4.6 Article

HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Supersplat-spliced RNA-seq alignment

Douglas W. Bryant et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

Graham A. Heap et al.

HUMAN MOLECULAR GENETICS (2010)

Review Multidisciplinary Sciences

Expansion of the eukaryotic proteome by alternative splicing

Timothy W. Nilsen et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

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

Hugues Richard et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biotechnology & Applied Microbiology

Global and unbiased detection of splice junctions from RNA-seq data

Adam Ameur et al.

GENOME BIOLOGY (2010)

Article Biochemical Research Methods

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

SOAP2: an improved ultrafast tool for short read alignment

Ruiqiang Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Review Biochemistry & Molecular Biology

The Spliceosome: Design Principles of a Dynamic RNP Machine

Markus C. Wahl et al.

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemical Research Methods

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

Daniel Ramskold et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Review Biotechnology & Applied Microbiology

The SR protein family

Peter J. Shepard et al.

GENOME BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

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

Ben Langmead et al.

GENOME BIOLOGY (2009)

Article Biochemical Research Methods

Optimal spliced alignments of short sequence reads

Fabio De Bona et al.

BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

Ryan Lister et al.

Article Biochemistry & Molecular Biology

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Heng Li et al.

GENOME RESEARCH (2008)

Article Multidisciplinary Sciences

Alternative isoform regulation in human tissue transcriptomes

Eric T. Wang et al.

NATURE (2008)

Article Multidisciplinary Sciences

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

Brian T. Wilhelm et al.

NATURE (2008)

Article Biochemical Research Methods

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Ali Mortazavi et al.

NATURE METHODS (2008)

Article Biochemistry & Molecular Biology

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

Juliane C. Dohm et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Multidisciplinary Sciences

The transcriptional landscape of the yeast genome defined by RNA sequencing

Ugrappa Nagalakshmi et al.

SCIENCE (2008)

Article Biotechnology & Applied Microbiology

cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome

Fangli Lu et al.

BMC GENOMICS (2007)

Article Biochemistry & Molecular Biology

ASD: a bioinformatics resource on alternative splicing

Stefan Stamm et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

KD Pruitt et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

GenBank: update

DA Benson et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)

Review Multidisciplinary Sciences

Genome sequence of the human malaria parasite Plasmodium falciparum

MJ Gardner et al.

NATURE (2002)

Review Multidisciplinary Sciences

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

S Kaul et al.

NATURE (2000)