photo

Eugenia Oshurko

PhD student at the ENS Lyon
(team PLUME, LIP)

Contact me

e-mail

My CV can be found here

My GitHub Github

My main research interests include rule-based modelling, knowledge representation, graph rewriting, graph databases as well as computational biology and modelling of complex systems in general.

Research

Journals

  • R. Harmer R., Le Cornec Y., Légaré S. and Oshurko E. (2019), Bio-curation for cellular signalling: the KAMI project. In IEEE/ACM Transactions on Computational Biology and Bioinformatics.

International Conferences

  • A. Bonifati, P. Furniss, A. Green, R. Harmer, E. Oshurko, H. Voigt (2019). Schema Validation and Evolution for Graph Databases. In Conceptual Modeling: 38th International Conference, ER 2019 (pp. 448-456). Springer Nature.
  • Harmer, R., Oshurko, E. (2019). KAMIStudio: An Environment for Biocuration of Cellular Signalling Knowledge. In International Conference on Computational Methods in Systems Biology (pp. 322-328). Springer, Cham.
  • Harmer, R., Oshurko, E. (2019). Knowledge Representation and Update in Hierarchies of Graphs. In International Conference on Graph Transformation (pp. 141-158). Springer, Cham.
  • Harmer, R., Le Cornec, Y. S., Légaré, S., Oshurko, I. (2017). Bio-Curation for Cellular Signalling: The KAMI Project. In International Conference on Computational Methods in Systems Biology (pp. 3-19). Springer, Cham.

Pre-prints

  • Bonifati, A., Furniss, P., Green, A., Harmer, R., Oshurko, E., & Voigt, H. (2019). Schema Validation and Evolution for Graph Databases. arXiv preprint arXiv:1902.06427.

Talks & Poster Presentations

  • Talk Schema Validation and Evolution for Graph Databases, 38th International Conference on Conceptual Modeling (ER 2019), Salvador, Bahia, Brazil, November 2019 [slides].
  • Talk KAMIStudio: an environment for bio-curation of cellular signalling knowledge, [BC]^2 Workshop 'Annotation and curation of computational models in biology', Basel, September 2019 [slides].
  • Talk Knowledge representation and update in hierarchies of graphs, ICGT 2019 - 12th International Conference on Graph Transformation, Eindhoven, July 2019 [slides].
  • Talk Schema Validation and Evolution for Graph Databases, Fifth openCypher Implementers Meeting (oCIM 5), Berlin, March 2019 [slides].
  • Poster presentation KAMI: a bio-curation tool for cellular signalling, ICSB 2018 - 19th International Conference on Systems Biology, Lyon, November 2018
  • [poster].
  • Talk Representation and aggregation of cellular signalling knowledge in KAMI, Meeting of Bioss Working Group in Symbolic Systems Biology, Marseille, July 2018
  • [slides].

Theses and Memoires

  • Oshurko I. (2017, June). Graph-based hierarchical knowledge representation (an application to rule-based modelling and bio-curation) [pdf]. Master 2 thesis at the ENS de Lyon.

Awards

  • The EATCS Best Paper Award at ICGT 2019, the 12th International Conference on Graph Transformation.

Software

Teaching

  • Fall 2019-2020, Programmation Web Client Riche (JavaScript, in French) course, lectures and practical sessions for L2 students, IUT Lyon 1
  • Spring 2018-2019, Distributed Systems course, practical sessions for Master 1 students of Fundamental Computer Science, ENS Lyon
  • Spring 2018-2019, Computational Complexity course, problem solving sessions for Master 1 students of Fundamental Computer Science, ENS Lyon
  • Fall 2018-2019, Information Theory course, problem solving sessions for Master 1 students of Fundamental Computer Science, ENS Lyon
  • Spring 2017-2018, Computational Complexity course, problem solving sessions for Master 1 students of Fundamental Computer Science, ENS Lyon
  • Fall 2017-2018, Information Theory course, problem solving sessions for Master 1 students of Fundamental Computer Science, ENS Lyon