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 …

CD8+ T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance

H Aoki, M Kitabatake, H Abe, P Xu, M Tsunoda… - Cell reports, 2024 - cell.com
Summary mRNA vaccines against the spike glycoprotein of severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) elicit strong T cell responses. However, a clonal …

Unveiling the power of high-dimensional cytometry data with cyCONDOR

C Kröger, S Müller, J Leidner, T Kröber… - Nature …, 2024 - nature.com
High-dimensional cytometry (HDC) is a powerful technology for studying single-cell
phenotypes in complex biological systems. Although technological developments and …

[HTML][HTML] Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues

DP Caron, WL Specht, D Chen, SB Wells, PA Szabo… - Cell Reports …, 2025 - cell.com
Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity
and transcriptional states, but transcriptomic profiles do not always delineate subsets …

scMMT: a multi-use deep learning approach for cell annotation, protein prediction and embedding in single-cell RNA-seq data

S Zhou, Y Li, W Wu, L Li - Briefings in Bioinformatics, 2024 - academic.oup.com
Accurate cell type annotation in single-cell RNA-sequencing data is essential for advancing
biological and medical research, particularly in understanding disease progression and …

Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro

Y Yin, M Yajima, JD Campbell - Nucleic Acids Research, 2024 - academic.oup.com
Assays such as CITE-seq can measure the abundance of cell surface proteins on individual
cells using antibody derived tags (ADTs). However, many ADTs have high levels of …

tagtango: an application to compare single-cell annotations

B Bramon Mora, H Lindsay, A Thiébaut… - …, 2025 - academic.oup.com
In this article, we present tagtango, an innovative R package and web application designed
for robust and intuitive comparison of single-cell clusters and annotations. It offers an …

CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replacement

H Aoki, M Kitabatake, H Abe, P Xu, M Tsunoda… - bioRxiv, 2022 - biorxiv.org
Abstract mRNA vaccines against the Spike glycoprotein of severe acute respiratory
syndrome type 2 coronavirus (SARS-CoV-2) elicit strong T-cell responses. However, it is …