Single-cell atlases: shared and tissue-specific cell types across human organs

R Elmentaite, C Domínguez Conde, L Yang… - Nature Reviews …, 2022 - nature.com
The development of single-cell and spatial transcriptomics methods was instrumental in the
conception of the Human Cell Atlas initiative, which aims to generate an integrated map of …

Genetics of human brain development

Y Zhou, H Song, G Ming - Nature Reviews Genetics, 2024 - nature.com
Brain development in humans is achieved through precise spatiotemporal genetic control,
the mechanisms of which remain largely elusive. Recently, integration of technological …

scGPT: toward building a foundation model for single-cell multi-omics using generative AI

H Cui, C Wang, H Maan, K Pang, F Luo, N Duan… - Nature …, 2024 - nature.com
Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens Consortium*, RC Jones… - Science, 2022 - science.org
Molecular characterization of cell types using single-cell transcriptome sequencing is
revolutionizing cell biology and enabling new insights into the physiology of human organs …

Intratumoral dendritic cell–CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma

A Magen, P Hamon, N Fiaschi, BY Soong, MD Park… - Nature medicine, 2023 - nature.com
Despite no apparent defects in T cell priming and recruitment to tumors, a large subset of T
cell rich tumors fail to respond to immune checkpoint blockade (ICB). We leveraged a …

[HTML][HTML] Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution

D Yang, MG Jones, S Naranjo, WM Rideout, KHJ Min… - Cell, 2022 - cell.com
Tumor evolution is driven by the progressive acquisition of genetic and epigenetic
alterations that enable uncontrolled growth and expansion to neighboring and distal tissues …

High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

S Salcher, G Sturm, L Horvath, G Untergasser… - Cancer cell, 2022 - cell.com
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …

The scverse project provides a computational ecosystem for single-cell omics data analysis

I Virshup, D Bredikhin, L Heumos, G Palla… - Nature …, 2023 - nature.com
Single-cell omics technologies have enabled the creation of comprehensive cell atlases
across tissues and species and delivered key insights into the biological mechanisms …

DestVI identifies continuums of cell types in spatial transcriptomics data

R Lopez, B Li, H Keren-Shaul, P Boyeau… - Nature …, 2022 - nature.com
Most spatial transcriptomics technologies are limited by their resolution, with spot sizes
larger than that of a single cell. Although joint analysis with single-cell RNA sequencing can …

Comparison and evaluation of statistical error models for scRNA-seq

S Choudhary, R Satija - Genome biology, 2022 - Springer
Background Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple
sources, including biological variation in cellular state as well as technical variation …