Results 21 to 30 of about 101,924 (212)

Classes of tree-based networks

Visual Computing for Industry, Biomedicine, and Art, 2020
Recently, so-called tree-based phylogenetic networks have attracted considerable attention. These networks can be constructed from a phylogenetic tree, called the base tree, by adding additional edges.
Mareike Fischer, Michelle Galla, Lina Herbst, Yangjing Long, Kristina Wicke   +4 more
doaj   +1 more source

Reconstructible phylogenetic networks: do not distinguish the indistinguishable. [PDF]

PLoS Computational Biology, 2015
Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays,
Fabio Pardi, Celine Scornavacca
doaj   +1 more source

Different evolutionary trajectories of vaccine-controlled and non-controlled avian infectious bronchitis viruses in commercial poultry. [PDF]

PLoS ONE, 2017
To determine the genetic and epidemiological relationship of infectious bronchitis virus (IBV) isolates from commercial poultry to attenuated live IBV vaccines we conducted a phylogenetic network analysis on the full-length S1 sequence for Arkansas (Ark),
Mark W Jackwood, Dong-Hun Lee
doaj   +1 more source

Algorithms for the Reconstruction of Genomic Structures with Proofs of Their Low Polynomial Complexity and High Exactness

Mathematics
The mathematical side of applied problems in multiple subject areas (biology, pattern recognition, etc.) is reduced to the problem of discrete optimization in the following mathematical method.
Konstantin Gorbunov, Vassily Lyubetsky
doaj   +1 more source

Extraction of phylogenetic network modules from the metabolic network

BMC Bioinformatics, 2006
Background In bio-systems, genes, proteins and compounds are related to each other, thus forming complex networks. Although each organism has its individual network, some organisms contain common sub-networks based on function.
Goto Susumu, Kanehisa Minoru, Yamada Takuji   +2 more
doaj   +1 more source

Extended Newick: it is time for a standard representation of phylogenetic networks

BMC Bioinformatics, 2008
Background Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events ...
Valiente Gabriel, Rosselló Francesc, Cardona Gabriel   +2 more
doaj   +1 more source

A network perspective on the topological importance of enzymes and their phylogenetic conservation

BMC Bioinformatics, 2007
Background A metabolic network is the sum of all chemical transformations or reactions in the cell, with the metabolites being interconnected by enzyme-catalyzed reactions. Many enzymes exist in numerous species while others occur only in a few.
Jordán Ferenc, Davis Andrew J, Lin Wen-hsien, Liu Wei-chung, Yang Hsih-te, Hwang Ming-jing   +5 more
doaj   +1 more source

Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks

Peer Community Journal, 2022
Whether interactions between species are conserved on evolutionary time-scales has spurred the development of both correlative and process-based approaches for testing phylogenetic signal in interspecific interactions: do closely related species interact
Perez-Lamarque, Benoît, Maliet, Odile, Pichon, Benoît, Selosse, Marc-André, Martos, Florent, Morlon, Hélène   +5 more
doaj   +1 more source

Rearrangement moves on rooted phylogenetic networks. [PDF]

PLoS Computational Biology, 2017
Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure.
Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, Celine Scornavacca   +5 more
doaj   +1 more source

From mice to humans—divergent strategies for intestinal homeostasis and regeneration

FEBS Letters, EarlyView.
Recent advances such as organoid genome editing, xenotransplantation, imaging, and whole‐genome sequencing have enabled direct studies of human intestinal stem cells (ISCs). These studies reveal species‐specific features, including slower ISC proliferation, distinct injury responses, slower somatic mutation accumulation in humans, and an inverse ...
Keiko Ishikawa, Shinya Sugimoto, Toshiro Sato   +2 more
wiley   +1 more source