Michael Skinnider's Publication Page

2021 (7)

Enabling reproducible re-analysis of single-cell data. Skinnider, M. A; Squair, J. W; and Courtine, G. 2021.
link bibtex

@misc{skinnider2021enabling,
  title={Enabling reproducible re-analysis of single-cell data},
  author={Skinnider, Michael A and Squair, Jordan W and Courtine, Gr{\'e}goire},
  year={2021},
  publisher={BioMed Central}
}

Chemical language models enable navigation in sparsely populated chemical space. Skinnider, M. A; Stacey, R G.; Wishart, D. S; and Foster, L. J Nature Machine Intelligence,1–12. 2021.
link bibtex

@article{skinnider2021chemical,
  title={Chemical language models enable navigation in sparsely populated chemical space},
  author={Skinnider, Michael A and Stacey, R Greg and Wishart, David S and Foster, Leonard J},
  journal={Nature Machine Intelligence},
  pages={1--12},
  year={2021},
  publisher={Nature Publishing Group}
}

Proteomic portraits reveal evolutionarily conserved and divergent responses to spinal cord injury. Skinnider, M. A; Rogalski, J.; Tigchelaar, S.; Manouchehri, N.; Prudova, A.; Jackson, A. M; Nielsen, K.; Jeong, J.; Chaudhary, S.; Shortt, K.; and others Molecular & Cellular Proteomics,100096. 2021.
link bibtex

@article{skinnider2021proteomic,
  title={Proteomic portraits reveal evolutionarily conserved and divergent responses to spinal cord injury},
  author={Skinnider, Michael A and Rogalski, Jason and Tigchelaar, Seth and Manouchehri, Neda and Prudova, Anna and Jackson, Angela M and Nielsen, Karina and Jeong, Jaihyun and Chaudhary, Shalini and Shortt, Katelyn and others},
  journal={Molecular \& Cellular Proteomics},
  pages={100096},
  year={2021},
  publisher={Elsevier}
}

An atlas of protein-protein interactions across mouse tissues. Skinnider, M. A; Scott, N. E; Prudova, A.; Kerr, C. H; Stoynov, N.; Stacey, R G.; Chan, Q. W.; Rattray, D.; Gsponer, J.; and Foster, L. J Cell. 2021.
link bibtex

@article{skinnider2021atlas,
  title={An atlas of protein-protein interactions across mouse tissues},
  author={Skinnider, Michael A and Scott, Nichollas E and Prudova, Anna and Kerr, Craig H and Stoynov, Nikolay and Stacey, R Greg and Chan, Queenie WT and Rattray, David and Gsponer, J{\"o}rg and Foster, Leonard J},
  journal={Cell},
  year={2021},
  publisher={Cell Press}
}

Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments. Skinnider, M. A; and Foster, L. J Nature Methods,1–10. 2021.
link bibtex

@article{skinnider2021meta,
  title={Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments},
  author={Skinnider, Michael A and Foster, Leonard J},
  journal={Nature Methods},
  pages={1--10},
  year={2021},
  publisher={Nature Publishing Group}
}

On the robustness of graph-based clustering to random network alterations. Stacey, R G.; Skinnider, M. A; and Foster, L. J Molecular & Cellular Proteomics, 20: 100002. 2021.
link bibtex

@article{stacey2021robustness,
  title={On the robustness of graph-based clustering to random network alterations},
  author={Stacey, R Greg and Skinnider, Michael A and Foster, Leonard J},
  journal={Molecular \& Cellular Proteomics},
  volume={20},
  pages={100002},
  year={2021},
  publisher={Elsevier}
}

PrInCE: an R/Bioconductor package for protein–protein interaction network inference from co-fractionation mass spectrometry data. Skinnider, M. A; Cai, C.; Stacey, R G.; and Foster, L. J Bioinformatics, 1: 3. 2021.
link bibtex

@article{skinnider2021prince,
  title={PrInCE: an R/Bioconductor package for protein--protein interaction network inference from co-fractionation mass spectrometry data},
  author={Skinnider, Michael A and Cai, Charley and Stacey, R Greg and Foster, Leonard J},
  journal={Bioinformatics},
  volume={1},
  pages={3},
  year={2021}
}

2020 (3)

Dynamic rewiring of the human interactome by interferon signaling. Kerr, C. H; Skinnider, M. A; Andrews, D. D.; Madero, A. M; Chan, Q. W.; Stacey, R G.; Stoynov, N.; Jan, E.; and Foster, L. J Genome biology, 21(1): 1–36. 2020.
link bibtex

@article{kerr2020dynamic,
  title={Dynamic rewiring of the human interactome by interferon signaling},
  author={Kerr, Craig H and Skinnider, Michael A and Andrews, Daniel DT and Madero, Angel M and Chan, Queenie WT and Stacey, R Greg and Stoynov, Nikolay and Jan, Eric and Foster, Leonard J},
  journal={Genome biology},
  volume={21},
  number={1},
  pages={1--36},
  year={2020},
  publisher={BioMed Central}
}

Cell type prioritization in single-cell data. Skinnider, M. A; Squair, J. W; Kathe, C.; Anderson, M. A; Gautier, M.; Matson, K. J.; Milano, M.; Hutson, T. H; Barraud, Q.; Phillips, A. A; and others Nature Biotechnology,1–5. 2020.
link bibtex

@article{skinnider2020cell,
  title={Cell type prioritization in single-cell data},
  author={Skinnider, Michael A and Squair, Jordan W and Kathe, Claudia and Anderson, Mark A and Gautier, Matthieu and Matson, Kaya JE and Milano, Marco and Hutson, Thomas H and Barraud, Quentin and Phillips, Aaron A and others},
  journal={Nature Biotechnology},
  pages={1--5},
  year={2020},
  publisher={Nature Publishing Group}
}

DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products. Merwin, N. J; Mousa, W. K; Dejong, C. A; Skinnider, M. A; Cannon, M. J; Li, H.; Dial, K.; Gunabalasingam, M.; Johnston, C.; and Magarvey, N. A Proceedings of the National Academy of Sciences, 117(1): 371–380. 2020.
link bibtex

@article{merwin2020deepripp,
  title={DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products},
  author={Merwin, Nishanth J and Mousa, Walaa K and Dejong, Chris A and Skinnider, Michael A and Cannon, Michael J and Li, Haoxin and Dial, Keshav and Gunabalasingam, Mathusan and Johnston, Chad and Magarvey, Nathan A},
  journal={Proceedings of the National Academy of Sciences},
  volume={117},
  number={1},
  pages={371--380},
  year={2020},
  publisher={National Acad Sciences}
}

2019 (1)

Evaluating measures of association for single-cell transcriptomics. Skinnider, M. A; Squair, J. W; and Foster, L. J Nature methods, 16(5): 381–386. 2019.
link bibtex

@article{skinnider2019evaluating,
  title={Evaluating measures of association for single-cell transcriptomics},
  author={Skinnider, Michael A and Squair, Jordan W and Foster, Leonard J},
  journal={Nature methods},
  volume={16},
  number={5},
  pages={381--386},
  year={2019},
  publisher={Nature Publishing Group}
}

2018 (5)

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. Squair, J. W; Tigchelaar, S.; Moon, K.; Liu, J.; Tetzlaff, W.; Kwon, B. K; Krassioukov, A. V; West, C. R; Foster, L. J; and Skinnider, M. A Elife, 7: e39188. 2018.
link bibtex

@article{squair2018integrated,
  title={Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury},
  author={Squair, Jordan W and Tigchelaar, Seth and Moon, Kyung-Mee and Liu, Jie and Tetzlaff, Wolfram and Kwon, Brian K and Krassioukov, Andrei V and West, Christopher R and Foster, Leonard J and Skinnider, Michael A},
  journal={Elife},
  volume={7},
  pages={e39188},
  year={2018},
  publisher={eLife Sciences Publications Limited}
}

Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis. Skinnider, M. A; Johnston, C. W; Merwin, N. J; Dejong, C. A; and Magarvey, N. A BMC genomics, 19(1): 45. 2018.
link bibtex

@article{skinnider2018global,
  title={Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis},
  author={Skinnider, Michael A and Johnston, Chad W and Merwin, Nishanth J and Dejong, Chris A and Magarvey, Nathan A},
  journal={BMC genomics},
  volume={19},
  number={1},
  pages={45},
  year={2018},
  publisher={Springer}
}

Predictors of sustained research involvement among MD/PhD programme graduates. Skinnider, M. A; Twa, D. D.; Squair, J. W; Rosenblum, N. D; Lukac, C. D; and Group, C. M. P. I. Medical Education, 52(5): 536–545. 2018.
link bibtex

@article{skinnider2018predictors,
  title={Predictors of sustained research involvement among MD/PhD programme graduates},
  author={Skinnider, Michael A and Twa, David DW and Squair, Jordan W and Rosenblum, Norman D and Lukac, Christine D and Canadian MD/PhD Program Investigation Group},
  journal={Medical Education},
  volume={52},
  number={5},
  pages={536--545},
  year={2018},
  publisher={Wiley Online Library}
}

Genomic data integration systematically biases interactome mapping. Skinnider, M. A; Stacey, R G.; and Foster, L. J PLoS computational biology, 14(10): e1006474. 2018.
link bibtex

@article{skinnider2018genomic,
  title={Genomic data integration systematically biases interactome mapping},
  author={Skinnider, Michael A and Stacey, R Greg and Foster, Leonard J},
  journal={PLoS computational biology},
  volume={14},
  number={10},
  pages={e1006474},
  year={2018},
  publisher={Public Library of Science San Francisco, CA USA}
}

Context-specific interactions in literature-curated protein interaction databases. Stacey, R G.; Skinnider, M. A; Chik, J. H.; and Foster, L. J BMC genomics, 19(1): 758. 2018.
link bibtex

@article{stacey2018context,
  title={Context-specific interactions in literature-curated protein interaction databases},
  author={Stacey, R Greg and Skinnider, Michael A and Chik, Jenny HL and Foster, Leonard J},
  journal={BMC genomics},
  volume={19},
  number={1},
  pages={758},
  year={2018},
  publisher={Springer}
}

2017 (7)

Characteristics and outcomes of Canadian MD/PhD program graduates: a cross-sectional survey. Skinnider, M. A; Squair, J. W; Twa, D. D.; Ji, J. X; Kuzyk, A.; Wang, X.; Steadman, P. E; Zaslavsky, K.; Dey, A. K; Eisenberg, M. J; and others CMAJ open, 5(2): E308. 2017.
link bibtex

@article{skinnider2017characteristics,
  title={Characteristics and outcomes of Canadian MD/PhD program graduates: a cross-sectional survey},
  author={Skinnider, Michael A and Squair, Jordan W and Twa, David DW and Ji, Jennifer X and Kuzyk, Alexandra and Wang, Xin and Steadman, Patrick E and Zaslavsky, Kirill and Dey, Ayan K and Eisenberg, Mark J and others},
  journal={CMAJ open},
  volume={5},
  number={2},
  pages={E308},
  year={2017},
  publisher={Canadian Medical Association}
}

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. Skinnider, M. A; Dejong, C. A; Franczak, B. C; McNicholas, P. D; and Magarvey, N. A Journal of Cheminformatics, 9(1): 46. 2017.
link bibtex

@article{skinnider2017comparative,
  title={Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm},
  author={Skinnider, Michael A and Dejong, Chris A and Franczak, Brian C and McNicholas, Paul D and Magarvey, Nathan A},
  journal={Journal of Cheminformatics},
  volume={9},
  number={1},
  pages={46},
  year={2017},
  publisher={Springer}
}

Cross-sectional-derived determinants of satisfaction with physician-scientist training among Canadian MD/PhD graduates. Twa, D. D.; Skinnider, M. A; Squair, J. W; Lukac, C. D; and Group, C. M. P. I. PloS one, 12(9): e0185218. 2017.
link bibtex

@article{twa2017cross,
  title={Cross-sectional-derived determinants of satisfaction with physician-scientist training among Canadian MD/PhD graduates},
  author={Twa, David DW and Skinnider, Michael A and Squair, Jordan W and Lukac, Christine D and Canadian MD/PhD Program Investigation Group},
  journal={PloS one},
  volume={12},
  number={9},
  pages={e0185218},
  year={2017},
  publisher={Public Library of Science San Francisco, CA USA}
}

Statistical reanalysis of natural products reveals increasing chemical diversity. Skinnider, M. A; and Magarvey, N. A Proceedings of the National Academy of Sciences, 114(31): E6271–E6272. 2017.
link bibtex

@article{skinnider2017statistical,
  title={Statistical reanalysis of natural products reveals increasing chemical diversity},
  author={Skinnider, Michael A and Magarvey, Nathan A},
  journal={Proceedings of the National Academy of Sciences},
  volume={114},
  number={31},
  pages={E6271--E6272},
  year={2017},
  publisher={National Acad Sciences}
}

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. Skinnider, M. A; Merwin, N. J; Johnston, C. W; and Magarvey, N. A Nucleic acids research, 45(W1): W49–W54. 2017.
link bibtex

@article{skinnider2017prism,
  title={PRISM 3: expanded prediction of natural product chemical structures from microbial genomes},
  author={Skinnider, Michael A and Merwin, Nishanth J and Johnston, Chad W and Magarvey, Nathan A},
  journal={Nucleic acids research},
  volume={45},
  number={W1},
  pages={W49--W54},
  year={2017},
  publisher={Oxford University Press}
}

A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). Stacey, R G.; Skinnider, M. A; Scott, N. E; and Foster, L. J BMC bioinformatics, 18(1): 1–14. 2017.
link bibtex

@article{stacey2017rapid,
  title={A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)},
  author={Stacey, R Greg and Skinnider, Michael A and Scott, Nichollas E and Foster, Leonard J},
  journal={BMC bioinformatics},
  volume={18},
  number={1},
  pages={1--14},
  year={2017},
  publisher={BioMed Central}
}

A targeted proteomics analysis of cerebrospinal fluid after acute human spinal cord injury. Streijger, F.; Skinnider, M. A; Rogalski, J. C; Balshaw, R.; Shannon, C. P; Prudova, A.; Belanger, L.; Ritchie, L.; Tsang, A.; Christie, S.; and others Journal of Neurotrauma, 34(12): 2054–2068. 2017.
link bibtex

@article{streijger2017targeted,
  title={A targeted proteomics analysis of cerebrospinal fluid after acute human spinal cord injury},
  author={Streijger, Femke and Skinnider, Michael A and Rogalski, Jason C and Balshaw, Robert and Shannon, Casey P and Prudova, Anna and Belanger, Lise and Ritchie, Leanna and Tsang, Angela and Christie, Sean and others},
  journal={Journal of Neurotrauma},
  volume={34},
  number={12},
  pages={2054--2068},
  year={2017},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

2016 (4)

Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching. Dejong, C. A; Chen, G. M; Li, H.; Johnston, C. W; Edwards, M. R; Rees, P. N; Skinnider, M. A; Webster, A. L.; and Magarvey, N. A Nature chemical biology, 12(12): 1007–1014. 2016.
link bibtex

@article{dejong2016polyketide,
  title={Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching},
  author={Dejong, Chris A and Chen, Gregory M and Li, Haoxin and Johnston, Chad W and Edwards, Mclean R and Rees, Philip N and Skinnider, Michael A and Webster, Andrew LH and Magarvey, Nathan A},
  journal={Nature chemical biology},
  volume={12},
  number={12},
  pages={1007--1014},
  year={2016},
  publisher={Nature Publishing Group}
}

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining. Skinnider, M. A; Johnston, C. W; Edgar, R. E; Dejong, C. A; Merwin, N. J; Rees, P. N; and Magarvey, N. A Proceedings of the National Academy of Sciences, 113(42): E6343–E6351. 2016.
link bibtex

@article{skinnider2016genomic,
  title={Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining},
  author={Skinnider, Michael A and Johnston, Chad W and Edgar, Robyn E and Dejong, Chris A and Merwin, Nishanth J and Rees, Philip N and Magarvey, Nathan A},
  journal={Proceedings of the National Academy of Sciences},
  volume={113},
  number={42},
  pages={E6343--E6351},
  year={2016},
  publisher={National Acad Sciences}
}

Assembly and clustering of natural antibiotics guides target identification. Johnston, C. W; Skinnider, M. A; Dejong, C. A; Rees, P. N; Chen, G. M; Walker, C. G; French, S.; Brown, E. D; Bérdy, J.; Liu, D. Y; and others Nature chemical biology, 12(4): 233–239. 2016.
link bibtex

@article{johnston2016assembly,
  title={Assembly and clustering of natural antibiotics guides target identification},
  author={Johnston, Chad W and Skinnider, Michael A and Dejong, Chris A and Rees, Philip N and Chen, Gregory M and Walker, Chelsea G and French, Shawn and Brown, Eric D and B{\'e}rdy, J{\'a}nos and Liu, Dennis Y and others},
  journal={Nature chemical biology},
  volume={12},
  number={4},
  pages={233--239},
  year={2016},
  publisher={Nature Publishing Group}
}

Informatic search strategies to discover analogues and variants of natural product archetypes. Johnston, C. W; Connaty, A. D; Skinnider, M. A; Li, Y.; Grunwald, A.; Wyatt, M. A; Kerr, R. G; and Magarvey, N. A Journal of industrial microbiology & biotechnology, 43(2-3): 293–298. 2016.
link bibtex

@article{johnston2016informatic,
  title={Informatic search strategies to discover analogues and variants of natural product archetypes},
  author={Johnston, Chad W and Connaty, Alex D and Skinnider, Michael A and Li, Yong and Grunwald, Alyssa and Wyatt, Morgan A and Kerr, Russell G and Magarvey, Nathan A},
  journal={Journal of industrial microbiology \& biotechnology},
  volume={43},
  number={2-3},
  pages={293--298},
  year={2016},
  publisher={Springer}
}

2015 (5)

The Canadian clinician-scientist training program must be reinstated. Twa, D. D.; Squair, J. W; Skinnider, M. A; Ji, J. X; and others The Journal of Clinical Investigation, 125(12): 4317–4319. 2015.
link bibtex

@article{twa2015canadian,
  title={The Canadian clinician-scientist training program must be reinstated},
  author={Twa, David DW and Squair, Jordan W and Skinnider, Michael A and Ji, Jennifer X and others},
  journal={The Journal of Clinical Investigation},
  volume={125},
  number={12},
  pages={4317--4319},
  year={2015},
  publisher={Am Soc Clin Investig}
}

Genomes to natural products prediction informatics for secondary metabolomes (PRISM). Skinnider, M. A; Dejong, C. A; Rees, P. N; Johnston, C. W; Li, H.; Webster, A. L.; Wyatt, M. A; and Magarvey, N. A Nucleic acids research, 43(20): 9645–9662. 2015.
link bibtex

@article{skinnider2015genomes,
  title={Genomes to natural products prediction informatics for secondary metabolomes (PRISM)},
  author={Skinnider, Michael A and Dejong, Chris A and Rees, Philip N and Johnston, Chad W and Li, Haoxin and Webster, Andrew LH and Wyatt, Morgan A and Magarvey, Nathan A},
  journal={Nucleic acids research},
  volume={43},
  number={20},
  pages={9645--9662},
  year={2015},
  publisher={Oxford University Press}
}

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. Johnston, C. W; Skinnider, M. A; Wyatt, M. A; Li, X.; Ranieri, M. R.; Yang, L.; Zechel, D. L; Ma, B.; and Magarvey, N. A Nature communications, 6(1): 1–11. 2015.
link bibtex

@article{johnston2015automated,
  title={An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products},
  author={Johnston, Chad W and Skinnider, Michael A and Wyatt, Morgan A and Li, Xiang and Ranieri, Michael RM and Yang, Lian and Zechel, David L and Ma, Bin and Magarvey, Nathan A},
  journal={Nature communications},
  volume={6},
  number={1},
  pages={1--11},
  year={2015},
  publisher={Nature Publishing Group}
}

Exploration of nonribosomal peptide families with an automated informatic search algorithm. Yang, L.; Ibrahim, A.; Johnston, C. W; Skinnider, M. A; Ma, B.; and Magarvey, N. A Chemistry & biology, 22(9): 1259–1269. 2015.
link bibtex

@article{yang2015exploration,
  title={Exploration of nonribosomal peptide families with an automated informatic search algorithm},
  author={Yang, Lian and Ibrahim, Ashraf and Johnston, Chad W and Skinnider, Michael A and Ma, Bin and Magarvey, Nathan A},
  journal={Chemistry \& biology},
  volume={22},
  number={9},
  pages={1259--1269},
  year={2015},
  publisher={Elsevier}
}

Automated identification of depsipeptide natural products by an informatic search algorithm. Skinnider, M. A; Johnston, C. W; Zvanych, R.; and Magarvey, N. A ChemBioChem, 16(2): 223–227. 2015.
link bibtex

@article{skinnider2015automated,
  title={Automated identification of depsipeptide natural products by an informatic search algorithm},
  author={Skinnider, Michael A and Johnston, Chad W and Zvanych, Rostyslav and Magarvey, Nathan A},
  journal={ChemBioChem},
  volume={16},
  number={2},
  pages={223--227},
  year={2015},
  publisher={Wiley Online Library}
}