Cancer proteogenomics: current impact and future prospects

DR Mani, K Krug, B Zhang, S Satpathy… - Nature Reviews …, 2022 - nature.com
Genomic analyses in cancer have been enormously impactful, leading to the identification of
driver mutations and development of targeted therapies. But the functions of the vast majority …

Feature selection revisited in the single-cell era

P Yang, H Huang, C Liu - Genome Biology, 2021 - Springer
Recent advances in single-cell biotechnologies have resulted in high-dimensional datasets
with increased complexity, making feature selection an essential technique for single-cell …

Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application

M Wang, W Song, C Ming, Q Wang, X Zhou… - Molecular …, 2022 - Springer
Alzheimer's disease (AD) is the most common form of dementia, characterized by
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …

[HTML][HTML] Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation

S Baek, I Lee - Computational and structural biotechnology journal, 2020 - Elsevier
Most genetic variations associated with human complex traits are located in non-coding
genomic regions. Therefore, understanding the genotype-to-phenotype axis requires a …

Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer

CY Wu, BT Lau, HS Kim, A Sathe, SM Grimes… - Nature …, 2021 - nature.com
Cancer progression is driven by both somatic copy number aberrations (CNAs) and
chromatin remodeling, yet little is known about the interplay between these two classes of …

scImmOmics: a manually curated resource of single-cell multi-omics immune data

YY Li, LW Zhou, FC Qian, QL Fang, ZM Yu… - Nucleic Acids …, 2025 - academic.oup.com
Single-cell sequencing technology has enabled the discovery and characterization of
subpopulations of immune cells with unique functions, which is critical for revealing immune …

Single-cell multiomics guided mechanistic understanding of Fontan-associated liver disease

P Hu, J Rychik, J Zhao, H Bai, A Bauer, W Yu… - Science translational …, 2024 - science.org
The Fontan operation is the current standard of care for single-ventricle congenital heart
disease. Individuals with a Fontan circulation (FC) exhibit central venous hypertension and …

A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing

E Lengyel, Y Li, M Weigert, L Zhu, H Eckart… - Cell Reports, 2022 - cell.com
As part of the Human Cell Atlas Initiative, our goal is to generate single-cell transcriptomics
(single-cell RNA sequencing [scRNA-seq], 86,708 cells) and regulatory (single-cell assay on …

Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance

H Fan, F Wang, A Zeng, A Murison, K Tomczak… - Communications …, 2023 - nature.com
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of
therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to …

scaDA: a novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data

F Zhao, X Ma, B Yao, Q Lu, L Chen - PLOS Computational Biology, 2024 - journals.plos.org
Single-cell ATAC-seq sequencing data (scATAC-seq) has been widely used to investigate
chromatin accessibility on the single-cell level. One important application of scATAC-seq …