Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Enablers and challenges of spatial omics, a melting pot of technologies

T Alexandrov, J Saez‐Rodriguez… - Molecular Systems …, 2023 - embopress.org
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of
publications presenting novel methods for obtaining spatially resolved information for any …

LIANA+ provides an all-in-one framework for cell–cell communication inference

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez-Mier… - Nature Cell …, 2024 - nature.com
The growing availability of single-cell and spatially resolved transcriptomics has led to the
development of many approaches to infer cell–cell communication, each capturing only a …

Advancing targeted protein degradation via multiomics profiling and artificial intelligence

M Duran-Frigola, M Cigler… - Journal of the American …, 2023 - ACS Publications
Only around 20% of the human proteome is considered to be druggable with small-molecule
antagonists. This leaves some of the most compelling therapeutic targets outside the reach …

The conundrum of Helicobacter pylori-associated apoptosis in gastric cancer

MCC Lim, P Jantaree, M Naumann - Trends in Cancer, 2023 - cell.com
Helicobacter pylori is a human microbial pathogen that colonizes the gastric epithelium and
causes type B gastritis with varying degrees of active inflammatory infiltrates. The underlying …

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions

E Farr, D Dimitrov, C Schmidt, D Turei… - Briefings in …, 2024 - academic.oup.com
From the catalytic breakdown of nutrients to signaling, interactions between metabolites and
proteins play an essential role in cellular function. An important case is cell–cell …

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system

PSL Schäfer, D Dimitrov, EJ Villablanca… - Nature …, 2024 - nature.com
The immune system comprises diverse specialized cell types that cooperate to defend the
host against a wide range of pathogenic threats. Recent advancements in single-cell and …

Current and future directions in network biology

M Zitnik, MM Li, A Wells, K Glass, DM Gysi… - arXiv preprint arXiv …, 2023 - arxiv.org
Network biology, an interdisciplinary field at the intersection of computational and biological
sciences, is critical for deepening understanding of cellular functioning and disease. While …

LIANA+: an all-in-one cell-cell communication framework

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez Mier… - BioRxiv, 2023 - biorxiv.org
The growing availability of single-cell and spatially-resolved transcriptomics has led to the
rapidly growing popularity of methods to infer cell-cell communication. Many approaches …

Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition

ML Burtscher, S Gade… - Molecular Systems …, 2024 - embopress.org
Complex disease phenotypes often span multiple molecular processes. Functional
characterization of these processes can shed light on disease mechanisms and drug effects …