Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants

A Wang, J Shen, AA Rodriguez, EJ Saunders, F Chen… - Nature …, 2023 - nature.com
The transferability and clinical value of genetic risk scores (GRSs) across populations
remain limited due to an imbalance in genetic studies across ancestrally diverse …

Big data and deep learning for RNA biology

H Hwang, H Jeon, N Yeo, D Baek - Experimental & Molecular Medicine, 2024 - nature.com
The exponential growth of big data in RNA biology (RB) has led to the development of deep
learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL …

Single-nucleotide variant calling in single-cell sequencing data with Monopogen

J Dou, Y Tan, KH Kock, J Wang, X Cheng, LM Tan… - Nature …, 2024 - nature.com
Single-cell omics technologies enable molecular characterization of diverse cell types and
states, but how the resulting transcriptional and epigenetic profiles depend on the cell's …

Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation

KL Kim, GJ Rahme, VY Goel, CA El Farran, AS Hansen… - Molecular Cell, 2024 - cell.com
Enhancer-gene communication is dependent on topologically associating domains (TADs)
and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying …

Epigenomic insights into common human disease pathology

CG Bell - Cellular and Molecular Life Sciences, 2024 - Springer
The epigenome—the chemical modifications and chromatin-related packaging of the
genome—enables the same genetic template to be activated or repressed in different …

Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement

PA Audano, CR Beck - Genome research, 2024 - genome.cshlp.org
High-quality genome assemblies and sophisticated algorithms have increased sensitivity for
a wide range of variant types, and breakpoint accuracy for structural variants (SVs,≥ 50 bp) …

Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning

A Hawkins-Hooker, G Visonà, T Narendra… - Nature …, 2023 - nature.com
Epigenetic modifications are dynamic mechanisms involved in the regulation of gene
expression. Unlike the DNA sequence, epigenetic patterns vary not only between …

Single-cell genomics and regulatory networks for 388 human brains

PS Emani, JJ Liu, D Clarke, M Jensen, J Warrell… - Science, 2024 - science.org
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the
brain. Yet little is understood about how genetic variants influence cell-level gene …

Haplotype Function Score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

W Song, Y Shi, GN Lin - Elife, 2024 - elifesciences.org
We propose a new framework for human genetic association studies: at each locus, a deep
learning model (in this study, Sei) is used to calculate the functional genomic activity score …

Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data

D Han, Y Li, L Wang, X Liang, Y Miao… - Briefings in …, 2024 - academic.oup.com
Non-coding variants associated with complex traits can alter the motifs of transcription factor
(TF)–deoxyribonucleic acid binding. Although many computational models have been …