Molecular tools for studying HIV transmission in sexual networks
暂无分享,去创建一个
[1] T. F. Rinke de Wit,et al. HIV Type 1 transmission networks among men having sex with men and heterosexuals in Kenya. , 2014, AIDS research and human retroviruses.
[2] M. Stanojevic,et al. Molecular typing of the local HIV-1 epidemic in Serbia. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[3] C. Verhofstede,et al. Transmission network of an HIV type 1 strain with K103N in young Belgian patients from different risk groups. , 2013, AIDS research and human retroviruses.
[4] M. Peeters,et al. HIV type 1 subtype C remains the predominant subtype in men having sex with men in Senegal. , 2013, AIDS research and human retroviruses.
[5] Min Zhang,et al. Identification of 3 Distinct HIV-1 Founding Strains Responsible for Expanding Epidemic Among Men Who Have Sex With Men in 9 Chinese Cities , 2013, Journal of acquired immune deficiency syndromes.
[6] T. Lam,et al. The rapidly expanding CRF01_AE epidemic in China is driven by multiple lineages of HIV-1 viruses introduced in the 1990s , 2013, AIDS.
[7] S. Ruță,et al. Transmitted HIV drug resistance in treatment‐naive Romanian patients , 2013, Journal of medical virology.
[8] T. Quinn,et al. Frequency and implications of HIV superinfection. , 2013, The Lancet. Infectious diseases.
[9] Y. Takebe,et al. Evolutionary History of HIV-1 Subtype B and CRF01_AE Transmission Clusters among Men Who Have Sex with Men (MSM) in Kuala Lumpur, Malaysia , 2013, PloS one.
[10] F. Vitale,et al. Dynamics and molecular evolution of HIV-1 strains in Sicily among antiretroviral naïve patients. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[11] Katy Robinson,et al. How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies , 2013, PLoS Comput. Biol..
[12] Á. Holguín,et al. Description of HIV-1 Group M Molecular Epidemiology and Drug Resistance Prevalence in Equatorial Guinea from Migrants in Spain , 2013, PloS one.
[13] Ann M. Dennis,et al. Social Network–Based Recruitment Successfully Reveals HIV-1 Transmission Networks Among High-Risk Individuals in El Salvador , 2013, Journal of acquired immune deficiency syndromes.
[14] Michel Roger,et al. Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. , 2013, AIDS.
[15] M. Salemi,et al. A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases , 2013, Journal of Virology.
[16] Min Chen,et al. Emerging Variability in HIV-1 Genetics among Recently Infected Individuals in Yunnan, China , 2013, PloS one.
[17] Erik M. Volz,et al. Modelling tree shape and structure in viral phylodynamics , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.
[18] W. Switzer,et al. Detailed Molecular Epidemiologic Characterization of HIV-1 Infection in Bulgaria Reveals Broad Diversity and Evolving Phylodynamics , 2013, PloS one.
[19] Wei Liu,et al. Subtype CRF01_AE dominate the sexually transmitted human immunodeficiency virus type 1 epidemic in Guangxi, China , 2013, Journal of medical virology.
[20] Z. Grossman,et al. Transmission Patterns of HIV-Subtypes A/AE versus B: Inferring Risk-Behavior Trends and Treatment-Efficacy Limitations from Viral Genotypic Data Obtained Prior to and during Antiretroviral Therapy , 2013, PloS one.
[21] D. Pillay,et al. Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[22] Trevor Bedford,et al. Viral Phylodynamics , 2013, PLoS Comput. Biol..
[23] C. Nielsen,et al. Phylogenetics of the Danish HIV Epidemic: The Role of Very Late Presenters in Sustaining the Epidemic , 2013, Journal of acquired immune deficiency syndromes.
[24] M. Poljak,et al. Limited cross-border infections in patients newly diagnosed with HIV in Europe , 2013, Retrovirology.
[25] Oliver Laeyendecker,et al. Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions. , 2012, The Journal of infectious diseases.
[26] Ramón Doallo,et al. CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.
[27] Oliver Laeyendecker,et al. The rates of HIV superinfection and primary HIV incidence in a general population in Rakai, Uganda. , 2012, The Journal of infectious diseases.
[28] Brian G. Williams,et al. HIV Treatment as Prevention: Debate and Commentary—Will Early Infection Compromise Treatment-as-Prevention Strategies? , 2012, PLoS medicine.
[29] Erik M. Volz,et al. Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection , 2012, PLoS Comput. Biol..
[30] Katrina A. Lythgoe,et al. New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels , 2012, Proceedings of the Royal Society B: Biological Sciences.
[31] B. Rannala,et al. Molecular phylogenetics: principles and practice , 2012, Nature Reviews Genetics.
[32] Huldrych F. Günthard,et al. Inferring Epidemic Contact Structure from Phylogenetic Trees , 2012, PLoS Comput. Biol..
[33] M. Suchard,et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.
[34] Maxim Teslenko,et al. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.
[35] Beda Joos,et al. Estimating the basic reproductive number from viral sequence data. , 2012, Molecular biology and evolution.
[36] P. Hraber,et al. Timing and source of subtype-C HIV-1 superinfection in the newly infected partner of Zambian couples with disparate viruses , 2012, Retrovirology.
[37] Lei Wang,et al. Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial. , 2011, The Journal of infectious diseases.
[38] Tanmoy Bhattacharya,et al. Role of donor genital tract HIV-1 diversity in the transmission bottleneck , 2011, Proceedings of the National Academy of Sciences.
[39] Niko Beerenwinkel,et al. Ultra-deep sequencing for the analysis of viral populations. , 2011, Current opinion in virology.
[40] M. Nei,et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.
[41] O. Laeyendecker,et al. Identification of HIV Superinfection in Seroconcordant Couples in Rakai, Uganda, by Use of Next-Generation Deep Sequencing , 2011, Journal of Clinical Microbiology.
[42] Timothy B. Stockwell,et al. Extensive Geographical Mixing of 2009 Human H1N1 Influenza A Virus in a Single University Community , 2011, Journal of Virology.
[43] J. Mullins,et al. Viral Linkage in HIV-1 Seroconverters and Their Partners in an HIV-1 Prevention Clinical Trial , 2011, PloS one.
[44] U. Unicef,et al. Global HIV/AIDS response: epidemic update and health sector progress towards universal access: progress report 2011. , 2011 .
[45] L. Frenkel,et al. Two Clusters of HIV-1 Infection, Rural Idaho, USA, 2008 , 2010, Emerging infectious diseases.
[46] Niko Beerenwinkel,et al. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies , 2010, Nucleic acids research.
[47] B. Grenfell,et al. Protocols for sampling viral sequences to study epidemic dynamics , 2010, Journal of The Royal Society Interface.
[48] Christl A. Donnelly,et al. HIV-1 Transmitting Couples Have Similar Viral Load Set-Points in Rakai, Uganda , 2010, PLoS pathogens.
[49] Alan S. Perelson,et al. High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men , 2010, PLoS pathogens.
[50] Hui Li,et al. Wide Variation in the Multiplicity of HIV-1 Infection among Injection Drug Users , 2010, Journal of Virology.
[51] M. Metzker. Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.
[52] Alexei J. Drummond,et al. Bayesian Phylogeography Finds Its Roots , 2009, PLoS Comput. Biol..
[53] David Dunn,et al. Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom , 2009, PLoS pathogens.
[54] Volker Roth,et al. Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction , 2009, RECOMB.
[55] Bette Korber,et al. HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC , 2009, PLoS pathogens.
[56] D. Pillay,et al. Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions. , 2009, The Journal of infectious diseases.
[57] Anne-Mieke Vandamme,et al. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing , 2009 .
[58] Hui Li,et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection , 2008, Proceedings of the National Academy of Sciences.
[59] A. Rambaut,et al. Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics , 2008, PLoS medicine.
[60] B. Korber,et al. Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing , 2008, Journal of Virology.
[61] Anne-Mieke Vandamme,et al. Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba. , 2007, AIDS research and human retroviruses.
[62] Michel Roger,et al. High rates of forward transmission events after acute/early HIV-1 infection. , 2007, The Journal of infectious diseases.
[63] O. Gascuel,et al. Neighbor-joining revealed. , 2006, Molecular biology and evolution.
[64] P. Ghys,et al. Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004 , 2006, AIDS.
[65] P. Lemey,et al. HIV evolutionary dynamics within and among hosts. , 2006, AIDS reviews.
[66] S. Ho,et al. Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.
[67] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[68] O. Laeyendecker,et al. Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda. , 2005, The Journal of infectious diseases.
[69] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[70] Bette T. Korber,et al. Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission , 2004, Science.
[71] O. Pybus,et al. Unifying the Epidemiological and Evolutionary Dynamics of Pathogens , 2004, Science.
[72] K. Anastos,et al. HIV-1 in genital tract and plasma of women: Compartmentalization of viral sequences, coreceptor usage, and glycosylation , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[73] T. Britton,et al. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. , 2003, Systematic biology.
[74] F. Lutzoni,et al. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. , 2003, Molecular biology and evolution.
[75] J. Green,et al. Viral genome characterisation by the heteroduplex mobility and heteroduplex tracking assays , 2000, Reviews in medical virology.
[76] M A Newton,et al. Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods , 1999, Biometrics.
[77] B. Rannala,et al. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. , 1997, Molecular biology and evolution.
[78] M. Uhlén,et al. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[79] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[80] F. Sanger,et al. DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.