Search filters

Authors whose works are in public domain in at least one jurisdiction

List of works by Art Poon

"Deep" sequencing accuracy and reproducibility using Roche/454 technology for inferring co-receptor usage in HIV-1.

scientific article

A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus.

scientific article published on 29 May 2008

A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation

scientific article published on 13 November 2017

A novel codon insert in protease of clade B HIV type 1.

scientific article published on May 2009

Absence of HIV-1 drug resistance mutations supports the use of dolutegravir in Uganda.

scientific article published on 21 January 2018

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

scientific article (publication date: March 2007)

Ageing in Escherichia coli requires damage by an extrinsic agent.

scientific article published on 15 March 2012

An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data

scientific article

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1

scientific article

An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

scientific article

Ancestral Reconstruction

scientific article

COMPENSATING FOR OUR LOAD OF MUTATIONS: FREEZING THE MELTDOWN OF SMALL POPULATIONS

scientific article published on 01 October 2000

Characterizing HIV transmission networks across the United States

scientific article

Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes.

scientific article published on 6 March 2013

Compensatory mutations are repeatable and clustered within proteins.

scientific article published on 25 February 2009

Correlation of the virological response to short-term maraviroc monotherapy with standard and deep-sequencing-based genotypic tropism prediction methods.

scientific article published on 5 December 2011

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

scientific article (publication date: October 2010)

Detecting signatures of selection from DNA sequences using Datamonkey.

scientific article

Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir

scientific article published on July 2015

Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction.

scientific article

Estimating selection pressures on HIV-1 using phylogenetic likelihood models.

scientific article published on October 2008

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

scientific article

Evolution of viral genomes: interplay between selection, recombination, and other forces.

scientific article published on January 2012

Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope

scientific article published on 8 December 2006

Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing.

scientific article published on 21 November 2012

First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda

article

Functional origins of fitness effect-sizes of compensatory mutations in the DNA bacteriophage phiX174.

scientific article

Genetic Cluster Analysis for HIV Prevention.

scientific article published on 19 February 2018

Genotypic susceptibility score (GSS) and CD4+ T cell recovery in HIV-1 patients with suppressed viral load.

scientific article published on 20 December 2016

Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations

scientific article

HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument

scientific article

Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection.

scientific article published on 18 January 2018

Immune-driven recombination and loss of control after HIV superinfection.

scientific article published on 14 July 2008

Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks.

scientific article published on July 2016

In vitro selection of clinically relevant bevirimat resistance mutations revealed by "deep" sequencing of serially passaged, quasispecies-containing recombinant HIV-1

scientific article

Limited evidence for alterations in Gag-mediated HIV replication capacity over the course of the North American epidemic (1979-present).

scientific article published on 13 September 2012

Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients.

scientific article

Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses

scientific article (publication date: 2013)

Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint.

scientific article published on 14 May 2013

Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study

scientific article published on 7 April 2016

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology.

scientific article

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

scientific article published on 07 October 2016

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

scientific article

Phylogenetic approach to recover integration dates of latent HIV sequences within-host

article published in the Proceedings of the National Academy of Sciences of the United States of America

Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada

scientific article

Promises and pitfalls of Illumina sequencing for HIV resistance genotyping

scientific article published on 16 December 2016

Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection

scientific article published on 01 January 2020

Quantifying the Aftermath: Recent Outbreaks Among People Who Inject Drugs and the Utility of Phylodynamics

scientific article published on 01 May 2018

Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays.

scientific article published on 5 July 2018

Reconstructing contact network parameters from viral phylogenies.

scientific article published on July 2016

Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries

scientific article published on 4 December 2017

Silent mutations are selected in HIV-1 reverse transcriptase and affect enzymatic efficiency.

scientific article published on November 2008

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.

scientific article published on 18 June 2008

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

article

The HIV nef protein within ARL is genetically and structurally distinct from those in the brain of patients with HAD.

scientific article published on 11 October 2010

The Influence of Hepatitis C Virus Genetic Region on Phylogenetic Clustering Analysis

scientific article published on 20 July 2015

The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood.

scientific article

The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada

scientific article

The rate of compensatory mutation in the DNA bacteriophage phiX174

scientific article

Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada

scientific article published on 25 February 2016

Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load

scientific article

Tuning intrinsic disorder predictors for virus proteins

scientific article published on 25 January 2021

Use of Cellular HIV DNA to Predict Virologic Response to Maraviroc: Performance of Population-Based and Deep Sequencing

scientific article published on 21 February 2013

What Proportion of Hiv-Infected Foreign-Born Individuals in The U.S. Have Been Infected After Immigrating to The U.S.?

scientific article published on 15 November 2017

sierra-local: A lightweight standalone application for drug resistance prediction

scientific article published on 25 January 2019

Paulina is supported by:

About Paulina

Help