Anton Afanassiev

DemuxHMM improves demultiplexing for large-scale single-cell datasets by modeling recombination patterns, enhancing scalability and accuracy in developmental studies.

The paper uses single-cell RNA sequencing to compare embryonic development in two sea urchin species, identifying evolutionary changes in cell fate specification and signaling.

The paper introduces GPS-seq, a theoretical framework for spatial transcriptomics that uses DNA barcodes to enable large-scale, optics-free imaging of tissue sections at single-cell resolution.

This paper introduces StationaryOT, an optimal transport method to infer cell trajectories from single snapshots of equilibrium systems, validated on simulated and Arabidopsis root data.

The paper uses scRNA-seq and computational methods to study developmental trajectories and gene regulatory networks in sea urchin embryos, revealing lineage diversification and timing differences between species.

The paper uses single cell RNA-seq to study human hematopoietic stem and progenitor cells (HSPCs) across development and aging, revealing age-related transcriptional changes and differentiation trajectories.