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Who we are dictates what we see as trivially true or inherently paradoxical, in other words, science has personality. Therefore, our projects are framed and continuously redirected by the people leading them. Our graduate students are strongly encouraged to become autonomous by following their own curiosity. As new tools become needed to tackle 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. Our goal is to understand how the genome encodes cell type identity and diversity, how various cell types assemble into complex tissue structures, and how the functional demands at the organismal level may lead to the creation of new cell types. To address these questions, we study a broad range of animals, from early-branching invertebrates to mammals, using single-cell multiomic sequencing, spatial transcriptomics, deep learning models, and genetic experiments. 

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

Systems biology of regeneration

Animals have the ability to heal wounds, but only some can regenerate from major tissue loss. We focus on those capable of whole-body regeneration —the ability to regenerate all body parts. We use functional genomic analysis to: (1) uncover the signaling circuits and gene regulatory networks controlling regeneration, (2) compare across species to pinpoint key cellular and genetic modifications driving regeneration success, and (3) identify molecular programs that prevent ectopic outgrowths in homeostatic tissues. 

Read more: Fan et al. Cell, 2023

Animal-algal photosymbiosis

Animal-algal symbiosis play a crucial role in sustaining biodiversity but has also become a vulnerable point of aquatic ecosystems under the pressure of climate change. Photosymbiosis, in particular, has evolved sustainable ways to exchange energy and nutrients between symbionts, offering a blueprint for sustainably powering biological machines from an engineering standpoint. We aim to understand the molecular and cellular mechanisms governing the establishment and control of photosymbiosis. For this, we study the acoel Convolutriloba longifissura, a marine worm that hosts Tetraselmis green algae as obligate symbionts. These algae reside between the acoel cells, making this relationship an extracellular endosymbiosis. We make progress using a set of sequencing and genetic tools and have recently incorporated Cryo-EM and mass spectrometry to characterize the physical and chemical interfaces between animal and algal cells.  

Read more: Nanes Sarfati Nature Communications, 2024

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