Filters








109 Hits in 9.1 sec

Coalescing times for IID random variables with applications to population biology

Ilan Adler, Hyun-Soo Ahn, Richard M. Karp, Sheldon M. Ross
2003 Random structures & algorithms (Print)  
Applications to population biology are noted.  ...  We consider a coalescing particle model where particles move in discrete time.  ...  ACKNOWLEDGMENTS We thank the referees for pointing out the connection of our model with the coalescent models of population biology.  ... 
doi:10.1002/rsa.10080 fatcat:b6lxramnprgflaf3yvxfg4tar4

The effective strength of selection in random environment [article]

Adrián González Casanova, Dario Spanò, Maite Wilke-Berenguer
2020 arXiv   pre-print
in the case of finite population size and in the scaling limit for large size.  ...  We analyse a family of two-types Wright-Fisher models with selection in a random environment and skewed offspring distribution.  ...  Acknowledgements We thank Martin Slowik for pointing out a mistake in an earlier version of this manuscript, which we corrected with Lemma 3.6.  ... 
arXiv:1903.12121v2 fatcat:2wsrl5v4engofet3e2zk67ey5u

The performance of coalescent-based species tree estimation methods under models of missing data

Michael Nute, Jed Chou, Erin K. Molloy, Tandy Warnow
2018 BMC Genomics  
Methods to estimate species trees in the presence of gene tree discord due to incomplete lineage sorting have been developed and proved to be statistically consistent when gene tree discord is due only  ...  Results: We establish statistical consistency of certain coalescent-based species tree estimation methods under some models of taxon deletion from genes.  ...  This work made use of the Illinois Campus Cluster, a computing resource that is operated by the Illinois Campus Cluster Program in conjunction with the National Center for Supercomputing Applications and  ... 
doi:10.1186/s12864-018-4619-8 pmid:29745854 pmcid:PMC5998899 fatcat:xi6e5fqh5vca5lvfvbd5uvgsii

Page 4013 of Mathematical Reviews Vol. , Issue 2004e [page]

2004 Mathematical Reviews  
times for iid random variables with applications to population biology.  ...  ) to discrete-time queues.”  ... 

Fitting stochastic epidemic models to gene genealogies using linear noise approximation [article]

Mingwei Tang, Gytis Dudas, Trevor Bedford, Vladimir N. Minin
2019 arXiv   pre-print
One important task in phylodynamics is to estimate changes in (effective) population size.  ...  To model changes in the number of infected individuals, current phylodynamic methods use non-parametric approaches, parametric approaches, and stochastic modeling in conjunction with likelihood-free Bayesian  ...  We are grateful to Michael Karcher and Julia Palacios for patiently answering questions about nonparametric phylodynamic inference and phylodyn package.  ... 
arXiv:1902.08877v1 fatcat:k45lpxd4nzbr5an3fxuunbjn2i

Hidden Markov Dirichlet process: modeling genetic inference in open ancestral space

Eric P. Xing, Kyung-Ah Sohn
2007 Bayesian Analysis  
of genome variations, with important applications to the genetic analysis of disease propensities and other complex traits.  ...  Statistical genetic methodologies developed so far mostly address these problems separately using specialized models ranging from coalescence and admixture models for population structures, to hidden Markov  ...  The computation time for analyzing this data set is comparable to that of the Daly data set. We applied HMDP to the union of the populations, with a random individual order.  ... 
doi:10.1214/07-ba220 fatcat:yn25v527vvgqxbdwjppxf2ehla

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts [article]

Andrew F. Magee, Sebastian Höhna, Tetyana I. Vasylyeva, Adam D. Leaché, Vladimir N. Minin
2019 biorxiv/medrxiv   pre-print
We use a piecewise-constant birth-death model, combined with both Gaussian Markov random field (GMRF) and horseshoe Markov random field (HSMRF) prior distributions, to approximate arbitrary changes in  ...  In general the HSMRF-based model has higher precision than its GMRF counterpart, with little to no loss of accuracy.  ...  Acknowledgments We are grateful to Arman Bilge, Jonathan Fintzi, Jean Feng, and Jared Grummer for helpful discussions, to James Faulkner for assistance with the MCMC samplers, and to Rebecca Magee for  ... 
doi:10.1101/853960 fatcat:brarox3lbjct5hu6qhiniyvd54

Statistical inference for the evolutionary history of cancer genomes [article]

Khanh N. Đinh, Roman Jaksik, Marek Kimmel, Amaury Lambert, Simon Tavaré
2019 biorxiv/medrxiv   pre-print
Reverse-time genealogical views of such models, commonly known as coalescents, have been used to infer aspects of the past of growing populations.  ...  We illustrate the theory with applications to several examples of The Cancer Genome Atlas tumors.  ...  AL thanks the Center for Interdisciplinary Research in Biology (CIRB, Collège de France) for funding. ST was supported in part by core funding to the Cancer Research UK Cambridge Institute.  ... 
doi:10.1101/722033 fatcat:mrbmnbarnvc7znqb4e56fcfqai

The Coalescence of Intrahost HIV Lineages Under Symmetric CTL Attack

Sivan Leviyang
2012 Bulletin of Mathematical Biology  
Cytotoxic T lymphocytes (CTLs) are immune system cells that are thought to play an important role in controlling HIV infection.  ...  Based on this stochastic model, we consider the effect of CTL attack on intrahost HIV lineages assuming CTLs attack several epitopes with equal strength.  ...  However, T h i − Ti = O(| log(δ)|) It then takes O( 1 ∆k | log(δ)|) time for the vi population to rise to O(1) levels, push out the vi−1 population, and near equilibrium with respect to h.  ... 
doi:10.1007/s11538-012-9737-x pmid:22644341 fatcat:elzkou5urff2nmwb2fisg5zs5i

A leader-election procedure using records [article]

Gerold Alsmeyer, Zakhar Kabluchko, Alexander Marynych
2016 arXiv   pre-print
., who generate iid random numbers from an arbitrary continuous distribution.  ...  The results are applied to study subsequential distributional limits for the number of collisions in the Poisson-Dirichlet coalescent.  ...  Acknowledgements The authors would like to express their sincere gratitude to two anonymous referees for numerous suggestions and inspiring comments on the first version of the manuscript.  ... 
arXiv:1512.04750v2 fatcat:jjto5do7gjfotfutqjj6fiswby

Why approximate Bayesian computational (ABC) methods cannot handle model choice problems [article]

Christian Robert, Jean-Michel Marin
2011 arXiv   pre-print
We advocated in Grelaud et al. (2009) the use of ABC for Bayesian model choice in the specific case of Gibbs random fields (GRF), relying on a sufficiency property mainly enjoyed by GRFs to show that the  ...  Approximate Bayesian computation (ABC), also known as likelihood-free methods, have become a favourite tool for the analysis of complex stochastic models, primarily in population genetics but also in financial  ...  The fundamental reason for this impossibility is that the statistical model associated with coalescent data needs to integrate over trees of extreme complexity.  ... 
arXiv:1101.5091v2 fatcat:n6em7y6uhbeftci2wmma2vlbx4

Lack of confidence in ABC model choice [article]

Christian P. Robert, Jean-Marie Cornuet, Natesh Pillai
2011 arXiv   pre-print
Earlier, Grelaud et al. (2009) advocated the use of ABC for Bayesian model choice in the specific case of Gibbs random fields, relying on a inter-model sufficiency property to show that the approximation  ...  Having implemented ABC-based model choice in a wide range of phylogenetic models in the DIY-ABC software (Cornuet et al., 2008), we now present theoretical background as to why a generic use of ABC for  ...  They are grateful to the reviewers and to Michael Stumpf for their comments. Computations were performed on the INRA CBGP and MIGALE clusters.  ... 
arXiv:1102.4432v4 fatcat:uid2nevhkbbqjm7rq7vm4w5jk4

Testing for Ancient Admixture between Closely Related Populations

Eric Y. Durand, Nick Patterson, David Reich, Montgomery Slatkin
2011 Molecular biology and evolution  
One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations.  ...  We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations.  ...  Acknowledgments We thank Anna-Sapfo Malaspinas for helpful discussions that helped improve the manuscript. E.Y.D and M.S were supported by a US National Institute of Health grant (R01-GM40282).  ... 
doi:10.1093/molbev/msr048 pmid:21325092 pmcid:PMC3144383 fatcat:ynmegadxizbl7a7frpvpbqudiy

The Coalescence of Intrahost HIV Lineages Under Symmetric CTL Attack [article]

Sivan Leviyang
2011 arXiv   pre-print
Cytotoxic T lymphocytes (CTLs) are immune system cells that are thought to play an important role in controlling HIV infection.  ...  Based on this stochastic model, we consider the effect of CTL attack on intrahost HIV lineages assuming CTLs attack several epitopes with equal strength.  ...  However, T h i − Ti = O(| log(δ)|) It then takes O( 1 ∆k | log(δ)|) time for the vi population to rise to O(1) levels, push out the vi−1 population, and near equilibrium with respect to h.  ... 
arXiv:1108.0686v1 fatcat:oyc3gty7undajjbrdwsy2r7bvi

EVIDENCE FOR CLIMATE-DRIVEN DIVERSIFICATION? A CAUTION FOR INTERPRETING ABC INFERENCES OF SIMULTANEOUS HISTORICAL EVENTS

Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron D. Siler, Mark T. Holder, Rafe M. Brown
2012 Evolution  
However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting  ...  Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene-driven diversification hypothesis.  ...  We also thank the Cincinnati Museum of Natural History, Field Museum of Natural History, National Museum of the Philippines, and Mindanao State University, along with each institution's staff, for providing  ... 
doi:10.1111/j.1558-5646.2012.01840.x pmid:23550751 fatcat:amduwttpvvawbfriaqlp3tztfm
« Previous Showing results 1 — 15 out of 109 results