Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Human disease models in drug development

A Loewa, JJ Feng, S Hedtrich - Nature reviews bioengineering, 2023 - nature.com
Biomedical research is undergoing a paradigm shift towards approaches centred on human
disease models owing to the notoriously high failure rates of the current drug development …

scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention

R Meng, S Yin, J Sun, H Hu, Q Zhao - Computers in biology and medicine, 2023 - Elsevier
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful
technique for investigating cellular heterogeneity and structure. However, analyzing scRNA …

A fast, scalable and versatile tool for analysis of single-cell omics data

K Zhang, NR Zemke, EJ Armand, B Ren - Nature methods, 2024 - nature.com
Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …

Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection

B Zhang, R Upadhyay, Y Hao, MI Samanovic… - Nature …, 2023 - nature.com
The immune response to SARS-CoV-2 antigen after infection or vaccination is defined by
the durable production of antibodies and T cells. Population-based monitoring typically …

[HTML][HTML] Single-cell immunology: Past, present, and future

F Ginhoux, A Yalin, CA Dutertre, I Amit - Immunity, 2022 - cell.com
The immune system is a complex, dynamic, and plastic ecosystem composed of multiple cell
types that constantly sense and interact with their local microenvironment to protect from …

Chromatin accessibility profiling methods

L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

Artificial intelligence-driven biomedical genomics

K Guo, M Wu, Z Soo, Y Yang, Y Zhang, Q Zhang… - Knowledge-Based …, 2023 - Elsevier
As genomic research becomes more complex and data-rich, artificial intelligence (AI) has
emerged as a crucial tool for processing and analyzing high-dimensional genomic data …

Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes

M Maitra, H Mitsuhashi, R Rahimian, A Chawla… - Nature …, 2023 - nature.com
Major depressive disorder (MDD) is a common, heterogenous, and potentially serious
psychiatric illness. Diverse brain cell types have been implicated in MDD etiology …

Understanding tumour cell heterogeneity and its implication for immunotherapy in liver cancer using single-cell analysis

S Heinrich, AJ Craig, L Ma, B Heinrich, TF Greten… - Journal of …, 2021 - Elsevier
Over the last decade, precision medicine and immunotherapeutic approaches have become
increasingly popular in oncology. Early clinical trials reported promising results, but …