# Michael Skinnider
**Michael Skinnider** (Michael A. Skinnider) is a Canadian computational biologist and physician-scientist who works on machine learning for drug discovery and precision medicine. According to his ORCID record, since September 2023 he has been an assistant professor at Princeton University's Lewis-Sigler Institute for Integrative Genomics and an assistant member of the Ludwig Institute for Cancer Research Princeton Branch, where he leads a laboratory that uses machine learning and mass spectrometry-based metabolomics to identify small molecules relevant to human health and disease.[1](https://orcid.org/0000-0002-2168-1621) • [2](https://ludwigcancer.princeton.edu/people/michael-skinnider)
| Key facts | |
|---|---|
| Position | Assistant professor, Lewis-Sigler Institute for Integrative Genomics, Princeton University, since September 2023[1](https://orcid.org/0000-0002-2168-1621); assistant member, Ludwig Princeton Branch (its first faculty hire), effective September 1, 2023[3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) |
| Training | B.ArtsSc., McMaster University, 2011–2015 |[1](https://orcid.org/0000-0002-2168-1621) • [4](https://open.library.ubc.ca/soa/cIRcle/collections/ubctheses/24/items/1.0398212)
| Signature work | *Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments*, Nature Methods, 2021[5](https://www.nature.com/articles/s41592-021-01194-4) |
| Measured result | DarkNPS deep generative model elucidates the exact structure of an unidentified novel psychoactive substance with 51% accuracy and 86% top-10 accuracy[6](https://michaelskinnider.com/files/Nat%20Mach%20Intell%202021%20-%20A%20deep%20generative%20model%20enables%20automated%20structure%20elucidation%20of%20novel%20psychoactive%20substances.pdf) |
| Industry | Research from his McMaster undergraduate years spun off into the biotechnology start-up Adapsyn Bioscience[3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) |
| Honors | 2025 Packard Fellowship for Science and Engineering ($875,000 over five years, one of 20 fellows)[7](https://www.princeton.edu/news/2025/10/15/michael-skinnider-wins-2025-packard-foundation-fellowship); 2025 Searle Scholar[8](https://searlescholars.org/michael-skinnider/); 2023 NOMIS & Science Young Explorer Award[9](https://www.aaas.org/news/ai-based-approach-used-fight-illicit-designer-drugs-epidemic) |
## Education and training
According to Ludwig Princeton, Skinnider was born in [Saskatoon](https://www.edgepedia.org/saskatoon), Canada, and raised in [Victoria, British Columbia](https://www.edgepedia.org/victoria-british-columbia).[3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) He entered [McMaster University](https://www.edgepedia.org/mcmaster-university)'s Bachelor of Arts & Science program in September 2011 and completed it in April 2015, graduating summa cum laude.[1](https://orcid.org/0000-0002-2168-1621) • [3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) His undergraduate research leveraged bacterial genomes and metabolomes to discover new antibiotics from nature.[10](https://memento.epfl.ch/event/ic-colloquium-machine-learning-approaches-to-hum-2/)
In August 2015 he began a combined MD/PhD at the [University of British Columbia](https://www.edgepedia.org/university-of-british-columbia), finishing in May 2023; the PhD was awarded in 2021 and the MD in 2023.[1](https://orcid.org/0000-0002-2168-1621) • [11](https://www.ludwigcancerresearch.org/scientist/michael-skinnider/) His doctoral thesis, *Understanding mammalian biology and disease through tissue-specific protein-protein interaction networks*, was supervised by [Leonard Foster](https://www.edgepedia.org/leonard-j-foster) in the Genome Science and Technology program.[4](https://open.library.ubc.ca/soa/cIRcle/collections/ubctheses/24/items/1.0398212) During the program he was also a visiting PhD student at the [École Polytechnique Fédérale de Lausanne](https://www.edgepedia.org/ecole-polytechnique-federale-de-lausanne) (EPFL) in Switzerland, where he was trained in single-cell and spatial transcriptomics.[11](https://www.ludwigcancerresearch.org/scientist/michael-skinnider/)
## Career
His McMaster research on microbial genomics and metabolomics for antibiotic discovery was spun off into the start-up biotechnology company Adapsyn Bioscience.[3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) By the time of his Princeton appointment he had published or had accepted about 30 peer-reviewed articles, some 20 of them as first author.[3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) He joined the Ludwig Princeton Branch as an assistant member effective September 1, 2023, the Branch's first faculty hire, with a joint appointment at the Lewis-Sigler Institute.[3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) • [1](https://orcid.org/0000-0002-2168-1621)
## Representative work
His 2021 [Nature Methods](https://www.edgepedia.org/nature-methods) paper *Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments* reanalyzed 206 co-fractionation mass spectrometry (CF-MS) experiments into a uniformly processed resource of over 11 million protein abundance measurements, predicted over 700,000 protein-protein interactions across 27 eukaryotic species or clades, and reconstructed a draft-quality human interactome by CF-MS.[5](https://www.nature.com/articles/s41592-021-01194-4) A follow-up resource, CFdb, harmonizes interaction proteomics data from 411 CF-MS datasets spanning 21,703 fractions, charting protein abundance, phosphorylation, and interactions across the tree of life.[12](https://pmc.ncbi.nlm.nih.gov/articles/PMC10724252/)
A related atlas from this co-fractionation work expanded the known mouse interactome by 37%, revealing over 26,000 novel interactions, and showed that rewiring of protein interactions across tissues is widespread and poorly predicted by gene expression or coexpression.[13](https://www.biorxiv.org/content/10.1101/351247v1)
## Machine learning for drug discovery and the dark metabolome
The Skinnider lab develops machine-learning approaches to identify known and unknown small molecules relevant to human health and disease, with mass spectrometry-based metabolomics as the primary analytical technique.[14](https://lsi.princeton.edu/people/michael-skinnider) Its stated aim is to illuminate metabolic dark matter: the large fraction of small molecules detected in metabolomic experiments whose structures are unknown, with a particular focus on unknown metabolites in cancer via germline risk factors and the human microbiome.[2](https://ludwigcancer.princeton.edu/people/michael-skinnider)
A second application works with forensic laboratories to identify new synthetic drugs of abuse.[14](https://lsi.princeton.edu/people/michael-skinnider) The 2021 Nature Machine Intelligence paper presented DarkNPS, a deep learning approach that elucidates the structures of unidentified designer drugs using only mass spectrometric data.[6](https://michaelskinnider.com/files/Nat%20Mach%20Intell%202021%20-%20A%20deep%20generative%20model%20enables%20automated%20structure%20elucidation%20of%20novel%20psychoactive%20substances.pdf) DarkNPS uses a [deep generative model](https://www.edgepedia.org/deep-generative-model) to learn a statistical probability distribution over unobserved structures, termed the structural prior, which allows it to elucidate the exact chemical structure of an unidentified novel psychoactive substance with 51% accuracy and 86% top-10 accuracy.[6](https://michaelskinnider.com/files/Nat%20Mach%20Intell%202021%20-%20A%20deep%20generative%20model%20enables%20automated%20structure%20elucidation%20of%20novel%20psychoactive%20substances.pdf) Combining the language model's predictions with mass spectrometric data allowed the model to elucidate the chemical structures of more than 30 new designer drugs, according to a report by AAAS; the approach was validated with the Danish national forensic laboratory and put into practice with law enforcement agencies and the BC Centre for Disease Control.[9](https://www.aaas.org/news/ai-based-approach-used-fight-illicit-designer-drugs-epidemic)
The lab also applies large language models trained on the structures of known human small molecules to look for related but unknown metabolites; with Princeton collaborators, it has experimentally discovered nearly 50 new small molecules in humans and mice.[15](https://csml.princeton.edu/news/michael-skinnider-using-generative-ai-accelerate-discovery-small-molecules)
## Honors and funding
In 2025 Skinnider received a Packard Fellowship for Science and Engineering, one of 20 fellows who each receive $875,000 over five years to pursue blue-sky research; the Packard Foundation lists his disciplines as biochemistry, biotechnology, and chemistry.[7](https://www.princeton.edu/news/2025/10/15/michael-skinnider-wins-2025-packard-foundation-fellowship) • [16](https://www.packard.org/fellow/michael-skinnider/) The fellowship funds work using AI to identify metabolite chemical structures in the human body and link them to human diseases including cancer.[7](https://www.princeton.edu/news/2025/10/15/michael-skinnider-wins-2025-packard-foundation-fellowship) He is also a 2025 Searle Scholar, with the project *Charting the unknown human metabolome with biochemical artificial intelligence*, which aims to develop AI models that transform metabolite discovery into a high-throughput endeavor and apply them to comprehensively map the mammalian metabolome.[8](https://searlescholars.org/michael-skinnider/) Earlier honors include the 2023 NOMIS & Science Young Explorer Award, which he won for the AI-based approach to identifying new designer drugs,[9](https://www.aaas.org/news/ai-based-approach-used-fight-illicit-designer-drugs-epidemic) the [Forbes 30 Under 30](https://www.edgepedia.org/forbes-30-under-30) list (2021, science category), the International Birnstiel Award, the Dan David Scholarship, and the Borealis AI Fellowship.[3](https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member) • [2](https://ludwigcancer.princeton.edu/people/michael-skinnider)
## Recent developments
Since moving to Princeton and launching his laboratory in 2023, his output has broadened from interaction proteomics toward metabolomics and single-cell biology: a 2025 Cell paper, *A clinical road map for single-cell omics*, with Skinnider as corresponding author, argues that despite initial forays into clinical settings, single-cell technologies are not yet routinely used to inform medical or surgical decision-making, and proposes combinatorial biomarkers that simultaneously quantify multiple cell-type-specific pathophysiological processes as a route into clinical decision-making.[17](https://www.cell.com/cell/fulltext/S0092-8674(25)00676-2) Recent publications listed on his ORCID record include a Science article on unbiased discovery of neuronal architectures (November 2025), a Nature article on language model-guided anticipation and discovery of mammalian metabolites (March 2026), and an Analytical Chemistry article on curation of small-molecule MS/MS libraries in Spectraverse (February 2026).[1](https://orcid.org/0000-0002-2168-1621)
## References
1. ORCID record 0000-0002-2168-1621. https://orcid.org/0000-0002-2168-1621
2. Michael Skinnider | Ludwig Princeton Branch. https://ludwigcancer.princeton.edu/people/michael-skinnider
3. Ludwig Princeton Branch Welcomes Skinnider as Assistant Member. https://ludwigcancer.princeton.edu/news/2023/ludwig-princeton-branch-welcomes-skinnider-assistant-member
4. Understanding mammalian biology and disease through tissue-specific protein-protein interaction networks (doctoral thesis, UBC). https://open.library.ubc.ca/soa/cIRcle/collections/ubctheses/24/items/1.0398212
5. Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments (Nature Methods, 2021). https://www.nature.com/articles/s41592-021-01194-4
6. A deep generative model enables automated structure elucidation of novel psychoactive substances (Nature Machine Intelligence, 2021). https://michaelskinnider.com/files/Nat%20Mach%20Intell%202021%20-%20A%20deep%20generative%20model%20enables%20automated%20structure%20elucidation%20of%20novel%20psychoactive%20substances.pdf
7. Michael Skinnider wins 2025 Packard Foundation Fellowship (Princeton University). https://www.princeton.edu/news/2025/10/15/michael-skinnider-wins-2025-packard-foundation-fellowship
8. Michael Skinnider – Searle Scholars Program. https://searlescholars.org/michael-skinnider/
9. AI-Based Approach Used to Fight Illicit Designer Drugs Epidemic (AAAS). https://www.aaas.org/news/ai-based-approach-used-fight-illicit-designer-drugs-epidemic
10. IC Colloquium: Machine learning approaches to human disease (EPFL). https://memento.epfl.ch/event/ic-colloquium-machine-learning-approaches-to-hum-2/
11. Michael Skinnider – Ludwig Cancer Research. https://www.ludwigcancerresearch.org/scientist/michael-skinnider/
12. Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry. https://pmc.ncbi.nlm.nih.gov/articles/PMC10724252/
13. An atlas of protein-protein interactions across mammalian tissues (bioRxiv). https://www.biorxiv.org/content/10.1101/351247v1
14. Michael Skinnider | Lewis-Sigler Institute. https://lsi.princeton.edu/people/michael-skinnider
15. Michael Skinnider: using generative AI to accelerate discovery of small molecules (Princeton CSML). https://csml.princeton.edu/news/michael-skinnider-using-generative-ai-accelerate-discovery-small-molecules
16. Michael Skinnider • The David and Lucile Packard Foundation. https://www.packard.org/fellow/michael-skinnider/
17. https://www.cell.com/cell/fulltext/S0092-8674(25)00676-2
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*Topic: Encyclopedia › Life and health › Life and health scientists › Life scientists › Researchers in computational biology, bioinformatics, and systems biology › Machine learning for drug discovery and precision medicine*
*Initially written Sep 21, 2026 · Reviewed: Sep 25, 2026 · Edited: Sep 25, 2026; Oct 11, 2026; Oct 15, 2026 · Last review: Sep 25, 2026*
*Copyright 2026 EdgeChat AI, a subsidiary of Biostate AI.*
License: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license