Preprints (highlighted are student collaborators):

3. Karcher, M, Palacios JA, Bedford T, Suchard MA, Minin VN. Quantifying and mitigating the effect of preferential sampling on phylodynamic inference, arXiv:1510.00775 [stat.ME]. phylodyn
2. Linkem CW, Minin VN, Leaché AD. Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae), bioRxiv.
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):

2015 and in press
34. Xu J, Guttorp P, Kato-Maede M, Minin VN. Likelihood-based inference for discretely observed birth-death-shift processes, with applications to evolution of mobile genetic elements, Biometrics, in press, arXiv:1411.0031 [stat.ME].
with a shorter version of this paper, Jason Xu won ASA Biometrics section student travel award to attend JSM 2015
33. Lan S, Palacios JA, Karcher, M, Minin VN, Babak Shahbaba. An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics, Bioinformatics, 31, 3282 – 3289. (arXiv:11412.0158 [stat.CO]) supplement
32. Xu J and Minin VN. Efficient transition probability computation for continuous-time branching processes via compressed sensing, Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, 952 – 961. (arXiv:1503.02644 [stat.CO]) supplement
31. Chi PB, Chattopadhyay S, Lemey P, Sokurenko EV, Minin VN. Synonymous and nonsynonymous distances help untangle convergent evolution and recombination, Statistical Applications in Genetics and Molecular Biology, 14, 375 – 389. (arXiv:1410.1263 [stat.ME]) supplement synDss
30. McCoy CO, Bedford T, Minin VN, Robins H, Matsen FA. Quantifying evolutionary constraints on B-cell affinity maturation, Philosophical Transactions of the Royal Society B: Biological Sciences, 370, 20140244. (arXiv:1403.3066 [q-bio.PE]) supplement startreerenaissance
29. 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, 71, 90 – 101. (UW Biostatistics Working Paper 401) supplement cthmm
28. 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, 111:E4736 – E4742. supplement indorigin
27. Irvahn J and Minin VN. Phylogenetic stochastic mapping without matrix exponentiation, Journal of Computational Biology, 21:676 – 690. (arXiv:1403.5040 [stat.CO]) 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
25. Leaché AD, Fujita MK, Minin VN, Bouckaert RR. Species delimitation using genome-wide SNP data, Systematic Biology, 63:534 – 542. (bioRxiv doi: 10.1101/123456) BFD*
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])
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]) 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.
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
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. 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]) 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.
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.
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.
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
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.
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)
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.
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
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)
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.
8. Minin VN and Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution, Journal of Mathematical Biology, 56:391 – 412.
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.
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. 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. 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.
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.
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.
1. Minin V, Abdo Z, Joyce P, and Sullivan J. Performance-based selection of likelihood models for phylogeny estimation, Systematic Biology, 52:674 – 683. 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].
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].

Selected Recent Conference Presentations and Posters:

Making the most of data augmentation in phylogenetics
invited talk at the Joint Statistical Meeting, Seattle, WA
August 2015.
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, 2015