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 …

Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023‏ - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications

J Cerneckis, H Cai, Y Shi - Signal Transduction and Targeted Therapy, 2024‏ - nature.com
The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and
holds great promise to advance regenerative medicine. iPSCs have the capacity for an …

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

C Bravo González-Blas, S De Winter, G Hulselmans… - Nature …, 2023‏ - nature.com
Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …

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 …

Spatially organized cellular communities form the develo** human heart

EN Farah, RK Hu, C Kern, Q Zhang, TY Lu, Q Ma… - Nature, 2024‏ - nature.com
The heart, which is the first organ to develop, is highly dependent on its form to function,.
However, how diverse cardiac cell types spatially coordinate to create the complex …

Predicting transcriptional outcomes of novel multigene perturbations with GEARS

Y Roohani, K Huang, J Leskovec - Nature Biotechnology, 2024‏ - nature.com
Understanding cellular responses to genetic perturbation is central to numerous biomedical
applications, from identifying genetic interactions involved in cancer to develo** methods …

[HTML][HTML] Single-cell brain organoid screening identifies developmental defects in autism

C Li, JS Fleck, C Martins-Costa, TR Burkard… - Nature, 2023‏ - nature.com
The development of the human brain involves unique processes (not observed in many
other species) that can contribute to neurodevelopmental disorders,,–. Cerebral organoids …

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

AA Pollen, U Kilik, CB Lowe, JG Camp - Nature Reviews Genetics, 2023‏ - nature.com
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled
humans to colonize diverse habitats, develop extraordinary technologies and reshape the …

[HTML][HTML] Human fetal brain self-organizes into long-term expanding organoids

D Hendriks, A Pagliaro, F Andreatta, Z Ma… - Cell, 2024‏ - cell.com
Human brain development involves an orchestrated, massive neural progenitor expansion
while a multi-cellular tissue architecture is established. Continuously expanding organoids …