ptRNApred: computational identification and classification of post-transcriptional RNA

Non-Coding RNAs: Functional Aspects and Diagnostic Utility in Oncology

(2013) Taiho Kim et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

mRNA secondary structure optimization using a correlated stem–loop prediction

(2013) Paulo Gaspar et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

LIBSVM

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

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features

(2011) Jiandong Ding et al.   BMC BIOINFORMATICS

Employing machine learning for reliable miRNA target identification in plants

(2011) Ashwani Jha et al.   BMC GENOMICS

Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes

(2011) Dominik Beck et al.   BMC Medical Genomics

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

TargetSpy: a supervised machine learning approach for microRNA target prediction

(2010) Martin Sturm et al.   BMC BIOINFORMATICS

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data

(2010) Chol-Hee Jung et al.   BMC GENOMICS

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

(2010) Z. J. Lu et al.   GENOME RESEARCH

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

DiProGB: the dinucleotide properties genome browser

(2009) M. Friedel et al.   BIOINFORMATICS

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

(2009) Roberto T Arrial et al.   BMC BIOINFORMATICS

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

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

miRNAminer: A tool for homologous microRNA gene search

(2008) Shay Artzi et al.   BMC BIOINFORMATICS

Non-protein coding RNA biomarkers and differential expression in cancers: a review

(2008) Massimo Mallardo et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH