Optimal transport for single-cell and spatial omics

C Bunne, G Schiebinger, A Krause, A Regev… - Nature Reviews …, 2024 - nature.com
High-throughput single-cell profiling provides an unprecedented ability to uncover the
molecular states of millions of cells. These technologies are, however, destructive to cells …

Spatiotemporal omics for biology and medicine

L Liu, A Chen, Y Li, J Mulder, H Heyn, X Xu - Cell, 2024 - cell.com
The completion of the Human Genome Project has provided a foundational blueprint for
understanding human life. Nonetheless, understanding the intricate mechanisms through …

An integrated transcriptomic cell atlas of human neural organoids

Z He, L Dony, JS Fleck, A Szałata, KX Li, I Slišković… - Nature, 2024 - nature.com
Human neural organoids, generated from pluripotent stem cells in vitro, are useful tools to
study human brain development, evolution and disease. However, it is unclear which parts …

Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon

DJ Otto, C Jordan, B Dury, C Dien, M Setty - Nature Methods, 2024 - nature.com
Cell-state density characterizes the distribution of cells along phenotypic landscapes and is
crucial for unraveling the mechanisms that drive diverse biological processes. Here, we …

scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features

J Samaran, G Peyré, L Cantini - Nature Communications, 2024 - nature.com
The abundance of unpaired multimodal single-cell data has motivated a growing body of
research into the development of diagonal integration methods. However, the state-of-the-art …

Nicheformer: a foundation model for single-cell and spatial omics

AC Schaar, A Tejada-Lapuerta, G Palla, R Gutgesell… - bioRxiv, 2024 - biorxiv.org
Tissue makeup relies fundamentally on the cellular microenvironment. Spatial single-cell
genomics allows probing the underlying cellular interactions in an unbiased, scalable …

CellRank 2: unified fate mapping in multiview single-cell data

P Weiler, M Lange, M Klein, D Pe'er, F Theis - Nature Methods, 2024 - nature.com
Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions
using expression similarity or RNA velocity to reconstruct state-change trajectories; however …

Spatial omics advances for in situ RNA biology

J Ren, S Luo, H Shi, X Wang - Molecular Cell, 2024 - cell.com
Spatial regulation of RNA plays a critical role in gene expression regulation and cellular
function. Understanding spatially resolved RNA dynamics and translation is vital for bringing …

Resource allocation in mammalian systems

HM Baghdassarian, NE Lewis - Biotechnology Advances, 2024 - Elsevier
Cells execute biological functions to support phenotypes such as growth, migration, and
secretion. Complementarily, each function of a cell has resource costs that constrain …

Generative Entropic Neural Optimal Transport To Map Within and Across Spaces

D Klein, T Uscidda, F Theis, M Cuturi - arXiv preprint arXiv:2310.09254, 2023 - arxiv.org
Learning measure-to-measure mappings is a crucial task in machine learning, featured
prominently in generative modeling. Recent years have witnessed a surge of techniques …