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

Whole-genome in-silico subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni

(2012) Julien Portela et al.   BMC GENOMICS

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host

(2011) Sophia J. Parker-Manuel et al.   PLoS Neglected Tropical Diseases

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

(2010) V. M. Bruno et al.   GENOME RESEARCH

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

(2010) B. Daines et al.   GENOME RESEARCH

New insights into the blood-stage transcriptome ofPlasmodium falciparumusing RNA-Seq

(2010) Thomas D. Otto et al.   MOLECULAR MICROBIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

(2010) Minou Nowrousian et al.   PLoS Genetics

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

(2009) L. W. Hillier et al.   GENOME RESEARCH

Evidence for Multiple Independent Origins of trans-Splicing in Metazoa

(2009) V. Douris et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Schistosoma japonicum genome reveals features of host–parasite interplay

(2009)   NATURE

The genome of the blood fluke Schistosoma mansoni

(2009) Matthew Berriman et al.   NATURE

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses

(2009) Jennifer M. Fitzpatrick et al.   PLoS Neglected Tropical Diseases

Genomic linkage map of the human blood fluke Schistosoma mansoni

(2009) Charles D Criscione et al.   GENOME BIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS