Results 61 to 70 of about 2,045,161 (322)

Evolutionarily divergent DUF4465 domains have a common vitamin B12‐binding function

FEBS Open Bio, EarlyView.
We show that DUF4465 family proteins, widespread across bacteria from gut microbiomes, hydrothermal vents, and soil, share a common vitamin B12‐binding function. These augmented β‐jellyroll proteins bind vitamin B12 via extended loops. Our findings establish sequence‐diverse DUF4465 proteins as a widespread class of B12‐binding proteins, highlighting ...
Charlea Clarke, Michal Banasik, Rokas Juodeikis, Martin J. Warren, Richard W. Pickersgill   +4 more
wiley   +1 more source

Cherry picking in forests: A new characterization for the unrooted hybrid number of two phylogenetic trees [PDF]

Discrete Mathematics & Theoretical Computer Science
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted} phylogenetic networks,
Katharina T. Huber, Simone Linz, Vincent Moulton   +2 more
doaj   +1 more source

Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees

, 2016
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$ and without ...
AD Gordon, AV Aho, C Scornavacca, D Bryant, D Lokshtanov, F Delsuc, J Felsenstein, M Frick, M Ng, M Steel, OR Bininda-Emonds, R Diestel, T Kloks, W Maddison   +13 more
core   +3 more sources

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

Nucleic Acids Res., 2012
The data and tools in PANTHER—a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org—have undergone continual, extensive improvement for over a decade.
H. Mi, A. Muruganujan, P. Thomas
semanticscholar   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees

BMC Bioinformatics, 2012
Background We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa.
Ramu Avinash, Kahveci Tamer, Burleigh J Gordon   +2 more
doaj   +1 more source

Operads and phylogenetic trees

Theory and Applications of Categories, 2017
We construct an operad $\mathrm{Phyl}$ whose operations are the edge-labelled trees used in phylogenetics. This operad is the coproduct of $\mathrm{Com}$, the operad for commutative semigroups, and $[0,\infty)$, the operad with unary operations corresponding to nonnegative real numbers, where composition is addition.
Baez, JC, Otter, N
openaire   +4 more sources

Aging Is a Key Driver for Adult Acute Myeloid Leukemia

Aging and Cancer, EarlyView.
Acute myeloid leukemia (AML) is a classical age‐related hematologic malignancy, and a key driver of AML is aging, which profoundly regulates intrinsic factors such as genomic instability, epigenetic reprogramming, and metabolic dysregulation, and alters bone marrow microenvironment.
Rong Yin, Haojian Zhang
wiley   +1 more source

Constructing Unrooted Phylogenetic Trees with Reinforcement Learning

Studia Universitatis Babes-Bolyai: Series Informatica, 2021
With the development of sequencing technologies, more and more amounts of sequence data are available. This poses additional challenges, such as processing them is usually a complex and time-consuming computational task.
Panna LIPTÁK, Attila KISS
doaj   +1 more source

TreeCluster: Clustering biological sequences using phylogenetic trees

bioRxiv, 2019
Clustering homologous sequences based on their similarity is a problem that appears in many bioinformatics applications. The fact that sequences cluster is ultimately the result of their phylogenetic relationships.
M. Balaban, Niema Moshiri, U. Mai, Xingfan Jia, S. Mirarab   +4 more
semanticscholar   +1 more source