Hidden network generating rules from partially observed complex networks

R Yang, F Sala, P Bogdan - Communications Physics, 2021 - nature.com
Complex biological, neuroscience, geoscience and social networks exhibit heterogeneous
self-similar higher order topological structures that are usually characterized as being …

Map** robust multiscale communities in chromosome contact networks

A Holmgren, D Bernenko, L Lizana - Scientific Reports, 2023 - nature.com
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome
capture methods such as Hi-C that measure the contact frequencies between all DNA …

Effective model of protein-mediated interactions in chromatin

F Borando, G Tiana - Physical Review E, 2024 - APS
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in
the nucleus, where they are responsible for the structuring of chromatin. We show through …

Towards forecasting epigenetic repression

MJ Lundkvist - 2024 - diva-portal.org
Multicellular organisms form many different cell types from one genome, which requires
differential gene activity. The Polycomb system upholds the correct gene expression …

Evidence of Kolmogorov like scalings and multifractality in the rainfall events

J GhoshDastider, D Pal, PK Mishra - arxiv preprint arxiv:2405.03463, 2024 - arxiv.org
In this paper we present a detailed statistical analysis related to the characterization of the
spatial and temporal fluctuations present in the rainfall patterns of North-East region …

ENT3C: an entropy-based similarity measure for Hi-C and micro-C derived contact matrices

X Lainscsek, L Taher - NAR Genomics and Bioinformatics, 2024 - academic.oup.com
Hi-C and micro-C sequencing have shed light on the profound importance of 3D genome
organization in cellular function by probing 3D contact frequencies across the linear …

Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA

X Lainscsek, L Taher - Briefings in Bioinformatics, 2023 - academic.oup.com
Abstract Three-dimensional (3D) genome architecture is characterized by multi-scale
patterns and plays an essential role in gene regulation. Chromatin conformation capturing …

Finding a target on DNA: interplay between the genomic sequence and 3D structure

L Hedström - 2024 - diva-portal.org
Cells are complex systems of interconnected machinery that maintains, repairs and furthers
the growth of themselves. In the center lies the instructions that coordinate it all—the DNA …

[PDF][PDF] Predicting 3D genome architecture directly from the nucleotide sequence with DNA-DDA

X Lainscsek, L Taher - 2022 - researchgate.net
The hierarchical three-dimensional (3D) architecture of the genome allows linearly distal loci
to interact with one another, thereby impacting genome function. Chromosome conformation …