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 am affiliated with the Loyola University Medical Center group of Harel Dahari since Aug. 2017.

Publications

  1. V. Reinharz, H. Dahari and D. Barash
    Numerical Schemes for Solving and Optimizing Multiscale Models with Age of Hepatitis C Virus Dynamics
    In Mathematical Biosciences, 2018.
    DOI: 10.1016/j.mbs.2018.03.011, Preprint, bibtex
  2. V. Reinharz, A. Soulé, E. Westhof, J. Waldispühl and A. Denise
    Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families
    In Nucleic Acids Research, 2018.
    DOI: 10.1093/nar/gky197, Preprint, bibtex
  3. V. Reinharz, A. Churkin, Harel Dahari and D. Barash
    A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics
    In Frontiers in Applied Mathematics and Statistics, 2017.
    DOI: 10.3389/fams.2017.00020, Preprint, bibtex
  4. J. Yao, V. Reinharz, F. Major and J. Waldispühl
    RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data
    In Nucleic Acids Research, 2017.
    DOI: 10.1093/nar/gkx429, Preprint, bibtex
  5. A. Churkin, M. D. Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl and D. Barash
    Design of RNAs: comparing programs for inverse RNA folding
    In Briefings in Bioinformatics, 2017.
    DOI: 10.1093/bib/bbw120, Preprint, bibtex
  6. O. Tremblay-Savard, V. Reinharz and J. Waldispühl
    Reconstruction of ancestral RNA sequences under multiple structural constraints
    In proceedings of 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: genomics, BMC Genomics, 2016.
    DOI: 10.1186/s12864-016-3105-4, Preprint, bibtex
  7. M.D. Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl and 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, bibtex
  8. V. Reinharz, Y. Ponty and 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, bibtex
  9. V. Reinharz, Y. Ponty and 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, bibtex
  10. V. Reinharz, Y. Ponty and 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.
    DOI: 10.1093/bioinformatics/btt217, Preprint, bibtex
    Recording of the presentation
  11. V. Reinharz, Y. Ponty and 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.
    DOI: 10.1007/978-3-642-37195-0_17, Preprint, bibtex
    Picture
  12. V. Reinharz, F. Major and 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.
    DOI: 10.1093/bioinformatics/BTS226, Preprint, bibtex
    Recording of the presentation

Preprints

  1. C. G. Oliver, V. Reinharz and J. Waldispühl
    The necessary emergence of structural complexity in self-replicating RNA populations
    On bioRχiv, 2017.
    DOI: 10.1101/218990, bibtex

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, bibtex

Softwares and Web servers

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

Richard Feynman - Ode To A Flower YouTube

ORCID iD iconorcid.org/0000-0001-8481-1094

You can contact me using one of the following emails: