From time-series transcriptomics to gene regulatory networks: A review on inference methods

M Marku, V Pancaldi - PLoS computational biology, 2023 - journals.plos.org
Inference of gene regulatory networks has been an active area of research for around 20
years, leading to the development of sophisticated inference algorithms based on a variety …

Combinatorial transcriptomic and genetic dissection of insulin/IGF‐1 signaling‐regulated longevity in Caenorhabditis elegans

S Ham, SS Kim, S Park, HC Kwon, SG Ha, Y Bae… - Aging …, 2024 - Wiley Online Library
Classical genetic analysis is invaluable for understanding the genetic interactions
underlying specific phenotypes, but requires laborious and subjective experiments to …

Cell-specific gene networks and drivers in rheumatoid arthritis synovial tissues

A Pelissier, T Laragione, PS Gulko… - Frontiers in …, 2024 - frontiersin.org
Rheumatoid arthritis (RA) is a common autoimmune and inflammatory disease
characterized by inflammation and hyperplasia of the synovial tissues. RA pathogenesis …

Identification of SPP1 + macrophages as an immune suppressor in hepatocellular carcinoma using single-cell and bulk transcriptomics

H **, W Kim, M Yuan, X Li, H Yang, M Li… - Frontiers in …, 2024 - frontiersin.org
Introduction Macrophages and T cells play crucial roles in liver physiology, but their
functional diversity in hepatocellular carcinoma (HCC) remains largely unknown. Methods …

[HTML][HTML] Gene network analyses identify co-regulated transcription factors and BACH1 as a key driver in rheumatoid arthritis fibroblast-like synoviocytes

A Pelissier, T Laragione, C Harris, MR Martínez… - …, 2024 - pmc.ncbi.nlm.nih.gov
RNA-sequencing and differential gene expression studies have significantly advanced our
understanding of pathogenic pathways underlying Rheumatoid Arthritis (RA). Yet, little is …

[HTML][HTML] The multiple dimensions of networks in cancer: A perspective

C Axenie, R Bauer, MR Martínez - Symmetry, 2021 - mdpi.com
This perspective article gathers the latest developments in mathematical and computational
oncology tools that exploit network approaches for the mathematical modelling, analysis …

Stochastic Modeling of the Humoral Immune Response: A Multi-scale Challenge

A Pelissier - 2023 - research-collection.ethz.ch
Understanding the mechanism underlying the immune system is crucial for tackling immune-
related diseases like cancer and autoimmune conditions. In this PhD thesis we address the …

[PDF][PDF] Building of cancer type-specific multi-layered molecular and patient similarity networks

M Manica, J Cadow, M Petrizzelli, A Zinovyev, D Cirillo - mpetrizzelli.github.io
Molecular and patient networks for specific cancertype enables an unbiased understanding
of disease mechanisms. We report the analysis performed on multiple omic levels for a …

[PDF][PDF] The Multiple Dimensions of Networks in Cancer: A Perspective. Symmetry 2021, 13, 1559

C Axenie, R Bauer, M Rodríguez Martínez - 2021 - academia.edu
This perspective article gathers the latest developments in mathematical and computational
oncology tools that exploit network approaches for the mathematical modelling, analysis …