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 …

Immune mechanisms linking metabolic injury to inflammation and fibrosis in fatty liver disease–novel insights into cellular communication circuits

M Peiseler, R Schwabe, J Hampe, P Kubes… - Journal of …, 2022 - Elsevier
Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disease and is
emerging as the leading cause of cirrhosis, liver transplantation and hepatocellular …

[HTML][HTML] Small molecule metabolites: discovery of biomarkers and therapeutic targets

S Qiu, Y Cai, H Yao, C Lin, Y Xie, S Tang… - Signal Transduction and …, 2023 - nature.com
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite
accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite …

The pentose phosphate pathway in health and disease

T TeSlaa, M Ralser, J Fan, JD Rabinowitz - Nature metabolism, 2023 - nature.com
The pentose phosphate pathway (PPP) is a glucose-oxidizing pathway that runs in parallel
to upper glycolysis to produce ribose 5-phosphate and nicotinamide adenine dinucleotide …

[HTML][HTML] Unbiased spatial proteomics with single-cell resolution in tissues

A Mund, AD Brunner, M Mann - Molecular Cell, 2022 - cell.com
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify
the entire complement of proteins in cells or tissues. Here, we review challenges and recent …

CD8+ T cell metabolism in infection and cancer

M Reina-Campos, NE Scharping… - Nature Reviews …, 2021 - nature.com
Cytotoxic CD8+ T cells play a key role in the elimination of intracellular infections and
malignant cells and can provide long-term protective immunity. In the response to infection …

SODB facilitates comprehensive exploration of spatial omics data

Z Yuan, W Pan, X Zhao, F Zhao, Z Xu, X Li, Y Zhao… - Nature …, 2023 - nature.com
Spatial omics technologies generate wealthy but highly complex datasets. Here we present
Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources …

[HTML][HTML] Image-based profiling for drug discovery: due for a machine-learning upgrade?

SN Chandrasekaran, H Ceulemans, JD Boyd… - Nature Reviews Drug …, 2021 - nature.com
Image-based profiling is a maturing strategy by which the rich information present in
biological images is reduced to a multidimensional profile, a collection of extracted image …

Artificial intelligence-based multi-omics analysis fuels cancer precision medicine

X He, X Liu, F Zuo, H Shi, J Jing - Seminars in Cancer Biology, 2023 - Elsevier
With biotechnological advancements, innovative omics technologies are constantly
emerging that have enabled researchers to access multi-layer information from the genome …

[HTML][HTML] Analyzing cell-type-specific dynamics of metabolism in kidney repair

G Wang, B Heijs, S Kostidis, A Mahfouz… - Nature …, 2022 - nature.com
A common drawback of metabolic analyses of complex biological samples is the inability to
consider cell-to-cell heterogeneity in the context of an organ or tissue. To overcome this …