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Items: 41

1.

19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology.

Fourment M, Magee AF, Whidden C, Bilge A, Matsen FA, Minin VN.

Syst Biol. 2019 Aug 28. pii: syz046. doi: 10.1093/sysbio/syz046. [Epub ahead of print]

PMID:
31504998
2.

Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori.

Chattopadhyay S, Chi PB, Minin VN, Berg DE, Sokurenko EV.

BMC Genomics. 2018 Nov 21;19(1):835. doi: 10.1186/s12864-018-5231-7.

3.

Predicting B cell receptor substitution profiles using public repertoire data.

Dhar A, Davidsen K, Matsen FA 4th, Minin VN.

PLoS Comput Biol. 2018 Oct 17;14(10):e1006388. doi: 10.1371/journal.pcbi.1006388. eCollection 2018 Oct.

4.

Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors.

Faulkner JR, Minin VN.

Bayesian Anal. 2018 Mar;13(1):225-252. doi: 10.1214/17-BA1050. Epub 2017 Feb 24.

5.

Using Genotype Abundance to Improve Phylogenetic Inference.

DeWitt WS 3rd, Mesin L, Victora GD, Minin VN, Matsen FA 4th.

Mol Biol Evol. 2018 May 1;35(5):1253-1265. doi: 10.1093/molbev/msy020.

6.

Birth/birth-death processes and their computable transition probabilities with biological applications.

Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA.

J Math Biol. 2018 Mar;76(4):911-944. doi: 10.1007/s00285-017-1160-3. Epub 2017 Jul 24.

7.

Myosin-independent cytokinesis in Giardia utilizes flagella to coordinate force generation and direct membrane trafficking.

Hardin WR, Li R, Xu J, Shelton AM, Alas GCM, Minin VN, Paredez AR.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5854-E5863. doi: 10.1073/pnas.1705096114. Epub 2017 Jul 5.

8.

Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time.

Dhar A, Minin VN.

J Comput Biol. 2017 May;24(5):377-399. doi: 10.1089/cmb.2016.0172. Epub 2017 Feb 8.

9.

Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data.

Fintzi J, Cui X, Wakefield J, Minin VN.

J Comput Graph Stat. 2017;26(4):918-929. doi: 10.1080/10618600.2017.1328365. Epub 2017 Oct 9.

10.

phylodyn: an R package for phylodynamic simulation and inference.

Karcher MD, Palacios JA, Lan S, Minin VN.

Mol Ecol Resour. 2017 Jan;17(1):96-100. doi: 10.1111/1755-0998.12630. Epub 2016 Nov 21.

11.

PREDICTIVE MODELING OF CHOLERA OUTBREAKS IN BANGLADESH.

Koepke AA, Longini IM Jr, Halloran ME, Wakefield J, Minin VN.

Ann Appl Stat. 2016 Jun;10(2):575-595. Epub 2016 Jul 22.

12.
13.

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.

Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN.

PLoS Comput Biol. 2016 Mar 3;12(3):e1004789. doi: 10.1371/journal.pcbi.1004789. eCollection 2016 Mar.

14.

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

Linkem CW, Minin VN, Leaché AD.

Syst Biol. 2016 May;65(3):465-77. doi: 10.1093/sysbio/syw001. Epub 2016 Jan 6.

15.

Quantifying evolutionary constraints on B-cell affinity maturation.

McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA 4th.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140244. doi: 10.1098/rstb.2014.0244.

16.

Likelihood-based inference for discretely observed birth-death-shift processes, with applications to evolution of mobile genetic elements.

Xu J, Guttorp P, Kato-Maeda M, Minin VN.

Biometrics. 2015 Dec;71(4):1009-21. doi: 10.1111/biom.12352. Epub 2015 Jul 6.

17.

An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics.

Lan S, Palacios JA, Karcher M, Minin VN, Shahbaba B.

Bioinformatics. 2015 Oct 15;31(20):3282-9. doi: 10.1093/bioinformatics/btv378. Epub 2015 Jun 20.

18.

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.

Chi PB, Chattopadhyay S, Lemey P, Sokurenko EV, Minin VN.

Stat Appl Genet Mol Biol. 2015 Aug;14(4):375-89. doi: 10.1515/sagmb-2014-0078.

19.

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid.

Pankey MS, Minin VN, Imholte GC, Suchard MA, Oakley TH.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):E4736-42. doi: 10.1073/pnas.1416574111. Epub 2014 Oct 21.

20.

Estimation for general birth-death processes.

Crawford FW, Minin VN, Suchard MA.

J Am Stat Assoc. 2014 Apr;109(506):730-747.

21.

A joint model for multistate disease processes and random informative observation times, with applications to electronic medical records data.

Lange JM, Hubbard RA, Inoue LYT, Minin VN.

Biometrics. 2015 Mar;71(1):90-101. doi: 10.1111/biom.12252. Epub 2014 Oct 15.

22.

Phylogenetic stochastic mapping without matrix exponentiation.

Irvahn J, Minin VN.

J Comput Biol. 2014 Sep;21(9):676-90. doi: 10.1089/cmb.2014.0062. Epub 2014 Jun 11.

23.

Heritability estimation of osteoarthritis in the pig-tailed macaque (Macaca nemestrina) with a look toward future data collection.

Chi PB, Duncan AE, Kramer PA, Minin VN.

PeerJ. 2014 May 1;2:e373. doi: 10.7717/peerj.373. eCollection 2014.

24.

Species delimitation using genome-wide SNP data.

Leaché AD, Fujita MK, Minin VN, Bouckaert RR.

Syst Biol. 2014 Jul;63(4):534-42. doi: 10.1093/sysbio/syu018. Epub 2014 Mar 12.

25.

A statistical approach to peptide identification from clustered tandem mass spectrometry data.

Ryu S, Goodlett DR, Noble WS, Minin VN.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2012 Oct 4:648-653.

26.

rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.

Irvahn J, Chattopadhyay S, Sokurenko EV, Minin VN.

Evol Bioinform Online. 2013 Jun 12;9:235-8. doi: 10.4137/EBO.S11945. Print 2013.

27.

Fitting and interpreting continuous-time latent Markov models for panel data.

Lange JM, Minin VN.

Stat Med. 2013 Nov 20;32(26):4581-95. doi: 10.1002/sim.5861. Epub 2013 Jun 5.

28.

Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies.

Palacios JA, Minin VN.

Biometrics. 2013 Mar;69(1):8-18. doi: 10.1111/biom.12003. Epub 2013 Feb 14.

PMID:
23409705
29.

Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting.

Doss CR, Suchard MA, Holmes I, Kato-Maeda M, Minin VN.

Ann Appl Stat. 2013;7(4):2315-2335.

30.

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.

Lemey P, Minin VN, Bielejec F, Kosakovsky Pond SL, Suchard MA.

Bioinformatics. 2012 Dec 15;28(24):3248-56. doi: 10.1093/bioinformatics/bts580. Epub 2012 Oct 12.

31.

Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model.

Sawaya SM, Lennon D, Buschiazzo E, Gemmell N, Minin VN.

Genome Biol Evol. 2012;4(6):636-47. doi: 10.1093/gbe/evs050. Epub 2012 May 16.

32.

Recombination between variants from genital tract and plasma: evolution of multidrug-resistant HIV type 1.

Kemal KS, Ramirez CM, Burger H, Foley B, Mayers D, Klimkait T, Hamy F, Anastos K, Petrovic K, Minin VN, Suchard MA, Weiser B.

AIDS Res Hum Retroviruses. 2012 Dec;28(12):1766-74. doi: 10.1089/AID.2011.0383. Epub 2012 Apr 10.

33.

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection.

Chattopadhyay S, Weissman SJ, Minin VN, Russo TA, Dykhuizen DE, Sokurenko EV.

Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12412-7. doi: 10.1073/pnas.0906217106. Epub 2009 Jul 15.

34.

Learning to count: robust estimates for labeled distances between molecular sequences.

O'Brien JD, Minin VN, Suchard MA.

Mol Biol Evol. 2009 Apr;26(4):801-14. doi: 10.1093/molbev/msp003. Epub 2009 Jan 8.

35.

Fast, accurate and simulation-free stochastic mapping.

Minin VN, Suchard MA.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3985-95. doi: 10.1098/rstb.2008.0176.

36.

Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.

Minin VN, Bloomquist EW, Suchard MA.

Mol Biol Evol. 2008 Jul;25(7):1459-71. doi: 10.1093/molbev/msn090. Epub 2008 Apr 11.

37.

Counting labeled transitions in continuous-time Markov models of evolution.

Minin VN, Suchard MA.

J Math Biol. 2008 Mar;56(3):391-412. Epub 2007 Sep 14.

PMID:
17874105
38.

Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes.

Minin VN, Dorman KS, Fang F, Suchard MA.

Genetics. 2007 Apr;175(4):1773-85. Epub 2006 Dec 28.

39.

cBrother: relaxing parental tree assumptions for Bayesian recombination detection.

Fang F, Ding J, Minin VN, Suchard MA, Dorman KS.

Bioinformatics. 2007 Feb 15;23(4):507-8. Epub 2006 Dec 4.

PMID:
17145740
40.

Dual multiple change-point model leads to more accurate recombination detection.

Minin VN, Dorman KS, Fang F, Suchard MA.

Bioinformatics. 2005 Jul 1;21(13):3034-42. Epub 2005 May 24.

PMID:
15914546
41.

Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation.

Abdo Z, Minin VN, Joyce P, Sullivan J.

Mol Biol Evol. 2005 Mar;22(3):691-703. Epub 2004 Nov 17. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1159.

PMID:
15548751

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