Publications by authors named "Alexander Churkin"

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The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3.
Rami Zakh, Alexander Churkin, Marina Parr, Tamir Tuller, Ohad Etzion

Brief Bioinform· August 2025

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Over time analysis of the codon usage of SARS-CoV-2 and its variants.
Alma Davidson, Marina Parr, Franziska Totzeck, Alexander Churkin, Danny Barash

Comput Struct Biotechnol J· May 2025

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RNA Design Using incaRNAfbinv Demonstrated with the Identification of Functional RNA Motifs in Hepatitis Delta Virus.
Rami Zakh, Alexander Churkin, Danny Barash

Methods Mol Biol· September 2024

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IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations.
Alexander Churkin, Yann Ponty, Danny Barash

BMC Bioinformatics· October 2022

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Modeling the Interplay between HDV and HBV in Chronic HDV/HBV Patients.
Adequate Mhlanga, Rami Zakh, Alexander Churkin, Vladimir Reinharz, Jeffrey S Glenn

Mathematics (Basel)· October 2022

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Advances in Parameter Estimation and Learning from Data for Mathematical Models of Hepatitis C Viral Kinetics.
Vladimir Reinharz, Alexander Churkin, Harel Dahari, Danny Barash

Mathematics (Basel)· June 2022

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Machine learning for mathematical models of HCV kinetics during antiviral therapy.
Alexander Churkin, Stephanie Kriss, Asher Uziel, Ashish Goyal, Rami Zakh

Math Biosci· January 2022

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A Mathematical Model for early HBV and -HDV Kinetics during Anti-HDV Treatment.
Rami Zakh, Alexander Churkin, William Bietsch, Menachem Lachiany, Scott J Cotler

Mathematics (Basel)· December 2021

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A Mathematical Analysis of HDV Genotypes: From Molecules to Cells.
Rami Zakh, Alexander Churkin, Franziska Totzeck, Marina Parr, Tamir Tuller

Mathematics (Basel)· September 2021

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HCVMultiscaleFit: A Simulator For Parameter Estimation in Multiscale Models Of Hepatitis C Virus Dynamics.
Alexander Churkin, Vladimir Reinharz, Stephanie Lewkiewicz, Harel Dahari, Danny Barash

AIP Conf Proc· November 2020

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Modeling-Based Response-Guided Glecaprevir-Pibrentasvir Therapy for Chronic Hepatitis C to Identify Patients for Ultrashort Treatment Duration.
Swikriti Dasgupta, Michio Imamura, Evan Gorstein, Takashi Nakahara, Masataka Tsuge, Alexander Churkin

J Infect Dis· September 2020

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Efficient Methods for Parameter Estimation of Ordinary and Partial Differential Equation Models of Viral Hepatitis Kinetics.
Alexander Churkin, Stephanie Lewkiewicz, Vladimir Reinharz, Harel Dahari, Danny Barash

Mathematics (Basel)· September 2020

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Modeling based response guided therapy in subjects with recent hepatitis C infection.
Evan Gorstein, Marianne Martinello, Alexander Churkin, Swikriti Dasgupta, Kevin Walsh

Antiviral Res· August 2020

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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

Bioinformatics· May 2020

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A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics.
Vladimir Reinharz, Alexander Churkin, Stephanie Lewkiewicz, Harel Dahari, Danny Barash

Bull Math Biol· October 2019

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Design of RNAs: comparing programs for inverse RNA folding.
Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl

Brief Bioinform· March 2018

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A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics.
Vladimir Reinharz, Alexander Churkin, Harel Dahari, Danny Barash

Front Appl Math Stat· October 2017

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Free energy minimization to predict RNA secondary structures and computational RNA design.
Alexander Churkin, Lina Weinbrand, Danny Barash

Methods Mol Biol· September 2015

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RNAthermsw: direct temperature simulations for predicting the location of RNA thermometers.
Alexander Churkin, Assaf Avihoo, Michal Shapira, Danny Barash

PLoS One· June 2015

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RNA dot plots: an image representation for RNA secondary structure analysis and manipulations.
Alexander Churkin, Danny Barash

Wiley Interdiscip Rev RNA· August 2013

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On topological indices for small RNA graphs.
Alexander Churkin, Idan Gabdank, Danny Barash

Comput Biol Chem· December 2012

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Efficient procedures for the numerical simulation of mid-size RNA kinetics.
Iddo Aviram, Ilia Veltman, Alexander Churkin, Danny Barash

Algorithms Mol Biol· September 2012

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RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences.
Assaf Avihoo, Alexander Churkin, Danny Barash

BMC Bioinformatics· August 2011

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The RNAmute web server for the mutational analysis of RNA secondary structures.
Alexander Churkin, Idan Gabdank, Danny Barash

Nucleic Acids Res· July 2011

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Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction.
Danny Barash, Alexander Churkin

Brief Bioinform· March 2011

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