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Vladimir Reinharz · SciRah

Researcher profile · Semantic Scholar

Vladimir Reinharz

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Vladimir Reinharz — researcher profile on SciRah

h-index: 12
Works: 49
Citations: 573

Most-cited papers

Design of RNAs: comparing programs for inverse RNA folding
A. Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty +2 more
2017Briefings Bioinform.94 citations Open access
Semantic Scholar
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution
Vladimir Reinharz, Yann Ponty, J. Waldispühl
2013Bioinform.70 citations Open access
Semantic Scholar
AlphaFold2 can predict single-mutation effects
John Mcbride, Konstantin Polev, Amirbek Abdirasulov, Vladimir Reinharz +2 more
2022bioRxiv60 citations Open access
Semantic Scholar
Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families
Vladimir Reinharz, A. Soulé, E. Westhof, J. Waldispühl +1 more
2018Nucleic Acids Research43 citations Open access
Semantic Scholar
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure
Vladimir Reinharz, F. Major, J. Waldispühl
2012Bioinform.41 citations Open access
Semantic Scholar
Augmented base pairing networks encode RNA-small molecule binding preferences
Carlos G. Oliver, Vincent Mallet, Roman Sarrazin Gendron, Vladimir Reinharz +3 more
2020Nucleic Acids Research28 citations Open access
Semantic Scholar
Understanding Hepatitis B Virus Dynamics and the Antiviral Effect of Interferon Alpha Treatment in Humanized Chimeric Mice
Vladimir Reinharz, Yuji Ishida, M. Tsuge, Karina Durso-Cain +6 more
2021Journal of Virology24 citations Open access
Semantic Scholar
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data
Jason Yao, Vladimir Reinharz, F. Major, J. Waldispühl
2017Nucleic Acids Res.22 citations Open access
Semantic Scholar
incaRNAfbinv: a web server for the fragment-based design of RNA sequences
Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, J. Waldispühl +1 more
2016Nucleic Acids Res.18 citations Open access
Semantic Scholar
Automated, customizable and efficient identification of 3D base pair modules with BayesPairing
Roman Sarrazin-Gendron, Vladimir Reinharz, Carlos G. Oliver, N. Moitessier +1 more
2019Nucleic Acids Research16 citations Open access
Semantic Scholar
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs
A. Soulé, Vladimir Reinharz, Roman Sarrazin-Gendron, A. Denise +1 more
2020bioRxiv14 citations Open access
Semantic Scholar
Numerical Schemes for Solving and Optimizing Multiscale Models with Age of Hepatitis C Virus Dynamics
Vladimir Reinharz, H. Dahari, D. Barash
2018Mathematical Biosciences14 citations Open access
Semantic Scholar
A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics
Vladimir Reinharz, A. Churkin, Stephanie M. Lewkiewicz, H. Dahari +1 more
2019Bulletin of Mathematical Biology12 citations Open access
Semantic Scholar
Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics
A. Hailegiorgis, Yuji Ishida, Nicholson T. Collier, M. Imamura +11 more
2023PLoS Comput. Biol.11 citations Open access
Semantic Scholar
Modeling of hepatitis B virus kinetics and accumulation of cccDNA in primary human hepatocytes
Louis M. Shekhtman, Yuji Ishida, M. Tsuge, Vladimir Reinharz +6 more
2024JHEP Reports9 citations Open access
Semantic Scholar
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs
Matan Drory Retwitzer, Vladimir Reinharz, A. Churkin, Y. Ponty +2 more
2020Bioinform.9 citations Open access
Semantic Scholar
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework
Gabriel Loyer, Vladimir Reinharz
2023bioRxiv7 citations Open access
Semantic Scholar
AlphaFold2 can predict structural and phenotypic effects of single mutations
John Mcbride, Konstantin Polev, Vladimir Reinharz, B. Grzybowski +1 more
20227 citations
Semantic Scholar
A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics
Vladimir Reinharz, A. Churkin, H. Dahari, D. Barash
2017Frontiers in Applied Mathematics and Statistics7 citations Open access
Semantic Scholar
Modeling the Interplay between HDV and HBV in Chronic HDV/HBV Patients
Adequate Mhlanga, Rami Zakh, A. Churkin, Vladimir Reinharz +6 more
2022Mathematics6 citations Open access
Semantic Scholar
Advances in Parameter Estimation and Learning from Data for Mathematical Models of Hepatitis C Viral Kinetics
Vladimir Reinharz, A. Churkin, H. Dahari, D. Barash
2022Mathematics6 citations Open access
Semantic Scholar
Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules Identification
Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver +2 more
2019bioRxiv6 citations Open access
Semantic Scholar
Modeling and predicting RNA three-dimensional structures.
J. Waldispühl, Vladimir Reinharz
2015Methods in molecular biology6 citations
Semantic Scholar
Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces
Vladimir Reinharz, Y. Ponty, J. Waldispühl
2016Nucleic Acids Research5 citations Open access
Semantic Scholar
Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique
Théo Boury, Yann Ponty, Vladimir Reinharz
2023Workshop on Algorithms in Bioinformatics4 citations
Semantic Scholar
A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures
Coline Gianfrotta, Vladimir Reinharz, D. Barth, A. Denise
2021The Sea4 citations Open access
Semantic Scholar
On the emergence of structural complexity in RNA replicators
Carlos G. Oliver, Vladimir Reinharz, J. Waldispühl
2017bioRxiv4 citations Open access
Semantic Scholar
On the predictibility of A-minor motifs from their local contexts
Coline Gianfrotta, Vladimir Reinharz, O. Lespinet, Dominique Barth +1 more
2022RNA Biology3 citations Open access
Semantic Scholar
Efficient Methods for Parameter Estimation of Ordinary and Partial Differential Equation Models of Viral Hepatitis Kinetics
A. Churkin, Stephanie M. Lewkiewicz, Vladimir Reinharz, H. Dahari +1 more
2020Mathematics3 citations Open access
Semantic Scholar
HCVMultiscaleFit: A Simulator For Parameter Estimation in Multiscale Models Of Hepatitis C Virus Dynamics
A. Churkin, Vladimir Reinharz, Stephanie M. Lewkiewicz, H. Dahari +1 more
2020AIP Conference Proceedings3 citations Open access
Semantic Scholar
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs
Vladimir Reinharz, Yann Ponty, J. Waldispühl
2013Annual International Conference on Research in Computational Molecular Biology3 citations
Semantic Scholar
Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs
Vladimir Reinharz, Yann Ponty, J. Waldispühl
2013J. Comput. Biol.3 citations Open access
Semantic Scholar
Parallel maximal common subgraphs with labels for molecular biology
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
2024bioRxiv2 citations Open access
Semantic Scholar
Classification and Identification of Non-canonical Base Pairs and Structural Motifs.
Roman Sarrazin-Gendron, J. Waldispühl, Vladimir Reinharz
2024Methods in molecular biology2 citations
Semantic Scholar
Extended RNA base pairing networks imprint small molecule binding preferences
Carlos G. Oliver, Vincent Mallet, Roman Sarrazin-Gendron, Vladimir Reinharz +3 more
2019bioRxiv2 citations Open access
Semantic Scholar
Reconstruction of ancestral RNA sequences under multiple structural constraints
Olivier Tremblay-Savard, Vladimir Reinharz, J. Waldispühl
2016BMC Genomics2 citations Open access
Semantic Scholar
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution
Vladimir Reinharz, Yann Ponty, J. Waldispühl
20132 citations
Semantic Scholar
Modeling and Predicting RNA Three-Dimensional Structures.
Vladimir Reinharz, Roman Sarrazin-Gendron, J. Waldispühl
2021Methods in molecular biology1 citations
Semantic Scholar
Mathematical Modeling of HDV RNA, HBV DNA, and HBsAg Dynamics During Lonafarnib-Based Therapy: Insights from the LOWR HDV-1 Study
A. Mhlanga, Louis M. Shekhtman, Rami Zakh, Sarah Duehren +9 more
2026Bulletin of Mathematical Biology0 citations
Semantic Scholar
Towards an improved mathematical model for HDV-HBV interaction during anti-HDV treatment
A. Mhlanga, Rami Zakh, A. Churkin, Vladimir Reinharz +2 more
2026AIP Conference Proceedings0 citations
Semantic Scholar
FASTiso: Fast Algorithm on Search state Tree for subgraph ISOmorphism in graphs of any size and density
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
2026bioRxiv0 citations Open access
Semantic Scholar
Reconstructing Ancestral Non-Coding RNAs of Multiple Families Using Sequence and Structural Information with Tree Decomposition
Song Hu, Vladimir Reinharz, Olivier Tremblay-Savard
2026J. Comput. Biol.0 citations
Semantic Scholar
Tree Decomposition for Reconstructing Ancestral RNA Sequences of Multiple Families
Song Hu, Vladimir Reinharz, Olivier Tremblay-Savard
2025RECOMB Comparative Genomics Satellite Conference0 citations
Semantic Scholar
Advances in parameter estimation for mathematical models of hepatitis C viral kinetics
Vladimir Reinharz, A. Churkin, H. Dahari, D. Barash
2023AIP Conference Proceedings0 citations
Semantic Scholar
Multiphasic hepatitis B virus kinetic patterns in humanized chimeric mice can be explained via stochastic agent-based modeling of intracellular virion production cycles
A. Hailegiorgis, Yuji Ishida, Nicholson T. Collier, M. Imamura +11 more
2022bioRxiv0 citations Open access
Semantic Scholar
Repliement de l'ARN
Y. Ponty, Vladimir Reinharz
20200 citations
Semantic Scholar
A graph-based approach to classify A-minor motifs in RNA structures according to their structural context
Coline Gianfrotta, Vladimir Reinharz, O. Lespinet, D. Barth +1 more
20200 citations Open access
Semantic Scholar
αβDCA method identifies unspecific binding but specific disruption of the group I intron by the StpA chaperone
Vladimir Reinharz, T. Tlusty
2019bioRxiv0 citations Open access
Semantic Scholar
HCVMultiscaleDyn: A simulator for the multiscale model of hepatitis C virus dynamics
A. Churkin, Vladimir Reinharz, H. Dahari, D. Barash
20180 citations
Semantic Scholar

Frequent co-authors

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J. Waldispühl×21
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J. Waldispühl — researcher profile on SciRah
H. Dahari×15
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H. Dahari — researcher profile on SciRah
D. Barash×14
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A. Churkin×12
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Yann Ponty — researcher profile on SciRah

Roman Sarrazin-Gendron×6

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A. Denise — researcher profile on SciRah

Carlos G. Oliver×5

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Yuji Ishida — researcher profile on SciRah

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