Anne-Mieke Vandamme

Bio: Anne-Mieke Vandamme is an academic researcher from Rega Institute for Medical Research. The author has contributed to research in topics: Drug resistance & Population. The author has an hindex of 79, co-authored 494 publications receiving 21929 citations. Previous affiliations of Anne-Mieke Vandamme include Instituto de Medicina Tropical Alexander von Humboldt & Nova Southeastern University.

Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update

Abstract: Programs that monitor local, national, and regional levels of transmitted HIV-1 drug resistance inform treatment guidelines and provide feedback on the success of HIV-1 treatment and prevention programs. To accurately compare transmitted drug resistance rates across geographic regions and times, the World Health Organization has recommended the adoption of a consensus genotypic definition of transmitted HIV-1 drug resistance. In January 2007, we outlined criteria for developing a list of mutations for drug-resistance surveillance and compiled a list of 80 RT and protease mutations meeting these criteria (surveillance drug resistance mutations; SDRMs). Since January 2007, several new drugs have been approved and several new drug-resistance mutations have been identified. In this paper, we follow the same procedures described previously to develop an updated list of SDRMs that are likely to be useful for ongoing and future studies of transmitted drug resistance. The updated SDRM list has 93 mutations including 34 NRTI-resistance mutations at 15 RT positions, 19 NNRTI-resistance mutations at 10 RT positions, and 40 PI-resistance mutations at 18 protease positions.

Human T-lymphotropic virus 1: recent knowledge about an ancient infection.

Abstract: Human T-lymphotropic virus 1 (HTLV-1) has infected human beings for thousands of years, but knowledge about the infection and its pathogenesis is only recently emerging. The virus can be transmitted from mother to child, through sexual contact, and through contaminated blood products. There are areas in Japan, sub-Saharan Africa, the Caribbean, and South America where more than 1% of the general population is infected. Although the majority of HTLV-1 carriers remain asymptomatic, the virus is associated with severe diseases that can be subdivided into three categories: neoplastic diseases (adult T-cell leukaemia/lymphoma), inflammatory syndromes (HTLV-1-associated myelopathy/tropical spastic paraparesis and uveitis among others), and opportunistic infections (including Strongyloides stercoralis hyperinfection and others). The understanding of the interaction between virus and host response has improved markedly, but there are still no clear surrogate markers for prognosis and there are few treatment options.

An automated genotyping system for analysis of HIV-1 and other microbial sequences

Abstract: Motivation: Genetic analysis of HIV-1 is important not only for vaccine development, but also to guide treatment strategies, track the emergence of new viral variants and ensure that diagnostic assays are contemporary and fully optimized. However, most genotyping methods are laborious and complex, and involve the use of multiple software applications. Here, we describe the development of an automated genotyping system that can be easily applied to HIV-1 and other rapidly evolving viral pathogens. Results: The new REGA subtyping tool, developed using Java programming and PERL scripts, combines phylogenetic analyses with bootscanning methods for the genetic subtyping of full-length and subgenomic fragments of HIV-1. When used to investigate the subtype of previously published reference datasets that were analysed using manual phylogenetic methods, the automated method correctly identified 97.5--100% of non-recombinant and circulating recombinant forms of HIV-1, including 108 full-length, 108 gag and 221 env sequences downloaded from the Los Alamos database. Availability: The tool, which can be easily downloaded and installed on either a UNIX or Linux-based computer system, is available at http://www.bioafrica.net/subtypetool/html/ Contact: tulio.deoliveira@zoology.oxford.ac.uk

The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing

Abstract: Part I. Introduction: 1. Basic concepts of molecular evolution Anne-Mieke Vandamme Part II. Data Preparation: 2. Sequence databases and database searching Guy Bottu, Marc Van Ranst and Philippe Lemey 3. Multiple sequence alignment Des Higgins and Philippe Lemey Part III. Phylogenetic Inference: 4. Nucleotide substitution models Korbinian Strimmer, Arndt von Haeseler and Marco Salemi 5. Phylogenetic inference based on distance methods Yves Van de Peer and Marco Salemi 6. Phylogenetic inference using maximum likelihood methods Heiko A. Schmidt and Arndt von Haeseler 7. Bayesian phylogenetic analysis using MRBAYES Fredrik Ronquist, Paul van der Mark and John P. Huelsenbeck 8. Phylogeny inference based on parsimony and other methods using PAUP* David L. Swofford and Jack Sullivan 9. Phylogenetic analysis using protein sequences Fred R. Opperdoes and Philippe Lemey Part IV. Testing Models and Trees: 10. Selecting models of evolution David Posada 11. Molecular clock analysis Philippe Lemey and David Posada 12. Testing tree topologies Heiko Schmidt Part V. Molecular Adaptation: 13. Natural selection and adaptation of molecular sequences Oliver G. Pybus and Beth Shapiro 14. Estimating selection pressures on alignments of coding sequences Sergei L. Kosakovsky Pond, Art F. Y. Poon, and Simon D. W. Frost Part VI. Recombination: 15. Introduction to recombination detection Philippe Lemey and David Posada 16. Detecting and characterizing individual recombination events Mika Salminen and Darren Martin Part VII. Population Genetics: 17. The coalescent: population genetic inference using genealogies Allen Rodrigo 18. Bayesian evolutionary analysis by sampling trees Alexei Drummond and Andrew Rambaut 19. LAMARC: estimating population genetic parameters from molecular data Mary K. Kuhner Part VIII. Additional Topics: 20. Assessing substitution saturation with DAMBE Xuhua Xia and Philippe Lemey 21. Split networks: a tool for exploring complex evolutionary relationships in molecular data Vincent Moulton and Katharina T. Huber.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

BEAST: Bayesian evolutionary analysis by sampling trees

Abstract: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Relaxed Phylogenetics and Dating with Confidence

Abstract: In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.