An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration

(2017) Soo-Yon Rhee et al.   EBioMedicine

Epidemic dispersion of HIV and HCV in a population of co-infected Romanian injecting drug users

(2017) Simona Paraschiv et al.   PLoS One

Additive methods for genomic signatures

(2016) Rallis Karamichalis et al.   BMC BIOINFORMATICS

Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study

(2016) John Gregson et al.   LANCET INFECTIOUS DISEASES

Virus classification in 60-dimensional protein space

(2016) Yongkun Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Recent HIV-1 Outbreak Among Intravenous Drug Users in Romania: Evidence for Cocirculation of CRF14_BG and Subtype F1 Strains

(2015) Iulia Niculescu et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests

(2015) Nazneen Aziz et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

An investigation into inter- and intragenomic variations of graphic genomic signatures

(2015) Rallis Karamichalis et al.   BMC BIOINFORMATICS

A high performance prediction of HPV genotypes by Chaos game representation and singular value decomposition

(2015) Watcharaporn Tanchotsrinon et al.   BMC BIOINFORMATICS

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology

(2015) Art F.Y. Poon   MOLECULAR BIOLOGY AND EVOLUTION

Mapping the Space of Genomic Signatures

(2015) Lila Kari et al.   PLoS One

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Global comparison of multiple-segmented viruses in 12-dimensional genome space

(2014) Hsin-Hsiung Huang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification

(2014) Daniel Struck et al.   NUCLEIC ACIDS RESEARCH

Alignment-free phylogenetics and population genetics

(2013) B. Haubold   BRIEFINGS IN BIOINFORMATICS

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

(2013) O. Bonham-Carter et al.   BRIEFINGS IN BIOINFORMATICS

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) Andrea-Clemencia Pineda-Peña et al.   INFECTION GENETICS AND EVOLUTION

Analysis of dinucleotide signatures in HIV-1 subtype B genomes

(2013) ARIDAMAN PANDIT et al.   JOURNAL OF GENETICS

Multi-class AdaBoost

(2013) Trevor Hastie et al.   Statistics and Its Interface

COMPARING VIRUS CLASSIFICATION USING GENOMIC MATERIALS ACCORDING TO DIFFERENT TAXONOMIC LEVELS

(2013) JING-DOO WANG   Journal of Bioinformatics and Computational Biology

Low Drug Resistance Levels Among Drug-Naive Individuals with Recent HIV Type 1 Infection in a Rural Clinical Cohort in Southwestern Uganda

(2012) Deogratius Ssemwanga et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping

(2012) Pandurang Kolekar et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Classification of HIV-1 Sequences Using Profile Hidden Markov Models

(2012) Sanjiv K. Dwivedi et al.   PLoS One

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

(2012) Kaustubh Raosaheb Patil et al.   PLoS One

Multifractal analysis of HIV-1 genomes

(2011) Aridaman Pandit et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease

(2010) Denis M Tebit et al.   LANCET INFECTIOUS DISEASES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

HIV-1 Epidemic in the Caribbean Is Dominated by Subtype B

(2009) Yuka Nadai et al.   PLoS One

Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method

(2009) G. A. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

(2009) Sergei L. Kosakovsky Pond et al.   PLoS Computational Biology

A novel feature-based method for whole genome phylogenetic analysis without alignment: Application to HEV genotyping and subtyping

(2008) Zhihua Liu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison

(2008) Qi Dai et al.   BIOINFORMATICS

Antiretroviral Drug Resistance Testing in Adult HIV‐1 Infection: 2008 Recommendations of an International AIDS Society–USA Panel

(2008) Martin S. Hirsch et al.   CLINICAL INFECTIOUS DISEASES

European AIDS Clinical Society (EACS) guidelines for the clinical management and treatment of HIV-infected adults

(2008) N Clumeck et al.   HIV MEDICINE

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey et al.   NATURE

The Challenge of HIV-1 Subtype Diversity

(2008) Barbara S. Taylor et al.   NEW ENGLAND JOURNAL OF MEDICINE