Published on 14 min read
Journal Safari #5. Malva makes 74 million single cells searchable by raw sequence, answering 24-mer queries in milliseconds, and it found oral bacteria outside a tumour section that a reference-based pipeline discards by construction. The engineering is excellent. What decides whether it still exists in 2036 isn't in the paper, and three of its four referees spent ten months saying so.
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Published on 12 min read
Microbial ecology spent twenty years learning that in low-biomass samples, the thing you measure is partly your reagents. Single-cell has the same exposure, most of the same tooling gaps, and none of the same scar tissue — and the field is moving into exactly the regime where it starts to matter.
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Published on 16 min read
Journal Safari #3. Pan-human Azimuth puts 27 million cells from 23 tissues on one annotation tree, then classifies them with a model 70× smaller than the foundation model I read in July — and wins. The contribution is not the model. It is the labels.
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Published on 8 min read
Kicking off Journal Safari, my biweekly close-read of one recent paper. First up: CellVQ, a 500-million-parameter single-cell foundation model that squashes every cell into a discrete code — and the peer reviews that quietly agreed with my doubts.
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