A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

A Hakimzadeh, A Abdala Asbun… - Molecular Ecology …, 2024 - Wiley Online Library
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for
monitoring biodiversity in ecology. However, taxa identifications produced through …

From multi-omics approaches to personalized medicine in myocardial infarction

C Zhan, T Tang, E Wu, Y Zhang, M He, R Wu… - Frontiers in …, 2023 - frontiersin.org
Myocardial infarction (MI) is a prevalent cardiovascular disease characterized by myocardial
necrosis resulting from coronary artery ischemia and hypoxia, which can lead to severe …

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Nucleic acids research, 2024 - academic.oup.com
Abstract Galaxy (https://galaxyproject. org) is deployed globally, predominantly through free-
to-use services, supporting user-driven research that broadens in scope each year. Users …

OME-Zarr: a cloud-optimized bioimaging file format with international community support

J Moore, D Basurto-Lozada, S Besson… - Histochemistry and Cell …, 2023 - Springer
A growing community is constructing a next-generation file format (NGFF) for bioimaging to
overcome problems of scalability and heterogeneity. Organized by the Open Microscopy …

Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits

DJ Beerling, DZ Epihov, IB Kantola, MD Masters… - Proceedings of the …, 2024 - pnas.org
Terrestrial enhanced weathering (EW) of silicate rocks, such as crushed basalt, on
farmlands is a promising scalable atmospheric carbon dioxide removal (CDR) strategy that …

Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets

NA O'Leary, E Cox, JB Holmes, WR Anderson, R Falk… - Scientific data, 2024 - nature.com
To explore complex biological questions, it is often necessary to access various data types
from public data repositories. As the volume and complexity of biological sequence data …

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023

J Alvarez-Jarreta, B Amos, C Aurrecoechea… - Nucleic acids …, 2024 - academic.oup.com
Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB,
https://veupathdb. org) is a Bioinformatics Resource Center funded by the National Institutes …

Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition

SE Murphy, AN Boettiger - Nature genetics, 2024 - nature.com
Polycomb group proteins have a critical role in silencing transcription during development. It
is commonly proposed that Polycomb-dependent changes in genome folding, which …

Kunitz-type protease inhibitor TFPI2 remodels stemness and immunosuppressive tumor microenvironment in glioblastoma

L Pang, M Dunterman, S Guo, F Khan, Y Liu… - Nature …, 2023 - nature.com
Glioblastoma (GBM) tumors consist of multiple cell populations, including self-renewing
glioblastoma stem cells (GSCs) and immunosuppressive microglia. Here we identified …

Bacterial cGAS senses a viral RNA to initiate immunity

DV Banh, CG Roberts, A Morales-Amador, BA Berryhill… - Nature, 2023 - nature.com
Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes
from viral (phage) attack through the production of cyclic oligonucleotides, which activate …