[HTML][HTML] MicrobiotaProcess: A comprehensive R package for deep mining microbiome
S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng… - The Innovation, 2023 - cell.com
The data output from microbiome research is growing at an accelerating rate, yet mining the
data quickly and efficiently remains difficult. There is still a lack of an effective data structure …
data quickly and efficiently remains difficult. There is still a lack of an effective data structure …
Using ggtree to visualize data on tree‐like structures
G Yu - Current protocols in bioinformatics, 2020 - Wiley Online Library
Ggtree is an R/Bioconductor package for visualizing tree‐like structures and associated
data. After 5 years of continual development, ggtree has been evolved as a package suite …
data. After 5 years of continual development, ggtree has been evolved as a package suite …
[HTML][HTML] Metagenomic analysis using phylogenetic placement—a review of the first decade
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and
interpret the tsunami of metagenomic sequencing data generated by high-throughput …
interpret the tsunami of metagenomic sequencing data generated by high-throughput …
Synthesis and scope of the role of postmating prezygotic isolation in speciation
MD Garlovsky, E Whittington… - Cold Spring …, 2023 - cshperspectives.cshlp.org
How barriers to gene flow arise and are maintained are key questions in evolutionary
biology. Speciation research has mainly focused on barriers that occur either before mating …
biology. Speciation research has mainly focused on barriers that occur either before mating …
ggtreeExtra: compact visualization of richly annotated phylogenetic data
S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou… - Molecular biology …, 2021 - academic.oup.com
We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic
tree in a circular or rectangular layout (https://www. bioconductor. org/packages/ggtreeExtra) …
tree in a circular or rectangular layout (https://www. bioconductor. org/packages/ggtreeExtra) …
[HTML][HTML] Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA
A new variant of Streptococcus pyogenes serotype M1 (designated 'M1UK') has been
reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase …
reported in the United Kingdom, linked with seasonal scarlet fever surges, marked increase …
[HTML][HTML] High-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …
ggmsa: A visual exploration tool for multiple sequence alignment and associated data
The identification of the conserved and variable regions in the multiple sequence alignment
(MSA) is critical to accelerating the process of understanding the function of genes. MSA …
(MSA) is critical to accelerating the process of understanding the function of genes. MSA …
Cycles of satellite and transposon evolution in Arabidopsis centromeres
Centromeres are critical for cell division, loading CENH3 or CENPA histone variant
nucleosomes, directing kinetochore formation and allowing chromosome segregation …
nucleosomes, directing kinetochore formation and allowing chromosome segregation …
[HTML][HTML] Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses
Nanoparticles for multivalent display and delivery of vaccine antigens have emerged as a
promising avenue for enhancing B cell responses to protein subunit vaccines. Here, we …
promising avenue for enhancing B cell responses to protein subunit vaccines. Here, we …