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Ancestral Reconstruction

PLoS computational biology, 2016-07, Vol.12 (7), p.e1004763-e1004763

2016

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

Bioinformatics, 2010-10, Vol.26 (19), p.2455-2457

2010

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Network science inspires novel tree shape statistics

PloS one, 2021-12, Vol.16 (12), p.e0259877-e0259877

2021

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Using networks to analyze and visualize the distribution of overlapping genes in virus genomes

PLoS pathogens, 2022-02, Vol.18 (2), p.e1010331-e1010331

2022

Volltextzugriff (PDF)

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

PLoS computational biology, 2022-11, Vol.18 (11), p.e1010745-e1010745

2022

Volltextzugriff (PDF)

Molecular source attribution

PLoS computational biology, 2022-11, Vol.18 (11), p.e1010649-e1010649

2022

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Molecular biology and evolution, 2020-01, Vol.37 (1), p.295-299

2020

Volltextzugriff (PDF)

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

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005868-e1005868

2017

Volltextzugriff (PDF)

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology

Molecular biology and evolution, 2015-09, Vol.32 (9), p.2483-2495

Poon, Art F Y

2015

Volltextzugriff (PDF)

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

PLoS computational biology, 2009-11, Vol.5 (11), p.e1000581-e1000581

2009

Volltextzugriff (PDF)

Detecting Amino Acid Coevolution with Bayesian Graphical Models

Methods in molecular biology (Clifton, N.J.), 2019-01, Vol.1851, p.105

2019

Volltextzugriff (PDF)

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

eLife, 2022-08, Vol.11

2022

Volltextzugriff (PDF)

Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks

Virus evolution, 2016-07, Vol.2 (2), p.vew031-vew031

Poon, Art F Y

2016

Volltextzugriff (PDF)

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

PloS one, 2018-11, Vol.13 (11), p.e0206409

2018

Volltextzugriff (PDF)

Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data

PLoS computational biology, 2012-11, Vol.8 (11), p.e1002753-e1002753

2012

Volltextzugriff (PDF)

Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses

Molecular biology and evolution, 2023-08, Vol.40 (8)

2023

Volltextzugriff (PDF)

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

PloS one, 2013-11, Vol.8 (11), p.e78122-e78122

2013

Volltextzugriff (PDF)

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

PLoS computational biology, 2007-11, Vol.3 (11), p.e231-e231

2007

Volltextzugriff (PDF)

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

The lancet HIV, 2016-05, Vol.3 (5), p.e231-e238

2016

Volltextzugriff (PDF)

Traversing missing links in the spread of HIV

eLife, 2022-09, Vol.11

2022

Volltextzugriff (PDF)

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

Proceedings of the National Academy of Sciences - PNAS, 2018-09, Vol.115 (38), p.E8958-E8967

2018

Volltextzugriff (PDF)

Comparative analysis of HIV sequences in real time for public health

Current opinion in HIV & AIDS, 2019-05, Vol.14 (3), p.213

2019

Volltextzugriff (PDF)

The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada

The Journal of infectious diseases, 2015-03, Vol.211 (6), p.926-935

2015

Volltextzugriff (PDF)

Genetic Cluster Analysis for HIV Prevention

Current HIV/AIDS reports, 2018-04, Vol.15 (2), p.182-189

2018

Volltextzugriff (PDF)

From components to communities: bringing network science to clustering for molecular epidemiology

Virus evolution, 2023, Vol.9 (1), p.vead026-vead026

2023

Volltextzugriff (PDF)

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Ancestral Reconstruction

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

Network science inspires novel tree shape statistics

Using networks to analyze and visualize the distribution of overlapping genes in virus genomes

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

Molecular source attribution

HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

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

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology

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

Detecting Amino Acid Coevolution with Bayesian Graphical Models

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks

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

Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data

Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses

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

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

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

Traversing missing links in the spread of HIV

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

Comparative analysis of HIV sequences in real time for public health

The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada

Genetic Cluster Analysis for HIV Prevention

From components to communities: bringing network science to clustering for molecular epidemiology

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