Publications

Spatial single-cell isotope tracing reveals heterogeneity of de novo fatty acid synthesis in cancer

This paper proposes a novel method for spatial & single-cell tracing of activity of key processes of lipid metabolism. It traces 13C carbon from labelled glucose in cell medium or food to the lipids synthesized de novo in cells. It does it by what can be called on-the-fly saponification or releasing fatty acids from intracellular lipids, detecting them for each cell, & mathematical modeling of fatty acids isotopologues. We evaluated & demonstrated method for liver cancer cells & brain tumors.

The paper was selected for a cover.

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SpaceM reveals metabolic states of single cells

This is the foundational paper for SpaceM, our method for single-cell metabolomics. The key idea of the method is to computationally integrate data from MALDI-imaging mass spectrometry and microscopy. The method can analyze monocultured or co-cultured cells of different types on glass slides & in situ. We evaluated the method & characterized metabolic states of human liver cells modelling stages of fatty liver disease.

The paper was highlighted in an editorial by Nature Methods & featured in Nature Seven Technologies to Watch in 2023.

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FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

This is the foundational paper for METASPACE, our cloud platform for spatial metabolomics. We proposed a novel method for metabolite & lipid annotation in imaging mass spectrometry data. The key distinguishing feature of the method is to be able to quantify the confidence in provided results by estimating the False Positive Rate.

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3D molecular cartography using LC-MS combined with Optimus and `ili software

This is the foundational paper for `ili, our visualization software for 3D molecular cartography. This software allows to visualize molecular data mapped on surfances & within 3D volume. `ili was developed following the original publication in PNAS mapping metabolites & microbes on the human skin & was used in a multitude of publications.

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