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

Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource

(2013) Donald B. Smith et al.   HEPATOLOGY

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

HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics

(2013) Ana B Abecasis et al.   Retrovirology

HIV-1 Subtype Is an Independent Predictor of Reverse Transcriptase Mutation K65R in HIV-1 Patients Treated with Combination Antiretroviral Therapy Including Tenofovir

(2012) K. Theys et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses

(2012) Leelavati Narlikar et al.   NUCLEIC ACIDS RESEARCH

Classification of HIV-1 Sequences Using Profile Hidden Markov Models

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

Global trends in molecular epidemiology of HIV-1 during 2000–2007

(2011) Joris Hemelaar et al.   AIDS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

MS4 - Multi-Scale Selector of Sequence Signatures: an alignment-free method for the classification of biological sequences

(2010) Eduardo Corel et al.   BMC BIOINFORMATICS

The role of recombination in the emergence of a complex and dynamic HIV epidemic

(2010) Ming Zhang et al.   Retrovirology

Effect of HIV‐1 Subtype on Virologic and Immunologic Response to Starting Highly Active Antiretroviral Therapy

(2009) Anna Maria Geretti et al.   CLINICAL INFECTIOUS DISEASES

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

Reliability of Rapid Subtyping Tools Compared to That of Phylogenetic Analysis for Characterization of Human Immunodeficiency Virus Type 1 Non-B Subtypes and Recombinant Forms

(2008) A. Holguin et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Effect of Human Immunodeficiency Virus Type 1 (HIV‐1) Subtype on Disease Progression in Persons from Rakai, Uganda, with Incident HIV‐1 Infection

(2008) Noah Kiwanuka et al.   JOURNAL OF INFECTIOUS DISEASES

The Challenge of HIV-1 Subtype Diversity

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

Identifying the Important HIV-1 Recombination Breakpoints

(2008) John Archer et al.   PLoS Computational Biology