Alex Gavryushkin
Overview
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
1.
Berling L, Klawitter J, Bouckaert R, Xie D, Gavryushkin A, Drummond A
PLoS Comput Biol
. 2025 Feb;
21(2):e1012789.
PMID: 39937844
Bayesian phylogenetic analysis with MCMC algorithms generates an estimate of the posterior distribution of phylogenetic trees in the form of a sample of phylogenetic trees and related parameters. The high...
2.
Truman K, Vaughan T, Gavryushkin A, Gavryushkina A
Syst Biol
. 2024 Oct;
74(1):112-123.
PMID: 39436077
Time-dependent birth-death sampling models have been used in numerous studies to infer past evolutionary dynamics in different biological contexts, for example, speciation and extinction rates in macroevolutionary studies, or effective...
3.
Berling L, Bouckaert R, Gavryushkin A
IEEE/ACM Trans Comput Biol Bioinform
. 2024 Sep;
21(6):2246-2257.
PMID: 39255085
Assessing convergence of Markov chain Monte Carlo (MCMC) based analyses is crucial but challenging, especially so in high dimensional and complex spaces such as the space of phylogenetic trees (treespace)....
4.
Berling L, Collienne L, Gavryushkin A
Bioinformatics
. 2024 Aug;
40(8).
PMID: 39177090
Motivation: Reconstructing evolutionary histories of biological entities, such as genes, cells, organisms, populations, and species, from phenotypic and molecular sequencing data is central to many biological, palaeontological, and biomedical disciplines....
5.
Collienne L, Whidden C, Gavryushkin A
Bull Math Biol
. 2024 Jan;
86(3):24.
PMID: 38294587
Phylogenetic trees are a mathematical formalisation of evolutionary histories between organisms, species, genes, cancer cells, etc. For many applications, e.g. when analysing virus transmission trees or cancer evolution, (phylogenetic) time...
6.
Elmes K, Heywood A, Huang Z, Gavryushkin A
PLoS Comput Biol
. 2022 Dec;
18(12):e1010730.
PMID: 36580499
Large-scale genotype-phenotype screens provide a wealth of data for identifying molecular alterations associated with a phenotype. Epistatic effects play an important role in such association studies. For example, siRNA perturbation...
7.
Moravec J, Lanfear R, Spector D, Diermeier S, Gavryushkin A
J Comput Biol
. 2022 Dec;
30(4):518-537.
PMID: 36475926
Phylogenetic methods are emerging as a useful tool to understand cancer evolutionary dynamics, including tumor structure, heterogeneity, and progression. Most currently used approaches utilize either bulk whole genome sequencing or...
8.
Chen K, Moravec J, Gavryushkin A, Welch D, Drummond A
Mol Biol Evol
. 2022 Jun;
39(8).
PMID: 35733333
Single-cell sequencing provides a new way to explore the evolutionary history of cells. Compared to traditional bulk sequencing, where a population of heterogeneous cells is pooled to form a single...
9.
Powell R, Pattison S, Moravec J, Bhat B, Guirguis N, Markie D, et al.
Cold Spring Harb Mol Case Stud
. 2022 Apr;
8(3).
PMID: 35483879
Tuberous sclerosis complex (TSC) is an inheritable disorder characterized by the formation of benign yet disorganized tumors in multiple organ systems. Germline mutations in the (hamartin) or more frequently (tuberin)...
10.
Gardner P, Paterson J, McGimpsey S, Ashari-Ghomi F, Umu S, Pawlik A, et al.
Genome Biol
. 2022 Feb;
23(1):56.
PMID: 35172880
Background: Computational biology provides software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for accuracy...