Publications

You can also find these on Google Scholar.

* co-first author, (co-)corresponding author

preprints

  1. Kerr, C.H.*, Skinnider, M.A.*, Madero, A.M., Andrews, D.D.T., Stacey, R.G., Chan, Q.W.T., Stoynov, N., Jan, E., Foster, L.J. “Dynamic rewiring of the human interactome by interferon signalling” bioRxiv, doi: 10.1101/766808.
  2. Skinnider, M.A.*, Scott, N.E.*, Prudova, A., Stoynov, N., Stacey, R.G., Gsponer, J., Foster, L.J. “An atlas of protein-protein interactions across mammalian tissues.” bioRxiv, doi: 10.1101/351247.

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]