Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition
Exploring the complexity of the epithelial-to-mesenchymal transition (EMT) unveils a
diversity of potential cell fates; however, the exact timing and mechanisms by which early …
diversity of potential cell fates; however, the exact timing and mechanisms by which early …
scNODE : generative model for temporal single cell transcriptomic data prediction
Measurement of single-cell gene expression at different timepoints enables the study of cell
development. However, due to the resource constraints and technical challenges associated …
development. However, due to the resource constraints and technical challenges associated …
Uncovering underlying physical principles and driving forces of cell differentiation and reprogramming from single-cell transcriptomics
L Zhu, S Yang, K Zhang, H Wang, X Fang… - Proceedings of the …, 2024 - pnas.org
Recent advances in single-cell sequencing technology have revolutionized our ability to
acquire whole transcriptome data. However, uncovering the underlying transcriptional …
acquire whole transcriptome data. However, uncovering the underlying transcriptional …
Detecting global and local hierarchical structures in cell-cell communication using CrossChat
Cell-cell communication (CCC) occurs across different biological scales, ranging from
interactions between large groups of cells to interactions between individual cells, forming a …
interactions between large groups of cells to interactions between individual cells, forming a …
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data
Q Jiang, L Wan - Bioinformatics, 2024 - academic.oup.com
Motivation: Learning cellular dynamics through reconstruction of the underlying cellular
potential energy landscape (aka Waddington landscape) from time-series single-cell RNA …
potential energy landscape (aka Waddington landscape) from time-series single-cell RNA …
Data‐and theory‐driven approaches for understanding paths of epithelial–mesenchymal transition
Reversible transitions between epithelial and mesenchymal cell states are a crucial form of
epithelial plasticity for development and disease progression. Recent experimental data and …
epithelial plasticity for development and disease progression. Recent experimental data and …
Single-cell RNA sequencing data analysis utilizing multi-type graph neural networks
L Xu, Z Li, J Ren, S Liu, Y Xu - Computers in Biology and Medicine, 2024 - Elsevier
Single-cell RNA sequencing (scRNA-seq) is the sequencing technology of a single cell
whose expression reflects the overall characteristics of the individual cell, facilitating the …
whose expression reflects the overall characteristics of the individual cell, facilitating the …
[HTML][HTML] Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation
Inferring gene regulatory networks from gene expression data is an important and
challenging problem in the biology community. We propose OTVelo, a methodology that …
challenging problem in the biology community. We propose OTVelo, a methodology that …
Learning Generalized Diffusions using an Energetic Variational Approach
Extracting governing physical laws from computational or experimental data is crucial across
various fields such as fluid dynamics and plasma physics. Many of those physical laws are …
various fields such as fluid dynamics and plasma physics. Many of those physical laws are …
[PDF][PDF] Generative AI models in time varying biomedical data: a systematic review
Background: Trajectory modeling is a longstanding challenge in the application of
computational methods to healthcare. However, traditional statistical and machine learning …
computational methods to healthcare. However, traditional statistical and machine learning …