Alex Khodaverdian

This paper develops two algorithms for exact phylogenetic reconstruction from CRISPR-Cas9 lineage tracing data and provides theoretical bounds on required recording sites.

The paper defines and solves the Time Conditioned Shortest Walk problem on temporal graphs, showing it is NP-Hard and introducing an integer linear program to address it.

The paper uses perturbation assays to study how regulatory elements guide neural differentiation over time, identifying sequence-driven activity and environmental effects on transcription.

The paper introduces Cassiopeia, a method for inferring single-cell phylogenies from lineage tracing data, and benchmarks it against traditional methods using a large experimental dataset.

The paper develops a molecular recorder to track lineage and define a mouse cell fate map using scRNA-seq, revealing transcriptional convergence of endodermal cells and estimating progenitor cell numbers.

The paper introduces the condition Steiner network problem to address dynamic biological networks across multiple conditions and develops an integer linear programming solver for it.