The influence of trematode parasite burden on gene expression in a mammalian host

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Human schistosomiasis

(2014) Daniel G Colley et al.   LANCET

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

(2014) Ryan P. Kelly et al.   PLoS One

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies

(2013) J. Andrew DeWoody et al.   Molecular Ecology Resources

QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data

(2013) Qian Zhou et al.   PLoS One

Break Out: Urogenital Schistosomiasis and Schistosoma haematobium Infection in the Post-Genomic Era

(2013) Paul J. Brindley et al.   PLoS Neglected Tropical Diseases

Schistosomiasis

(2012) Bruno Gryseels   INFECTIOUS DISEASE CLINICS OF NORTH AMERICA

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

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni

(2012) Anna V. Protasio et al.   PLoS Neglected Tropical Diseases

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

(2010) Shawn T O'Neil et al.   BMC GENOMICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

No evidence for lateral gene transfer between salmonids and schistosomes

(2010) Christoph Grunau et al.   NATURE GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Immunopathogenesis of human schistosomiasis

(2009) M. L. BURKE et al.   PARASITE IMMUNOLOGY

Schistosomiasis and liver fibrosis

(2009) Z. A. ANDRADE   PARASITE IMMUNOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY