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Vladimir Reinharz
Vladimir Reinharz
Assistant Professor, Computer Science Department, Université du Québec à Montréal
Verified email at uqam.ca - Homepage
Title
Cited by
Cited by
Year
Design of RNAs: comparing programs for inverse RNA folding
A Churkin, MD Retwitzer, V Reinharz, Y Ponty, J Waldispühl, D Barash
Briefings in bioinformatics 19 (2), 350-358, 2018
672018
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure
V Reinharz, F Major, J Waldispühl
Bioinformatics 28 (12), i207-i214, 2012
612012
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution
V Reinharz, Y Ponty, J Waldispühl
Bioinformatics 29 (13), i308-i315, 2013
572013
Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families
V Reinharz, A Soulé, E Westhof, J Waldispühl, A Denise
Nucleic acids research 46 (8), 3841-3851, 2018
532018
Augmented base pairing networks encode RNA-small molecule binding preferences
C Oliver, V Mallet, RS Gendron, V Reinharz, WL Hamilton, N Moitessier, ...
Nucleic acids research 48 (14), 7690-7699, 2020
342020
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data
J Yao, V Reinharz, F Major, J Waldispühl
Nucleic acids research 45 (W1), W440-W444, 2017
222017
AlphaFold2 can predict single-mutation effects
JM McBride, K Polev, A Abdirasulov, V Reinharz, BA Grzybowski, T Tlusty
Physical Review Letters 131 (21), 218401, 2023
20*2023
Automated, customizable and efficient identification of 3D base pair modules with BayesPairing
R Sarrazin-Gendron, V Reinharz, CG Oliver, N Moitessier, J Waldispühl
Nucleic acids research 47 (7), 3321-3332, 2019
192019
Stochastic sampling of structural contexts improves the scalability and accuracy of RNA 3d module identification
R Sarrazin-Gendron, HT Yao, V Reinharz, CG Oliver, Y Ponty, ...
Research in Computational Molecular Biology: 24th Annual International …, 2020
162020
incaRNAfbinv: a web server for the fragment-based design of RNA sequences
M Drory Retwitzer, V Reinharz, Y Ponty, J Waldispühl, D Barash
Nucleic acids research 44 (W1), W308-W314, 2016
152016
Numerical schemes for solving and optimizing multiscale models with age of hepatitis C virus dynamics
V Reinharz, H Dahari, D Barash
Mathematical biosciences 300, 1-13, 2018
142018
Understanding hepatitis B virus dynamics and the antiviral effect of interferon alpha treatment in humanized chimeric mice
V Reinharz, Y Ishida, M Tsuge, K Durso-Cain, TL Chung, C Tateno, ...
Journal of Virology 95 (14), 10.1128/jvi. 00492-20, 2021
132021
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs
A Soulé, V Reinharz, R Sarrazin-Gendron, A Denise, J Waldispühl
PLoS computational biology 17 (5), e1008990, 2021
112021
A parameter estimation method for multiscale models of hepatitis C virus dynamics
V Reinharz, A Churkin, S Lewkiewicz, H Dahari, D Barash
Bulletin of mathematical biology 81, 3675-3721, 2019
92019
A robust and efficient numerical method for RNA-mediated viral dynamics
V Reinharz, A Churkin, H Dahari, D Barash
Frontiers in applied mathematics and statistics 3, 20, 2017
72017
Modeling and predicting RNA three-dimensional structures
J Waldispühl, V Reinharz
RNA Bioinformatics, 101-121, 2015
72015
On the emergence of structural complexity in RNA replicators
CG Oliver, V Reinharz, J Waldispühl
Rna 25 (12), 1579-1591, 2019
62019
Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces
V Reinharz, Y Ponty, J Waldispühl
Nucleic acids research 44 (11), e104-e104, 2016
62016
Using structural and evolutionary information to detect and correct pyrosequencing errors in non-coding RNAs
V Reinharz, Y Ponty, J Waldispühl
Journal of Computational Biology doi:10.1089/cmb.2013.0085, 2013
62013
A graph-based similarity approach to classify recurrent complex motifs from their context in RNA structures
C Gianfrotta, V Reinharz, D Barth, A Denise
19th Symposium on Experimental Algorithms, 2021
52021
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Articles 1–20