Molecular quantitative trait loci

F Aguet, K Alasoo, YI Li, A Battle, HK Im… - Nature reviews …, 2023 - nature.com
Understanding functional effects of genetic variants is one of the key challenges in human
genetics, as much of disease-associated variation is located in non-coding regions with …

Deep learning for computational biology

C Angermueller, T Pärnamaa, L Parts… - Molecular systems …, 2016 - embopress.org
Technological advances in genomics and imaging have led to an explosion of molecular
and cellular profiling data from large numbers of samples. This rapid increase in biological …

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 …

Exaggerated false positives by popular differential expression methods when analyzing human population samples

Y Li, X Ge, F Peng, W Li, JJ Li - Genome biology, 2022 - Springer
When identifying differentially expressed genes between two conditions using human
population RNA-seq samples, we found a phenomenon by permutation analysis: two …

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease

H Liu, T Doke, D Guo, X Sheng, Z Ma, J Park, HMT Vy… - Nature …, 2022 - nature.com
More than 800 million people suffer from kidney disease, yet the mechanism of kidney
dysfunction is poorly understood. In the present study, we define the genetic association with …

The GTEx Consortium atlas of genetic regulatory effects across human tissues

GTEx Consortium - Science, 2020 - science.org
The Genotype-Tissue Expression (GTEx) project was established to characterize genetic
effects on the transcriptome across human tissues and to link these regulatory mechanisms …

Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies

J Zhang, D Dutta, A Köttgen, A Tin, P Schlosser… - Nature Genetics, 2022 - nature.com
Improved understanding of genetic regulation of the proteome can facilitate identification of
the causal mechanisms for complex traits. We analyzed data on 4,657 plasma proteins from …

Genetic map** across autoimmune diseases reveals shared associations and mechanisms

MR Lincoln, N Connally, PP Axisa, C Gasperi… - Nature …, 2024 - nature.com
Autoimmune and inflammatory diseases are polygenic disorders of the immune system.
Many genomic loci harbor risk alleles for several diseases, but the limited resolution of …

Identification of constrained sequence elements across 239 primate genomes

LFK Kuderna, JC Ulirsch, S Rashid, M Ameen… - Nature, 2024 - nature.com
Noncoding DNA is central to our understanding of human gene regulation and complex
diseases,, and measuring the evolutionary sequence constraint can establish the functional …

Genome‐wide map** of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease

C Yao, G Chen, C Song, J Keefe, M Mendelson… - Nature …, 2018 - nature.com
Identifying genetic variants associated with circulating protein concentrations (protein
quantitative trait loci; pQTLs) and integrating them with variants from genome-wide …