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* co-first author, corresponding author


  1. Skinnider, M.A.*, Gautier, M.*, Teo, A.Y.Y., Kathe, C., Hutson, T., Laskaratos, A., de Coucy, A., Regazzi, N., Aureli, V., James, N.D., Schneider, B., Sofroniew, M., Barraud, Q., Bloch, J., Anderson, M.A., Squair, J.W., Courtine, G. “The Tabulae Paralytica: Multimodal single-cell and spatial atlases of spinal cord injury.” bioRxiv, doi: 10.1101/2023.06.23.544348.


  1. (news & views) Skinnider, M.A. “Spectrum of the past.” Nature Reviews Chemistry, 8, 85–86. [pdf]


  1. Skinnider, M.A., Akinlaja, M.O., Foster, L.J. “Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.” Nature Communications, 14, 8365. [pdf]
  2. Wang, F., Pasin, D., Skinnider, M.A., Liigand, J., Kleis, J.-N., Brown, D., Oler, E., Sajed, T., Gautam, V., Harrison, S., Greiner, R., Foster, L.J., Dalsgaard, P.W., Wishart, D.S. “Deep learning-enabled MS/MS spectrum prediction facilitates automated identification of novel psychoactive substances.” Analytical Chemistry, 95, 18326–18334 (2023). [pdf]
  3. Skinnider, M.A., Merette, S.A.M., Pasin, D., Rogalski, J., Foster, L.J., Scheuermeyer, F., Shapiro, A.M. “Identification of emerging novel psychoactive substances by retrospective analysis of population-scale mass spectrometry data sets.” Analytical Chemistry, 95, 17300–17310 (2023). [pdf]
  4. (essay) Skinnider, M.A. “Hallucinating hallucinogens.” Science, 382, 656–657 (2023). [pdf]
  5. (essay) Skinnider, M.A. “From single cells to neural circuits.” Science, 382, 528 (2023). [pdf]
  6. Squair, J.W.*, Milano, M.*, Gautier, M., de Coucy, A., Skinnider, M.A., James, N.D., Cho, N., Lasne, A., Kathe, C., Hutson, T., Ceto, S., Baud, L., Galan, K., Barraud, Q., Deming, T.J., Schneider, B., He, Z., Sofroniew, M.V., Courtine, G., Anderson, M.A. “Recovery of walking after paralysis by regenerating characterized neurons to their natural target region.” Science, 381, 1338–1345 (2023). [pdf]
  7. (review) Mullowney, M.W.*, Duncan, K.R.*, Elsayed, S.S.*, Garg, N.*, van der Hooft, J.J.J.*, Martin, N.I.*, Meijer, D.*, Terlouw, B.*, [...] Skinnider, M.A., [...] van Westen, G., Hirsch, A.K.H., Linington, R.G., Robinson, S.L., Medema, M.H. “Artificial intelligence for natural product drug discovery.” Nature Reviews Drug Discovery, 22, 895–916 (2023). [pdf]
  8. Stukas, S., Cooper, J., Gill, J., Fallah, N., Skinnider, M.A., Belanger, L., Ritchie, L., Tsang, A., Dong, K., Streijger, F., Street, J., Paquette, S., Ailon, T., Dea, N., Charest-Morin, R., Fisher, C.G., Bailey, C.S., Dhall, S., Mac-Thiong, J.-M., Wilson, J.R., Christie, S., Dvorak, M.F., Wellington, C., Kwon, B.K. “Association of CSF and serum neurofilament light and glial fibrillary acidic protein and injury severity and outcome in patients with acute spinal cord injury.” Neurology, 100, e1221–e1233 (2023). [pdf]


  1. Kathe, C.*, Skinnider, M.A.*, Hutson, T.H.*, Regazzi, N., Gautier, M., Demesmaeker, R., Komi, S., Ceto, S., James, N.D., Cho, N., Baud, L., Galan, K., Matson, K.J.E., Rowald, A., Kim, K., Wang, R., Prior, J.O., Asboth, L., Barraud, Q., Lacour, S.P., Levine, A.J., Wagner, F., Bloch, J., Squair, J.W., Courtine, G. “The neurons that restore walking after paralysis.” Nature, 611, 540–547 (2022). [pdf]


  1. Skinnider, M.A., Wang, F., Pasin, D., Greiner, R., Foster, L.J., Dalsgaard, P.W., Wishart, D.S. “A deep generative model enables automated structure elucidation of novel psychoactive substances.” Nature Machine Intelligence, 3, 973–984 (2021). [pdf]
  2. Squair, J.W., Gautier, M., Kathe, C., Anderson, M.A., James, N.D., Hutson, T.H., Hudelle, R., Qaiser, T., Matson, K.J.E., Barraud, Q., Levine, A.J., La Manno, G., Skinnider, M.A., Courtine, G. “Confronting false discoveries in single-cell differential expression.” Nature Communications, 18, 5692 (2021). [pdf]
  3. (editorial) Skinnider, M.A., Squair, J.W., Courtine, G. “Enabling reproducible re-analysis of single-cell data.” Genome Biology, 22, 215 (2021). [pdf]
  4. Skinnider, M.A., Stacey, R.G., Wishart, D.S., Foster, L.J. “Chemical language models enable navigation in sparsely populated chemical space.” Nature Machine Intelligence, 3, 759–770 (2021). [pdf]
  5. Skinnider, M.A.*, Scott, N.E.*, Prudova, A., Kerr, C.H., Stoynov, N., Stacey, R.G., Chan, Q.W.T., Rattray, D., Gsponer, J., Foster, L.J. “An atlas of protein-protein interactions across mammalian tissues.” Cell, 184, 4073–4089 (2021). [pdf]
  6. Skinnider, M.A., Foster, L.J. “Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments.” Nature Methods, 18, 806–815 (2021). [pdf]
  7. Squair, J.W.*, Skinnider, M.A.*, Gautier, M., Foster, L.J., Courtine, G. “Prioritization of cell types responsive to biological perturbations in single-cell data with Augur.” Nature Protocols, 16, 3836–3873 (2021). [pdf]
  8. Skinnider, M.A., Rogalski, J., Tigchelaar, S., Manouchehri, N., Prudova, A., Jackson, A.M., Nielsen, K., Jeong, J., Chaudhary, S., Shortt, K., Gallagher-Kurtzke, Y., So, K., Fong, A., Gupta, R., Okon, E.B., Rizzuto, M.A., Dong, K., Streijger, F., Belanger, L., Ritchie, L., Tsang, A., Christie, S., Mac-Thiong, J.-M., Bailey, C., Ailon, T., Charest-Morin, R., Dea, N., Wilson, J.R., Dhall, S., Paquette, S., Street, J., Fisher, C.G., Dvorak, M.F., Shannon, C.P., Borchers, C., Balshaw, R., Foster, L.J., Kwon, B.K. “Proteomic portraits reveal evolutionarily conserved and divergent responses to spinal cord injury.” Molecular & Cellular Proteomics, 20, 100096 (2021). [pdf]
  9. Skinnider, M.A., Cai, C., Stacey, R.G., Foster, L.J. “PrInCE: an R/Bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data.” Bioinformatics, 37, 2775–2777 (2021). [pdf]
  10. Skinnider, M.A.*, Squair, J.W.*, Kathe, C., Anderson, M.A., Gautier, M., Matson, K.J.E., Milano, M., Hutson, T.H., Barraud, Q., Phillips, A.A., Foster, L.J., La Manno, G., Levine, A.J., Courtine, G. “Cell type prioritization in single-cell data.” Nature Biotechnology, 39, 30–34 (2021). [pdf]
  11. Stacey, R.G., Skinnider, M.A., Foster, L.J. “On the robustness of graph-based clustering to random network alterations.” Molecular & Cellular Proteomics, 20, 100002 (2021). [pdf]


  1. Skinnider, M.A., Johnston, C.W., Gunabalasingam, M., Merwin, N.J., Kieliszek, A.M., MacLellan, R.J., Li, H., Ranieri, M.R.M., Webster, A.L.H., Cao, M.P.T., Pfeifle, A., Spencer, N., To, Q.H., Wallace, D.P., Dejong, C.A., Magarvey, N.A. “Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.” Nature Communications, 11, 6058 (2020). [pdf]
  2. Kerr, C.H.*, Skinnider, M.A.*, Andrews, D.D.T., Madero, A.M., Chan, Q.W.T., Stacey, R.G., Stoynov, N., Jan, E., Foster, L.J. “Dynamic rewiring of the human interactome by interferon signalling.” Genome Biology, 21, 140 (2020). [pdf]
  3. Merwin, N.J.*, Mousa, W.K.*, Dejong, C.A., Skinnider, M.A., Cannon, M.J., Li, H., Dial, K., Gunabalasingam, M., Johnston, C.W., Magarvey, N.A. “DeepRiPP integrates multi-omics data to automate discovery of novel ribosomally synthesized natural products.” Proceedings of the National Academy of Sciences of the USA, 117, 371–380 (2020). [pdf]


  1. Skinnider, M.A., Squair, J.W., Foster, L.J. “Evaluating measures of association for single-cell transcriptomics.” Nature Methods, 16, 381–386 (2019). [pdf]


  1. Stacey, R.G., Skinnider, M.A., Chik, J.H.L., Foster, L.J. “Conditional interactions in literature-curated protein interaction databases.” BMC Genomics, 19, 758 (2018). [pdf]
  2. Skinnider, M.A., Stacey, R.G., Foster, L.J. “Genomic data integration systematically biases interactome mapping.” PLoS Computational Biology, 14, e1006474 (2018). [pdf]
  3. Squair, J.W.*, Tigchelaar, S., Moon, K.M., Liu, J., Tetzlaff, W., Kwon, B.K., Krassioukov, A.V., West, C.R., Foster, L.J., Skinnider, M.A.*. “Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury.” eLife, 7, e39188 (2018). [pdf]
  4. Skinnider, M.A., Twa, D.D.W., Squair, J.W., Rosenblum, N.D., Lukac, C.D. “Predictors of sustained research involvement among Canadian MD/PhD program graduates.” Medical Education, 52, 536–545 (2018). [pdf]
  5. Skinnider, M.A., Johnston, C.W., Merwin, N.J., Dejong, C..A., Magarvey, N.A. “Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis.” BMC Genomics, 19, 45 (2018). [pdf]


  1. Stacey, R.G., Skinnider, M.A., Scott, N.E., Foster, L.J. “A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).” BMC Bioinformatics, 18, 457 (2017). [pdf]
  2. Twa, D.D.W., Skinnider, M.A., Squair, J.W., Lukac, C.D. “Cross-sectional-derived determinants of satisfaction with physician-scientist training among Canadian MD/PhD graduates. PLoS ONE, 12, e0185218 (2017). [pdf]
  3. Skinnider, M.A., Dejong, C.A., Franczak, B.C., McNicholas, P.D., Magarvey, N.A. “Comparative analysis of molecular similarity methods for modular natural products with a hypothetical structure enumeration algorithm.” Journal of Cheminformatics, 9, 46 (2017). [pdf]
  4. (letter) Skinnider, M.A., Magarvey, N.A. “Statistical reanalysis of natural products reveals increasing chemical diversity.” Proceedings of the National Academy of Sciences of the USA, 114, E6271–E6272 (2017). [pdf]
  5. Skinnider, M.A., Merwin, N.J., Johnston, C.W., Magarvey, N.A. “PRISM 3: An expanded resource for the automated prediction of microbial secondary metabolomes.” Nucleic Acids Research, 45, W49–W54 (2017). [pdf]
  6. Skinnider, M.A.*, Squair, J.W.*, Twa, D.D.W.*, Ji, J.X.*, Kuzyk, A., Wang, X., Steadman, P.E., Zaslavsky, K., Dey, A.K., Eisenberg, M.J., Gagné, E.R., HayGlass, K.T., Lewis, J.F., Margetts, P.J., Underhill, D.A., Rosenblum, N.D., Raymond, L.A. “Characteristics and outcomes of Canadian MD/PhD program graduates: a cross-sectional survey.” CMAJ Open, 5, E308–E314 (2017). [pdf]
  7. Streijger, F., Skinnider, M.A., Rogalski, J.C., Balshaw, R., Shannon, C.P., Prudova, A., Belanger, L., Ritchie, L., Tsang, A., Christie, S., Parent, S., Thiong, J.M., Bailey, C., Urquhart, J., Ailon, T., Paquette, S., Boyd, M., Street, J., Fisher, C.G., Dvorak, M.F., Borchers, C.H., Foster, L.J., Kwon, B.K. “Targeted proteomic analysis of human cerebrospinal fluid after acute spinal cord injury.” Journal of Neurotrauma, 34, 2054–2068 (2017). [pdf]


  1. Skinnider, M.A.*, Johnston, C.W.*, Edgar, R.E., Dejong, C.A., Merwin, N.J., Rees, P.N., Magarvey, N.A. “Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining.” Proceedings of the National Academy of Sciences of the USA, 113, E6343–E6351 (2016). [pdf]
  2. Dejong, C.A.*, Chen, G.M.*, Li, H.*, Johnston, C.W., Edwards, M., Rees, P.N., Skinnider, M.A., Webster, A.L.H., Magarvey, N.A. “Retrobiosynthesis of polyketide and nonribosomal peptide natural product chemistry and global alignment to biosynthetic clusters.” Nature Chemical Biology, 12, 1007–1014 (2016). [pdf]
  3. Johnston, C.W., Skinnider, M.A., Dejong, C.A., Rees, P.N., Chen, G.M., Walker, C., French, S., Brown, E.D., Bérdy, J., Liu, D.Y., Magarvey, N.A. “Assembly and clustering of natural antibiotics guides target identification.” Nature Chemical Biology, 12, 233–239 (2016). [pdf]
  4. Johnston, C.W., Connaty, A.D., Skinnider, M.A., Li, Y.C., Grunwald, A., Wyatt, M.A., Kerr, R.G., Magarvey, N.A. “Informatic search strategies to discover analogues and variants of natural product archetypes.” Journal of Industrial Microbiology and Biotechnology, 43, 293–298 (2016). [pdf]


  1. Johnston, C.W.*, Skinnider, M.A.*, Wyatt, M.A., Li, X., Ranieri, M.R.M., Yang, L., Zechel, D.L., Ma, B., Magarvey, N.A. “An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products.” Nature Communications, 6, 8421 (2015). [pdf]
  2. (perspective) Twa, D.D.W.*, Squair, J.W.*, Skinnider, M.A.*, Ji, J.X.*. “The Canadian clinician-scientist training program must be reinstated.” Journal of Clinical Investigation, 125, 4317–4319 (2015). [pdf]
  3. Skinnider, M.A., Dejong, C.A., Rees, P.N., Johnston, C.W., Li, H., Webster, A.L.H., Wyatt, M.A., Magarvey, N.A. “Genomes to natural products prediction informatics for secondary metabolomes (PRISM).” Nucleic Acids Research, 43, 9645–9662 (2015). [pdf]
  4. Yang, L.*, Ibrahim, A.*, Johnston, C.W.*, Skinnider, M.A., Ma, B., Magarvey, N.A. “Exploration of nonribosomal peptide families with an automated search algorithm.” Chemistry & Biology, 22, 1259–1269 (2015). [pdf]
  5. Skinnider, M.A.*, Johnston, C.W.*, Zvanych, R., Magarvey, N.A. “Automated identification of depsipeptide natural products by an informatic search algorithm.” ChemBioChem, 16, 223–227 (2015). [pdf]