Hypergraph geometry reflects higher-order dynamics in protein interaction networks

KA Murgas, E Saucan, R Sandhu - Scientific Reports, 2022 - nature.com
Protein interactions form a complex dynamic molecular system that shapes cell phenotype
and function; in this regard, network analysis is a powerful tool for studying the dynamics of …

Discrete curvature on graphs from the effective resistance

K Devriendt, R Lambiotte - Journal of Physics: Complexity, 2022 - iopscience.iop.org
This article introduces a new approach to discrete curvature based on the concept of
effective resistances. We propose a curvature on the nodes and links of a graph and present …

Multi-scale geometric network analysis identifies melanoma immunotherapy response gene modules

KA Murgas, R Elkin, N Riaz, E Saucan, JO Deasy… - Scientific Reports, 2024 - nature.com
Melanoma response to immune-modulating therapy remains incompletely characterized at
the molecular level. In this study, we assess melanoma immunotherapy response using a …

[HTML][HTML] Curvature-enhanced graph convolutional network for biomolecular interaction prediction

C Shen, P Ding, J Wee, J Bi, J Luo, K Xia - Computational and Structural …, 2024 - Elsevier
Geometric deep learning has demonstrated a great potential in non-Euclidean data
analysis. The incorporation of geometric insights into learning architecture is vital to its …

Inferring functional communities from partially observed biological networks exploiting geometric topology and side information

J Sia, W Zhang, E Jonckheere, D Cook, P Bogdan - Scientific Reports, 2022 - nature.com
Cellular biological networks represent the molecular interactions that shape function of living
cells. Uncovering the organization of a biological network requires efficient and accurate …

Graph geometry from effective resistances

K Devriendt - 2022 - ora.ox.ac.uk
The main subject of this thesis is the effective resistance—a measure of distance between
the nodes of a graph which reflects how close or well-connected two nodes are, taking into …

[图书][B] Classical and Discrete Differential Geometry: Theory, Applications and Algorithms

DX Gu, E Saucan - 2023 - taylorfrancis.com
This book introduces differential geometry and cutting-edge findings from the discipline by
incorporating both classical approaches and modern discrete differential geometry across …

Beyond pairwise interactions: Higher-order dynamics in protein interaction networks

KA Murgas, E Saucan, R Sandhu - bioRxiv, 2022 - biorxiv.org
Protein interactions form a complex dynamic system that shapes cell phenotype and
function; in this regard, network analysis is a powerful tool for studying the dynamics of …

[PDF][PDF] Higher-Order Dynamics in Protein Interaction Networks

KA Murgas, R Sandhu - q-bio.org
Network analysis is a powerful tool for studying the dynamics of cellular processes. Graph-
based models are limited, however, in that these models consider only pairwise …