A new approach to bias correction in RNA-Seq

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

(2011) Anitha D. Jayaprakash et al.   NUCLEIC ACIDS RESEARCH

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

FRT-seq: amplification-free, strand-specific transcriptome sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

(2010) Sudeep Srivastava et al.   NUCLEIC ACIDS RESEARCH

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

(2010) Anna Wetterbom et al.   GENOME BIOLOGY

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH