The triumphs and limitations of computational methods for scRNA-seq

PV Kharchenko - Nature methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …

Regulation of immune responses by the airway epithelial cell landscape

RJ Hewitt, CM Lloyd - Nature Reviews Immunology, 2021 - nature.com
The community of cells lining our airways plays a collaborative role in the preservation of
immune homeostasis in the lung and provides protection from the pathogens and pollutants …

CellRank 2: unified fate map** in multiview single-cell data

P Weiler, M Lange, M Klein, D Pe'er, F Theis - Nature Methods, 2024 - nature.com
Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions
using expression similarity or RNA velocity to reconstruct state-change trajectories; however …

Dictionary learning for integrative, multimodal and scalable single-cell analysis

Y Hao, T Stuart, MH Kowalski, S Choudhary… - Nature …, 2024 - nature.com
Map** single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

Pan-cancer single-cell landscape of tumor-infiltrating T cells

L Zheng, S Qin, W Si, A Wang, B **s derived from single-cell sequencing data that represent highly
granular, distinct cell states. Here we present single-cell aggregation of cell states …

Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development

A Sur, Y Wang, P Capar, G Margolin, MK Prochaska… - Developmental Cell, 2023 - cell.com
During development, animals generate distinct cell populations with specific identities,
functions, and morphologies. We mapped transcriptionally distinct populations across …

A new genomic framework to categorize pediatric acute myeloid leukemia

M Umeda, J Ma, T Westover, Y Ni, G Song… - Nature Genetics, 2024 - nature.com
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific
driver alterations, many of which are underrepresented in the current classification schemas …