Transcriptome analysis of the parasite Encephalitozoon cuniculi: an in-depth examination of pre-mRNA splicing in a reduced eukaryote

Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites

(2012) J.-F. Pombert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts

(2011) K. Sorber et al.   NUCLEIC ACIDS RESEARCH

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

(2010) Ashish Agarwal et al.   BMC GENOMICS

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

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

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

Patterns of 5′ Untranslated Region Length Distribution in Encephalitozoon cuniculi: Implications for Gene Regulation and Potential Links Between Transcription and Splicing

(2010) CAMERON J. GRISDALE et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Splicing and Transcription Differ between Spore and Intracellular Life Stages in the Parasitic Microsporidia

(2010) E. E. Gill et al.   MOLECULAR BIOLOGY AND EVOLUTION

Constrained Intron Structures in a Microsporidian

(2010) R. C. H. Lee et al.   MOLECULAR BIOLOGY AND EVOLUTION

Defining transcribed regions using RNA-seq

(2010) Brian T Wilhelm et al.   Nature Protocols

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

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

(2009) Ben Langmead 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

Comparative profiling of overlapping transcription in the compacted genomes of microsporidia Antonospora locustae and Encephalitozoon cuniculi

(2008) Nicolas Corradi et al.   GENOMICS

Kinetics of Encephalitozoon Spp. Infection of Human Macrophages

(2008) Jeffrey Fischer et al.   JOURNAL OF PARASITOLOGY

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components

(2008) Marcela Dávila López et al.   NUCLEIC ACIDS RESEARCH

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Evolutionary Convergence on Highly-Conserved 3′ Intron Structures in Intron-Poor Eukaryotes and Insights into the Ancestral Eukaryotic Genome

(2008) Manuel Irimia et al.   PLoS Genetics