New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum

(2013) Chunzhao Zhao et al.   BMC GENOMICS

TheAspergillusGenome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

(2013) Gustavo C. Cerqueira et al.   NUCLEIC ACIDS RESEARCH

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

(2012) Richard J O'Connell et al.   NATURE GENETICS

RNA-Seq vs Dual- and Single-Channel Microarray Data: Sensitivity Analysis for Differential Expression and Clustering

(2012) Alina Sîrbu et al.   PLoS One

Sequential Delivery of Host-Induced Virulence Effectors by Appressoria and Intracellular Hyphae of the Phytopathogen Colletotrichum higginsianum

(2012) Jochen Kleemann et al.   PLoS Pathogens

Design and validation issues in RNA-seq experiments

(2011) Z. Fang et al.   BRIEFINGS IN BIOINFORMATICS

Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome

(2011) E. Tisserant et al.   NEW PHYTOLOGIST

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

When and how to kill a plant cell: Infection strategies of plant pathogenic fungi

(2010) Ralf Horbach et al.   JOURNAL OF PLANT PHYSIOLOGY

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

(2010) Bin Wang et al.   NUCLEIC ACIDS RESEARCH

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS 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

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Sfp-Type 4'-Phosphopantetheinyl Transferase Is Indispensable for Fungal Pathogenicity

(2009) R. Horbach et al.   PLANT CELL

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

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

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

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

(2008) T. Mituyama et al.   NUCLEIC ACIDS RESEARCH

Cross-kingdom patterns of alternative splicing and splice recognition

(2008) Abigail M McGuire et al.   GENOME BIOLOGY