Aug 2026· Nature Biotechnology· 0 citations· 45 references
Medicine
TL;DR
This approach uncovers epigenomic priming of basal cells in the mammary gland and captures the dynamics of basal-to-luminal transdifferentiation, suggesting that epigenomic and transcriptional remodeling do not occur in complete synchrony during cell-fate conversion.
Accurate identification of cell types and states is essential for reliable single-cell RNA-sequencing analyses, yet current methods remain sensitive to continuous biological states, data preprocessing choices, and reference selection. Here we present ClustoCell, a reference-free method that resolves cell identity using...
Abbas Salavaty, M. Foroutan, N. Pretel et al.· bioRxiv· 0 citations
The cell cycle phase is the major source of variability in transcription within a division cycle, and combining this with the analysis of key transcription factors and chromatin modifier state enables accurate prediction of transcriptional output during zygotic genome activation in individual cells.
Max Hess, M. Wyss, Edlyn Wu et al.· Nature Communications· 0 citations
This study established an integrative strategy enabling high confidence cell identity assignment in sparse epigenomic data, and revealed the roles of B cell subtypes in the regulation of tumor immunity.
Chen-Yu Wang, Qi-Xin Hu, Jian Chen et al.· The Innovation Oncology· 0 citations
This chapter outlines a comprehensive protocol for joint embedding of chromatin accessibility and transcriptomic data using best practices developed in laboratories, along with detailed parameter tuning at each step to fully leveraging this pipeline.
Avinash M. Veerappa, C. Guda· Methods in molecular biology· 0 citations
This manuscript explores the current landscape of single-cell RNA sequencing (scRNA-seq), highlighting key studies that have leveraged this technology to advance biological understanding for clinical purposes through the construction of gene regulatory networks (GRNs) from single-cell transcriptomic data.
J. López-Castiblanco, L. López-Kleine, Yesid Cuesta-Astroz· Journal of Investigative Med...· 0 citations
MeadBRYO is presented: a method for continuous stable isotope labeling (SILAC) of newly synthesized proteins throughout the live embryo at the hour-timescales of developmental phenotypes, thereby accessing the proteome of neurogenesis in the forebrain ex utero.
Marta Couce-Iglesias, Eleonora Oliani, R. Kerridge et al.· bioRxiv· 0 citations
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