Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Applications of single-cell RNA sequencing in drug discovery and development

B Van de Sande, JS Lee, E Mutasa-Gottgens… - Nature Reviews Drug …, 2023 - nature.com
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods,
together with associated computational tools and the growing availability of public data …

Transfer learning enables predictions in network biology

CV Theodoris, L Xiao, A Chopra, MD Chaffin… - Nature, 2023 - nature.com
Mapping gene networks requires large amounts of transcriptomic data to learn the
connections between genes, which impedes discoveries in settings with limited data …

Identification of a tumour immune barrier in the HCC microenvironment that determines the efficacy of immunotherapy

Y Liu, Z Xun, K Ma, S Liang, X Li, S Zhou, L Sun… - Journal of …, 2023 - Elsevier
Background & Aims The tumour microenvironment (TME) is a crucial mediator of cancer
progression and therapeutic outcome. The TME subtype correlates with patient response to …

Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer

J Qi, H Sun, Y Zhang, Z Wang, Z Xun, Z Li… - Nature …, 2022 - nature.com
Colorectal cancer (CRC) is among the most common malignancies with limited treatments
other than surgery. The tumor microenvironment (TME) profiling enables the discovery of …

[HTML][HTML] Organization of the human intestine at single-cell resolution

JW Hickey, WR Becker, SA Nevins, A Horning… - Nature, 2023 - nature.com
The intestine is a complex organ that promotes digestion, extracts nutrients, participates in
immune surveillance, maintains critical symbiotic relationships with microbiota and affects …

The role of goblet cells and mucus in intestinal homeostasis

JK Gustafsson, MEV Johansson - Nature reviews Gastroenterology & …, 2022 - nature.com
The intestinal tract faces numerous challenges that require several layers of defence. The
tight epithelium forms a physical barrier that is further protected by a mucus layer, which …

Cancer-associated fibroblasts in the single-cell era

D Lavie, A Ben-Shmuel, N Erez, R Scherz-Shouval - Nature cancer, 2022 - nature.com
Cancer-associated fibroblasts (CAFs) are central players in the microenvironment of solid
tumors, affecting cancer progression and metastasis. CAFs have diverse phenotypes …

Impact of the Human Cell Atlas on medicine

JE Rood, A Maartens, A Hupalowska, SA Teichmann… - Nature medicine, 2022 - nature.com
Single-cell atlases promise to provide a 'missing link'between genes, diseases and
therapies. By identifying the specific cell types, states, programs and contexts where disease …

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

KA Jagadeesh, KK Dey, DT Montoro, R Mohan… - Nature …, 2022 - nature.com
Genome-wide association studies provide a powerful means of identifying loci and genes
contributing to disease, but in many cases, the related cell types/states through which genes …