Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

A compendium of uniformly processed human gene expression and splicing quantitative trait loci

N Kerimov, JD Hayhurst, K Peikova, JR Manning… - Nature …, 2021 - nature.com
Many gene expression quantitative trait locus (eQTL) studies have published their summary
statistics, which can be used to gain insight into complex human traits by downstream …

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

G Eraslan, E Drokhlyansky, S Anand, E Fiskin… - Science, 2022 - science.org
Understanding gene function and regulation in homeostasis and disease requires
knowledge of the cellular and tissue contexts in which genes are expressed. Here, we …

Single-cell eQTL models reveal dynamic T cell state dependence of disease loci

A Nathan, S Asgari, K Ishigaki, C Valencia, T Amariuta… - Nature, 2022 - nature.com
Non-coding genetic variants may cause disease by modulating gene expression. However,
identifying these expression quantitative trait loci (eQTLs) is complicated by differences in …

From GWAS to function: using functional genomics to identify the mechanisms underlying complex diseases

E Cano-Gamez, G Trynka - Frontiers in genetics, 2020 - frontiersin.org
Genome-wide association studies (GWAS) have successfully mapped thousands of loci
associated with complex traits. These associations could reveal the molecular mechanisms …

Brain Chimeroids reveal individual susceptibility to neurotoxic triggers

N Antón-Bolaños, I Faravelli, T Faits, S Andreadis… - Nature, 2024 - nature.com
Interindividual genetic variation affects the susceptibility to and progression of many
diseases,. However, efforts to study how individual human brains differ in normal …

Principles and challenges of modeling temporal and spatial omics data

B Velten, O Stegle - Nature Methods, 2023 - nature.com
Studies with temporal or spatial resolution are crucial to understand the molecular dynamics
and spatial dependencies underlying a biological process or system. With advances in high …

Where are the disease-associated eQTLs?

BD Umans, A Battle, Y Gilad - Trends in Genetics, 2021 - cell.com
Most disease-associated variants, although located in putatively regulatory regions, do not
have detectable effects on gene expression. One explanation could be that we have not …

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

AA Pollen, U Kilik, CB Lowe, JG Camp - Nature Reviews Genetics, 2023 - nature.com
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled
humans to colonize diverse habitats, develop extraordinary technologies and reshape the …