4.6 Article

Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology

Related references

Note: Only part of the references are listed.
Article Immunology

Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host

Brittany Rife Magalis et al.

Summary: This study investigated the dynamic nature of the SIV population in the SIV/macaque model of AIDS, highlighting the adaptive immune response as the key factor explaining the behavior of the virus population. The relationship between the virus and immune cell populations revealed a predator-prey dynamic, with viral adaptation occurring in response to varying immune pressures over the course of infection progression.

FRONTIERS IN IMMUNOLOGY (2021)

Article Microbiology

Rapid progression is associated with lymphoid follicle dysfunction in SIV-infected infant rhesus macaques

Matthew P. Wood et al.

Summary: This study evaluated immunological and virological parameters in 25 SIV-infected infant rhesus macaques and found that RP infants exhibited low levels of plasma anti-SIV antibody and high viral loads, with 11 out of 25 macaques showing an RP phenotype. Abnormalities in various immune cell populations in RP infants contributed to immune system impairment, ultimately leading to rapid disease progression.

PLOS PATHOGENS (2021)

Article Virology

Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness

Guinevere Q. Lee

Summary: HIV persists by integrating viral DNA into the human genome, and understanding the viral persistence is crucial. Next-generation deep sequencing technologies have developed FLIP-seq and MIP-seq assays to capture information about the viral DNA pool.

VIRUSES-BASEL (2021)

Review Immunology

HIV-1 Tat: Role in Bystander Toxicity

David Ajasin et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)

Correction Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (vol 37, pg 1530, 2020)

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Review Microbiology

New Frontiers in Measuring and Characterizing the HIV Reservoir

Shane D. Falcinelli et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

Steven Weaver et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Infectious Diseases

Molecular Signatures of HIV-1 Envelope Associated with HIV-Associated Neurocognitive Disorders

Teresa H. Evering

CURRENT HIV/AIDS REPORTS (2018)

Article Virology

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Marc A. Suchard et al.

VIRUS EVOLUTION (2018)

Article Neurosciences

HIV-1 Viral Protein R Activates NLRP3 Inflammasome in Microglia: implications for HIV-1 Associated Neuroinflammation

Manmeet K. Mamik et al.

JOURNAL OF NEUROIMMUNE PHARMACOLOGY (2017)

Article Computer Science, Artificial Intelligence

A Survey on Evolutionary Computation Approaches to Feature Selection

Bing Xue et al.

IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION (2016)

Editorial Material Microbiology

HIV Whole-Genome Sequencing Now: Answering Still-Open Questions

Karin J. Metzner

JOURNAL OF CLINICAL MICROBIOLOGY (2016)

Article Multidisciplinary Sciences

Persistent HIV-1 replication maintains the tissue reservoir during therapy

Ramon Lorenzo-Redondo et al.

NATURE (2016)

Review Clinical Neurology

HIV-associated neurocognitive disorder - pathogenesis and prospects for treatment

Deanna Saylor et al.

NATURE REVIEWS NEUROLOGY (2016)

Article Multidisciplinary Sciences

Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic

Gonzalo Yebra et al.

SCIENTIFIC REPORTS (2016)

Article Virology

Non-human primate models of SIV infection and CNS neuropathology

Kenneth Williams et al.

CURRENT OPINION IN VIROLOGY (2016)

Article Virology

Phenotypic Correlates of HIV-1 Macrophage Tropism

Kathryn T. Arrildt et al.

JOURNAL OF VIROLOGY (2015)

Article Infectious Diseases

Compartmentalization, Viral Evolution, and Viral Latency of HIV in the CNS

Maria M. Bednar et al.

CURRENT HIV/AIDS REPORTS (2015)

Article Biochemical Research Methods

AliView: a fast and lightweight alignment viewer and editor for large datasets

Anders Larsson

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS

Samantha L. Strickland et al.

JOURNAL OF GENERAL VIROLOGY (2014)

Article Biochemical Research Methods

Directional Darwinian Selection in proteins

David A. McClellan

BMC BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

Ben Murrell et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Rheumatology

The phenotypic and genetic signatures of common musculoskeletal pain conditions

Luda Diatchenko et al.

NATURE REVIEWS RHEUMATOLOGY (2013)

Article Virology

Within-host and between-host evolutionary rates across the HIV-1 genome

Samuel Alizon et al.

RETROVIROLOGY (2013)

Review Biotechnology & Applied Microbiology

Random forests for genomic data analysis

Xi Chen et al.

GENOMICS (2012)

Article Biochemistry & Molecular Biology

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Alexei J. Drummond et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Genetics & Heredity

Detecting Individual Sites Subject to Episodic Diversifying Selection

Ben Murrell et al.

PLOS GENETICS (2012)

Review Immunology

Editorial NeuroAIDS review

Paul Shapshak et al.

Article Immunology

Significant Genetic Heterogeneity of the SIVmac251 Viral Swarm Derived from Different Sources

Samantha L. Strickland et al.

AIDS RESEARCH AND HUMAN RETROVIRUSES (2011)

Article Biochemical Research Methods

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

Filip Bielejec et al.

BIOINFORMATICS (2011)

Article Infectious Diseases

HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues

Susanna L. Lamers et al.

INFECTION GENETICS AND EVOLUTION (2011)

Review Biochemistry & Molecular Biology

HIV-1 Envelope Glycoprotein Biosynthesis, Trafficking, and Incorporation

Mary Ann Checkley et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Immunology

Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design

Susan Zolla-Pazner et al.

NATURE REVIEWS IMMUNOLOGY (2010)

Article Biochemical Research Methods

Bayesian Phylogeography Finds Its Roots

Philippe Lemey et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics

Vladimir N. Minin et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemical Research Methods

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

Art F. Y. Poon et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Multidisciplinary Sciences

Structural definition of a conserved neutralization epitope on HIV-1 gp120

Tongqing Zhou et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

Relaxed phylogenetics and dating with confidence

Alexei J. Drummond et al.

PLOS BIOLOGY (2006)

Article Multidisciplinary Sciences

Solving the protein sequence metric problem

WR Atchley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Bayesian coalescent inference of past population dynamics from molecular sequences

AJ Drummond et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Virology

Development and characterization of positively selected brain-adapted SIV

Peter J. Gaskill et al.

VIROLOGY JOURNAL (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)