A machine learning approach for viral genome classification.

PubWeight™: 0.75‹?›

🔗 View Article (PMID 28399797)

Published in BMC Bioinformatics on April 11, 2017

Authors

Mohamed Amine Remita1,2, Ahmed Halioui1,2, Abou Abdallah Malick Diouara1,2, Bruno Daigle1,2, Golrokh Kiani1,2, Abdoulaye Baniré Diallo3,4

Author Affiliations

1: Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada.
2: Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada.
3: Laboratoire de bioinformatique, département d'informatique, Université du Québec à Montréal, Montreal, P.O. Box 8888 Downtown Station, H3C 3P8, Qc, Canada. diallo.abdoulaye@uqam.ca.
4: Pharmaqam Center, Université du Québec à Montréal (Québec), Montréal (Quebec), PO BOX 8888 Downtown Station, H3C 3P8, Canada. diallo.abdoulaye@uqam.ca.

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97

Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med (2003) 31.67

The contributions of hepatitis B virus and hepatitis C virus infections to cirrhosis and primary liver cancer worldwide. J Hepatol (2006) 10.21

Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology (2010) 7.24

HIV-1 nomenclature proposal. Science (2000) 6.61

Alignment-free sequence comparison-a review. Bioinformatics (2003) 6.29

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics (2010) 5.70

An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics (2005) 5.60

Identification and assessment of known and novel human papillomaviruses by polymerase chain reaction amplification, restriction fragment length polymorphisms, nucleotide sequence, and phylogenetic algorithms. J Infect Dis (1994) 4.89

A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol (1998) 3.65

A new human immunodeficiency virus derived from gorillas. Nat Med (2009) 3.47

REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res (2014) 2.84

Hepatitis B virus taxonomy and hepatitis B virus genotypes. World J Gastroenterol (2007) 2.50

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2015) 2.44

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin Microbiol Rev (2001) 2.37

Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification. Arch Virol (2014) 2.09

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res (2009) 2.06

Estimation of phylogenetic relationships from DNA restriction patterns and selection of endonuclease cleavage sites. Proc Natl Acad Sci U S A (1982) 1.98

Hepatitis B virus genotype assignment using restriction fragment length polymorphism patterns. FEBS Lett (1999) 1.96

Typing of hepatitis C virus genomes by restriction fragment length polymorphism. J Gen Virol (1991) 1.74

Class-imbalanced classifiers for high-dimensional data. Brief Bioinform (2012) 1.36

Class prediction for high-dimensional class-imbalanced data. BMC Bioinformatics (2010) 1.34

Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type 1 by using restriction fragment length polymorphism analysis. Virus Genes (1996) 1.33

Machine learning applications in genetics and genomics. Nat Rev Genet (2015) 1.32

Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J Virol (2012) 1.31

COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification. Nucleic Acids Res (2014) 1.15

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Brief Bioinform (2013) 1.06

Complete genotyping of mucosal human papillomavirus using a restriction fragment length polymorphism analysis and an original typing algorithm. J Clin Virol (2008) 0.94

An alternative method for electrophoretic gel image analysis in the GelMaster software. Comput Methods Programs Biomed (2005) 0.92

A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. Biochem Biophys Res Commun (2008) 0.90

Real time classification of viruses in 12 dimensions. PLoS One (2013) 0.90

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. BMC Bioinformatics (2010) 0.87

A computerized methodology for improved virus typing by PCR-RFLP gel electrophoresis. IEEE Trans Biomed Eng (2011) 0.76