Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications

M Su, T Pan, QZ Chen, WW Zhou, Y Gong, G Xu… - Military Medical …, 2022 - Springer
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has
advanced our understanding of the pathogenesis of disease and provided valuable insights …

Tumor heterogeneity: preclinical models, emerging technologies, and future applications

M Proietto, M Crippa, C Damiani, V Pasquale… - Frontiers in …, 2023 - frontiersin.org
Heterogeneity describes the differences among cancer cells within and between tumors. It
refers to cancer cells describing variations in morphology, transcriptional profiles …

Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

A Wagner, C Wang, J Fessler, D DeTomaso… - Cell, 2021 - cell.com
Metabolism is a major regulator of immune cell function, but it remains difficult to study the
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …

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 …

Machine and deep learning meet genome-scale metabolic modeling

G Zampieri, S Vijayakumar, E Yaneske… - PLoS computational …, 2019 - journals.plos.org
Omic data analysis is steadily growing as a driver of basic and applied molecular biology
research. Core to the interpretation of complex and heterogeneous biological phenotypes …

A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data

N Alghamdi, W Chang, P Dang, X Lu, C Wan… - Genome …, 2021 - genome.cshlp.org
The metabolic heterogeneity and metabolic interplay between cells are known as significant
contributors to disease treatment resistance. However, with the lack of a mature high …

Decoding aging hallmarks at the single-cell level

S Ma, X Chi, Y Cai, Z Ji, S Wang, J Ren… - Annual Review of …, 2023 - annualreviews.org
Organismal aging exhibits wide-ranging hallmarks in divergent cell types across tissues,
organs, and systems. The advancement of single-cell technologies and generation of rich …

Deciphering metabolic heterogeneity by single-cell analysis

TMJ Evers, M Hochane, SJ Tans, RMA Heeren… - 2019 - ACS Publications
Single-cell analysis provides insights into cellular heterogeneity and dynamics of individual
cells. This Feature highlights recent developments in key analytical techniques suited for …

[HTML][HTML] Toward modeling metabolic state from single-cell transcriptomics

K Hrovatin, DS Fischer, FJ Theis - Molecular metabolism, 2022 - Elsevier
Background Single-cell metabolic studies bring new insights into cellular function, which can
often not be captured on other omics layers. Metabolic information has wide applicability …

A review of computational strategies for denoising and imputation of single-cell transcriptomic data

L Patruno, D Maspero, F Craighero… - Briefings in …, 2021 - academic.oup.com
Motivation The advancements of single-cell sequencing methods have paved the way for
the characterization of cellular states at unprecedented resolution, revolutionizing the …