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 …

A pathology foundation model for cancer diagnosis and prognosis prediction

X Wang, J Zhao, E Marostica, W Yuan, J **, J Zhang… - Nature, 2024 - nature.com
Histopathology image evaluation is indispensable for cancer diagnoses and subtype
classification. Standard artificial intelligence methods for histopathology image analyses …

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 …

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 …

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 …

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 …

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 …

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation

J Linder, D Srivastava, H Yuan, V Agarwal, DR Kelley - Nature Genetics, 2025 - nature.com
Sequence-based machine-learning models trained on genomics data improve genetic
variant interpretation by providing functional predictions describing their impact on the cis …