miRBoost: boosting support vector machines for microRNA precursor classification

RNA
Van Du T TranFariza Tahi

Abstract

Identification of microRNAs (miRNAs) is an important step toward understanding post-transcriptional gene regulation and miRNA-related pathology. Difficulties in identifying miRNAs through experimental techniques combined with the huge amount of data from new sequencing technologies have made in silico discrimination of bona fide miRNA precursors from non-miRNA hairpin-like structures an important topic in bioinformatics. Among various techniques developed for this classification problem, machine learning approaches have proved to be the most promising. However these approaches require the use of training data, which is problematic due to an imbalance in the number of miRNAs (positive data) and non-miRNAs (negative data), which leads to a degradation of their performance. In order to address this issue, we present an ensemble method that uses a boosting technique with support vector machine components to deal with imbalanced training data. Classification is performed following a feature selection on 187 novel and existing features. The algorithm, miRBoost, performed better in comparison with state-of-the-art methods on imbalanced human and cross-species data. It also showed the highest ability among the tested methods for discov...Continue Reading

References

May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Oct 27, 2001·Science·M Lagos-QuintanaT Tuschl
Apr 4, 2003·Genes & Development·Lee P LimDavid P Bartel
Jul 8, 2003·Genome Biology·Eric C LaiGerald M Rubin
Oct 29, 2004·Bioinformatics·Matthieu LegendreDaniel Gautheret
Jun 10, 2005·Nature·Lin HeScott M Hammond
Jul 1, 2005·Nucleic Acids Research·Jin-Wu NamByoung-Tak Zhang
Jul 5, 2005·Bioinformatics·Xiaowo WangYanda Li
Nov 9, 2005·BMC Bioinformatics·Alain SewerMihaela Zavolan
Jul 29, 2006·Bioinformatics·Jana Hertel, Peter F Stadler
Jul 4, 2007·Circulation·Thomas ThumJohann Bauersachs
Dec 20, 2007·BMC Bioinformatics·Markus Brameier, Carsten Wiuf
Jun 5, 2008·Biochemical and Biophysical Research Communications·Sonika TyagiAlok Bhattacharya
Jul 1, 2008·Bioinformatics·Yunpen XuWeixiong Zhang
Oct 18, 2008·Nucleic Acids Research·Qinghua JiangYunlong Liu
Jan 6, 2009·BMC Bioinformatics·Darby Tien-Hao ChangJian-Wei Chen
Feb 24, 2009·Bioinformatics·Rukshan Batuwita, Vasile Palade
Apr 7, 2009·Leukemia & Lymphoma·Marek MrazJiri Mayer
Apr 14, 2009·Nature Genetics·Angeles MencíaMiguel Angel Moreno-Pelayo
Nov 3, 2009·Current Genomics·Olivier C MaesHyman M Schipper
Mar 5, 2010·BMC Bioinformatics·Sumeet AgarwalAshwin Srinivasan
Nov 3, 2010·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Jan 22, 2011·Circulation Research·Eva van Rooij
Mar 25, 2011·Advances in Experimental Medicine and Biology·Daniel PasailăLiviu Ciortuz
Mar 26, 2011·Bioinformatics·Yuanwei ZhangQinghua Shi
Mar 1, 2012·Nucleic Acids Research·Sébastien Tempel, Fariza Tahi
Sep 27, 2012·Nucleic Acids Research·Supatcha LertampaipornMarasri Ruengjitchatchawalya
Mar 19, 2013·BMC Bioinformatics·Adam GudyśIzabela Makałowska

❮ Previous
Next ❯

Citations

Jun 1, 2016·Nucleic Acids Research·Christophe TavFariza Tahi
Apr 1, 2017·Interdisciplinary Sciences, Computational Life Sciences·Anjana RajendiranArchana Pan
Jan 19, 2019·BMC Genomics·Michal ReichertEwa Borzym
Jun 13, 2020·Scientific Reports·Georgios K GeorgakilasPanagiotis Alexiou
Mar 24, 2017·Briefings in Functional Genomics·Vaibhav ShuklaKapaettu Satyamoorthy
Nov 10, 2020·Evolution; International Journal of Organic Evolution·Shotaro HiraseWataru Iwasaki
Jun 6, 2019·Artificial Intelligence in Medicine·Zhenqiu LiuSteven Piantadosi
May 11, 2021·Briefings in Bioinformatics·Dalwinder SinghJoy Roy

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.