Prediction of plant lncRNA by ensemble machine learning classifiers

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

(2017) Yu-Jian Kang et al.   NUCLEIC ACIDS RESEARCH

Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants

(2017) Dong Wang et al.   PLANT JOURNAL

nRC: non-coding RNA Classifier based on structural features

(2017) Antonino Fiannaca et al.   BioData Mining

iRSpot-EL: identify recombination spots with an ensemble learning approach

(2016) Bin Liu et al.   BIOINFORMATICS

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

(2016) Elena Rivas et al.   NATURE METHODS

COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features

(2016) Long Hu et al.   NUCLEIC ACIDS RESEARCH

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

Pseudogene-derived lncRNAs: emerging regulators of gene expression

(2015) Michael J. Milligan et al.   Frontiers in Genetics

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

(2015) Lei Sun et al.   PLoS One

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Characterization of stress-responsive lncRNAs inArabidopsis thalianaby integrating expression, epigenetic and structural features

(2014) Chao Di et al.   PLANT JOURNAL

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis

(2013) Zhu-Hong You et al.   BMC BIOINFORMATICS

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the classification of long non-coding RNAs

(2013) Lina Ma et al.   RNA Biology

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Mechanisms guiding Polycomb activities during gene silencing in Arabidopsis thaliana

(2013) Chongsheng He et al.   Frontiers in Plant Science

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

(2012) T. Derrien et al.   GENOME RESEARCH

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs

(2012) F. Niazi et al.   RNA

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

(2011) Michael J Axtell et al.   GENOME BIOLOGY

Identification and classification of ncRNA molecules using graph properties

(2009) Liam Childs et al.   NUCLEIC ACIDS RESEARCH

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE