Deciphering cell–cell interactions and communication from gene expression

E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments

L Gatto, R Aebersold, J Cox, V Demichev, J Derks… - Nature …, 2023 - nature.com
Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently
become technically feasible. While such analysis has the potential to accurately quantify …

Single-cell transcriptomic characterization of a gastrulating human embryo

RCV Tyser, E Mahammadov, S Nakanoh, L Vallier… - Nature, 2021 - nature.com
Gastrulation is the fundamental process in all multicellular animals through which the basic
body plan is first laid down,,–. It is pivotal in generating cellular diversity coordinated with …

scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention

R Meng, S Yin, J Sun, H Hu, Q Zhao - Computers in biology and medicine, 2023 - Elsevier
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful
technique for investigating cellular heterogeneity and structure. However, analyzing scRNA …

High-throughput total RNA sequencing in single cells using VASA-seq

F Salmen, J De Jonghe, TS Kaminski, A Alemany… - Nature …, 2022 - nature.com
Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated
transcripts, capturing only a small fraction of the total cellular transcriptome. This precludes …

Role of the gut–brain axis in energy and glucose metabolism

HR Wachsmuth, SN Weninger, FA Duca - Experimental & molecular …, 2022 - nature.com
The gastrointestinal tract plays a role in the development and treatment of metabolic
diseases. During a meal, the gut provides crucial information to the brain regarding …

Direct cell reprogramming: approaches, mechanisms and progress

H Wang, Y Yang, J Liu, L Qian - Nature Reviews Molecular Cell Biology, 2021 - nature.com
The reprogramming of somatic cells with defined factors, which converts cells from one
lineage into cells of another, has greatly reshaped our traditional views on cell identity and …

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

P Ma, HM Amemiya, LL He, SJ Gandhi, R Nicol… - Cell, 2023 - cell.com
We introduce BacDrop, a highly scalable technology for bacterial single-cell RNA
sequencing that has overcome many challenges hindering the development of scRNA-seq …

Pathway paradigms revealed from the genetics of inflammatory bowel disease

DB Graham, RJ Xavier - Nature, 2020 - nature.com
Inflammatory bowel disease (IBD) is a complex genetic disease that is instigated and
amplified by the confluence of multiple genetic and environmental variables that perturb the …

A human liver cell atlas reveals heterogeneity and epithelial progenitors

N Aizarani, A Saviano, null Sagar, L Mailly, S Durand… - Nature, 2019 - nature.com
The human liver is an essential multifunctional organ. The incidence of liver diseases is
rising and there are limited treatment options. However, the cellular composition of the liver …