Genome-resolved metagenomics: a game changer for microbiome medicine

N Kim, J Ma, W Kim, J Kim, P Belenky… - Experimental & Molecular …, 2024 - nature.com
Recent substantial evidence implicating commensal bacteria in human diseases has given
rise to a new domain in biomedical research: microbiome medicine. This emerging field …

[HTML][HTML] Tau PTM profiles identify patient heterogeneity and stages of Alzheimer's disease

H Wesseling, W Mair, M Kumar, CN Schlaffner, S Tang… - Cell, 2020 - cell.com
To elucidate the role of Tau isoforms and post-translational modification (PTM) stoichiometry
in Alzheimer's disease (AD), we generated a high-resolution quantitative proteomics map of …

Evolution of buffering in a genetic circuit controlling plant stem cell proliferation

D Rodriguez-Leal, C Xu, CT Kwon, C Soyars… - Nature …, 2019 - nature.com
Precise control of plant stem cell proliferation is necessary for the continuous and
reproducible development of plant organs,. The peptide ligand CLAVATA3 (CLV3) and its …

MCUB regulates the molecular composition of the mitochondrial calcium uniporter channel to limit mitochondrial calcium overload during stress

JP Lambert, TS Luongo, D Tomar, P Jadiya, E Gao… - Circulation, 2019 - Am Heart Assoc
Background: The mitochondrial calcium uniporter (mtCU) is an≈ 700-kD multisubunit
channel residing in the inner mitochondrial membrane required for mitochondrial Ca2+ …

Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation

JL Steenwyk, A Rokas - Frontiers in microbiology, 2018 - frontiersin.org
In recent years, copy number (CN) variation has emerged as a new and significant source of
genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants …

Hypoxia Inducible Factor (HIF) transcription factor family expansion, diversification, divergence and selection in eukaryotes

AM Graham, JS Presnell - PloS one, 2017 - journals.plos.org
Hypoxia inducible factor (HIF) transcription factors are crucial for regulating a variety of
cellular activities in response to oxygen stress (hypoxia). In this study, we determine the …

The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction

M Stamboulian, RF Guerrero, MW Hahn… - …, 2020 - academic.oup.com
Motivation The computational prediction of gene function is a key step in making full use of
newly sequenced genomes. Function is generally predicted by transferring annotations from …

Pairwise comparisons across species are problematic when analyzing functional genomic data

CW Dunn, F Zapata, C Munro… - Proceedings of the …, 2018 - National Acad Sciences
There is considerable interest in comparing functional genomic data across species. One
goal of such work is to provide an integrated understanding of genome and phenotype …

Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway

BT Piatkowski, K Imwattana, EA Tripp… - Molecular Phylogenetics …, 2020 - Elsevier
The flavonoids, one of the largest classes of plant secondary metabolites, are found in
lineages that span the land plant phylogeny and play important roles in stress responses …

Not Only for Egg Yolk—Functional and Evolutionary Insights from Expression, Selection, and Structural Analyses of Formica Ant Vitellogenins

C Morandin, H Havukainen, J Kulmuni… - Molecular biology …, 2014 - academic.oup.com
Vitellogenin (Vg), a storage protein, has been extensively studied for its egg-yolk precursor
role, and it has been suggested to be fundamentally involved in caste differences in social …