Vladimir N Minin

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics
    Vladimir N Minin
    Department of Statistics, University of Washington, USA
    Mol Biol Evol 25:1459-71. 2008
  2. pmc Fast, accurate and simulation-free stochastic mapping
    Vladimir 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
  3. pmc Species delimitation using genome-wide SNP data
    Adam 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
  4. doi request reprint Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies
    Julia A Palacios
    Department of Statistics, University of Washington, Seattle, Washington 98195 4322, USA
    Biometrics 69:8-18. 2013
  5. pmc Fitting and interpreting continuous-time latent Markov models for panel data
    Jane M Lange
    Department of Biostatistics, University of Washington, Seattle, WA, U S A
    Stat Med 32:4581-95. 2013
  6. doi request reprint phylodyn: an r package for phylodynamic simulation and inference
    Michael D Karcher
    Department of Statistics, University of Washington, Seattle, WA, USA
    Mol Ecol Resour . 2016
  7. pmc Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference
    Michael D Karcher
    Department of Statistics, University of Washington, Seattle, Washington, United States of America
    PLoS Comput Biol 12:e1004789. 2016
  8. pmc Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting
    Charles R Doss
    University of Washington, Seattle
    Ann Appl Stat 7:2315-2335. 2013
  9. pmc A joint model for multistate disease processes and random informative observation times, with applications to electronic medical records data
    Jane M Lange
    Department of Bioststatistics, University of Washington, Seattle, Washington, U S A
    Biometrics 71:90-101. 2015
  10. pmc Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes
    Vladimir N Minin
    Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genetics 175:1773-85. 2007

Collaborators

Detail Information

Publications13

  1. pmc Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics
    Vladimir 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...
  2. pmc Fast, accurate and simulation-free stochastic mapping
    Vladimir 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...
  3. pmc Species delimitation using genome-wide SNP data
    Adam 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.]. ..
  4. doi request reprint Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies
    Julia 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...
  5. pmc Fitting and interpreting continuous-time latent Markov models for panel data
    Jane 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...
  6. doi request reprint phylodyn: an r package for phylodynamic simulation and inference
    Michael 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...
  7. pmc Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference
    Michael 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. ..
  8. pmc Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting
    Charles R Doss
    University of Washington, Seattle
    Ann Appl Stat 7:2315-2335. 2013
    ....
  9. pmc A joint model for multistate disease processes and random informative observation times, with applications to electronic medical records data
    Jane 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. ..
  10. pmc Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes
    Vladimir 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...
  11. ncbi request reprint cBrother: relaxing parental tree assumptions for Bayesian recombination detection
    Fang 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...
  12. ncbi request reprint Dual multiple change-point model leads to more accurate recombination detection
    Vladimir 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...
  13. ncbi request reprint Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation
    Zaid 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...