Volodymyr Minin, Ph.D. - Publications

Affiliations: 
2007 University of California, Los Angeles, Los Angeles, CA 
Area:
Biostatistics Biology, Genetics

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Magee AF, Höhna S, Vasylyeva TI, Leaché AD, Minin VN. Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts. Plos Computational Biology. 16: e1007999. PMID 33112848 DOI: 10.1371/journal.pcbi.1007999  0.01
2020 Karcher MD, Carvalho LM, Suchard MA, Dudas G, Minin VN. Estimating effective population size changes from preferentially sampled genetic sequences. Plos Computational Biology. 16: e1007774. PMID 33044955 DOI: 10.1371/journal.pcbi.1007774  0.92
2020 Dhar A, Ralph DK, Minin VN, Matsen FA. A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis. Plos Computational Biology. 16: e1008030. PMID 32804924 DOI: 10.1371/Journal.Pcbi.1008030  0.04
2020 Faulkner JR, Magee AF, Shapiro B, Minin VN. Rejoinder for discussion on "Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories". Biometrics. PMID 32378741 DOI: 10.1111/Biom.13273  0.01
2020 Faulkner JR, Magee AF, Shapiro B, Minin VN. Horseshoe-based bayesian nonparametric estimation of effective population size trajectories. Biometrics. PMID 32277713 DOI: 10.1111/Biom.13276  0.01
2019 Fourment M, Magee AF, Whidden C, Bilge A, Matsen FA, Minin VN. 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology. Systematic Biology. PMID 31504998 DOI: 10.1093/Sysbio/Syz046  0.04
2019 Oaks JR, Cobb KA, Minin VN, Leaché AD. Marginal likelihoods in phylogenetics: a review of methods and applications. Systematic Biology. PMID 30668834 DOI: 10.1093/Sysbio/Syz003  0.01
2018 Chattopadhyay S, Chi PB, Minin VN, Berg DE, Sokurenko EV. Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori. Bmc Genomics. 19: 835. PMID 30463511 DOI: 10.1186/s12864-018-5231-7  0.01
2018 Dhar A, Davidsen K, Matsen FA, Minin VN. Predicting B cell receptor substitution profiles using public repertoire data. Plos Computational Biology. 14: e1006388. PMID 30332400 DOI: 10.1371/Journal.Pcbi.1006388  0.04
2018 Faulkner JR, Minin VN. Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors. Bayesian Analysis. 13: 225-252. PMID 29755638 DOI: 10.1214/17-Ba1050  0.01
2018 DeWitt WS, Mesin L, Victora GD, Minin VN, Matsen FA. Using genotype abundance to improve phylogenetic inference. Molecular Biology and Evolution. PMID 29474671 DOI: 10.1093/Molbev/Msy020  0.04
2017 Fintzi J, Cui X, Wakefield J, Minin VN. Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data. Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. 26: 918-929. PMID 30515026 DOI: 10.1080/10618600.2017.1328365  0.01
2017 Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA. Birth/birth-death processes and their computable transition probabilities with biological applications. Journal of Mathematical Biology. PMID 28741177 DOI: 10.1007/S00285-017-1160-3  0.92
2017 Hardin WR, Li R, Xu J, Shelton AM, Alas GCM, Minin VN, Paredez AR. Myosin-independent cytokinesis in Giardia utilizes flagella to coordinate force generation and direct membrane trafficking. Proceedings of the National Academy of Sciences of the United States of America. PMID 28679631 DOI: 10.1073/Pnas.1705096114  0.4
2017 Dhar A, Minin VN. Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 28177780 DOI: 10.1089/Cmb.2016.0172  0.01
2016 Karcher MD, Palacios JA, Lan S, Minin VN. phylodyn: an R package for phylodynamic simulation and inference. Molecular Ecology Resources. PMID 27801980 DOI: 10.1111/1755-0998.12630  0.48
2016 Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN. Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. Plos Computational Biology. 12: e1004789. PMID 26938243 DOI: 10.1371/Journal.Pcbi.1004789  0.92
2016 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). Systematic Biology. PMID 26738927 DOI: 10.1093/Sysbio/Syw001  0.01
2016 Koepke AA, Longini IM, Halloran ME, Wakefield J, Minin VN. Predictive modeling of cholera outbreaks in Bangladesh Annals of Applied Statistics. 10: 575-595. DOI: 10.1214/16-AOAS908  0.92
2015 Xu J, Minin VN. Efficient Transition Probability Computation for Continuous-Time Branching Processes via Compressed Sensing. Uncertainty in Artificial Intelligence : Proceedings of the ... Conference. Conference On Uncertainty in Artificial Intelligence. 2015: 952-961. PMID 26949377  0.92
2015 McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FA. Quantifying evolutionary constraints on B-cell affinity maturation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370. PMID 26194758 DOI: 10.1098/Rstb.2014.0244  0.92
2015 Xu J, Guttorp P, Kato-Maeda M, Minin VN. Likelihood-based inference for discretely observed birth-death-shift processes, with applications to evolution of mobile genetic elements. Biometrics. 71: 1009-21. PMID 26148963 DOI: 10.1111/Biom.12352  0.92
2015 Lan S, Palacios JA, Karcher M, Minin VN, Shahbaba B. An Efficient Bayesian Inference Framework for Coalescent-Based Nonparametric Phylodynamics. Bioinformatics (Oxford, England). PMID 26093147 DOI: 10.1093/Bioinformatics/Btv378  0.92
2015 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. PMID 26061623 DOI: 10.1515/Sagmb-2014-0078  0.92
2015 Lange JM, Hubbard RA, Inoue LY, 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. PMID 25319319 DOI: 10.1111/Biom.12252  0.92
2014 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 of the United States of America. 111: E4736-42. PMID 25336755 DOI: 10.1073/Pnas.1416574111  0.92
2014 Crawford FW, Minin VN, Suchard MA. Estimation for general birth-death processes. Journal of the American Statistical Association. 109: 730-747. PMID 25328261 DOI: 10.1080/01621459.2013.866565  0.92
2014 Irvahn J, Minin VN. Phylogenetic stochastic mapping without matrix exponentiation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 21: 676-90. PMID 24918812 DOI: 10.1089/Cmb.2014.0062  0.92
2014 Chi PB, Duncan AE, 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. PMID 24860700 DOI: 10.7717/Peerj.373  0.92
2014 Leaché AD, Fujita MK, Minin VN, Bouckaert RR. Species delimitation using genome-wide SNP data. Systematic Biology. 63: 534-42. PMID 24627183 DOI: 10.1093/Sysbio/Syu018  0.92
2013 Doss CR, Suchard MA, Holmes I, Kato-Maeda M, Minin VN. Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting. The Annals of Applied Statistics. 7: 2315-2335. PMID 26702330 DOI: 10.1214/13-Aoas673  0.92
2013 Irvahn J, Chattopadhyay S, Sokurenko EV, Minin VN. rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection. Evolutionary Bioinformatics Online. 9: 235-8. PMID 23818749 DOI: 10.4137/Ebo.S11945  0.92
2013 Lange JM, Minin VN. Fitting and interpreting continuous-time latent Markov models for panel data. Statistics in Medicine. 32: 4581-95. PMID 23740756 DOI: 10.1002/Sim.5861  0.92
2013 Palacios JA, Minin VN. Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies. Biometrics. 69: 8-18. PMID 23409705 DOI: 10.1111/Biom.12003  0.92
2013 Leaché AD, Palacios JA, Minin VN, Bryson RW. Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south-eastern Mexico Biological Journal of the Linnean Society. 110: 852-865. DOI: 10.1111/Bij.12172  0.92
2012 Ryu S, Goodlett DR, Noble WS, Minin VN. A statistical approach to peptide identification from clustered tandem mass spectrometry data. Proceedings. Ieee International Conference On Bioinformatics and Biomedicine. 648-653. PMID 23828149 DOI: 10.1109/BIBMW.2012.6470214  0.92
2012 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 (Oxford, England). 28: 3248-56. PMID 23064000 DOI: 10.1093/Bioinformatics/Bts580  0.92
2012 Sawaya SM, Lennon D, Buschiazzo E, Gemmell N, Minin VN. Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model. Genome Biology and Evolution. 4: 636-47. PMID 22593552 DOI: 10.1093/Gbe/Evs050  0.92
2012 Kemal KS, Ramirez CM, Burger H, Foley B, Mayers D, 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 type 1. Aids Research and Human Retroviruses. 28: 1766-74. PMID 22364185 DOI: 10.1089/Aid.2011.0383  0.92
2012 Palacios JA, Minin VN. Integrated nested laplace approximation for bayesian nonparametric phylodynamics Uncertainty in Artificial Intelligence - Proceedings of the 28th Conference, Uai 2012. 726-735.  0.92
2011 Minin VN, O'Brien JD, Seregin A. Imputation estimators partially correct for model misspecification Statistical Applications in Genetics and Molecular Biology. 10. DOI: 10.2202/1544-6115.1650  0.92
2009 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 of the United States of America. 106: 12412-7. PMID 19617543 DOI: 10.1073/Pnas.0906217106  0.92
2009 O'Brien JD, Minin VN, Suchard MA. Learning to count: robust estimates for labeled distances between molecular sequences. Molecular Biology and Evolution. 26: 801-14. PMID 19131426 DOI: 10.1093/Molbev/Msp003  0.92
2008 Minin VN, Suchard MA. Fast, accurate and simulation-free stochastic mapping. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3985-95. PMID 18852111 DOI: 10.1098/Rstb.2008.0176  0.92
2008 Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology and Evolution. 25: 1459-71. PMID 18408232 DOI: 10.1093/Molbev/Msn090  0.92
2008 Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. Journal of Mathematical Biology. 56: 391-412. PMID 17874105 DOI: 10.1007/S00285-007-0120-8  0.92
2007 Minin VN, Dorman KS, Fang F, Suchard MA. Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes. Genetics. 175: 1773-85. PMID 17194781 DOI: 10.1534/Genetics.106.066258  0.92
2007 Fang F, Ding J, Minin VN, Suchard MA, Dorman KS. cBrother: relaxing parental tree assumptions for Bayesian recombination detection. Bioinformatics (Oxford, England). 23: 507-8. PMID 17145740 DOI: 10.1093/Bioinformatics/Btl613  0.92
2007 Rajaram ML, Minin VN, Suchard MA, Dorman KS. Hot and cold: Spatial fluctuation in HIV-1 recombination rates Proceedings of the 7th Ieee International Conference On Bioinformatics and Bioengineering, Bibe. 707-714. DOI: 10.1109/BIBE.2007.4375638  0.92
2005 Minin VN, Dorman KS, Fang F, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics (Oxford, England). 21: 3034-42. PMID 15914546 DOI: 10.1093/Bioinformatics/Bti459  0.92
2005 Abdo Z, Minin VN, Joyce P, 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. PMID 15548751 DOI: 10.1093/Molbev/Msi050  0.92
2004 Liu X, Minin V, Huang Y, Seligson DB, Horvath S. Statistical methods for analyzing tissue microarray data. Journal of Biopharmaceutical Statistics. 14: 671-85. PMID 15468758 DOI: 10.1081/Bip-200025657  0.92
2003 Minin V, Abdo Z, Joyce P, Sullivan J. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology. 52: 674-83. PMID 14530134 DOI: 10.1080/10635150390235494  0.92
2001 Pikaev AK, Ponomarev AV, Bludenko AV, Minin VN, Elizar'eva LM. Combined electron-beam and coagulation purification of molasses distillery slops. Features of the method, technical and economic evaluation of large-scale facility Radiation Physics and Chemistry. 61: 81-87. DOI: 10.1016/S0969-806X(00)00377-7  0.01
1996 Pikaev AK, Bludenko AV, Makarov IE, Ponomarev AV, Minin VN, Ponomarev VI, Linnik OA. Electron-beam treatment of highly-coloured river water Radiation Physics and Chemistry. 48: 75-80. DOI: 10.1016/0969-806X(95)00425-W  0.01
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