The emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

Spatial biology of cancer evolution

Z Seferbekova, A Lomakin, LR Yates… - Nature Reviews …, 2023 - nature.com
The natural history of cancers can be understood through the lens of evolution given that the
driving forces of cancer development are mutation and selection of fitter clones. Cancer …

Spatially informed cell-type deconvolution for spatial transcriptomics

Y Ma, X Zhou - Nature biotechnology, 2022 - nature.com
Many spatially resolved transcriptomic technologies do not have single-cell resolution but
measure the average gene expression for each spot from a mixture of cells of potentially …

A cellular hierarchy in melanoma uncouples growth and metastasis

P Karras, I Bordeu, J Pozniak, A Nowosad, C Pazzi… - Nature, 2022 - nature.com
Although melanoma is notorious for its high degree of heterogeneity and plasticity,, the
origin and magnitude of cell-state diversity remains poorly understood. Equally, it is unclear …

Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses

T Hirz, S Mei, H Sarkar, Y Kfoury, S Wu… - Nature …, 2023 - nature.com
The treatment of low-risk primary prostate cancer entails active surveillance only, while high-
risk disease requires multimodal treatment including surgery, radiation therapy, and …

Cell segmentation in imaging-based spatial transcriptomics

V Petukhov, RJ Xu, RA Soldatov, P Cadinu… - Nature …, 2022 - nature.com
Single-molecule spatial transcriptomics protocols based on in situ sequencing or
multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However …

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 …

RNA velocity—current challenges and future perspectives

V Bergen, RA Soldatov, PV Kharchenko… - Molecular systems …, 2021 - embopress.org
RNA velocity has enabled the recovery of directed dynamic information from single‐cell
transcriptomics by connecting measurements to the underlying kinetics of gene expression …

Lineage tracing meets single-cell omics: opportunities and challenges

DE Wagner, AM Klein - Nature Reviews Genetics, 2020 - nature.com
A fundamental goal of developmental and stem cell biology is to map the developmental
history (ontogeny) of differentiated cell types. Recent advances in high-throughput single …

RNA velocity unraveled

G Gorin, M Fang, T Chari, L Pachter - PLOS Computational …, 2022 - journals.plos.org
We perform a thorough analysis of RNA velocity methods, with a view towards
understanding the suitability of the various assumptions underlying popular …