Papers currently undergoing peer review

Nothing to report here, I should probably start doing something if I want to finish my PhD.

Peer-reviewed papers

  • A. Soulé, V. Reinharz, R. Sarrazin-Gendron, A. Denise, J. Waldispühl. Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs, PLOS Computational Biology (2021) full text

  • C.G. Oliver, V. Mallet, R. Sarrazin-Gendron, V. Reinharz, W.L. Hamilton, N. Moitessier, J. Waldispühl. Augmented base pairing networks encode RNA-small molecule binding preferences. Nucleic acids research (2020) full text

  • R. Sarrazin-Gendron, H. Yao, V. Reinharz, C. Oliver, Y. Ponty and J. Waldispühl. Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification, RECOMB Proceedings (2020) full text.

  • R. Sarrazin-Gendron, V. Reinharz, C. G. Oliver, N. Moitessier and J. Waldispühl. Automated, customizable and efficient identification of 3D base pair modules with BayesPairing. Nucleic acids research (2019) full text.

  • K. Kenyon-Dean, E. Ahmed, S. Fujimoto, …, R. Sarrazin-Gendron et al. Sentiment Analysis: It’s Complicated!. NAACL 2018 full text

Textbook Chapters

Modeling and Predicting RNA Three-Dimensional Structures, RNA Bioinformatics, Springer (2021). preprint full text.

Software and web-servers

Automatic identification of 3D structural modules in RNA sequences.


  • M.Sc. Thesis (full text)
  • Ph.D. Comprehensive Exam Literature Review (PDF)