lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine

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

(2016) Kun Sun et al.   BMC GENOMICS

Prediction and classification of ncRNAs using structural information

(2014) Bharat Panwar et al.   BMC GENOMICS

eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

(2014) Luana Micallef et al.   PLoS One

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

(2014) Yolanda Sánchez et al.   Nature Communications

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

(2013) J. R. Alvarez-Dominguez et al.   BLOOD

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study

(2012) Lei Sun et al.   BMC BIOINFORMATICS

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

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

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

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

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

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology