Results 51 to 60 of about 2,113,711 (315)
Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
bioRxiv, 2020 A new generation of scalable single cell whole genome sequencing (scWGS) methods allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cell populations.
Sohrab Salehi +14 more
semanticscholar +1 more source
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations [PDF]
Bioinform., 2018 Summary TreeGrafter is a new software tool for annotating protein sequences using pre‐annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily.
Haiming Tang, R. Finn, P. Thomas
semanticscholar +1 more source
phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)
bioRxiv, 2023 Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of ...
L. Revell
semanticscholar +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 +13 more
core +3 more sources
Novel metric for hyperbolic phylogenetic tree embeddings
bioRxiv, 2020 Advances in experimental technologies such as DNA sequencing have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of ...
Hirotaka Matsumoto +2 more
semanticscholar +1 more source
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
Nucleic Acids Res., 2019 The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models.
C. J. Norsigian +6 more
semanticscholar +1 more source
Molecular bases of circadian magnesium rhythms across eukaryotes
FEBS Letters, EarlyView.Circadian rhythms in intracellular [Mg2+] exist across eukaryotic kingdoms. Central roles for Mg2+ in metabolism suggest that Mg2+ rhythms could regulate daily cellular energy and metabolism. In this Perspective paper, we propose that ancestral prokaryotic transport proteins could be responsible for mediating Mg2+ rhythms and posit a feedback model ...
Helen K. Feord, Gerben van Ooijen
wiley +1 more source
Darwintree: A Molecular Data Analysis and Application Environment for Phylogenetic Study
Data Science Journal, 2015 DarwinTree (http://www.darwintree.cn) provides an integrated bioinformatics platform that supports all phases of the analytical pathway for phylogenetic study from data collections, phylogenetic tree constructions, visualization of the tree of life, and ...
Zhen Meng +6 more
doaj +1 more source
Molecular Oncology, EarlyView.In this exploratory study, we investigated the relationship between the gut microbiota and outcome in patients with metastatic hormone receptor‐positive breast cancer, treated in a randomized clinical trial with chemotherapy alone or chemotherapy in combination with immune checkpoint blockade.
Andreas Ullern +7 more
wiley +1 more source
Protein O‐glycosylation in the Bacteroidota phylum
FEBS Open Bio, EarlyView.Species of the Bacteroidota phylum exhibit a unique O‐glycosylation system. It modifies noncytoplasmic proteins on a specific amino acid motif with a shared glycan core but a species‐specific outer glycan. A locus of multiple glycosyltransferases responsible for the synthesis of the outer glycan has been identified.
Lonneke Hoffmanns +2 more
wiley +1 more source