Vladimir N Minin
Affiliation: University of Washington
- Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamicsVladimir N Minin
Department of Statistics, University of Washington, USA
Mol Biol Evol 25:1459-71. 2008..Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons...
- Fast, accurate and simulation-free stochastic mappingVladimir N Minin
Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
Philos Trans R Soc Lond B Biol Sci 363:3985-95. 2008..We conclude by mapping synonymous and non-synonymous mutations onto branches of an HIV intrahost phylogenetic tree and comparing selection pressure on terminal and internal tree branches...
- Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogiesJulia A Palacios
Department of Statistics, University of Washington, Seattle, Washington 98195 4322, USA
Biometrics 69:8-18. 2013..In both cases, we recover more believed aspects of the viral demographic histories than the GMRF approach. We also find that our GP method produces more reasonable uncertainty estimates than the GMRF method...
- Fitting and interpreting continuous-time latent Markov models for panel dataJane M Lange
Department of Biostatistics, University of Washington, Seattle, WA, U S A
Stat Med 32:4581-95. 2013..Finally, we illustrate the interpretive power of latent CTMC models for describing disease processes on a dataset of lung transplant patients. We hope our work will encourage wider use of these models in the biomedical setting...
- Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processesVladimir N Minin
Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
Genetics 175:1773-85. 2007..We then proceed with the analysis of 42 human immunodeficiency virus (HIV) intersubtype gag recombinants and identify a putative recombination hotspot...
- Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimationZaid Abdo
Initiative in Bioinformatics and Evolutionary Studies IBEST, University of Idaho, Moscow
Mol Biol Evol 22:691-703. 2005..That is, LRT, Extended-AIC, and AIC result in more complicated models that do not contribute to the performance of the phylogenetic inference, yet cause a significant increase in the time required for data analysis...
- Dual multiple change-point model leads to more accurate recombination detectionVladimir N Minin
Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, CA 90095 1766, USA
Bioinformatics 21:3034-42. 2005..Statistical analysis is done in a Bayesian framework using reversible jump Markov chain Monte Carlo sampling to approximate the joint posterior distribution of all model parameters...
- cBrother: relaxing parental tree assumptions for Bayesian recombination detectionFang Fang
Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
Bioinformatics 23:507-8. 2007..Availability: cBrother can be freely downloaded from http://www.biomath.org/dormanks/ and can be compiled on Linux, Macintosh and Windows operating systems. Online documentation and a tutorial are also available at the site...