I study how living systems build themselves through cell fate decisions and self-organization. I approach
both questions from opposite ends of the spatial scale, from reconstituted molecular systems up to
whole embryos and tissues. My work sits at the interface of quantitative biology, developmental
biology, and molecular engineering, drawing heavily on tools from high-dimensional data analysis and
physics.
Cell fate decisions in development
How a single cell gives rise to the full diversity of an organism remains a central question in
biology. Cell fate is specified as cells integrate their internal state with signals from neighboring
cells and their physical environment. I track this process in the zebrafish embryo, focusing on
three interconnected layers of control:
- Transcriptional regulation: how gene regulatory networks resolve competing inputs into a
single stable cell state.
- The mRNA post-transcriptional landscape: how transcripts are processed, stabilized and
degraded after synthesis to control cell fate and the timing of commitments.
- Mechanosensing and signal transduction: how physical forces and tissue geometry are
converted into transcriptional programs, creating a dynamic feedback loop between form and
function.
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Measuring and modeling cells in space and time
Fate decisions play out across space and time, yet standard measurements usually force a trade-off
between them. I develop and apply multimodal approaches that preserve both — in embryos,
tissues, and tumors. Three ingredients add a spatial and temporal axis to sequencing:
- Metabolic labeling of new transcripts: separates newly made RNA from older pools, dating
when a gene was switched on and tracking what becomes of its transcripts afterwards.
- Spatial-lineage recording: places each cell where it sits in the tissue and reconstructs
where it came from.
- Multimodal integration: aligns live microscopy, single-cell RNA-seq, and spatial
transcriptomics across the same system.
Measured densely enough, these complex dynamics can be modeled quantitatively.
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Self-organization of biological matter
Living matter organizes itself across scales. To understand how this works, I build reconstituted
systems held far from equilibrium, in which striking patterns, flows, and physical forms emerge
spontaneously from a handful of simple molecular rules:
- Reaction–diffusion patterning: a few programmed reactions producing fronts, waves,
and stationary patterns, for example in DNA-based reaction networks.
- Active matter: components consuming energy to generate flows, contraction, and shape, for
example in reconstituted cytoskeletal networks.
Chemistry and mechanics constantly feed back on one another, deforming, wrinkling, and sculpting the
material. Because every component in these systems is defined, they can be modeled with mathematical
precision. The organizational principles that emerge offer direct insight into how tissues pattern
themselves in vivo.
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Synthetic biology & molecular programming
Synthetic and engineering-based approaches allow us to deconstruct, modify, and repurpose biological
processes. I design custom molecular programs such as riboregulators, synthetic gene
circuits, and enzymatic DNA reaction networks, which serve two ends:
- As models: minimal, fully controllable versions of tissue patterning, used to test which
ingredients are actually necessary.
- As tools: functional instruments in their own right, such as molecular barcodes for
single-cell identification.
My current work expands into protein engineering, developing molecular architectures designed to
record transcriptional histories and to rewire signaling pathways inside living cells.
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