Me from really close
Me from really close

Vladimir Reinharz

I am an Azrieli and FQRNT postdoctoral fellow at Ben-Gurion University of the Negev in the group of Danny Barash since Sept. 2016.

I received my Ph.D. from McGill in Aug. 2016 under the supervision of Jérôme Waldispühl and Yann Ponty, funded by an Alexander Graham Bell Canada (CGS D3) scholarship.
I visited the Laboratoire de Recherche en Informatique under the supervision of Alain Denise at Paris-Sud from January to June 2013 thanks to a TEE Erasmus scholarship.

Publications

  1. O. Tremblay-Savard, V. Reinharz, J. Waldispühl, Reconstruction of ancestral RNA sequences under multiple structural constraints
    In BMC Genomics, 2016.
    DOI: 10.1186/s12864-016-3105-4, Preprint
  2. M.D. Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, D. Barash, incaRNAfbinv: a web server for the fragment-based design of RNA sequences
    In Nucleic acids research, 2016.
    DOI: 10.1093/nar/gkw440, Preprint
  3. V. Reinharz, Y. Ponty, J. Waldispühl, Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces
    In Nucleic Acids Research, 2016.
    DOI: 10.1093/nar/gkw217 , Preprint
  4. V. Reinharz, Y. Ponty, J. Waldispühl, Using structural and evolutionary information to detect and correct pyrosequencing errors in non-coding RNAs
    Extended version of A linear inside-outside algorithm for correcting sequencing errors in structured RNAs
    In the Journal of Computational Biology, 2013.
    DOI: 10.1089/cmb.2013.0085, Preprint
  5. V. Reinharz, Y. Ponty, J. Waldispühl, A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution
    In proceedings of the 21st Annual International Conference on Intelligent Systems for Molecual Biology / 12th European Conference on Computational Biology (ISMB/ECCB), Bioinformatics, 2013. [Acceptance rate 16%]
    DOI: 10.1093/bioinformatics/btt217, Preprint
    Recording of the presentation
  6. V. Reinharz, Y. Ponty, J. Waldispühl, A linear inside-outside algorithm for correcting sequencing errors in structured RNAs
    In proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Research in Computational Molecular Biology, Lecture Notes in Computer Science, 2013. [Acceptance rate 20%]
    DOI: 10.1007/978-3-642-37195-0_17, Preprint
    Picture
  7. V. Reinharz, F. Major, J. Waldispühl, Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure
    In proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics, 2012. [Acceptance rate 13%]
    DOI: 10.1093/bioinformatics/BTS226, Preprint
    Recording of the presentation

Book Chapters

  1. J. Waldispühl and V. Reinharz, Modeling and Predicting RNA Three-dimensional Structures
    In RNA Bioinformatics, Series: Methods in Molecular Biology, Vol. 1269. Humana Press, 2015.
    ISBN: 978-1-4939-2290-1, DOI: 10.1007/978-1-4939-2291-8_6, Preprint

Miscellaneous

  1. Ph.D. Thesis
    Algorithmic Properties of Evolved Structured RNAs PDF (defence slides)
  2. MSc Thesis
    Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure PDF
  3. BSc projet final
    Classes de Complexité & Problèmes de Satisfaction de Contraintes PDF

Other

My plant Lazarus

You can contact me using one of the following emails: