Network models of chromatin structure

V Pancaldi - Current Opinion in Genetics & Development, 2023 - Elsevier
Highlights•Networks are a useful framework to study chromatin structure
datasets.•Chromatin networks can be used to visualize the 3D epigenome and integrate …

[HTML][HTML] From DNA human sequence to the chromatin higher order organisation and its biological meaning: using biomolecular interaction networks to understand the …

M Chiliński, K Sengupta, D Plewczynski - Seminars in cell & developmental …, 2022 - Elsevier
The three-dimensional structure of the human genome has been proven to have a
significant functional impact on gene expression. The high-order spatial chromatin is …

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

V Robin, A Bodein, MP Scott-Boyer… - Frontiers in Molecular …, 2022 - frontiersin.org
At the heart of the cellular machinery through the regulation of cellular functions, protein–
protein interactions (PPIs) have a significant role. PPIs can be analyzed with network …

Assessment of GO-based protein interaction affinities in the large-scale human–coronavirus family interactome

SS Bandyopadhyay, AK Halder, S Saha, P Chatterjee… - Vaccines, 2023 - mdpi.com
SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host
proteins. As a result, identifying virus and host protein-protein interactions could help …

PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms

K Sengupta, S Saha, AK Halder, P Chatterjee… - Frontiers in …, 2022 - frontiersin.org
Protein function prediction is gradually emerging as an essential field in biological and
computational studies. Though the latter has clinched a significant footprint, it has been …

[HTML][HTML] Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

K Sengupta, M Denkiewicz, M Chiliński… - Computational and …, 2022 - Elsevier
The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The
DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of …

FuzzyPPI: Large-Scale Interaction of Human Proteome at Fuzzy Semantic Space

AK Halder, SS Bandyopadhyay… - … Transactions on Big …, 2024 - ieeexplore.ieee.org
Large-scale protein-protein interaction (PPI) network of an organism provides key insights
into its cellular and molecular functionalities, signaling pathways and underlying disease …

JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment

AK Halder, SS Bandyopadhyay… - IEEE/ACM …, 2020 - ieeexplore.ieee.org
Over the years, several methods have been proposed for the computational PPI prediction
with different performance evaluation strategies. While attempting to benchmark …

[PDF][PDF] 企业股东网络对盈余管理行为影响的研究

孙宸, 庄新田 - 管理学报, 2023 - manu68.magtech.com.cn
基于社会网络理论, 以2013~ 2019 年我国沪深A 股上市公司为研究对象, 分析了股东网络对企业
盈余管理行为的影响. 研究结果发现, 股东网络能带来信息优势, 可以抑制企业盈余管理行为; …

Exploration of the inhibitory mechanism of PC190723 on FtsZ protein by molecular dynamics simulation

Y Ma, S Zhang, L Zhou, L Zhang, P Zhang… - Journal of Molecular …, 2022 - Elsevier
Bacterial resistance caused by widespread use and abuse of antibiotics is threatening
human health, and the development of new antibacterial agents with novel antibacterial …