Aviezer Lifshitz

Abstract Single-cell mapping of chromosomal accessibility patterns has recently led to improved predictive modelling of epigenomic activity from sequence. However, quantitative models explaining the epigenome using directly interpretable components are still lacking. Here we develop IceQream (IQ), a modelling strategy and inference algorithm for regressing accessibility from sequences using physical models of transcription factor (TF) binding.

Abstract The developing placenta, which in mice originates through the extraembryonic ectoderm (ExE), is essential for mammalian embryonic development. Yet unbiased characterization of the differentiation dynamics of the ExE and its interactions with the embryo proper remains incomplete. Here we develop a temporal single-cell model of mouse gastrulation that maps continuous and parallel differentiation in embryonic and extraembryonic lineages.

Abstract Hematopoietic stem and progenitor cells (HSPCs) deliver life-long multi-lineage output. However, with aging, we exhibit certain characteristic blood count changes and accumulation of clonal disorders. Better understanding of inter-individual variation in HSPC behavior is needed to understand these age-related phenomena and the transition from health to chronic and acute hematological malignancies.