Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms

L Zhao, F Gao, S Gao, Y Liang, H Long, Z Lv… - Science China Life …, 2021 - Springer
Evolutionary developmental biology, or Evo-Devo for short, has become an established field
that, broadly speaking, seeks to understand how changes in development drive major …

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics

D Podlesny, M Durdevic, S Paramsothy… - Cell Reports …, 2022 - cell.com
Fecal microbiota transplantation (FMT) is a promising therapeutic approach for microbiota-
associated pathologies, but our understanding of the post-FMT microbiome assembly …

Codon usage bias and environmental adaptation in microbial organisms

D Arella, M Dilucca, A Giansanti - Molecular Genetics and Genomics, 2021 - Springer
In each genome, synonymous codons are used with different frequencies; this general
phenomenon is known as codon usage bias. It has been previously recognised that codon …

[HTML][HTML] Strain inheritance and neonatal gut microbiota development: a meta-analysis

D Podlesny, WF Fricke - International Journal of Medical Microbiology, 2021 - Elsevier
As many inflammatory and metabolic disorders have been associated with structural deficits
of the human gut microbiota, the principles and mechanisms that govern its initialization and …

Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer

Y Bromberg, AA Aptekmann, Y Mahlich, L Cook… - Science …, 2022 - science.org
Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-
guided sequence analysis of proteins, we explored the patterns of evolution of enzymes …

Functional comparison of metabolic networks across species

C Ramon, J Stelling - Nature Communications, 2023 - nature.com
Metabolic phenotypes are pivotal for many areas, but disentangling how evolutionary history
and environmental adaptation shape these phenotypes is an open problem. Especially for …

HFSP: high speed homology-driven function annotation of proteins

Y Mahlich, M Steinegger, B Rost, Y Bromberg - Bioinformatics, 2018 - academic.oup.com
Motivation The rapid drop in sequencing costs has produced many more (predicted) protein
sequences than can feasibly be functionally annotated with wet-lab experiments. Thus …

Computational analysis on the dissemination of non-B DNA structural motifs in promoter regions of 1180 cellular genomes

VR Yella, A Vanaja - Biochimie, 2023 - Elsevier
The promoter regions of gene regulation are under evolutionary constraints and earlier
studies uncovered that they are characterized by enrichment of functional non-B DNA …

Assembling bacterial puzzles: piecing together functions into microbial pathways

HC Chung, I Friedberg… - NAR Genomics and …, 2024 - academic.oup.com
Functional metagenomics enables the study of unexplored bacterial diversity, gene families,
and pathways essential to microbial communities. However, discovering biological insights …

The Diverse Mycorrizal Morphology of Rhododendron dauricum, the Fungal Communities Structure and Dynamics from the Mycorrhizosphere

J Liu, Y Xu, YJ Si, BQ Li, P Chen, LL Wu, P Guo, RQ Ji - Journal of Fungi, 2024 - mdpi.com
It is generally believed that mycorrhiza is a microecosystem composed of mycorrhizal fungi,
host plants and other microscopic organisms. The mycorrhiza of Rhododendron dauricum is …