Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases

F Ratajczak, M Joblin, M Hildebrandt… - Nature …, 2023 - nature.com
Understanding phenotype-to-genotype relationships is a grand challenge of 21st century
biology with translational implications. The recently proposed “omnigenic” model postulates …

A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

S Ramdas, J Judd, SE Graham, S Kanoni… - The American Journal of …, 2022 - cell.com
A major challenge of genome-wide association studies (GWASs) is to translate phenotypic
associations into biological insights. Here, we integrate a large GWAS on blood lipids …

Improved functional mapping of complex trait heritability with GSA-MiXeR implicates biologically specific gene sets

O Frei, G Hindley, AA Shadrin, D van der Meer… - Nature Genetics, 2024 - nature.com
While genome-wide association studies are increasingly successful in discovering genomic
loci associated with complex human traits and disorders, the biological interpretation of …

Genetically personalised organ-specific metabolic models in health and disease

C Foguet, Y Xu, SC Ritchie, SA Lambert… - Nature …, 2022 - nature.com
Understanding how genetic variants influence disease risk and complex traits (variant-to-
function) is one of the major challenges in human genetics. Here we present a model-driven …

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

S Kanoni, SE Graham, Y Wang, I Surakka, S Ramdas… - Genome biology, 2022 - Springer
Background Genetic variants within nearly 1000 loci are known to contribute to modulation
of blood lipid levels. However, the biological pathways underlying these associations are …

De novo discovery of traits co-occurring with chronic obstructive pulmonary disease

E Golovina, T Fadason, RK Jaros… - Life Science …, 2023 - life-science-alliance.org
Chronic obstructive pulmonary disease (COPD) is a heterogeneous group of chronic lung
conditions. Genome-wide association studies have identified single-nucleotide …

Estimation of causal effects of genes on complex traits using a Bayesian-network-based framework applied to GWAS data

L Yin, Y Feng, Y Shi, A Lau, J Qiu, PC Sham… - Nature Machine …, 2024 - nature.com
Deciphering the relationships between genes and complex traits can enhance our
understanding of phenotypic variations and disease mechanisms. However, determining the …

Topology prediction and structural controllability analysis of complex networks without connection information

D Yang, Y Sun, Q Wei, H Zhang… - IEEE Transactions on …, 2021 - ieeexplore.ieee.org
In this article, we consider complex networks without connection information. The absence of
global structure induces a great obstacle in the structural controllability analysis of these …

Leveraging cell-type-specific regulatory networks to interpret genetic variants in abdominal aortic aneurysm

S Ma, X Chen, X Zhu, PS Tsao… - Proceedings of the …, 2022 - National Acad Sciences
Abdominal aortic aneurysm (AAA) is a common degenerative cardiovascular disease whose
pathobiology is not clearly understood. The cellular heterogeneity and cell-type-specific …

SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

KK Dey, S Gazal, B van de Geijn, SS Kim, J Nasser… - Cell genomics, 2022 - cell.com
We assess contributions to autoimmune disease of genes whose regulation is driven by
enhancer regions (enhancer-related) and genes that regulate other genes in trans …