James D. R. Knight, PhD

Cultivarium
Watertown, Massachusetts, United States

Experience

Principal Software Engineer

Cultivarium
April 2022 - present
Boston, Massachusetts, United States
  • Architect, develop and manage a web portal for the aggregation of existing microorganism data as well as data generated by our team
  • Manage cloud infrastructure and develop operational tools for data management
  • Mentor the engineering and computational biology teams

Bioinformatician

Lunenfeld-Tanenbaum Research Institute
September 2015 - April 2022
Toronto, Ontario, Canada
Supervisor: Dr. Anne-Claude Gingras
  • Performed data analysis for large-scale proteomic projects in the lab
  • Developed software to aid molecular biologists with analysis, visualization and productivity
  • Created web resources for the management, analysis and distribution of data

Postdoctoral fellow

Lunenfeld-Tanenbaum Research Institute
September 2011 - August 2015
Toronto, Ontario, Canada
Supervisor: Dr. Anne-Claude Gingras
  • Studied cerebral cavernous malformations, a vascular disease of the central nervous system
  • Identified novel interactors and functions for the three CCM proteins that cause genetic forms of this disease
  • Generated a large protein-interaction network for CCM and related proteins that covers multiple cell types and organisms
  • Developed computation tools for the visualization of proteomics data

PhD thesis

Ottawa Hospital Research Institute
September 2005 - August 2011
Ottawa, Ontario, Canada
Supervisor: Dr. Rashmi Kothary
  • Characterized through computational approaches the structural heterogeneity that exists within the protein kinase superfamily
  • Discovered structural water molecule conversation across the kinase superfamily
  • Developed a technique for kinase-substrate finding that allows for the substrates of a kinase to be specifically determined from any cell type of interest

Summer student

McMaster University
May - August 2002, August - September 2003
Hamilton, Ontario, Canada
Supervisor: Dr. David J. D. Earn
  • Studied the effects of migration between isolated organism populations using individual- and population-based computer models

Summer student

University of York
June - August 2003
York, UK
Supervisor: Dr. Jon W. Pitchford
  • Developed a mathematical model for a non-equilibrium soil food-web and explored the effects of system dynamics and spatial heterogeneity as part of a wider national research program involving soil biodiversity

Undergraduate thesis

McMaster University
September 2001 - April 2002
Hamilton, Ontario, Canada
Supervisor: Dr. G. Brian Golding
  • Developed a mathematical algorithm for detecting functional divergence between homologous protein sequences

Summer student

McMaster University
May - August 2000, May - August 2001
Hamilton, Ontario, Canada
Supervisor: Dr. G. Brian Golding
  • Worked on quantifying amino acid substitution rate heterogeneity at the structural protein level across large phylogenetic trees

Academic Degrees

PhD
2011
Cellular and Molecular Medicine, University of Ottawa
BA
2005
English and History, University of York (United Kingdom)
BSc
2002
Biology and Mathematics, McMaster University

Awards

2015
Travel award to attend Human Proteome Organization World Congress
Awarding Body: Canadian National Proteomics Network
2015
TD Bank Health Research Fellowship at the LTRI
Awarding Body: Lunenfeld-Tanenbaum Research Institute
2012 - 2014
Postdoctoral Research Fellowship
Awarding Body: Heart and Stroke Foundation of Canada
2011
Faculty of Graduate and Postdoctoral Studies Dean’s Scholarship
Awarding Body: University of Ottawa
2009 - 2011
Vanier Canada Graduate Scholarship
Awarding Body: Canadian Institutes of Health Research
2006 - 2009
Canada Research Studentship
Awarding Body: Multiple Sclerosis Society of Canada
2005 - 2011
Excellence Scholarship
Awarding Body: University of Ottawa
2005
Canada Graduate Scholarship Master’s award
Awarding Body: Canadian Institutes of Health Research
2002
Undergraduate Student Research Award
Awarding Body: National Science and Engineering Research Council
For research to be undertaken with the supervision of Dr David Earn
2001
The George P. and Leatha M. Keys Scholarship
Awarding Body: McMaster University
Awarded for outstanding achievement in Honours Mathematics
2001
The Herbert A. Ricker Scholarship
Awarding Body: McMaster University
Awarded for scholarship and character in Science
2001
Undergraduate Student Research Award
Awarding Body: National Science and Engineering Research Council
For research to be undertaken with the supervision of Dr Brian Golding
2000
Senate Scholarship
Awarding Body: McMaster University
2000
Undergraduate Student Research Award
Awarding Body: National Science and Engineering Research Council
For research to be undertaken with the supervision of Dr Brian Golding
1998
Science Incentive Scholarship
Awarding Body: McMaster University

Publications

First authored

  1. Go C*, Knight JDR*, Rajasekharan A, Rathod B, Hesketh GG, Abe KT, Youn JY, Samavarchi-Tehrani P, Zhang H, Zhu LY, Popiel E, Lambert JP, Coyaud E, Cheung SWT, Rajendran D, Wong CJ, Antonicka H, Pelletier LP, Palazzo AF, Shoubridge EA, Raught B, and Gingras AC (2021). A proximity-dependent biotinylation map of a human cell. Nature, 595:120-124.
  2. Knight JDR, Samavarchi-Tehrani P, Tyers M, and Gingras AC (2019). Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. Nature Methods, 16:665-666.
  3. Knight JDR, Choi H, Gupta G, Pelletier L, Raught B, Nesvizhskii AI, and Gingras AC (2017). ProHits-viz: a suite of web-tools for visualizing interaction proteomics data. Nature Methods, 14:645-646.
  4. Knight JDR, Liu G, Zhang JP, Pasculescu A, Choi H, and Gingras AC (2015). A web-tool for visualizing quantitative protein-protein interaction data. Proteomics, 15:1432-1436.
  5. Knight JDR, Pawson T, and Gingras AC (2013). Profiling the kinome: current capabilities and future challenges. Journal of Proteomics, 81:43-55.
  6. Knight JDR, and Kothary R (2012). The extracellular kinome. Kinome, 1:1-3.
  7. Knight JDR, Tian R, Lee REC, Wang F, Beauvais A, Zou H, Megeney LA, Gingras AC, Pawson T, Figeys D, and Kothary R (2012). A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts. Skeletal Muscle, 2:5.
  8. Knight JDR, and Kothary R (2011). The myogenic kinome: protein kinases critical to mammalian skeletal myogenesis. Skeletal Muscle, 1:29.
  9. Knight JDR, Hamelberg D, McCammon JA, and Kothary R (2009). The role of conserved water molecules in the catalytic domain of protein kinases. Proteins: Structure, Function, and Bioinformatics, 76:527-535.
  10. Knight JDR, Qian B, Baker D, and Kothary R (2007). Conservation, variability and the modeling of active protein kinases. PLoS ONE, 2:e982.
* co-first author

Co-authored

  1. Samavarchi-Tehrani P, Abdouni H, Knight JDR, Astori A, Samson R, Lin ZY, Kim DK, Knapp JJ, St-Germain J, Go CD, Larsen B, Wong CJ, Cassonnet P, Demeret C, Jacob Y, Roth FP, Raught B, and Gingras AC (2020). A SARS-CoV-2 – host proximity interactome. bioRχiv.
  2. Hesketh GG, Papazotos F, Pawling J, Rajendran D, Knight JDR, Martinez S, Taipale M, Schramek D, Dennis J, and Gingras AC (2020). Free and lysosome-derived amino acids activate mTORC1 through distinct pathways. Science, 370:351-356.
  3. Youn JY, Dyakov BJA, Zhang JP, Knight JDR, Vernon RM, Forman-Kay JD, and Gingras AC (2019). Proteomic landscapes of stress granules and P-bodies. Molecular Cell, 76:286-294.
  4. Lambert JP, Picaud S, Fujisawa T, Hou H, Savitsky P, Uusküla-Reimand L, Gupta G, Abdouni H, Lin ZY, Tucholska M, Knight JDR, Gonzalez-Badillo B, St-Denis N, Newman J, Stucki M, Pelletier L, Bandeira N, Wilson M, Filippakopoulos P, and Gingras AC (2019). Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains. Molecular Cell, 73:621-638.
  5. Youn JY, Dunham WH, Hong SJ, Knight JDR, Chen GI, Bagci H, Bashkurov M, Rathod B, MacLeod G, Eng SWM, Angers S, Morris Q, Fabian M, Côté JF, and Gingras AC (2018). High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies. Molecular Cell, 69:517-532.
  6. Couzens AL, Xiong S, Knight JDR, Mao DY, Guettler S, Picaud S, Kurinov I, Filippakopoulos P, Sicheri F, and Gingras AC (2017). MOB1 mediated phospho-recognition in the core mammalian Hippo pathway. Molecular and Cellular Proteomics, 16:1098-1110.
  7. St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JDR, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SWT, Pelletier L, and Gingras AC (2016). Phenotypic and interaction profiling of the human phosphatases identifies diverse mitotic regulators. Cell Reports, 17: 2488-2501.
  8. Liu G, Knight JDR, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii A, Choi H, and Gingras AC (2016). Data Independent Acquisition analysis in ProHits 4.0. J Proteomics, 149: 64-68.
  9. Teo G, Koh H, Fermin D, Lambert JP, Knight JDR, Gingras AC, and Choi HW (2016). SAINTq: Scoring protein-protein interactions in affinity purification – mass spectrometry experiments with fragment or peptide intensity data. Proteomics, 16: 15-16.
  10. De Kreuk BJ, Gingras AR, Knight JDR, Liu JJ, Gingras AC, and Ginsberg MH (2016). Heart of Glass Anchors Rasip1 at Endothelial Cell-Cell Junctions to Support Vascular Integrity. eLife, 5: e11394.
  11. Gupta GD, Coyaud É, Gonçalves J, Mojarad BA, Liu Y, Wu Q, Gheiratmand L, Comartin D, Tkach JM, Cheung SW, Bashkurov M, Hasegan M, Knight JDR, Lin ZY, Schueler M, Hildebrandt F, Moffat J, Gingras AC, Raught B, and Pelletier L (2015). A dynamic protein interaction landscape of the human centrosome-cilium interface. Cell, 163: 1484-99.
  12. Wang J, Tucholska M, Knight JDR, Lambert JP, Larsen B, Tate S, Gingras AC, and Bandeira N (2015). MSPLIT-DIA: Sensitive peptide identification for data-independent acquisition. Nature Methods, 12: 1106-8.
  13. Lambert JP, Tucholska M, Go C, Knight JDR, and Gingras AC (2015). Proximity biotinylation and affinity purification are complimentary approaches for the interactome mapping of chromatin-associated protein complexes. Journal of Proteomics, 118:81-94.
  14. Lant B, Yu B, Goudreault M, Holmyard D, Knight JDR, Xu P, Zhao X, Chin K, Wallace E, Zhen M, Gingras AC, and Derry WB (2015). CCM-3/STRIPAK promotes seamless tube extension through endosome recycling. Nature Communications, 6:6449.
  15. Turowec JP, Zukowsli SA, Knight JDR, Smalley DM, Graves LM, Johnson GL, Li SS, Lajoie GA, and Litchfield DW (2014). An unbiased, proteomic screen reveals caspase cleavage is positively and negatively regulated by substrate phosphorylation. Molecular and Cellular Proteomics, 13:1184-97.
  16. Couzens AL, Knight JDR, Kean MJ, Teo G, Weiss A, Dunham W, Lin Z-Y, Bagshaw RD, Sicheri F, Pawson T, Wrana J, Choi H, and Gingras AC (2013). Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions. Science Signaling, 6: rs15.
  17. Costa B, Kean MJ, Ast V, Knight JDR, Mett A, Levy Z, Ceccarelli DF, Badillo BG, Eils R, König R, Gingras AC, and Fainzilber M (2012). STK25 mediates TrkA and CCM2 dependent death in pediatric tumor cells of neural origin. Journal of Biological Chemistry, 287: 29285–29289.
  18. Fukuda K, Knight JDR, Piszczek G, Kothary R, and Qin J (2011). Biochemical, proteomic, structural, and thermodynamic characterizations of ILK: Cross-validation of the pseudokinase. Journal of Biological Chemistry, 286:21886–21895.

Talks

  1. Knight JDR, Choi H, Raught B, Nesvizhskii AI, and Gingras AC (2017). ProHits-viz: a suite of web-tools for visualizing interaction proteomics data. The 9th Annual CNPN Symposium: "Next Generation Proteomics: Functional Organization of the Human Proteome", Toronto, Canada.
  2. Knight JDR (2017). CNPN ProHits workshop. The 9th Annual CNPN Symposium: "Next Generation Proteomics: Functional Organization of the Human Proteome", Toronto, Canada.
  3. Knight JDR, Liu G, Zhang JP, Youn JY, Go C, Choi HW, and Gingras AC (2016). ProHits-viz: Interactively visualizing and analyzing protein interactome data. The 8th Annual CNPN Symposium: "Proteomic Advances in Health and Diseases", Montreal, Canada.
  4. Knight JDR, Ceccarelli D, Sicheri F, Pawson T, and Gingras AC (2013). Proteomic charactization of CCM3-GCKIII complexes. 9th Annual Angioma Alliance CCM Scientific Meeting, Washington, DC, USA.
  5. Knight JDR, Couzens A, Ceccarelli D, Guettler S, Sicheri F, Pawson T, and Gingras AC (2013). Elucidating signaling networks for the Mammalian Ste20-like (MST) kinases using interaction proteomics and substrate screening. Proteins Kinases and Protein Phosphorylation, Niagara Falls, NY, USA.
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© James Knight, 2023.