Michal Klein

OmniPath: integrated knowledgebase for multi-omics analysis

OmniPath integrates molecular knowledge from 168 resources to support multi-omics analysis, offering curated data, predictions, and tools for causal modeling across bulk, single-cell, and spatial data.

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.

Mapping lineage-traced cells across time points with moslin

The paper introduces moslin, a method that combines lineage and gene expression data across time points to predict cell fate and decision driver genes.

Unified fate mapping in multiview single-cell data

The paper introduces CellRank 2, a framework for analyzing multiview single-cell data to study cellular fate, showing it recovers terminal states and fate probabilities across modalities in hematopoiesis and endodermal development.

Squidpy: a scalable framework for spatial omics analysis

Squidpy extends Scanpy/AnnData with spatial neighbor graphs and a lazy-loading image container, enabling spatial statistics, ligand-receptor tests, image features, and ~10-fold faster neighborhood enrichment than Giotto.

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.

Integrated intra- and intercellular signaling knowledge for multicelullar omics analysis

The paper integrates intra- and intercellular signaling knowledge into a database for multicellular omics analysis, demonstrating its application to SARS-CoV-2 infection and ulcerative colitis.