Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. - Vladimir Reinharz; François Major; Jérôme Waldispühl (Bioinform., 2012)

A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (RECOMB, 2013)

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (Bioinform., 2013)

Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (J. Comput. Biol., 2013)

incaRNAfbinv: a web server for the fragment-based design of RNA sequences. - Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Nucleic Acids Res., 2016)

A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics. - Vladimir Reinharz; Alexander Churkin; Harel Dahari; Danny Barash (Frontiers Appl. Math. Stat., 2017)

RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. - Jason Yao; Vladimir Reinharz; François Major; Jérôme Waldispühl (Nucleic Acids Res., 2017)

Design of RNAs: comparing programs for inverse RNA folding. - Alexander Churkin; Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Briefings Bioinform., 2018)

Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. - Roman Sarrazin-Gendron; Hua-Ting Yao; Vladimir Reinharz; Carlos G. Oliver; Yann Ponty; Jérôme Waldispühl (RECOMB, 2020)

incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. - Matan Drory Retwitzer; Vladimir Reinharz; Alexander Churkin; Yann Ponty; Jérôme Waldispühl; Danny Barash (Bioinform., 2020)

A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures. - Coline Gianfrotta; Vladimir Reinharz; Dominique Barth; Alain Denise (SEA, 2021)

Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs. - Antoine Soulé; Vladimir Reinharz; Roman Sarrazin-Gendron; Alain Denise; Jérôme Waldispühl (PLoS Comput. Biol., 2021)

Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. - Théo Boury; Yann Ponty; Vladimir Reinharz (WABI, 2023)

Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics. - Atesmachew Hailegiorgis; Yuji Ishida; Nicholson T. Collier; Michio Imamura; Zhenzhen Shi; Vladimir Reinharz; Masataka Tsuge; Danny Barash; Nobuhiko Hiraga; Hiroshi Yokomichi; Chise Tateno; Jonathan Ozik; et al. (PLoS Comput. Biol., 2023)

Parallel Maximal Common Subgraphs with Labels for Molecular Biology. - Wilfried Agbeto; Camille Coti; Vladimir Reinharz (PPAM (1), 2024)

Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework. - Gabriel Loyer; Vladimir Reinharz (Bioinform., 2024)