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Latest publications
Coherent Raman imaging of live, unfixed _Saccharomyces cerevisiae_ and mutants _aah1∆ and rad6∆_
We acquired single-cell coherent Raman microscopy data (SRS and CARS) from wild-type budding yeast and two mutants. Our aim was to collect spatially resolved biochemical data on living yeast cells. We’re sharing the data and code for others to visualize and explore it!
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Morphological transformation of _Chlamydomonas smithii_ grown in Marine Broth medium
Marine Broth induces extreme morphological transformation in _C. smithii_: Cells shift from typical ellipsoid shape to amorphous forms with thin wisp-like appendages containing mitochondria, revealing unexpected cellular plasticity.
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A tractability atlas for experimental organism selection
We’ve mapped experimental tractability for ~15,000 diverse organisms. By aggregating data on community activity, infrastructure, tooling, throughput, and logistics, our interactive atlas helps researchers navigate trade-offs when deciding which organisms to use for their work.
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Biology needs to become prospective
Since biological data are often non-independent, more data doesn't always mean more insight. We argue that a prospective approach is needed to uncover the deepest principles of life.
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Strategizing the search for bio-utility: A framework for evolution-integrated _in silico_ bioprospecting
To accurately and efficiently identify instances of useful biological variation, we must establish an evolution-integrated bioprospecting framework. This will enable us to better interpret biological datasets and direct future sampling efforts to solve societal challenges.
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MSA-based pLMs encode evolutionary distance but don’t reliably exploit it
We characterize how MSA Pairformer encodes phylogenetic relationships. Sequence weights correlate with evolutionary distance, with distinct layers specializing as phylogenetic filters. Yet uniform averaging often outperforms learned weights for contact prediction.
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