Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite

Phylogenomic and biogeographic reconstruction of the Trichinella complex

(2016) Pasi K. Korhonen et al.   Nature Communications

WormBase 2016: expanding to enable helminth genomic research

(2015) Kevin L. Howe et al.   NUCLEIC ACIDS RESEARCH

The evolution of parasite genomes and the origins of parasitism

(2015) ANDREW P. JACKSON   PARASITOLOGY

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

‘Degraded’ RNA profiles in Arthropoda and beyond

(2015) Sean D. McCarthy et al.   PeerJ

Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout

(2015) Mohamed Salem et al.   PLoS One

Landscape Genetics of Schistocephalus solidus Parasites in Threespine Stickleback (Gasterosteus aculeatus) from Alaska

(2015) C. Grace Sprehn et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

On the optimal trimming of high-throughput mRNA sequence data

(2014) Matthew D. MacManes   Frontiers in Genetics

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly

(2013) Warren R Francis et al.   BMC GENOMICS

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

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

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Pfam: the protein families database

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

Diverse effects of parasites in ecosystems: linking interdependent processes

(2012) Melanie J Hatcher et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

(2012) V. CAHAIS et al.   Molecular Ecology Resources

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

In vitro transition of Schistocephalus solidus (Cestoda) from coracidium to procercoid and from procercoid to plerocercoid

(2011) P.J. Jakobsen et al.   EXPERIMENTAL PARASITOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Diel vertical movements, and effects of infection by the cestode Schistocephalus solidus on daytime proximity of three-spined sticklebacks Gasterosteus aculeatus to the surface of a large Alaskan lake

(2011) T. P. Quinn et al.   OECOLOGIA

Evolutionary significance of fecundity reduction in threespine stickleback infected by the diphyllobothriidean cestode Schistocephalus solidus

(2010) DAVID C. HEINS et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity

(2009) NADIA AUBIN-HORTH et al.   MOLECULAR ECOLOGY

The three-spined stickleback- Schistocephalus solidus system: an experimental model for investigating host-parasite interactions in fish

(2009) I. BARBER et al.   PARASITOLOGY

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

(2008) Brian J Haas et al.   GENOME BIOLOGY