Vladimir Reinharz

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Jérôme WaldispühlAssociate Professor of Computer Science, McGill UniversityVerified email at mcgill.ca
Danny BarashBen-Gurion UniversityVerified email at bgu.ac.il
Yann PontyResearch director at CNRS & Ecole PolytechniqueVerified email at lix.polytechnique.fr
Alexander ChurkinSenior Lecturer, Sami Shamoon College of Engineering, Department of Software EngineeringVerified email at sce.ac.il
Harel DahariAssociate Professor, PhD, Loyola University Chicago Medical CenterVerified email at luc.edu
Roman Sarrazin-GendronAssistant Professor of Computer Science, UQAMVerified email at uqam.ca
Carlos OliverAssistant Professor of Molecular Physiology and Biophysics, Computer Science Vanderbilt UniversityVerified email at vanderbilt.edu
Alain DeniseUniversité Paris-SaclayVerified email at lri.fr
Matan Drory RetwitzerAssoc. Director, Data ScienceVerified email at mammothbiosci.com
Nicolas MoitessierMcGill UniversityVerified email at mcgill.ca
Tsvi TlustyDistinguished Professor of Physics, UNISTVerified email at unist.ac.kr
Susan L. UprichardLoyola University Chicago Medical CenterVerified email at luc.edu
Francois MajorUniversite de MontrealVerified email at umontreal.ca
Antoine SouléPostDoc at McGill UniversityVerified email at mail.mcgill.ca
Vincent MalletCBIO, Mines Paris - PSL, Institut CurieVerified email at mail.mcgill.ca
Stephanie M. LewkiewiczTemple UniversityVerified email at temple.edu
John M. McBrideResearch Fellow, IBS, CSLM, South KoreaVerified email at unist.ac.kr
Bartosz GrzybowskiUNIST, Distinguished Professor of Chemistry, Director of the IBS CARS CenterVerified email at unist.ac.kr
Eric WesthofArchitecture et Réactivité de l'ARN Université de Strasbourg Institut de biologieVerified email at unistra.fr
William L HamiltonAssistant Professor of Computer Science, McGill University and MilaVerified email at cs.mcgill.ca

Vladimir Reinharz

Assistant Professor, Computer Science Department, Université du Québec à Montréal

Verified email at uqam.ca - Homepage

RNA Viral dynamic Evolution Computational Biology


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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	97	2018
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	68	2013
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	61	2012
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	60	2023
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	59	2018
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	50	2020
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	24	2021
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	23	2017
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	22	2019
`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	20	2016
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	18	2018
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, ... International Conference on Research in Computational Molecular Biology, 186-201, 2020	17	2020
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	16	2021
`incaRNAfbinv 2.0`: a webserver and software with motif control for fragment-based design of RNAs MD Retwitzer, V Reinharz, A Churkin, Y Ponty, J Waldispühl, D Barash Bioinformatics 36 (9), 2920-2922, 2020	12	2020
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 (10), 3675-3721, 2019	11	2019
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	9	2017
Modeling and predicting RNA three-dimensional structures J Waldispühl, V Reinharz RNA Bioinformatics, 101-121, 2015	8	2015
Modelling Agile Backlogs as Composable Artifacts to support Developers and Product Owners. S Mosser, C Pulgar, V Reinhar J. Object Technol. 21 (3), 3:1-15, 2022	7	2022
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	7	2016
On the emergence of structural complexity in RNA replicators CG Oliver, V Reinharz, J Waldispühl Rna 25 (12), 1579-1591, 2019	6	2019

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