RNAMute: RNA Secondary Structure Mutation Analysis Tool. - Alexander Churkin; Ornit Elgad; Oshrat Petgho; Danny Barash (CSB Workshops, 2005)

Pattern Recognition Method to Detect Vulnerable Spots in an RNA Sequence for Bacterial Resistance to the Antibiotic Spectinomycin. - Alexander Churkin; Danny Barash (CVPR Workshops, 2005)

RNAmute: RNA secondary structure mutation analysis tool. - Alexander Churkin; Danny Barash (BMC Bioinform., 2006)

Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute. - Alexander Churkin; Danny Barash (EURASIP J. Adv. Signal Process., 2006)

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions. - Alexander Churkin; Danny Barash (BMC Bioinform., 2008)

Bioinformatic Analysis of the Neutrality of RNA Secondary Structure Elements across genotypes reveals Evidence for Direct Evolution of Genetic Robustness in HCV. - Alexander Churkin; Moriah Cohen; Yonat Shemer-Avni; Danny Barash (J. Bioinform. Comput. Biol., 2010)

Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. - Danny Barash; Alexander Churkin (Briefings Bioinform., 2011)

RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. - Assaf Avihoo; Alexander Churkin; Danny Barash (BMC Bioinform., 2011)

The RNAmute web server for the mutational analysis of RNA secondary structures. - Alexander Churkin; Idan Gabdank; Danny Barash (Nucleic Acids Res., 2011)

Efficient procedures for the numerical simulation of mid-size RNA kinetics. - Iddo Aviram; Ilia Veltman; Alexander Churkin; Danny Barash (Algorithms Mol. Biol., 2012)

On topological indices for small RNA graphs. - Alexander Churkin; Idan Gabdank; Danny Barash (Comput. Biol. Chem., 2012)

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

A Biologically Meaningful Extension of the Efficient Method for Deleterious Mutations Prediction in RNAs: Insertions and Deletions in Addition to Substitution Mutations. - Alexander Churkin; Danny Barash (ISBRA, 2018)

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)

The HHD Dataset. - Irina Rabaev; Berat Kurar Barakat; Alexander Churkin; Jihad El-Sana (ICFHR, 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)

IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. - Alexander Churkin; Yann Ponty; Danny Barash (BMC Bioinform., 2022)

Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans. - Alma Davidson; Marina Parr; Franziska Totzeck; Alexander Churkin; Danny Barash; Dmitrij Frishman; Tamir Tuller (RECOMB-CG, 2024)