SA-REPC - Sequence Alignment with Regular Expression Path Constraint. - Nimrod Milo; Tamar Pinhas; Michal Ziv-Ukelson (LATA, 2010)

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

StemSearch: RNA search tool based on stem identification and indexing. - Sivan Yogev; Nimrod Milo; Michal Ziv-Ukelson (BIBM, 2013)

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)

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)

Algorithms for path-constrained sequence alignment. - Tamar Pinhas; Nimrod Milo; Gregory Kucherov; Michal Ziv-Ukelson (J. Discrete Algorithms, 2014)

Learning Heuristics for Mining RNA Sequence-Structure Motifs. - Achiya Elyasaf; Pavel Vaks; Nimrod Milo; Moshe Sipper; Michal Ziv-Ukelson (GPTP, 2015)