Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis

H Huang, C Liu, MM Wagle, P Yang - Genome Biology, 2023 - Springer
Background Feature selection is an essential task in single-cell RNA-seq (scRNA-seq) data
analysis and can be critical for gene dimension reduction and downstream analyses, such …

A comparison of marker gene selection methods for single-cell RNA sequencing data

JM Pullin, DJ McCarthy - Genome Biology, 2024 - Springer
Background The development of single-cell RNA sequencing (scRNA-seq) has enabled
scientists to catalog and probe the transcriptional heterogeneity of individual cells in …

Vascular senescence and leak are features of the early breakdown of the blood–brain barrier in Alzheimer's disease models

KK Ting, P Coleman, HJ Kim, Y Zhao, J Mulangala… - Geroscience, 2023 - Springer
Alzheimer's disease (AD) is an age-related disease, with loss of integrity of the blood–brain
barrier (BBB) being an early feature. Cellular senescence is one of the reported nine …

Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era

A Tran, P Yang, JYH Yang… - Briefings in Functional …, 2022 - academic.oup.com
Recent advances in direct cell reprogramming have made possible the conversion of one
cell type to another cell type, offering a potential cell-based treatment to many major …

Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas

H Robertson, HJ Kim, J Li, N Robertson, P Robertson… - Nature Medicine, 2024 - nature.com
The pathogenesis of allograft (dys) function has been increasingly studied using 'omics'-
based technologies, but the focus on individual organs has created knowledge gaps that …

Time-series single-cell transcriptomic profiling of luteal-phase endometrium uncovers dynamic characteristics and its dysregulation in recurrent implantation failures

D Cao, Y Liu, Y Cheng, J Wang, B Zhang… - Nature …, 2025 - nature.com
Understanding human endometrial dynamics in the establishment of endometrial receptivity
remains a challenge, which limits early diagnosis and treatment of endometrial-factor …

Comprehensive characterization of fetal and mature retinal cell identity to assess the fidelity of retinal organoids

HJ Kim, M O'Hara-Wright, D Kim, TH Loi, BY Lim… - Stem Cell Reports, 2023 - cell.com
Characterizing cell identity in complex tissues such as the human retina is essential for
studying its development and disease. While retinal organoids derived from pluripotent stem …

scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction

Y Cao, Y Lin, E Patrick, P Yang, JYH Yang - Bioinformatics, 2022 - academic.oup.com
Motivation With the recent surge of large-cohort scale single cell research, it is of critical
importance that analytical methods can fully utilize the comprehensive characterization of …

Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging

H Zheng, J Vijg, AT Fard, JC Mar - Genome biology, 2023 - Springer
Background Single-cell RNA-sequencing (scRNA-seq) technologies enable the capture of
gene expression heterogeneity and consequently facilitate the study of cell-to-cell variability …

scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq

L Chen, Z Guo, T Deng, H Wu - Genome Biology, 2024 - Springer
Single-cell RNA-sequencing (scRNA-seq) provides gene expression profiles of individual
cells from complex samples, facilitating the detection of cell type-specific marker genes. In …