Current progress and open challenges for applying deep learning across the biosciences

N Sapoval, A Aghazadeh, MG Nute… - Nature …, 2022 - nature.com
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand
challenges in computational biology: the half-century-old problem of protein structure …

Emerging roles and functional mechanisms of PIWI-interacting RNAs

X Wang, A Ramat, M Simonelig, MF Liu - Nature Reviews Molecular …, 2023 - nature.com
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with
proteins of the PIWI clade of the Argonaute family. First identified in animal germ line cells …

A genomic mutational constraint map using variation in 76,156 human genomes

S Chen, LC Francioli, JK Goodrich, RL Collins, M Kanai… - Nature, 2024 - nature.com
The depletion of disruptive variation caused by purifying natural selection (constraint) has
been widely used to investigate protein-coding genes underlying human disorders,,–, but …

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens Consortium*, RC Jones… - Science, 2022 - science.org
Molecular characterization of cell types using single-cell transcriptome sequencing is
revolutionizing cell biology and enabling new insights into the physiology of human organs …

Genome-wide prediction of disease variant effects with a deep protein language model

N Brandes, G Goldman, CH Wang, CJ Ye, V Ntranos - Nature Genetics, 2023 - nature.com
Predicting the effects of coding variants is a major challenge. While recent deep-learning
models have improved variant effect prediction accuracy, they cannot analyze all coding …

FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations

N Zhou, X Yuan, Q Du, Z Zhang, X Shi… - Nucleic acids …, 2023 - academic.oup.com
Ferroptosis is a mode of regulated cell death characterized by iron-dependent accumulation
of lipid peroxidation. It is closely linked to the pathophysiological processes in many …

Genetic diversity fuels gene discovery for tobacco and alcohol use

GRB Saunders, X Wang, F Chen, SK Jang, M Liu… - Nature, 2022 - nature.com
Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of
worldwide deaths, respectively, due largely to broad increased risk for disease and injury …

Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration

V Moiseeva, A Cisneros, V Sica, O Deryagin, Y Lai… - Nature, 2023 - nature.com
Tissue regeneration requires coordination between resident stem cells and local niche
cells,. Here we identify that senescent cells are integral components of the skeletal muscle …

The sequences of 150,119 genomes in the UK Biobank

BV Halldorsson, HP Eggertsson, KHS Moore… - Nature, 2022 - nature.com
Detailed knowledge of how diversity in the sequence of the human genome affects
phenotypic diversity depends on a comprehensive and reliable characterization of both …

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

S Chen, LC Francioli, JK Goodrich, RL Collins, M Kanai… - BioRxiv, 2022 - biorxiv.org
The depletion of disruptive variation caused by purifying natural selection (constraint) has
been widely used to investigate protein-coding genes underlying human disorders, but …