publications

2023

1. Association of CSF and Serum Neurofilament Light and Glial Fibrillary Acidic Protein, Injury Severity, and Outcome in Spinal Cord Injury

   Sophie Stukas, Jennifer Cooper, Jasmine Gill, Nader Fallah, Michael A Skinnider, Lise Belanger, Leanna Ritchie, Angela Tsang, Kevin Dong, Femke Streijger, and  others

   Neurology, 2023
2. The Tabulae Paralytica: Multimodal single-cell and spatial atlases of spinal cord injury

   Michael A Skinnider*, Matthieu Gautier*, Alan Yue Yang Teo, Claudia Kathe, Thomas Hutson, Achilleas Laskaratos, Alexandra Coucy, Nicola Regazzi, Viviana Aureli, Nicholas D James, Bernard Schneider, Michael Sofroniew, Quentin Barraud, Jocelyne Bloch, and 3 more authors

   bioRxiv, 2023

2022

1. The neurons that restore walking after paralysis

   Claudia Kathe*, Michael A Skinnider*, Thomas H Hutson*, Nicola Regazzi, Matthieu Gautier, Robin Demesmaeker, Salif Komi, Steven Ceto, Nicholas D James, Newton Cho, and  others

   Nature, 2022

2021

1. On the robustness of graph-based clustering to random network alterations

   R Greg Stacey, Michael A Skinnider, and Leonard J Foster

   Mol. Cell. Proteomics, 2021
2. Cell type prioritization in single-cell data

   Michael A Skinnider*, Jordan W Squair*, Claudia Kathe, Mark A Anderson, Matthieu Gautier, Kaya JE Matson, Marco Milano, Thomas H Hutson, Quentin Barraud, Aaron A Phillips, and  others

   Nature Biotechnology, 2021
3. PrInCE: an R/Bioconductor package for protein–protein interaction network inference from co-fractionation mass spectrometry data

   Michael A Skinnider, Charley Cai, R Greg Stacey, and Leonard J Foster

   Bioinformatics, 2021
4. Confronting false discoveries in single-cell differential expression

   Jordan W Squair, Matthieu Gautier, Claudi Kathe, Mark A Anderson, Nicholas D James, Thomas H Hutson, Rémi Hudelle, Taha Qaiser, Kaya JE Matson, Quentin Barraud, and  others

   Nature Communications, 2021
5. A deep generative model enables automated structure elucidation of novel psychoactive substances

   Michael A Skinnider, Fei Wang, Daniel Pasin, Russell Greiner, Leonard J Foster, Petur W Dalsgaard, and David S Wishart

   Nat. Mach. Intell., 2021
6. Proteomic portraits reveal evolutionarily conserved and divergent responses to spinal cord injury

   Michael A Skinnider, Jason Rogalski, Seth Tigchelaar, Neda Manouchehri, Anna Prudova, Angela M Jackson, Karina Nielsen, Jaihyun Jeong, Shalini Chaudhary, Katelyn Shortt, and  others

   Mol. Cell. Proteomics, 2021
7. Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

   Jordan W Squair*, Michael A Skinnider*, Matthieu Gautier, Leonard J Foster, and Grégoire Courtine

   Nature Protocols, 2021
8. Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments

   Michael A Skinnider, and Leonard J Foster

   Nature Methods, 2021
9. An atlas of protein-protein interactions across mouse tissues

   Michael A Skinnider*, Nichollas E Scott*, Anna Prudova, Craig H Kerr, Nikolay Stoynov, R Greg Stacey, Queenie WT Chan, David Rattray, Jörg Gsponer, and Leonard J Foster

   Cell, 2021
10. Chemical language models enable navigation in sparsely populated chemical space

    Michael A Skinnider, R Greg Stacey, David S Wishart, and Leonard J Foster

    Nat. Mach. Intell., 2021
11. Enabling reproducible re-analysis of single-cell data

    Michael A Skinnider, Jordan W Squair, and Grégoire Courtine

    Genome Biol., 2021

2020

1. DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products

   Nishanth J Merwin*, Walaa K Mousa*, Chris A Dejong, Michael A Skinnider, Michael J Cannon, Haoxin Li, Keshav Dial, Mathusan Gunabalasingam, Chad Johnston, and Nathan A Magarvey

   Proc. Natl. Acad. Sci. U.S.A., 2020
2. Dynamic rewiring of the human interactome by interferon signaling

   Craig H Kerr*, Michael A Skinnider*, Daniel DT Andrews, Angel M Madero, Queenie WT Chan, R Greg Stacey, Nikolay Stoynov, Eric Jan, and Leonard J Foster

   Genome Biol., 2020
3. Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences

   Michael A Skinnider, Chad W Johnston, Mathusan Gunabalasingam, Nishanth J Merwin, Agata M Kieliszek, Robyn J MacLellan, Haoxin Li, Michael RM Ranieri, Andrew LH Webster, My PT Cao, and  others

   Nat. Commun., 2020

2019

1. Evaluating measures of association for single-cell transcriptomics

   Michael A Skinnider, Jordan W Squair, and Leonard J Foster

   Nat. Methods, 2019

2018

1. Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis

   Michael A Skinnider, Chad W Johnston, Nishanth J Merwin, Chris A Dejong, and Nathan A Magarvey

   BMC Genomics, 2018
2. Genomic data integration systematically biases interactome mapping

   Michael A Skinnider, R Greg Stacey, and Leonard J Foster

   PLoS Comput. Biol., 2018
3. Predictors of sustained research involvement among MD/PhD programme graduates

   Michael A Skinnider, David DW Twa, Jordan W Squair, Norman D Rosenblum, Christine D Lukac, and Canadian MD/PhD Program Investigation Group

   Med. Educ., 2018
4. Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury

   Jordan W Squair, Seth Tigchelaar, Kyung-Mee Moon, Jie Liu, Wolfram Tetzlaff, Brian K Kwon, Andrei V Krassioukov, Christopher R West, Leonard J Foster, and Michael A Skinnider

   eLife, 2018
5. Context-specific interactions in literature-curated protein interaction databases

   R Greg Stacey, Michael A Skinnider, Jenny HL Chik, and Leonard J Foster

   BMC Genomics, 2018

2017

1. A targeted proteomics analysis of cerebrospinal fluid after acute human spinal cord injury

   Femke Streijger, Michael A Skinnider, Jason C Rogalski, Robert Balshaw, Casey P Shannon, Anna Prudova, Lise Belanger, Leanna Ritchie, Angela Tsang, Sean Christie, and  others

   J. Neurotrauma, 2017
2. PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

   Michael A Skinnider, Nishanth J Merwin, Chad W Johnston, and Nathan A Magarvey

   Nucleic Acids Res., 2017
3. Characteristics and outcomes of Canadian MD/PhD program graduates: a cross-sectional survey

   Michael A Skinnider*, Jordan W Squair*, David DW Twa*, Jennifer X Ji*, Alexandra Kuzyk, Xin Wang, Patrick E Steadman, Kirill Zaslavsky, Ayan K Dey, Mark J Eisenberg, and  others

   CMAJ Open, 2017
4. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)

   R Greg Stacey, Michael A Skinnider, Nichollas E Scott, and Leonard J Foster

   BMC Bioinformatics, 2017
5. Statistical reanalysis of natural products reveals increasing chemical diversity

   Michael A Skinnider, and Nathan A Magarvey

   Proc. Natl. Acad. Sci. U.S.A., 2017
6. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

   Michael A Skinnider, Chris A Dejong, Brian C Franczak, Paul D McNicholas, and Nathan A Magarvey

   J. Cheminform., 2017
7. Cross-sectional-derived determinants of satisfaction with physician-scientist training among Canadian MD/PhD graduates

   David DW Twa, Michael A Skinnider, Jordan W Squair, Christine D Lukac, and Canadian MD/PhD Program Investigation Group

   PloS ONE, 2017

2016

1. Informatic search strategies to discover analogues and variants of natural product archetypes

   Chad W Johnston, Alex D Connaty, Michael A Skinnider, Yong Li, Alyssa Grunwald, Morgan A Wyatt, Russell G Kerr, and Nathan A Magarvey

   J. Indust. Microbiol. Biotechnol., 2016
2. Assembly and clustering of natural antibiotics guides target identification

   Chad W Johnston, Michael A Skinnider, Chris A Dejong, Philip N Rees, Gregory M Chen, Chelsea G Walker, Shawn French, Eric D Brown, János Bérdy, Dennis Y Liu, and  others

   Nat. Chem. Biol., 2016
3. Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching

   Chris A Dejong*, Gregory M Chen*, Haoxin Li*, Chad W Johnston, Mclean R Edwards, Philip N Rees, Michael A Skinnider, Andrew LH Webster, and Nathan A Magarvey

   Nat. Chem. Biol., 2016
4. Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

   Michael A Skinnider*, Chad W Johnston*, Robyn E Edgar, Chris A Dejong, Nishanth J Merwin, Philip N Rees, and Nathan A Magarvey

   Proc. Natl. Acad. Sci. U.S.A., 2016

2015

1. Automated identification of depsipeptide natural products by an informatic search algorithm

   Michael A Skinnider*, Chad W Johnston*, Rostyslav Zvanych, and Nathan A Magarvey

   ChemBioChem, 2015
2. Exploration of nonribosomal peptide families with an automated informatic search algorithm

   Lian Yang*, Ashraf Ibrahim*, Chad W Johnston*, Michael A Skinnider, Bin Ma, and Nathan A Magarvey

   Chemistry & Biology, 2015
3. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

   Chad W Johnston*, Michael A Skinnider*, Morgan A Wyatt, Xiang Li, Michael RM Ranieri, Lian Yang, David L Zechel, Bin Ma, and Nathan A Magarvey

   Nat. Commun., 2015
4. Genomes to natural products Prediction informatics for secondary metabolomes (PRISM)

   Michael A Skinnider, Chris A Dejong, Philip N Rees, Chad W Johnston, Haoxin Li, Andrew LH Webster, Morgan A Wyatt, and Nathan A Magarvey

   Nucleic Acids Res., 2015
5. The Canadian clinician-scientist training program must be reinstated

   David DW Twa*, Jordan W Squair*, Michael A Skinnider*, and Jennifer X Ji*

   J. Clin. Invest., 2015

1967

1. 

   Letters on wave mechanics

   Albert Einstein, Erwin Schrödinger, Max Planck, Hendrik Antoon Lorentz, and Karl Przibram

   1967

   Bib

   @book{przibram1967letters,
     title = {Letters on wave mechanics},
     author = {Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl},
     year = {1967},
     publisher = {Vision},
   }

1956

1. 

   Investigations on the Theory of the Brownian Movement

   Albert Einstein

   1956

   Bib

   @book{einstein1956investigations,
     title = {Investigations on the Theory of the Brownian Movement},
     author = {Einstein, Albert},
     year = {1956},
     publisher = {Courier Corporation},
   }

1950

1. AJP

   The meaning of relativity

   Albert Einstein, and AH Taub

   American Journal of Physics, 1950

   Bib

   @article{einstein1950meaning,
     title = {The meaning of relativity},
     author = {Einstein, Albert and Taub, AH},
     journal = {American Journal of Physics},
     volume = {18},
     number = {6},
     pages = {403--404},
     year = {1950},
     publisher = {American Association of Physics Teachers}
   }

1935

1. PhysRev

   Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?

   A. Einstein, B. Podolsky, and N. Rosen

   Phys. Rev., May 1935

   Abs HTML PDF

   In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.

1905

1. Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen

   A. Einstein

   Annalen der physik, May 1905
2. Ann. Phys.

   Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat

   A. Einstein

   Ann. Phys., May 1905
3. On the electrodynamics of moving bodies

   A. Einstein

   May 1905