Probing transient memory of cellular states using single-cell lineages

A Singh, M Saint-Antoine - Frontiers in microbiology, 2023 - frontiersin.org
The inherent stochasticity in the gene product levels can drive single cells within an
isoclonal population to different phenotypic states. The dynamic nature of this intercellular …

Virus infection variability by single-cell profiling

M Suomalainen, UF Greber - Viruses, 2021 - mdpi.com
Cell-to-cell variability of infection has long been known, yet it has remained one of the least
understood phenomena in infection research. It impacts on disease onset and development …

Transiently heritable fates and quorum sensing drive early IFN-I response dynamics

LC Van Eyndhoven, VPG Verberne, CVC Bouten… - Elife, 2023 - elifesciences.org
Abstract Type I interferon (IFN-I)-mediated antiviral responses are central to host defense
against viral infections. Crucial is the tight and well-orchestrated control of cellular decision …

Preexisting cell state rather than stochastic noise confers high or low infection susceptibility of human lung epithelial cells to adenovirus

A Petkidis, M Suomalainen, V Andriasyan, A Singh… - Msphere, 2024 - journals.asm.org
Viruses display large variability across all stages of their life cycle, including entry, gene
expression, replication, assembly, and egress. We previously reported that the immediate …

Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets

AS Eisele, M Tarbier, AA Dormann, V Pelechano… - nature …, 2024 - nature.com
Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has
transformed our understanding of differentiation during development, regeneration, and …

A fluctuation-based approach to infer kinetics and topology of cell-state switching

M Saint-Antoine, R Grima, A Singh - bioRxiv, 2022 - biorxiv.org
In the noisy cellular environment, RNAs and proteins are subject to considerable stochastic
fluctuations in copy numbers over time. As a consequence, single cells within the same …

A modified fluctuation test for elucidating drug resistance in microbial and cancer cells

P Bokes, A Singh - European Journal of Control, 2021 - Elsevier
Clonal populations of microbial and cancer cells are often driven into a drug-tolerant
persister state in response to drug therapy, and these persisters can subsequently adapt to …

Barcode-free prediction of cell lineages from scRNA-seq datasets

AS Eisele, M Tarbier, AA Dormann, V Pelechano… - bioRxiv, 2022 - biorxiv.org
The integration of lineage tracing with scRNA-seq has transformed our understanding of
gene expression heritability during development, regeneration, and disease. However …

Revising immune cell coordination: Origins and importance of single‐cell variation

LC Van Eyndhoven, J Tel - European Journal of Immunology, 2022 - Wiley Online Library
Moving from the optimalization of single‐cell technologies to the interpretation of the multi‐
complex single‐cell data, the field of immunoengineering is granted with numerous …

Fluctuation-based approaches to infer kinetics of cell-state switching

M Saint-Antoine, R Grima… - 2022 IEEE 61st …, 2022 - ieeexplore.ieee.org
In the noisy cellular environment, RNAs and proteins are subject to considerable stochastic
fluctuations in copy numbers over time. As a consequence, single cells within the same …