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 …
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 …
publications presenting novel methods for obtaining spatially resolved information for any …
LIANA+ provides an all-in-one framework for cell–cell communication inference
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 …
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 …
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 …
causes type B gastritis with varying degrees of active inflammatory infiltrates. The underlying …
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions
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 …
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
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 …
host against a wide range of pathogenic threats. Recent advancements in single-cell and …
Current and future directions in network biology
Network biology, an interdisciplinary field at the intersection of computational and biological
sciences, is critical for deepening understanding of cellular functioning and disease. While …
sciences, is critical for deepening understanding of cellular functioning and disease. While …
LIANA+: an all-in-one cell-cell communication framework
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 …
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 …
characterization of these processes can shed light on disease mechanisms and drug effects …