IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

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

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

(2010) Soohyun Lee et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Jun Li et al.   GENOME BIOLOGY

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

A multivariate regression approach to association analysis of a quantitative trait network

(2009) S. Kim et al.   BIOINFORMATICS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

Genome-wide association analysis by lasso penalized logistic regression

(2009) Tong Tong Wu et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Comparison of next generation sequencing technologies for transcriptome characterization

(2009) P Kerr Wall et al.   BMC GENOMICS

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

(2009) M. Yassour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

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

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

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

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

(2008) Brian T. Wilhelm et al.   NATURE

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

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

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE