UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq

TACO produces robust multisample transcriptome assemblies from RNA-seq

(2016) Yashar S Niknafs et al.   NATURE METHODS

Long noncoding and circular RNAs in lung cancer: advances and perspectives

(2016) Weijia Xie et al.   Epigenomics

iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data

(2016) Kun Sun et al.   BMC GENOMICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

High-throughput long noncoding RNA profiling for diagnostic and prognostic markers in cancer: opportunities and challenges

(2015) Zhifu Sun   Epigenomics

Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

(2015) Akanksha Verma et al.   Genome Medicine

Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs) - Application in Human Skeletal Muscle Cells

(2014) Kun Sun et al.   PLoS One

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

(2013) Y. Liao et al.   BIOINFORMATICS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

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

Genome-wide computational identification and manual annotation of human long noncoding RNA genes

(2010) H. Jia et al.   RNA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS