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...
- Species delimitation using genome-wide SNP dataAdam D Leaché
Department of Biology, University of Washington, Seattle, WA 98195, USA Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
Syst Biol 63:534-42. 2014..Bayes factor; model testing; phylogeography; RADseq; simulation; speciation.]. ..
- 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...
- phylodyn: an r package for phylodynamic simulation and inferenceMichael D Karcher
Department of Statistics, University of Washington, Seattle, WA, USA
Mol Ecol Resour . 2016..We compare the performance and outputs of various methods implemented in phylodyn and outline their strengths and weaknesses. r package phylodyn is available at https://github.com/mdkarcher/phylodyn...
- Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic InferenceMichael D Karcher
Department of Statistics, University of Washington, Seattle, Washington, United States of America
PLoS Comput Biol 12:e1004789. 2016..Finally, we compare the performance of the currently used phylodynamic methods with our proposed model through clinically-relevant, seasonal human influenza examples. ..
- Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA FingerprintingCharles R Doss
University of Washington, Seattle
Ann Appl Stat 7:2315-2335. 2013....
- A joint model for multistate disease processes and random informative observation times, with applications to electronic medical records dataJane M Lange
Department of Bioststatistics, University of Washington, Seattle, Washington, U S A
Biometrics 71:90-101. 2015..We apply the model to a study of secondary breast cancer events, utilizing mammography and biopsy records from a sample of women with a history of primary breast cancer. ..
- 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...
- 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...
- 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...
- 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...