#3 · Structural bio & protein design
Reproducible environments, DNA library design and standard formats for biology tools
The dominant thread is making computational procedures explicit and portable. REBEL resolves system and transitive dependencies across CRAN, Bioconductor and PyPI and archives packages locally for offline rebuilds, while Biochef exports its drag-and-drop genomic workflows as reproducible bash and config files. Antimony 3 extends a human-readable model language to SBML Level 3 Core and several packages through a C/C++ library, and PoolParty encodes DNA oligo pool designs as computational graphs of over 50 operations for MPRA and DMS experiments. The items differ in domain and emphasis, so the shared element is declarative specification of computation rather than a single common standard. What is new is the application of this pattern to library design and systems biology model exchange, alongside environment resolution and workflow export.
Published papers
Spatial single-cell mapping of transcriptional differences across genetic backgrounds in mouse brains.
ATLAS, a scalable spatial mapping method using scRNA-seq-derived probe signatures, profiles 40M cells across mouse brains to compare cell-type distributions by…
Preprints
CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition
CEP-IP with CMRF on SEA-AD microglia snRNA-seq links a mitochondrial MT-CO3 module to cognition; R package cepip released.
Single-Nucleus Profiling Reveals Neuronal Metabolic Collapse During the Transition to Alzheimer's Disease Dementia
New normalization for snRNA-seq and multiome data links neuronal mitochondrial biogenesis suppression to Alzheimer's dementia.
Cellular context defines brain-specific functions of genes associated with neurodevelopmental disorders
Harmonized transcriptome framework finds ~10% of NDD genes brain-preferential; QRICH1 brain-specific interactions validated.
Proteomic clocks reveal organ-specific signatures of aging in mice
Organ-specific proteomic aging clocks for eight mouse organs, applied to RNA and spatial transcriptomes with organ-dependent age signals.
Joint localization and testing reveals spatial context of differential expression
SpaceDX jointly tests subject-level differential expression and localizes spatial patterns via gene-specific attention weighting, outperforming cluster-based…
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