Shanjun Deng

This paper reconstructs whole-organism cell phylogenies with resolved ancestral transcriptional states in zebrafish larvae using a novel computational framework called LEAP.

This study identifies and quantifies developmental canals in C. elegans embryogenesis that suppress noise and stabilize development, revealing how cell-level stochasticity affects phenotypic outcomes.

This paper introduces a coalescent method, i-coalescent analysis, that is insensitive to population structure and demonstrates its ability to accurately reconstruct population size dynamics in structured populations.

This study uses scLOESS to trace lineage commitments in zebrafish embryos, revealing development histories and ongoing lineage events through single-cell analysis.

The paper shows that gene deletion effects can be split into clustered and distributed effects, with only clustered effects aligning with known biochemical functions and distributed effects being evolutionarily decoupled.

The paper analyzes sex ratio dynamics in Tetrahymena thermophila using a population genetics model and experimental validation, showing support for theoretical predictions about sex coexistence and fixation.