Michael Skinnider

Michael Skinnider

Assistant professor at Princeton University

Publications

You can also find these on Google Scholar.

* co-first author, † corresponding author

preprints

  1. Qiang, H.*, Wang, F.*, Lu, W., Xing, X., Kim, H., Merette, S.A.M., Ayres, L.B., Oler, E., AbuSalim, J.E., Roichman, A., Neinast, M., Cordova, R.A., Lee, W.D., Herbst, E., Gupta, V., Neff, S., Hiebert-Giesbrecht, M., Young, A., Gautam, V., Tian, S., Wang, B., Röst, H., Greiner, R., Chen, L., Johnston, C.W., Foster, L.J., Shapiro, A.M., Wishart, D.S., Rabinowitz, J.D., Skinnider, M.A.† “Language model-guided anticipation and discovery of unknown metabolites.” bioRxiv, doi: 10.1101/2024.11.13.623458.
  2. Teo, Y.Y., Gautier, M., Brock, L., Tsai, J.Y.J., de Coucy, A., Laskaratos, A., Regazzi, N., Barraud, Q., Sofroniew, M.V., Anderson, M.A., Courtine, G.†, Squair, J.W.†, Skinnider, M.A.† “Identification of perturbation-responsive regions and genes in comparative spatial transcriptomics atlases.” bioRxiv, doi: 10.1101/2024.06.13.598641.
  3. Soriano, J.E.*, Hudelle, R.*, Mahe, L., Gautier, M., Teo, Y.Y., Skinnider, M.A., Laskaratos, A., Ceto, S., Kathe, C., Hutson, T., Charbonneau, R., Girgis, F., Casha, S., Rimok, J., Tso, M., Larkin-Kaiser, K., Hankov, N., Gandhi, A.P., Amir, S., Kang, X., Vyza, Y., Martin-Moraud, E., Lacour, S., Demesmaeker, R., Asboth, L., Barraud, Q., Anderson, M.A., Bloch, J., Squair, J.W., Phillips, A.A., Courtine, G. “The neuronal architecture of autonomic dysreflexia.” bioRxiv, doi: 10.1101/2024.05.06.592781.

2024

  1. (commentary) Skinnider, M.A. “Hiding in plain sight: a research parasite’s perspective on new lessons in old data.” GigaScience, 13, 1–3 (2024). [pdf]
  2. Cho, N.*, Squair, J.W.*, Aureli, V., James, N.D., Bole-Feysot, L., Dewany, I., Hankov, N., Baud, L., Leonhartsberger, A., Sveistyte, K., Skinnider, M.A., Gautier, M., Laskaratos, A., Galan, K., Goubran, M., Ravier, J., Merlos, F., Batti, L., Pages, S., Berard, N., Intering, N., Varescon, C., Carda, S., Bartholdi, K.A., Hutson, T.H., Kathe, C., Hodara, M., Anderson, M.A., Draganski, B., Demesmaeker, R., Asboth, L., Barraud, Q., Bloch, J., Courtine, G. “Hypothalamic deep brain stimulation augments walking after spinal cord injury.” Nature Medicine, 30, 3676–3686 (2024). [pdf]
  3. Teo, A.Y.Y., Squair, J.W.†, Courtine, G.†, Skinnider, M.A.† “Best practices for differential accessibility analysis in single-cell epigenomics.” Nature Communications, 15, 8805 (2024). [pdf]
  4. 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. “Single-cell and spatial atlases of spinal cord injury in the Tabulae Paralytica.” Nature, 631, 150–163 (2024). [pdf]
  5. Skinnider, M.A. “Invalid SMILES are beneficial rather than detrimental to chemical language models.” Nature Machine Intelligence, 6, 437–448 (2024). [pdf]
  6. (news & views) Skinnider, M.A. “Spectrum of the past.” Nature Reviews Chemistry, 8, 85–86 (2024). [pdf]

2023

  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 (2023). [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]

2022

  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]

2021

  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]

2020

  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]

2019

  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]

2018

  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]

2017

  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]

2016

  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]

2015

  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]