Mostafa Bakhti

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

TERRA is a foundation model for spatial transcriptomics that predicts tissue behavior under perturbation and identifies multi-scale biological insights across tissues.

Mapping cells through time and space with moscot

moscot unifies optimal transport for temporal, spatial and spatiotemporal single-cell mapping, using multimodal cost spaces and low-rank solvers to scale to 1.7 million mouse embryo cells.

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

This paper integrates multiple scRNA-seq datasets to create a mouse islet atlas, revealing new insights into β-cell states and differences across diabetes models.

Synaptotagmin 13 orchestrates pancreatic endocrine cell egression and islet morphogenesis

This study identifies Synaptotagmin 13 as a key regulator of endocrine cell egression and islet formation through its role in cell polarity and basement membrane remodeling.

CellRank for directed single-cell fate mapping

CellRank maps cell fates in single-cell RNA sequencing data by integrating RNA velocity and trajectory inference, revealing novel regeneration trajectories in lung injury.

Generation of a novel Nkx6-1 Venus fusion reporter mouse line

This paper generates a Nkx6-1 Venus fusion reporter mouse line to track and isolate Nkx6-1-expressing cells, including pancreatic β-cells, during development and in adult tissues.

Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

The paper introduces pseudodynamics, a framework to model real-time cellular development using time-series and genetic knock-out data, applied to thymic T-cell maturation.