(Q50062934)

24 February 2018

title

HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens (English)

1 reference

24 February 2018

Sergei L. Kosakovsky Pond

main subject

epidemiology of HIV/AIDS

1 reference

1 reference

1

object named as

Sergei L Kosakovsky Pond

1 reference

24 February 2018

Joel O Wertheim

4

object named as

Joel O Wertheim

1 reference

24 February 2018

Andrew J Leigh Brown

3

object named as

Andrew J Leigh Brown

1 reference

24 February 2018

author name string

Steven Weaver

2

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24 February 2018

publication date

31 January 2018

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24 February 2018

Molecular Biology and Evolution

published in

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24 February 2018

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes

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26 August 2018

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Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases.

26 August 2018

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Detailed Transmission Network Analysis of a Large Opiate-Driven Outbreak of HIV Infection in the United States

26 August 2018

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Identification of major routes of HIV transmission throughout Mesoamerica

26 August 2018

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A Phylogenetic Analysis of HIV-1 Sequences in Kiev: Findings among Key Populations.

26 August 2018

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Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network

26 August 2018

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Defining HIV-1 transmission clusters based on sequence data

26 August 2018

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Social and Genetic Networks of HIV-1 Transmission in New York City

26 August 2018

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

26 August 2018

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A molecular transmission network of recent hepatitis C infection in people with and without HIV: Implications for targeted treatment strategies

26 August 2018

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Identifying Transmission Clusters with Cluster Picker and HIV-TRACE.

26 August 2018

1 reference

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HIV Infection Linked to Injection Use of Oxymorphone in Indiana, 2014-2015.

26 August 2018

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The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States

26 August 2018

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Phylogenetically resolving epidemiologic linkage.

26 August 2018

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Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States

26 August 2018

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Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States

26 August 2018

1 reference

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Sampling through time and phylodynamic inference with coalescent and birth-death models

26 August 2018

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IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies

26 August 2018

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

26 August 2018

1 reference

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Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

26 August 2018

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Using HIV networks to inform real time prevention interventions

26 August 2018

1 reference

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Molecular tools for studying HIV transmission in sexual networks

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Inferring the source of transmission with phylogenetic data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

The global transmission network of HIV-1

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Modelling tree shape and structure in viral phylodynamics.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Characterizing HIV transmission networks across the United States

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Bayesian phylogenetics with BEAUti and the BEAST 1.7

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Comparison of methods to detect HIV dual infection

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

FastTree 2--approximately maximum-likelihood trees for large alignments

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Biopython: freely available Python tools for computational molecular biology and bioinformatics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

A public health model for the molecular surveillance of HIV transmission in San Diego, California

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Episodic sexual transmission of HIV revealed by molecular phylodynamics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

The emergence of HIV/AIDS in the Americas and beyond

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Likelihood-based inference for stochastic models of sexual network formation

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1).

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

Identification of common molecular subsequences

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5995201

26 August 2018

Identifiers

DOI

10.1093/MOLBEV/MSY016

1 reference

24 February 2018

PMC publication ID

5995201

0 references

1 reference

24 February 2018