Edit Distance with Duplications and Contractions Revisited. - Tamar Pinhas; Dekel Tsur; Shay Zakov; Michal Ziv-Ukelson (CPM, 2011)

Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach. - Shay Zakov; Dekel Tsur; Michal Ziv-Ukelson (Algorithms Mol. Biol., 2011)

Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis. - Kfir Wolfson; Shay Zakov; Moshe Sipper; Michal Ziv-Ukelson (Genet. Program. Evolvable Mach., 2011)

Rich Parameterization Improves RNA Structure Prediction. - Shay Zakov; Yoav Goldberg; Michael Elhadad; Michal Ziv-Ukelson (J. Comput. Biol., 2011)

Sparse RNA folding: Time and space efficient algorithms. - Rolf Backofen; Dekel Tsur; Shay Zakov; Michal Ziv-Ukelson (J. Discrete Algorithms, 2011)

RNA Tree Comparisons via Unrooted Unordered Alignments. - Nimrod Milo; Shay Zakov; Erez Katzenelson; Eitan Bachmat; Yefim Dinitz; Michal Ziv-Ukelson (WABI, 2012)

Unrooted unordered homeomorphic subtree alignment of RNA trees. - Nimrod Milo; Shay Zakov; Erez Katzenelson; Eitan Bachmat; Yefim Dinitz; Michal Ziv-Ukelson (Algorithms Mol. Biol., 2013)

Efficient edit distance with duplications and contractions. - Tamar Pinhas; Shay Zakov; Dekel Tsur; Michal Ziv-Ukelson (Algorithms Mol. Biol., 2013)

Evaluating genome architecture of a complex region via generalized bipartite matching. - Christine Lo; Sangwoo Kim; Shay Zakov; Vineet Bafna (BMC Bioinform., 2013)

An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. - Shay Zakov; Marcus Kinsella; Vineet Bafna (Proc. Natl. Acad. Sci. USA, 2013)

Recent Results on Three Problems in Comparative Structural RNAomics. - Shay Zakov; Nimrod Milo; Tamar Pinhas; Sivan Yogev; Erez Katzenelson; Eitan Bachmat; Yefim Dinitz; Dekel Tsur; Michal Ziv-Ukelson (CMSR@ECCB, 2014)

Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele. - Roy Ronen; Glenn Tesler; Ali Akbari; Shay Zakov; Noah A. Rosenberg; Vineet Bafna (RECOMB, 2015)

Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. - Shay Zakov; Vineet Bafna (J. Comput. Biol., 2015)

Shortest Longest-Path Graph Orientations. - Yuichi Asahiro; Jesper Jansson 001; Avraham A. Melkman; Eiji Miyano; Hirotaka Ono 001; Quan Xue; Shay Zakov (COCOON (1), 2023)

Shortest Longest-Path Graph Orientations for Trees. - Yuichi Asahiro; Jesper Jansson 001; Avraham A. Melkman; Eiji Miyano; Hirotaka Ono 001; Quan Xue; Yoshichika Yano; Shay Zakov (SOFSEM (1), 2025)