Zobrazeno 1 - 10
of 36
pro vyhledávání: '"Jeremy G. Sumner"'
Publikováno v:
Journal of Bioinformatics and Computational Biology. 19
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position paradigm", in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::df69c418c885386db5cf0916b2225608
https://doi.org/10.1142/s0219720021400151
https://doi.org/10.1142/s0219720021400151
Publikováno v:
Journal of Molecular Evolution. 88:136-150
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching history of the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a9ec9743b85077ae2b1846be0af8ea10
https://doi.org/10.1007/s00239-019-09918-z
https://doi.org/10.1007/s00239-019-09918-z
Autor:
Peter D. Jarvis, Jeremy G. Sumner
Publikováno v:
Journal of Mathematical Biology. 82
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f6fe57e4646b5780b9fc12c4ad2152a7
https://doi.org/10.1007/s00285-021-01625-y
https://doi.org/10.1007/s00285-021-01625-y
Autor:
Michael Baake, Jeremy G. Sumner
The representation problem of finite-dimensional Markov matrices in Markov semigroups is revisited, with emphasis on concrete criteria for matrix subclasses of theoretical or practical relevance, such as equal-input, circulant, symmetric or doubly st
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c970007a8685da9eb42364afc0f6bbb5
https://doi.org/10.1016/j.laa.2020.02.016
https://doi.org/10.1016/j.laa.2020.02.016
Autor:
Venta Terauds, Jeremy G. Sumner
Publikováno v:
Bulletin of Mathematical Biology. 81:535-567
The calculation of evolutionary distance via models of genome rearrangement has an inherent combinatorial complexity. Various algorithms and estimators have been used to address this; however, many of these set quite specific conditions for the under
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a3b5b62cc1df17563c05aeed5331586c
https://doi.org/10.1007/s11538-018-0511-6
https://doi.org/10.1007/s11538-018-0511-6
A matrix Lie algebra is a linear space of matrices closed under the operation $ [A, B] = AB-BA $. The "Lie closure" of a set of matrices is the smallest matrix Lie algebra which contains the set. In the context of Markov chain theory, if a set of rat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f204f68232f83be394dd0d9e9dfaefd4
http://arxiv.org/abs/1804.11249
http://arxiv.org/abs/1804.11249
Publikováno v:
Systematic biology. 67(5)
We give a non-technical introduction to convergence–divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more sim
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ddbf8f3c9ed47b16da066dedf51e7ff4
https://pubmed.ncbi.nlm.nih.gov/29788496
https://pubmed.ncbi.nlm.nih.gov/29788496
Autor:
Jeremy G. Sumner, Michael D. Woodhams
Publikováno v:
Bulletin of mathematical biology. 81(2)
We present and explore a general method for deriving a Lie-Markov model from a finite semigroup. If the degree of the semigroup is $k$, the resulting model is a continuous-time Markov chain on $k$ states and, as a consequence of the product rule in t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a5dc9d7a4e0c02c209a93b8be55c3cf8
https://pubmed.ncbi.nlm.nih.gov/30073568
https://pubmed.ncbi.nlm.nih.gov/30073568
Autor:
Barbara R. Holland, Peter D. Jarvis, Attila Egri-Nagy, Stuart Serdoz, Andrew R. Francis, Jeremy G. Sumner, Mark M. Tanaka
Publikováno v:
Journal of theoretical biology. 423
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. Distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genom
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::338f3792688518fc7b1c47b6c0781053
https://pubmed.ncbi.nlm.nih.gov/28435014
https://pubmed.ncbi.nlm.nih.gov/28435014
"Phylogenetics" is the systematic study of reconstructing the past evolutionary history of extant species or taxa, based on present-day data, such as morphologies or molecular information (sequence data). This evolutionary history or phylogeny is ide
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6376ef00162b8a73a7ed52b22f55c664
https://doi.org/10.1016/b978-0-12-809633-8.06903-x
https://doi.org/10.1016/b978-0-12-809633-8.06903-x