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 …

A biologist's guide to planning and performing quantitative bioimaging experiments

RA Senft, B Diaz-Rohrer, P Colarusso, L Swift… - PLoS …, 2023 - journals.plos.org
Technological advancements in biology and microscopy have empowered a transition from
bioimaging as an observational method to a quantitative one. However, as biologists are …

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 …

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 …

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

D Larivière, L Abueg, N Brajuka, C Gallardo-Alba… - Nature …, 2024 - nature.com
The Earth BioGenome Project aims to produce reference genomes for all~ 1.8 million known
eukaryotic species over the next decade 1–4. Achieving this goal will require the current …

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 …

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 …

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

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

hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS)

HE Salapa, PA Thibault, CD Libner, Y Ding… - Nature …, 2024 - nature.com
Neurodegeneration is the primary driver of disease progression in multiple sclerosis (MS)
resulting in permanent disability, creating an urgent need to discover its underlying …

SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing

S Pan, XM Zhao, LP Coelho - Bioinformatics, 2023 - academic.oup.com
Motivation Metagenomic binning methods to reconstruct metagenome-assembled genomes
(MAGs) from environmental samples have been widely used in large-scale metagenomic …