al.   PLoS One

RNAseq Analysis of the Parasitic Nematode Strongyloides stercoralis Reveals Divergent Regulation of Canonical Dauer Pathways

(2012) Jonathan D. Stoltzfus et al.   PLoS Neglected Tropical Diseases

Genome-Wide Analysis of Germline Signaling Genes Regulating Longevity and Innate Immunity in the Nematode Pristionchus pacificus

(2012) Robbie Rae et al.   PLoS Pathogens

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

The draft genome of the parasitic nematode Trichinella spiralis

(2011) Makedonka Mitreva et al.   NATURE GENETICS

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

(2010) N. Borchert et al.   GENOME RESEARCH

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

The genetic basis of evolutionary change in gene expression levels

(2010) J. J. Emerson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

(2010) Jean-François Gout et al.   PLoS Genetics

A Conserved Endocrine Mechanism Controls the Formation of Dauer and Infective Larvae in Nematodes

(2008) Akira Ogawa et al.   CURRENT BIOLOGY

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

(2008) Christoph Dieterich et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH