Alex Gavryushkin
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Explore the profile of Alex Gavryushkin including associated specialties, affiliations and a list of published articles.
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18
Citations
310
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Recent Articles
11.
Collienne L, Elmes K, Fischer M, Bryant D, Gavryushkin A
J Math Biol
. 2021 Nov;
83(5):60.
PMID: 34739608
In many phylogenetic applications, such as cancer and virus evolution, time trees, evolutionary histories where speciation events are timed, are inferred. Of particular interest are clock-like trees, where all leaves...
12.
Elmes K, Schmich F, Szczurek E, Jenkins J, Beerenwinkel N, Gavryushkin A
PLoS One
. 2021 Jul;
16(7):e0254491.
PMID: 34255784
The treatment of complex diseases often relies on combinatorial therapy, a strategy where drugs are used to target multiple genes simultaneously. Promising candidate genes for combinatorial perturbation often constitute epistatic...
13.
Collienne L, Gavryushkin A
J Math Biol
. 2021 Jan;
82(1-2):8.
PMID: 33492606
Many popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where...
14.
Gould A, Zhang V, Lamberti L, Jones E, Obadia B, Korasidis N, et al.
Proc Natl Acad Sci U S A
. 2018 Dec;
115(51):E11951-E11960.
PMID: 30510004
Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what...
15.
Lienkaemper C, Lamberti L, Drain J, Beerenwinkel N, Gavryushkin A
J Math Biol
. 2018 May;
77(4):951-970.
PMID: 29736875
We present an efficient computational approach for detecting genetic interactions from fitness comparison data together with a geometric interpretation using polyhedral cones associated to partial orderings. Genetic interactions are defined...
16.
Crona K, Gavryushkin A, Greene D, Beerenwinkel N
Elife
. 2017 Dec;
6.
PMID: 29260711
Darwinian fitness is a central concept in evolutionary biology. In practice, however, it is hardly possible to measure fitness for all genotypes in a natural population. Here, we present quantitative...
17.
Gavryushkin A, Whidden C, Matsen 4th F
J Math Biol
. 2017 Jul;
76(5):1101-1121.
PMID: 28756523
A time-tree is a rooted phylogenetic tree such that all internal nodes are equipped with absolute divergence dates and all leaf nodes are equipped with sampling dates. Such time-trees have...
18.
Gavryushkin A, Drummond A
J Theor Biol
. 2016 May;
403:197-208.
PMID: 27188249
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution...
19.
Stadler T, Vaughan T, Gavryushkin A, Guindon S, Kuhnert D, Leventhal G, et al.
Proc Biol Sci
. 2015 Apr;
282(1806):20150420.
PMID: 25876846
One of the central objectives in the field of phylodynamics is the quantification of population dynamic processes using genetic sequence data or in some cases phenotypic data. Phylodynamics has been...