A5015045944- Genomics and Phylogenetic Studies
- HIV Research and Treatment
- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- HIV/AIDS drug development and treatment
- RNA and protein synthesis mechanisms
- Hepatitis C virus research
- HIV/AIDS Research and Interventions
- Evolution and Paleontology Studies
- Bacteriophages and microbial interactions
- Herpesvirus Infections and Treatments
- Gut microbiota and health
- Hepatitis B Virus Studies
- Evolutionary Game Theory and Cooperation
- Identification and Quantification in Food
- Cancer Genomics and Diagnostics
- Bayesian Methods and Mixture Models
- Gene expression and cancer classification
- Genetic Mapping and Diversity in Plants and Animals
- Animal Disease Management and Epidemiology
- Chromosomal and Genetic Variations
- Microbial Community Ecology and Physiology
- vaccines and immunoinformatics approaches
- Virology and Viral Diseases
- Molecular Biology Techniques and Applications
University of Auckland
2008-2024
Australian National University
2016-2024
Badji Moktar-Annaba University
2019
Universidad de Oviedo
2019
Duke University
2011-2017
Universidad Autónoma de Madrid
2017
United States Geological Survey
2017
Hospital Universitario Fundación Jiménez Díaz
2017
National Evolutionary Synthesis Center
2012-2016
Auckland City Hospital
2013
Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is Kishino-Hasegawa test. However, assumptions that to be made ensure validity Kishino–Hasegawa test place important restrictions on its applicability. In particular, it only valid when topologies being compared are specified priori. Unfortunately, this means may severely biased in many cases which now used: example, any case...
Abstract Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and ancient subfossil fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation mutation rate population size that incorporates uncertainty in genealogy such temporally spaced by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used describe time...
To understand the high variability of asymptomatic interval between primary human immunodeficiency virus type 1 (HIV-1) infection and development AIDS, we studied evolution C2-V5 region HIV-1 env gene T-cell subsets in nine men with a moderate or slow rate disease progression. They were monitored from time seroconversion for period 6 to 12 years until advanced seven men. Based on analysis viral divergence founder strain, population diversity within sequential points, outgrowth viruses...
A new obligately anaerobic, extremely thermophilic, cellulolytic bacterium is described. The strain designated Tp8T 6331 differentiated from thermophilic clostridia on the basis of physiological characteristics and phylogenetic position within Bacillus/Clostridium subphylum Gram-positive bacteria. Strain assigned to a genus Caldicellulosiruptor, as Caldicellulosiruptor saccharolyticus gen., nov., sp. nov.
The unambiguous footprint of positive Darwinian selection in protein-coding DNA sequences is revealed by an excess nonsynonymous substitutions over synonymous compared with the neutral expectation. Methods for analyzing patterns and usually rely on stochastic models which regime may vary across sequence but remains constant lineages any amino acid position. Despite some work that has relaxed constraint remain time, no model provides a strong statistical framework to deal switches between...
Measureable rates of genome evolution are well documented in human pathogens but less understood bacterial the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly poultry recently jumped to wild house finches (Carpodacus mexicanus), common North American songbird. For first time we characterize measure House Finch isolates MG, as outgroups. Using whole-genome sequences 12 across 13-year serial sample an...
We analyze a maximum likelihood approach for combining phylogenetic trees into larger "supertree." This is based on simple exponential model of error, which ensures that ML supertrees have combinatorial description (as median tree, minimizing weighted sum distances to the input trees). show this supertree reconstruction statistically consistent (it converges true species as more are combined), in contrast widely used MRP method, we can be inconsistent under error model. also statistical...
We present ViPRA-Haplo, a de novo strain-specific assembly workflow for reconstructing viral haplotypes in population from paired-end next generation sequencing (NGS) data. The proposed Viral Path Reconstruction Algorithm (ViPRA) generates subset of paths De Bruijn graph reads using the pairing information reads. generated by ViPRA are an over-estimation true contigs. propose two refinement methods to obtain optimal set contigs representing haplotypes. first method clusters reconstructed...
For the rapid genetic analysis of feline immunodeficiency virus (FIV), we developed a heteroduplex mobility assay (HMA) that utilizes PCR-amplified fragment FIV envelope gene spanning third and fourth variable regions surface protein coding sequence. Viral sequences were successfully amplified from blood specimens 98 naturally infected cats Australia, Canada, Germany, Italy, South Africa, United States. Eighty clearly assignable to A or B sequence subtypes. Three belonged subtype C, one was...
Abstract Recombinants of preexisting human immunodeficiency virus type 1 (HIV-1) strains are now circulating globally. To increase our understanding the importance these recombinants, we assessed recombination within an individual infected from a single source by studying linkage patterns auxiliary genes HIV-1 subtype B. Maximum-likelihood phylogenetic techniques revealed evidence for topological incongruence among adjacent genes. Coalescent methods were then used to estimate in vivo rate....
ABSTRACT The development of viral diversity during the course human immunodeficiency virus type 1 (HIV-1) infection may significantly influence pathogenesis. paradigm for HIV-1 evolution is based primarily on studies male cohorts in which individuals were presumably infected with a single variant subtype B HIV-1. In this study, we evaluated sequence information V1, V2, and V3 portions clade A envelope genes obtained from peripheral blood cervical secretions three women genetically...
Polymerase chain reaction-based limiting dilution assays (PLDAs), commonly called end-point dilutions, are frequently used to quantify the copy numbers of human immunodeficiency virus (HIV) and other viruses in biological samples; however, way which these done, mathematical method estimate numbers, vary from laboratory laboratory. Here, we describe a statistical for estimating number copies associated standard error estimate, using PLDA. The is estimated by value that maximizes goodness fit...
Using likelihood-based evolutionary methods, we demonstrate that the broad genetic diversity of human immunodeficiency virus type 1 (HIV-1) in an infected individual is a consequence site-specific positive selection for diversity, likely immune recognition. In particular, extent appears to be good predictor disease duration. Positively selected sites along HIV-1 partial env sequences are numerous but not distributed uniformly. sample eight patients studied longitudinally, proportion per...
ABSTRACT Human immunodeficiency virus type 1 (HIV-1) is a difficult target for vaccine development, in part because of its ever-expanding genetic diversity and attendant capacity to escape immunologic recognition. Vaccine efficacy might be improved by maximizing immunogen antigenic similarity viruses likely encountered vaccinees. To this end, we designed prototype HIV-1 envelope using deduced ancestral state the env gene. The reconstruction method was shown >95% accurate computer...
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different may have evolutionary histories due incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even not be treelike recombination. To overcome this shortcoming, we introduce an implementation multi-tree mixture model call mixtures across sites and trees (MAST). This...
The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model viral dynamics and was found to be on the order one two days per generation. Here, we describe new method based coalescence theory that allows estimate times derived by nucleotide sequence data reconstructed genealogy sequences obtained over time. is applied from long-term nonprogressing individual at five sampling occasions. coalescent 1.2 close modeling (1.8 generation), thus...
Abstract Cladograms for the same group of taxa derived using different datasets often agree extensively but are seldom identical. This disagreement may be due to fact that cladograms sampling estimates true phylogeny and as a result differ only because error. A protocol is proposed test null hypothesis two trees estimate or parametric no more than would expected In event rejected, pruned remove potentially confounding information, repeated. If cannot method combining cladistic information...