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Latest publications
A benchmark for the next generation of genotype–phenotype mapping
Despite their limitations, linear methods dominate the field of G–P mapping. In this study, we assess the performance of common linear methods at phenotype and variant effect prediction as a benchmark for more sophisticated methods.
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Assembly and annotation artifacts can lead to problematic protein structural inferences
Protein structures inferred by protein structure prediction algorithms have incredible potential, but can contain errors stemming from incorrect input sequences. Here, we investigate one such case in which tandem-domain proteins appear to have been erroneously inferred.
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Spontaneous Raman spectroscopy detects chemical perturbation of protein structure
Using 785 nm spontaneous Raman benchmarked against size-exclusion chromatography, we detected disulfide bond reduction, metal chelation effects, and pH-induced changes in diverse proteins.
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Leave-one-batch-out cross-validation reveals strong batch effects in Raman spectroscopy of yeast cultures
We acquired spontaneous Raman spectra of several strains and species of yeast. We found that experimental batch effects dominate strain-level biological signals in our dataset, yielding misleadingly high classification accuracy under standard cross-validation.
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Modular CRISPR landing pads for _Chlamydomonas reinhardtii_
We propose a two-stage CRISPR landing pad system for _Chlamydomonas reinhardtii_ that combines one-time, QC-intensive installation at a safe-harbor locus with repeatable, high-throughput HDR-based payload swapping to enable consistent, comparable nuclear expression at scale.
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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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