Mikhail V. Pachkov

Bonsai provides a tree-based visualization method for single-cell omics data that accurately represents distances and structures without distortion, offering novel biological insights.

The paper maps transcriptional dynamics in murine cortical development, identifying lineage shifts and gene regulatory networks in neural stem cells, basal progenitors, and newborn neurons.

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

This paper introduces a new model for transcription factor binding site prediction that accounts for pairwise dependencies between positions, outperforming existing methods on ChIP-seq and HT-SELEX data.