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Automated analysis of phylogenetic clusters

BMC bioinformatics, 2013-11, Vol.14 (1), p.317-317, Article 317

2013

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Drug resistance mutations in HIV: new bioinformatics approaches and challenges

Current opinion in virology, 2021-12, Vol.51, p.56-64

2021

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Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina

The Journal of infectious diseases, 2020-03, Vol.221 (8), p.1321-1330

2020

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A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK

AIDS (London), 2015-09, Vol.29 (15), p.1917-1925

2015

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Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji

Nature communications, 2021-03, Vol.12 (1), p.1671-1671, Article 1671

2021

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Phenotypic properties of envelope glycoproteins of transmitted HIV-1 variants from patients belonging to transmission chains

AIDS (London), 2018-09, Vol.32 (14), p.1917-1926

2018

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External Validation of an MRI-Derived Radiomics Model to Predict Biochemical Recurrence after Surgery for High-Risk Prostate Cancer

Cancers, 2020-03, Vol.12 (4), p.814

2020

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Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs

Proceedings of the National Academy of Sciences - PNAS, 2022-09, Vol.119 (38), p.1-e2210604119

2022

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Poxvirus genomes: a phylogenetic analysis

Journal of general virology, 2004-01, Vol.85 (1), p.105-117

2004

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The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance

Bioinformatics, 2009-05, Vol.25 (9), p.1197-1198

2009

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Ross River Virus Antibody Prevalence, Fiji Islands, 2013-2015

Emerging infectious diseases, 2019-04, Vol.25 (4), p.827-830

2019

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G2/M cell cycle arrest correlates with primate lentiviral Vpr interaction with the SLX4 complex

Journal of virology, 2015, Vol.89 (1), p.230-240

2015

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Phylogenetic Analysis of Murine Leukemia Virus Sequences from Longitudinally Sampled Chronic Fatigue Syndrome Patients Suggests PCR Contamination Rather than Viral Evolution

Journal of Virology, 2011-10, Vol.85 (20), p.10909-10913

2011

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HIV Transmission Patterns Among Immigrant Latinos Illuminated by the Integration of Phylogenetic and Migration Data

AIDS research and human retroviruses, 2015-10, Vol.31 (10), p.973

2015

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Positive Selection Analysis of Overlapping Reading Frames Is Invalid

AIDS research and human retroviruses, 2015-10, Vol.31 (10), p.947

2015

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Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain

Infection, genetics and evolution, 2013-03, Vol.14, p.232-239

2013

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Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history

BMC genomics, 2017-10, Vol.18 (1), p.829-829, Article 829

2017

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Preservation of Tetherin and CD4 Counter-Activities in Circulating Vpu Alleles despite Extensive Sequence Variation within HIV-1 Infected Individuals: e1003895

PLoS pathogens, 2014-01, Vol.10 (1)

2014

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Rising prevalence of non-B HIV-1 subtypes in North Carolina and evidence for local onward transmission

Virus evolution, 2017-01, Vol.3 (1), p.vex013-vex013

2017

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Demonstration of Sustained Drug-Resistant Human Immunodeficiency Virus Type 1 Lineages Circulating among Treatment-Naïve Individuals

Journal of Virology, 2009-03, Vol.83 (6), p.2645-2654

2009

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Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions

AIDS (London), 2014-08, Vol.28 (13), p.1967-1975

2014

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Hepatitis B virus candidate subgenotype I1 varies in distribution throughout Guangxi, China and may have originated in Long An county, Guangxi

Journal of medical virology, 2013-05, Vol.85 (5), p.799-807

2013

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Preservation of tetherin and CD4 counter-activities in circulating Vpu alleles despite extensive sequence variation within HIV-1 infected individuals

PLoS pathogens, 2014-01, Vol.10 (1), p.e1003895-e1003895

2014

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Low risk of a sexually-transmitted Zika virus outbreak

The Lancet infectious diseases, 2016-10, Vol.16 (10), p.1100-1102

2016

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Leveraging Phylogenetics to Understand HIV Transmission and Partner Notification Networks

Journal of acquired immune deficiency syndromes (1999), 2018-08, Vol.78 (4), p.367

2018

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Automated analysis of phylogenetic clusters

Drug resistance mutations in HIV: new bioinformatics approaches and challenges

Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina

A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK

Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji

Phenotypic properties of envelope glycoproteins of transmitted HIV-1 variants from patients belonging to transmission chains

External Validation of an MRI-Derived Radiomics Model to Predict Biochemical Recurrence after Surgery for High-Risk Prostate Cancer

Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs

Poxvirus genomes: a phylogenetic analysis

The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance

Ross River Virus Antibody Prevalence, Fiji Islands, 2013-2015

G2/M cell cycle arrest correlates with primate lentiviral Vpr interaction with the SLX4 complex

Phylogenetic Analysis of Murine Leukemia Virus Sequences from Longitudinally Sampled Chronic Fatigue Syndrome Patients Suggests PCR Contamination Rather than Viral Evolution

HIV Transmission Patterns Among Immigrant Latinos Illuminated by the Integration of Phylogenetic and Migration Data

Positive Selection Analysis of Overlapping Reading Frames Is Invalid

Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history

Preservation of Tetherin and CD4 Counter-Activities in Circulating Vpu Alleles despite Extensive Sequence Variation within HIV-1 Infected Individuals: e1003895

Rising prevalence of non-B HIV-1 subtypes in North Carolina and evidence for local onward transmission

Demonstration of Sustained Drug-Resistant Human Immunodeficiency Virus Type 1 Lineages Circulating among Treatment-Naïve Individuals

Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions

Hepatitis B virus candidate subgenotype I1 varies in distribution throughout Guangxi, China and may have originated in Long An county, Guangxi

Preservation of tetherin and CD4 counter-activities in circulating Vpu alleles despite extensive sequence variation within HIV-1 infected individuals

Low risk of a sexually-transmitted Zika virus outbreak

Leveraging Phylogenetics to Understand HIV Transmission and Partner Notification Networks

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