A Structure-Based Flexible Search Method for Motifs in RNA. - Isana Veksler-Lublinsky; Michal Ziv-Ukelson; Danny Barash; Klara Kedem (J. Comput. Biol., 2007)

Computational Identification of Three-Way Junctions in Folded RNAs: A Case Study in Arabidopsis. - Adaya N. Cohen; Samuel Bocobza; Isana Veksler; Idan Gabdank; Danny Barash; Asaph Aharoni; Michal Shapira; Klara Kedem (Silico Biol., 2008)

FASH: A web application for nucleotides sequence search. - Isana Veksler-Lublinsky; Danny Barash; Chai Avisar; Einav Troim; L. Paul Chew; Klara Kedem (Source Code Biol. Medicine, 2008)

Gene bi-targeting by viral and human miRNAs. - Isana Veksler-Lublinsky; Yonat Shemer-Avni; Klara Kedem; Michal Ziv-Ukelson (BMC Bioinform., 2010)

Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV). - Isana Veksler-Lublinsky; Yonat Shemer-Avni; Eti Meiri; Zvi Bentwich; Klara Kedem; Michal Ziv-Ukelson (BMC Bioinform., 2012)

Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes. - Jonathan Engel; Isana Veksler-Lublinsky; Michal Ziv-Ukelson (J. Comput. Biol., 2019)

minMLST: machine learning for optimization of bacterial strain typing. - Shani Cohen; Lior Rokach; Yair Motro; Jacob Moran-Gilad; Isana Veksler-Lublinsky (Bioinform., 2021)

Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species. - Gilad Ben Or; Isana Veksler-Lublinsky (BMC Bioinform., 2021)

sInterBase: a comprehensive database of Escherichia coli sRNA-mRNA interactions. - Shani Cohen; Eden Maximof; Shay Rokach; Mor Tadeski; Isana Veksler-Lublinsky (Bioinform., 2023)

Dataset of GraphRNA scores for sRNA-mRNA interactions in E. coli. - Shani Cohen; Lior Rokach; Isana Veksler-Lublinsky (Zenodo, 2023)

Datasets and predictions for sRNA-mRNA interactions in E. coli - kGraphRNA, GraphRNA, sInterRF, and sInterXGB models. - Shani Cohen; Lior Rokach; Isana Veksler-Lublinsky (Zenodo, 2024)

Datasets and predictions for sRNA-mRNA interactions in E. coli - kGraphRNA, GraphRNA, sInterRF, and sInterXGB models. - Shani Cohen; Lior Rokach; Isana Veksler-Lublinsky (Zenodo, 2024)

Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions. - Efrat Cohen-Davidi; Isana Veksler-Lublinsky (PLoS Comput. Biol., 2024)

GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions. - Shani Cohen; Lior Rokach; Isana Veksler-Lublinsky (BMC Bioinform., 2025)