Optimal transport for single-cell and spatial omics
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 …
molecular states of millions of cells. These technologies are, however, destructive to cells …
Spatiotemporal omics for biology and medicine
The completion of the Human Genome Project has provided a foundational blueprint for
understanding human life. Nonetheless, understanding the intricate mechanisms through …
understanding human life. Nonetheless, understanding the intricate mechanisms through …
An integrated transcriptomic cell atlas of human neural organoids
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 …
study human brain development, evolution and disease. However, it is unclear which parts …
Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon
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 …
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
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 …
research into the development of diagonal integration methods. However, the state-of-the-art …
Nicheformer: a foundation model for single-cell and spatial omics
Tissue makeup relies fundamentally on the cellular microenvironment. Spatial single-cell
genomics allows probing the underlying cellular interactions in an unbiased, scalable …
genomics allows probing the underlying cellular interactions in an unbiased, scalable …
CellRank 2: unified fate mapping in multiview single-cell data
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 …
using expression similarity or RNA velocity to reconstruct state-change trajectories; however …
Spatial omics advances for in situ RNA biology
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 …
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 …
secretion. Complementarily, each function of a cell has resource costs that constrain …
Generative Entropic Neural Optimal Transport To Map Within and Across Spaces
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 …
prominently in generative modeling. Recent years have witnessed a surge of techniques …