Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning

C Zuo, Y Zhang, C Cao, J Feng, M Jiao… - Nature …, 2022 - nature.com
Spatially resolved transcriptomics (SRT) technology enables us to gain novel insights into
tissue architecture and cell development, especially in tumors. However, lacking …

Molecular biomarkers, network biomarkers, and dynamic network biomarkers for diagnosis and prediction of rare diseases

S Tang, K Yuan, L Chen - Fundamental Research, 2022 - Elsevier
The difficulty of converting scientific research findings into novel pharmacological treatments
for rare and life-threatening diseases is enormous. Biomarkers related to multiple biological …

New Possibilities for Evaluating the Development of Age-Related Pathologies Using the Dynamical Network Biomarkers Theory

K Akagi, K Koizumi, M Kadowaki, I Kitajima, S Saito - Cells, 2023 - mdpi.com
Aging is the slowest process in a living organism. During this process, mortality rate
increases exponentially due to the accumulation of damage at the cellular level. Cellular …

Oxidative stress-triggered Wnt signaling perturbation characterizes the tipping point of lung adeno-to-squamous transdifferentiation

Z Fang, X Han, Y Chen, X Tong, Y Xue, S Yao… - … and Targeted Therapy, 2023 - nature.com
Lkb1 deficiency confers the Kras-mutant lung cancer with strong plasticity and the potential
for adeno-to-squamous transdifferentiation (AST). However, it remains largely unknown how …

Multi-modal molecular determinants of clinically relevant osteoporosis subtypes

C Yuan, XT Yu, J Wang, B Shu, XY Wang, C Huang… - Cell Discovery, 2024 - nature.com
Due to a rapidly aging global population, osteoporosis and the associated risk of bone
fractures have become a wide-spread public health problem. However, osteoporosis is very …

Latent space search based multimodal optimization with personalized edge-network biomarker for multi-purpose early disease prediction

J Liang, ZW Li, ZN Sun, Y Bi, H Cheng… - Briefings in …, 2023 - academic.oup.com
Considering that cancer is resulting from the comutation of several essential genes of
individual patients, researchers have begun to focus on identifying personalized edge …

Application of the dynamical network biomarker theory to raman spectra

T Haruki, S Yonezawa, K Koizumi, Y Yoshida… - Biomolecules, 2022 - mdpi.com
The dynamical network biomarker (DNB) theory detects the early warning signals of state
transitions utilizing fluctuations in and correlations between variables in complex systems …

The single-sample network module biomarkers (sNMB) method reveals the pre-deterioration stage of disease progression

J Zhong, H Liu, P Chen - Journal of Molecular Cell Biology, 2022 - academic.oup.com
The progression of complex diseases generally involves a pre-deterioration stage that
occurs during the transition from a healthy state to disease deterioration, at which a drastic …

Using single-sample networks to identify the contrasting patterns of gene interactions and reveal the radiation dose-dependent effects in multiple tissues of spaceflight …

Y Zhang, L Zhao, Y Sun - npj Microgravity, 2024 - nature.com
Transcriptome profiles are sensitive to space stressors and serve as valuable indicators of
the biological effects during spaceflight. Herein, we transformed the expression profiles into …

Intrinsic entropy model for feature selection of scRNA-seq data

L Li, H Tang, R Xia, H Dai, R Liu… - Journal of Molecular Cell …, 2022 - academic.oup.com
Recent advances of single-cell RNA sequencing (scRNA-seq) technologies have led to
extensive study of cellular heterogeneity and cell-to-cell variation. However, the high …