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Who we are dictates what we see as trivially true and what we see as inherently paradoxical, in other words, science has personality. Therefore, our projects are framed and continuously redirected by people who are leading them. Our graduate students are strongly encouraged to become autonomous by following their own curiosity. As new tools become needed to attack a given problem, we also spend time to develop them (examples here).

Cell type evolution

Cell types are the fundamental building blocks of multicellular life, and their diversity and identity are determined by the collective activities of genes. Our goal is to uncover how the conservation and divergence of gene regulation modify cell type identity and lead to the creation of new cell types, as well as how these cell types assemble into the diverse, complex tissue structures. To attain these objectives, we study a broad range of animals from basal invertebrates to mammals using single-cell multiomic sequencing and deep learning models. 

Read more: Tarashansky et al. eLife, 2021 | Li et al. Nature Communications, 2021

Comparative systems biology of regeneration

Animals have the ability to heal wounds, but only some can regenerate from major tissue loss. Our focus is on animals with whole-body regeneration (the ability to regenerate all body parts), a phenomenon that remains one of the greatest mysteries in biology. Mastering this process would be a moonshot triumph for bioengineering. We use functional genomic analysis to: (1) uncover signaling circuits and gene regulatory networks that control whole-body regeneration, and (2) compare across species to identify crucial cellular and genetic modifications that contribute to regeneration success. 

Read more: Fan et al. Cell, 2023

Emergent properties of neuropeptide communication

neuropeptide image

Neuropeptides serve as neurotransmitters in diverse nervous systems and play a key role in regulating a variety of animal behaviors. Unlike small molecule neurotransmitters such as monoamines and acetylcholine, which operate at synapses over fast timescales and short distances due to their rapid reuptake and extracellular degradation, neuropeptides can be secreted throughout the entire neuronal body and diffuse for up to minutes over hundreds of microns, potentially signaling to many neurons with matching receptors. Our goal is to explore the impact of the long-range diffusion and slow time scales of neuropeptide communication on the emergence of surprising neural structures, functions, and behavioral output.  

Read more: Khariton et al. Nature Physics, 2020