Ilia Kats

MOFA-FLEX is a flexible factor analysis framework that integrates multi-omics data with prior knowledge, improving robustness and disentangling variation in scRNA-seq and CITE-seq data.

SpatialData, a Zarr/OME-NGFF-based format plus Python library, unifies images, labels, points, shapes and tables across spatial omics platforms with coordinate alignment, lazy loading and cross-modal aggregation.

This study creates a spatially resolved single-cell multiomics atlas of human trophoblast differentiation in early pregnancy, revealing key regulatory programs and cell-cell communication events involved in EVT invasion and arterial transformation.

The paper introduces MUON, a framework for organizing, analyzing, and visualizing multimodal omics data, enabling flexible multi-omics analysis and interoperability with existing standards.

SpatialDE2 unifies tissue zone mapping and spatially variable gene detection for spatial transcriptomics within a fast Bayesian framework that directly models Poisson count noise.

The paper identifies Bfr1 as a regulator of Pmt1 and Pmt2 translation, affecting unfolded protein O-mannosylation in yeast.

The paper uses a fluorescent timer to analyze Bicoid gradient dynamics in Drosophila embryos, revealing parameters consistent with the synthesis-diffusion-degradation model.

The paper describes a C-SWAT library for high-throughput tagging of yeast ORFs and validates it by tagging the yeast proteome with fluorescent proteins.