An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes
暂无分享,去创建一个
Lila Kari | Stephen Solis-Reyes | Mariano Avino | Art Poon | L. Kari | A. Poon | Mariano Avino | Stephen Solis-Reyes
[1] Anil K. Jain,et al. Small Sample Size Effects in Statistical Pattern Recognition: Recommendations for Practitioners , 1991, IEEE Trans. Pattern Anal. Mach. Intell..
[2] Khalid Sayood,et al. Computational Genomic Signatures , 2011, Computational Genomic Signatures.
[3] Yang Young Lu,et al. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data , 2017, Microbiome.
[4] Troy Hernandez,et al. Real Time Classification of Viruses in 12 Dimensions , 2013, PloS one.
[5] Xiao Sun,et al. A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. , 2008, Biochemical and Biophysical Research Communications - BBRC.
[6] Sung-Hou Kim,et al. Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs) , 2011, Proceedings of the National Academy of Sciences.
[7] S Karlin,et al. Heterogeneity of genomes: measures and values. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[8] Ziheng Yang,et al. INDELible: A Flexible Simulator of Biological Sequence Evolution , 2009, Molecular biology and evolution.
[9] Achuthsankar S. Nair,et al. Combined classifier for unknown genome classification using chaos game representation features , 2010 .
[10] P. Musoke,et al. Impact of human immunodeficiency virus type 1 (hiv-1) subtype on women receiving single-dose nevirapine prophylaxis to prevent hiv-1 vertical transmission (hiv network for prevention trials 012 study). , 2001, The Journal of infectious diseases.
[11] Huldrych F. Günthard,et al. Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration , 2017, EBioMedicine.
[12] J. Mullins,et al. HIV Sequence Compendium 2010 , 2010 .
[13] Changchuan Yin,et al. Virus classification in 60-dimensional protein space. , 2016, Molecular phylogenetics and evolution.
[14] W. Blattner,et al. HIV-1 Epidemic in the Caribbean Is Dominated by Subtype B , 2009, PloS one.
[15] Sanjiv K. Dwivedi,et al. Classification of HIV-1 Sequences Using Profile Hidden Markov Models , 2012, PloS one.
[16] Christophe Combet,et al. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes , 2005, Hepatology.
[17] A. Izenman. Linear Discriminant Analysis , 2013 .
[18] Jonas S. Almeida,et al. Alignment-free sequence comparison: benefits, applications, and tools , 2017, Genome Biology.
[19] Achuthsankar S. Nair,et al. ANN Based Classification of Unknown Genome Fragments Using Chaos Game Representation , 2010, 2010 Second International Conference on Machine Learning and Computing.
[20] A. Poon. Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology , 2015, Molecular biology and evolution.
[21] Tulio de Oliveira,et al. An automated genotyping system for analysis of HIV-1 and other microbial sequences , 2005, Bioinform..
[22] ARIDAMAN PANDIT,et al. Analysis of dinucleotide signatures in HIV-1 subtype B genomes , 2013, Journal of Genetics.
[23] S. Karlin,et al. Over- and under-representation of short oligonucleotides in DNA sequences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[24] Tong Zhang,et al. Solving large scale linear prediction problems using stochastic gradient descent algorithms , 2004, ICML.
[25] Troy Hernandez,et al. Global comparison of multiple-segmented viruses in 12-dimensional genome space. , 2014, Molecular phylogenetics and evolution.
[26] Patrick J. F. Groenen,et al. Modern Multidimensional Scaling: Theory and Applications , 2003 .
[27] S. Karlin,et al. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[28] Jie Ren,et al. Prediction of virus-host infectious association by supervised learning methods , 2017, BMC Bioinformatics.
[29] Ahmed Halioui,et al. A machine learning approach for viral genome classification , 2017, BMC Bioinformatics.
[30] Anders Larsson,et al. AliView: a fast and lightweight alignment viewer and editor for large datasets , 2014, Bioinform..
[31] Wolfgang Preiser,et al. Moderate levels of preantiretroviral therapy drug resistance in a generalized epidemic: time for better first-line ART? , 2017, AIDS.
[32] Jimmy Ba,et al. Adam: A Method for Stochastic Optimization , 2014, ICLR.
[33] Huldrych F. Günthard,et al. Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study , 2016 .
[34] Y. S. Thushana. Texture features from Chaos Game Representation Images of Genomes , 2013 .
[35] Leo Breiman,et al. Random Forests , 2001, Machine Learning.
[36] Trevor Hastie,et al. Multi-class AdaBoost ∗ , 2009 .
[37] S Karlin,et al. Comparisons of eukaryotic genomic sequences. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[38] Anil K. Jain,et al. 39 Dimensionality and sample size considerations in pattern recognition practice , 1982, Classification, Pattern Recognition and Reduction of Dimensionality.
[39] Somdatta Sinha,et al. Multifractal analysis of HIV-1 genomes. , 2012, Molecular phylogenetics and evolution.
[40] Lila Kari,et al. An investigation into inter- and intragenomic variations of graphic genomic signatures , 2015, BMC Bioinformatics.
[41] Nikesh S. Dattani,et al. Mapping the Space of Genomic Signatures , 2014, PloS one.
[42] WolfElizabeth,et al. Short Communication: Phylogenetic Evidence of HIV-1 Transmission Between Adult and Adolescent Men Who Have Sex with Men. , 2016 .
[43] S. Hammer,et al. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. , 2008, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[44] Wei-Yin Loh,et al. Classification and regression trees , 2011, WIREs Data Mining Knowl. Discov..
[45] F. Raffi,et al. European AIDS Clinical Society (EACS) guidelines for the clinical management and treatment of HIV‐infected adults , 2008, HIV medicine.
[46] Chidchanok Lursinsap,et al. A high performance prediction of HPV genotypes by Chaos game representation and singular value decomposition , 2015, BMC Bioinformatics.
[47] Ming Zhang,et al. A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes , 2006, BMC Bioinformatics.
[48] Bernhard Haubold,et al. Alignment-free phylogenetics and population genetics , 2014, Briefings Bioinform..
[49] I. Williams,et al. Development of a novel human immunodeficiency virus type 1 subtyping tool, Subtype Analyzer (STAR): analysis of subtype distribution in London. , 2004, AIDS research and human retroviruses.
[50] Birgit Funke,et al. College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. , 2015, Archives of pathology & laboratory medicine.
[51] Se-Ran Jun,et al. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions , 2009, Proceedings of the National Academy of Sciences.
[52] Tiee-Jian Wu,et al. Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences , 2005, Bioinform..
[53] Diana D. Huang,et al. Sequence characterization of the protease and partial reverse transcriptase proteins of the NED panel, an international HIV type 1 subtype reference and standards panel. , 2003, AIDS research and human retroviruses.
[54] G. Learn,et al. HIV-1 Nomenclature Proposal , 2000, Science.
[55] Jun S. Liu,et al. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome , 2007, Proceedings of the National Academy of Sciences.
[56] B. Blaisdell. A measure of the similarity of sets of sequences not requiring sequence alignment. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[57] A. Mchardy,et al. The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences , 2012, PloS one.
[58] Chidchanok Lursinsap,et al. An Efficient Prediction of HPV Genotypes from Partial Coding Sequences by Chaos Game Representation and Fuzzy k-Nearest Neighbor Technique , 2017 .
[59] S. Hammer,et al. The challenge of HIV-1 subtype diversity. , 2008, The New England journal of medicine.
[60] Giovanni Felici,et al. MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification , 2016, BioData Mining.
[61] Tiee-Jian Wu,et al. Statistical Measures of DNA Sequence Dissimilarity under Markov Chain Models of Base Composition , 2001, Biometrics.
[62] Alina A. von Davier,et al. Cross-Validation , 2014 .
[63] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[64] E. Arts,et al. Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease. , 2011, The Lancet. Infectious diseases.
[65] Gaël Varoquaux,et al. Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..
[66] Gene H. Golub,et al. Matrix computations , 1983 .
[67] S Karlin,et al. Compositional biases of bacterial genomes and evolutionary implications , 1997, Journal of bacteriology.
[68] S. Salzberg,et al. Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov Models , 2009, Nature Methods.
[69] Nello Cristianini,et al. An Introduction to Support Vector Machines and Other Kernel-based Learning Methods , 2000 .
[70] E. Krause. Taxicab Geometry: An Adventure in Non-Euclidean Geometry , 1987 .
[71] Dan Otelea,et al. Recent HIV-1 Outbreak Among Intravenous Drug Users in Romania: Evidence for Cocirculation of CRF14_BG and Subtype F1 Strains. , 2015, AIDS research and human retroviruses.
[72] Pandurang Kolekar,et al. Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping. , 2012, Molecular phylogenetics and evolution.
[73] Yoav Freund,et al. A decision-theoretic generalization of on-line learning and an application to boosting , 1995, EuroCOLT.
[74] Ehsaneddin Asgari,et al. Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics , 2015, PloS one.
[75] Jing-Doo Wang,et al. Comparing Virus Classification using genomic Materials According to Different Taxonomic Levels , 2013, J. Bioinform. Comput. Biol..
[76] Geoffrey E. Hinton. Connectionist Learning Procedures , 1989, Artif. Intell..
[77] Ramón Doallo,et al. CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.
[78] Fereidoun Azizi,et al. Fast Food Intake Increases the Incidence of Metabolic Syndrome in Children and Adolescents: Tehran Lipid and Glucose Study , 2015, PloS one.
[79] Achuthsankar S. Nair,et al. Hurst CGR (HCGR) - A Novel Feature Extraction Method from Chaos Game Representation of Genomes , 2011, ACC.
[80] Sergei L. Kosakovsky Pond,et al. An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1 , 2009, PLoS Comput. Biol..
[81] Steven Wolinsky,et al. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960 , 2008, Nature.
[82] Giovanni Felici,et al. LAF: Logic Alignment Free and its application to bacterial genomes classification , 2015, BioData Mining.
[83] Anne-Mieke Vandamme,et al. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[84] Kristof Theys,et al. Epidemic dispersion of HIV and HCV in a population of co-infected Romanian injecting drug users , 2017, PloS one.
[85] O. Gascuel,et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.
[86] N. Altman. An Introduction to Kernel and Nearest-Neighbor Nonparametric Regression , 1992 .
[87] G. Golub,et al. Updating formulae and a pairwise algorithm for computing sample variances , 1979 .
[88] Pontiano Kaleebu,et al. Low drug resistance levels among drug-naive individuals with recent HIV type 1 infection in a rural clinical cohort in southwestern Uganda. , 2012, AIDS research and human retroviruses.
[89] B. Blaisdell,et al. Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarity of natural sequences , 1989, Journal of Molecular Evolution.
[90] Glenn Lawyer,et al. COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification , 2014, Nucleic acids research.
[91] Sung-Hou Kim,et al. Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method , 2009, Proceedings of the National Academy of Sciences.
[92] Oludayo O. Olugbara,et al. Identification of Pathogenic Viruses Using Genomic Cepstral Coefficients with Radial Basis Function Neural Network , 2015, NaBIC.
[93] Tatiana A. Tatusova,et al. A web-based genotyping resource for viral sequences , 2004, Nucleic Acids Res..
[94] Yanchun Yang,et al. Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison , 2008, Bioinform..
[95] Lila Kari,et al. Additive methods for genomic signatures , 2016, BMC Bioinformatics.
[96] R. Tibshirani,et al. Diagnosis of multiple cancer types by shrunken centroids of gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[97] Brian T. Foley,et al. HIV-1 Subtype and Circulating Recombinant Form (CRF) Reference Sequences, 2005 , 2005 .
[98] Richard H. Liang,et al. Origin and Evolution of Human Immunodeficiency Viruses , 2015 .
[99] Leo Breiman,et al. Classification and Regression Trees , 1984 .
[100] Lila Kari,et al. MoDMaps3D: an interactive webtool for the quantification and 3D visualization of interrelationships in a dataset of DNA sequences , 2017, Bioinform..
[101] D. Burke,et al. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. , 1995, AIDS research and human retroviruses.
[102] S. Karlin,et al. Dinucleotide relative abundance extremes: a genomic signature. , 1995, Trends in genetics : TIG.
[103] Jonas S. Almeida,et al. Alignment-free sequence comparison-a review , 2003, Bioinform..
[104] Dhundy Bastola,et al. Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis , 2014, Briefings Bioinform..
[105] E V Koonin,et al. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. , 1997, Nucleic acids research.
[106] W. Chantratita,et al. Surveillance of Genotypic Resistance Mutations in Chronic HIV-1 Treated Individuals After Completion of the National Access to Antiretroviral Program in Thailand , 2007, Infection.