Preprints (highlighted are student collaborators):

3. Chi PB, Chattopadhyay S, Lemey P, Sokurenko EV, Minin VN. Synonymous and nonsynonymous distances help untangle convergent evolution and recombination, arXiv:1410.1263 [stat.ME]. synDss
2. McCoy CO, Bedford T, Minin VN, Robins H, Matsen FA. Substitution and site-specific selection driving B cell affinity maturation is consistent across individuals, arXiv:1403.3066 [q-bio.PE].
1. Koepke AA, Longini, IM, Halloran ME, Wakefield J, Minin VN. Predictive modeling of cholera outbreaks in Bangladesh, arXiv:1402.0536 [stat.AP]. bayessir

Book Chapters (highlighted are student collaborators):

1. Palacios JA, Gill MS, Suchard MA, and Minin VN. Bayesian nonparametric phylodynamics, in Bayesian Phylogenetics: Methods, Algorithms, and Applications, edited by Chen MH, Kuo L, Lewis PO. 2014

Refereed Articles (highlighted are student collaborators):

29. Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH. Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid, Proceedings of the National Academy of Sciences, USA, in press. 201x supplement indorigin
28. Lange JM, Hubbard RA, Inoue LYT, Minin VN. A joint model for multistate disease processes and random informative observation times, with applications to electronic medical records data, Biometrics, in press. (UW Biostatistics Working Paper 401) 201x cthmm
27. Irvahn J and Minin VN. Phylogenetic stochastic mapping without matrix exponentiation, Journal of Computational Biology, 21:676 – 690. (arXiv:1403.5040 [stat.CO]) 2014 supplement phylomap
26. Chi PB, Duncan A, Kramer PA, Minin VN. Heritability estimation of osteoarthritis in the pig-tailed macaque (Macaca nemestrina) with a look toward future data collection, PeerJ, 2, e373. (PeerJ PrePrints 2:e284v1)
with a shorter version of this paper, Peter Chi was a runner-up in 2012 WNAR student written paper competition
2014
25. Leaché AD, Fujita MK, Minin VN, Remco RB. Species delimitation using genome-wide SNP data, Systematic Biology, 63:534 – 542. (bioRxiv doi: 10.1101/123456) 2014 BFD*
cover
24. Crawford FW, Minin VN, Suchard MA. Estimation for general birth-death processes, Journal of the American Statistical Association, 109:730 – 747. (arXiv:1111.4954v1 [stat.ME]) 2014
23. Doss CR, Suchard MA, Holmes I, Kato-Maeda M, Minin VN. Fitting birth-death processes to panel data with applications to bacterial DNA fingerprinting, Annals of Applied Statistics, 7:2315 – 2335. (arXiv:1009.0893 [stat.CO]) 2013 supplement DOBAD
22. Leaché AD, Palacios JA, Minin VN, Bryson RW. Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of southeastern Mexico, Biological Journal of the Linnean Society, 110:852 – 865. 2013
21. Lange JM and Minin VN. Fitting and interpreting continuous-time latent Markov models for panel data, Statistics in Medicine, 32:4581 – 4595. (UW Biostatistics Working Paper 382)
with a shorter version of this paper, Jane Lange won 2012 WNAR student written paper competition
2013 supplement cthmm
20. Irvahn J, Chattopadhyay S, Sokurenko EV, Minin VN. rbrothers: R package for Bayesian multiple change-point recombination detection, Evolutionary Bioinformatics, 9:235 – 238. 2013 rbrothers
19. Palacios JA and Minin VN. Gaussian process-based Bayesian nonparametric inference of population trajectories from gene genealogies, Biometrics, 69: 8 – 18. (arXiv:1112.4138 [stat.ME]) 2013 supplement
18. Lemey P, Minin VN, Bielejec F, Kosakovsky Pond SL, Suchard MA. A counting renaissance: Combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection, Bioinformatics, 28: 3248 – 3256.
2012
17. Ryu S, Goodlett DR, Noble WS, Minin VN. A statistical approach to peptide identification from clustered tandem mass spectrometry data, IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), 648 – 653.
2012
16. Palacios JA and Minin VN. Integrated nested Laplace approximation for Bayesian nonparametric phylodynamics, Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence, 726 – 735.
2012
15. Sawaya SM*, Lennon D*, Buschiazza G, Gemmell N, Minin VN. Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model, Genome Biology and Evolution, 4: 636 – 647.
* - joint first authors
2012 supplement McSMAC
14. Kemal K, Kitchen C, Burger H, Foley B, Klimkait T, Hamy F, Anastos, K, Petrovic K, Minin VN, Suchard MA, Weiser B. Recombination between variants from genital tract and plasma: Evolution of multidrug-resistant HIV-1, AIDS Research and Human Retroviruses, 28:1766 – 1774. 2012
13. Minin VN, O'Brien JD, Seregin A. Imputation estimators partially correct for model misspecification, Statistical Applications in Genetics and Molecular Biology, 10:1 – 24. (an earlier version with a beta-binomial example: arXiv:0911.0939v1) 2011
12. Chattopadhyay S, Weissman SJ, Minin VN, Russo TA, Dykhuizen DE, Sokurenko EV. High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection, Proceedings of the National Academy of Sciences, USA, 106:12412 – 12417. 2009
11. O'Brien JD*, Minin VN*, and Suchard MA. Learning to count: robust estimates for labeled distances between molecular sequences, Molecular Biology and Evolution, 26:801 – 814.
* - joint first authors
2009
10. Minin VN and Suchard MA. Fast, accurate and simulation-free stochastic mapping, Philosophical Transactions of the Royal Society B: Biological Sciences, 363:3985 – 3995. (an earlier version with more details) 2008
9. Minin VN, Bloomquist EW, and Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics, Molecular Biology and Evolution, 25:1459 – 1471. 2008
8. Minin VN and Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution, Journal of Mathematical Biology, 56:391 – 412. 2008
7. Rajaram ML, Minin VN, Suchard MA, and Dorman KS. Hot and cold: spatial fluctuation in HIV-1 recombination rates, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 707 – 714. 2007
6. Minin VN, Dorman KS, Fang F, and Suchard MA. Phylogenetic mapping of recombination hot-spots in HIV via spatially smoothed change-point processes, Genetics, 175:1773 – 1785. 2007 highlighted article
5. Fang F, Ding J, Minin VN, Suchard MA, and Dorman KS. cBrother: Relaxing parental tree assumptions for Bayesian recombination detection, Bioinformatics, 23:507 – 508. 2007 cBrother
4. Minin VN, Dorman KS, Fang F, and Suchard MA. Dual multiple change-point model leads to more accurate recombination detection, Bioinformatics, 21:3034 – 3042. 2005
3. Abdo Z, Minin VN, Joyce P, and Sullivan J. Accounting for uncertainty in the tree topology has little effect on the decision theoretic approach to model selection in phylogeny estimation, Molecular Biology and Evolution, 22:691 – 703. 2004
2. Liu X, Minin V, Huang Y, Selingson D, and Horvath S. Statistical methods for analyzing tissue microarray data, Journal of Biopharmaceutical Statistics, 14:671 – 685. 2004
1. Minin V, Abdo Z, Joyce P, and Sullivan J. Performance-based selection of likelihood models for phylogeny estimation, Systematic Biology, 52:674 – 683. 2003 DTModSel

Unrefereed Publications:

2. Fang F, Minin VN, Suchard MA, Dorman KS. A Bayesian phylogenetic model for counting recombination events, 2005 Proceedings of the American Statistical Association, Bayesian Statistical Science Section, [CD-ROM]. 2005
1. Minin VN, Dorman KS, Suchard MA. Bayesian recombination identification: new models for incorporating prior information, 2004 Proceedings of the American Statistical Association, Bayesian Statistical Science Section, [CD-ROM]. 2004

Selected Recent Conference Presentations and Posters:

Balancing statistical and computational trade-offs when extracting selection signal from a large number of DNA sequences
contributed talk at the Joint Statistical Meeting, Boston, MA
August 2014.
Bayesian inference for Kingman's coalescent process via thinning
invited talk at the 36th Conference on Stochastic Processes and Their Applications, Boulder, CO
August 2013.


Last modified: October, 2014