Zobrazeno 1 - 10
of 1 135
pro vyhledávání: '"LEMEY, PHILIPPE"'
Autor:
Brusselmans, Marius, Carvalho, Luiz Max, Hong, Samuel L., Gao, Jiansi, Matsen IV, Frederick A., Rambaut, Andrew, Lemey, Philippe, Suchard, Marc A., Dudas, Gytis, Baele, Guy
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of t
Externí odkaz:
http://arxiv.org/abs/2402.11657
Autor:
Lin, Chin-Yi, Chen, Kuo-Chin, Lemey, Philippe, Suchard, Marc A., Holbrook, Andrew J., Hsieh, Min-Hsiu
Multiproposal Markov chain Monte Carlo (MCMC) algorithms choose from multiple proposals at each iteration in order to sample from challenging target distributions more efficiently. Recent work demonstrates the possibility of quadratic quantum speedup
Externí odkaz:
http://arxiv.org/abs/2312.01402
Autor:
Magee, Andrew F., Holbrook, Andrew J., Pekar, Jonathan E., Caviedes-Solis, Itzue W., Matsen IV, Fredrick A., Baele, Guy, Wertheim, Joel O., Ji, Xiang, Lemey, Philippe, Suchard, Marc A.
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time
Externí odkaz:
http://arxiv.org/abs/2303.13642
Autor:
Gangavarapu, Karthik, Ji, Xiang, Baele, Guy, Fourment, Mathieu, Lemey, Philippe, Matsen IV, Frederick A., Suchard, Marc A.
The rapid growth in genomic pathogen data spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters inc
Externí odkaz:
http://arxiv.org/abs/2303.04390
Autor:
Crits-Christoph, Alexander, Levy, Joshua I., Pekar, Jonathan E., Goldstein, Stephen A., Singh, Reema, Hensel, Zach, Gangavarapu, Karthik, Rogers, Matthew B., Moshiri, Niema, Garry, Robert F., Holmes, Edward C., Koopmans, Marion P.G., Lemey, Philippe, Peacock, Thomas P., Popescu, Saskia, Rambaut, Andrew, Robertson, David L., Suchard, Marc A., Wertheim, Joel O., Rasmussen, Angela L., Andersen, Kristian G., Worobey, Michael, Débarre, Florence
Publikováno v:
In Cell 19 September 2024 187(19):5468-5482
Autor:
Zhang, Zhenyu, Nishimura, Akihiko, Trovão, Nídia S., Cherry, Joshua L., Holbrook, Andrew J., Ji, Xiang, Lemey, Philippe, Suchard, Marc A.
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The state-of-the-art approach
Externí odkaz:
http://arxiv.org/abs/2201.07291
Autor:
Ji, Xiang, Fisher, Alexander A., Su, Shuo, Thorne, Jeffrey L., Potter, Barney, Lemey, Philippe, Baele, Guy, Suchard, Marc A.
Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian phylogenetic
Externí odkaz:
http://arxiv.org/abs/2110.13298
Autor:
Hassler, Gabriel W., Gallone, Brigida, Aristide, Leandro, Allen, William L., Tolkoff, Max R., Holbrook, Andrew J., Baele, Guy, Lemey, Philippe, Suchard, Marc A.
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the evolutionary his
Externí odkaz:
http://arxiv.org/abs/2107.01246
Autor:
Paredes, Miguel I., Ahmed, Nashwa, Figgins, Marlin, Colizza, Vittoria, Lemey, Philippe, McCrone, John T., Müller, Nicola, Tran-Kiem, Cécile, Bedford, Trevor
Publikováno v:
In Cell 14 March 2024 187(6):1374-1386
Local clock models propose that the rate of molecular evolution is constant within phylogenetic sub-trees. Current local clock inference procedures scale poorly to large taxa problems, impose model misspecification, or require a priori knowledge of t
Externí odkaz:
http://arxiv.org/abs/2105.07119