@article{fujisaki1992online,
title = {{Online recognition of unconstrained handprinting: a stroke-based system and its evaluation}},
author = {Fujisaki, T. and Beigi, HSM and Tappert, CC and Ukelson, M. and Wolf, CG},
journal = {From Pixels to Features III: Frontiers in Handwriting Recognition. Elsevier Science Publishers},
year = {1992}
}
@conference{ziv1998dictionary,
title = {{A dictionary matching algorithm fast on the average for terms of varying length}},
author = {Ziv-Ukelson, M. and Kershenbaum, A.},
booktitle = {Combinatorial Pattern Matching},
pages = {34--54},
year = {1998},
organization = {Springer}
}
@conference{landau2000shared,
title = {{On the shared substring alignment problem}},
author = {Landau, G.M. and Ziv-Ukelson, M.},
booktitle = {PROC ANNU ACM SIAM SYMP DISCRETE ALGORITHMS},
pages = {804--814},
year = {2000}
}
@conference{landau2003sparse,
title = {{Sparse LCS common substring alignment}},
author = {Landau, G.M. and Schieber, B. and Ziv-Ukelson, M.},
booktitle = {Combinatorial Pattern Matching: 14th Annual Symposium, CPM 2003, Morelia, Michoac{\'a}n, Mexico, June 25-27, 2003. Proceedings},
pages = {1017--1017},
year = {2003},
organization = {Springer}
}
@conference{landau2004two,
title = {{Two algorithms for LCS consecutive suffix alignment}},
author = {Landau, G.M. and Myers, E. and Ziv-Ukelson, M.},
booktitle = {Combinatorial Pattern Matching},
pages = {173--193},
year = {2004},
organization = {Springer}
}
@conference{pinter2004approximate,
title = {{Approximate labelled subtree homeomorphism}},
author = {Pinter, R.Y. and Rokhlenko, O. and Tsur, D. and Ziv-Ukelson, M.},
booktitle = {Combinatorial Pattern Matching},
pages = {59--73},
year = {2004},
organization = {Springer}
}
@article{kent2006complexity,
title = {{On the complexity of sparse exon assembly}},
author = {Kent, C. and Landau, G.M. and Ziv-Ukelson, M.},
journal = {Journal of Computational Biology},
volume = {13},
number = {5},
pages = {1013--1027},
issn = {1066-5277},
year = {2006},
publisher = {Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@conference{kent2005complexity,
title = {{On the complexity of sparse exon assembly}},
author = {Kent, C. and Landau, G.M. and Ziv-Ukelson, M.},
booktitle = {Combinatorial Pattern Matching},
pages = {201--218},
year = {2005},
organization = {Springer}
}
@conference{zilberstein2005high,
title = {{A high-throughput approach for associating microRNAs with their activity conditions}},
author = {Zilberstein, C.B.Z. and Ziv-Ukelson, M. and Pinter, R.Y. and Yakhini, Z.},
booktitle = {Research in Computational Molecular Biology},
pages = {133--151},
year = {2005},
organization = {Springer}
}
@article{zilberstein2005dynamic,
title = {{Dynamic de-novo prediction of microRNAs associated with cell conditions: A search pruned by expression}},
author = {Zilberstein, C. and Ziv-Ukelson, M.},
journal = {Algorithms in Bioinformatics},
pages = {13--26},
year = {2005},
publisher = {Springer}
}
@conference{wexler2006study,
title = {{A study of accessible motifs and rna folding complexity}},
author = {Wexler, Y. and Zilberstein, C. and Ziv-Ukelson, M.},
booktitle = {Research in Computational Molecular Biology},
pages = {473--487},
year = {2006},
organization = {Springer}
}
@article{wexler2007study,
title = {{A study of accessible motifs and RNA folding complexity}},
author = {Wexler, Y. and Zilberstein, C. and Ziv-Ukelson, M.},
journal = {Journal of Computational Biology},
volume = {14},
number = {6},
pages = {856--872},
issn = {1066-5277},
year = {2007},
publisher = {Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@article{swidan2006repeatP,
title = {{On the repeat-annotated phylogenetic tree reconstruction problem}},
author = {Swidan, F. and Ziv-Ukelson, M. and Pinter, R.Y.},
journal = {Journal of Computational Biology},
volume = {13},
number = {8},
pages = {1397--1418},
issn = {1066-5277},
year = {2006},
publisher = {Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@conference{swidan2006repeat,
title = {{On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem}},
author = {Swidan, F. and Ziv-Ukelson, M. and Pinter, R.},
booktitle = {Combinatorial Pattern Matching},
pages = {141--152},
year = {2006},
organization = {Springer}
}
@conference{mozes2007speeding,
title = {{Speeding up HMM decoding and training by exploiting sequence repetitions}},
author = {Mozes, S. and Weimann, O. and Ziv-Ukelson, M.},
booktitle = {Combinatorial Pattern Matching},
pages = {4--15},
year = {2007},
organization = {Springer}
}
@article{lifshits2009speeding,
title = {{Speeding up HMM decoding and training by exploiting sequence repetitions}},
author = {Lifshits, Y. and Mozes, S. and Weimann, O. and Ziv-Ukelson, M.},
journal = {Algorithmica},
volume = {54},
number = {3},
pages = {379--399},
issn = {0178-4617},
year = {2009},
publisher = {Springer}
}
@article{lozano2007seeded,
title = {{Seeded tree alignment and planar tanglegram layout}},
author = {Lozano, A. and Pinter, R. and Rokhlenko, O. and Valiente, G. and Ziv-Ukelson, M.},
journal = {Algorithms in Bioinformatics},
pages = {98--110},
year = {2007},
publisher = {Springer}
}
@conference{mozes2008fast,
title = {{Fast algorithms for computing tree lcs}},
author = {Mozes, S. and Tsur, D. and Weimann, O. and Ziv-Ukelson, M.},
booktitle = {Combinatorial Pattern Matching},
pages = {230--243},
year = {2008},
organization = {Springer}
}
@article{ziv2008faster,
title = {{A faster algorithm for RNA co-folding}},
author = {Ziv-Ukelson, M. and Gat-Viks, I. and Wexler, Y. and Shamir, R.},
journal = {Algorithms in Bioinformatics},
pages = {174--185},
year = {2008},
publisher = {Springer}
}
@conference{backofen2009time,
title = {{Sparse RNA Folding: Time and Space Efficient Algorithms}},
author = {Backofen, R. and Tsur, D. and Zakov, S. and Ziv-Ukelson, M.},
booktitle = {Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching},
pages = {249--262},
year = {2009}
}
@article{backofen2010sparse,
title = {{Sparse RNA folding: Time and space efficient algorithms}},
author = {Backofen, R. and Tsur, D. and Zakov, S. and Ziv-Ukelson, M.},
journal = {Journal of Discrete Algorithms},
issn = {1570-8667},
year = {2010},
publisher = {Elsevier}
}
@article{milo2010sa,
title = {{SA-REPC--Sequence Alignment with Regular Expression Path Constraint}},
author = {Milo, N. and Pinhas, T. and Ziv-Ukelson, M.},
journal = {Language and Automata Theory and Applications},
pages = {451--462},
year = {2010},
publisher = {Springer}
}
@article{kucherov2011re,
title = {{Regular Language Constrained Sequence Alignment Revisited}},
author = {Kucherov, G. and Pinhas, T. and Ziv-Ukelson, M.},
journal = {Journal of Computational Biology (to appear)},
year = {2011},
publisher = {Mary Ann Liebert, Inc.}
}
@article{zakov2010reducing,
title = {{Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant’s Approach}},
author = {Zakov, S. and Tsur, D. and Ziv-Ukelson, M.},
journal = {Algorithms in Bioinformatics},
pages = {65--77},
year = {2010},
publisher = {Springer},
url = {http://www.cs.bgu.ac.il/~dekelts/publications/vmt.pdf}
}
@inproceedings{ContextFold,
author = {Shay Zakov and Yoav Goldberg and Michael Elhadad and Michal
Ziv-Ukelson},
title = {Rich Parameterization Improves RNA Structure Prediction},
booktitle = {RECOMB 2011: Proceedings of the 15th Annual
International Conference on Research in Computational Molecular
Biology},
year = {2011},
location = {Vancouver, Canada},
url = {http://www.cs.bgu.ac.il/~negevcb/contextfold/}
}
@inproceedings{PTZZ,
author = {T. Pinhas, D. Tsur, S. Zakov and M. Ziv-Ukelson},
title = {Edit Distance with Duplications and Contractions Revisited},
booktitle = {Proc. CPM 2011 (The 22nd Annual Symposium on Combinatorial Pattern Matching)},
year = {2011},
location = {Palermo, Italy}
}
@article{crochemore2re,
title = {{Re-use dynamic programming for sequence alignment: An algorithmic toolkit}},
author = {Crochemore, M. and Landau, G.M. and Schieber, B. and Ziv-Ukelson, M.},
journal = {String Algorithmics},
volume = {2},
pages = {19--60},
publisher = {Citeseer}
}
@article{landau2001common,
title = {{On the Common Substring Alignment Problem* 1}},
author = {Landau, G.M. and Ziv-Ukelson, M.},
journal = {Journal of Algorithms},
volume = {41},
number = {2},
pages = {338--359},
issn = {0196-6774},
year = {2001},
publisher = {Elsevier}
}
@article{crochemore2003subquadratic,
title = {{A subquadratic sequence alignment algorithm for unrestricted scoring matrices}},
author = {Crochemore, M. and Landau, G.M. and Ziv-Ukelson, M.},
journal = {SIAM Journal on Computing},
volume = {32},
number = {6},
pages = {1654--1676},
issn = {0097-5397},
year = {2003},
publisher = {Citeseer}
}
@article{landau2003sparseP,
title = {{Sparse LCS Common Substring Alignment}},
author = {Landau, G.M. and Schieber, B. and Ziv-Ukelson, M.},
journal = {Information Processing Letters},
volume = {88},
number = {6},
pages = {259--270},
issn = {0020-0190},
year = {2003},
publisher = {Elsevier}
}
@article{pinter2005alignment,
title = {{Alignment of metabolic pathways}},
author = {Pinter, R.Y. and Rokhlenko, O. and Yeger-Lotem, E. and Ziv-Ukelson, M.},
journal = {Bioinformatics},
volume = {21},
number = {16},
pages = {3401},
issn = {1367-4803},
year = {2005},
publisher = {Oxford Univ Press}
}
@article{zilberstein2006high,
title = {{A high-throughput approach for associating microRNAs with their activity conditions}},
author = {Zilberstein, C.B.Z. and Ziv-Ukelson, M. and Pinter, R.Y. and Yakhini, Z.},
journal = {Journal of Computational Biology},
volume = {13},
number = {2},
pages = {245--266},
issn = {1066-5277},
year = {2006},
publisher = {Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@article{landau2007two,
title = {{Two algorithms for LCS consecutive suffix alignment}},
author = {Landau, G.M. and Myers, E. and Ziv-Ukelson, M.},
journal = {Journal of Computer and System Sciences},
volume = {73},
number = {7},
pages = {1095--1117},
issn = {0022-0000},
year = {2007},
publisher = {Elsevier}
}
@article{veksler2007structure,
title = {{A structure-based flexible search method for motifs in RNA}},
author = {Veksler-Lublinsky, I. and Ziv-Ukelson, M. and Barash, D. and Kedem, K.},
journal = {Journal of Computational Biology},
volume = {14},
number = {7},
pages = {908--926},
issn = {1066-5277},
year = {2007},
publisher = {Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA},
url = {http://www.liebertonline.com/doi/abs/10.1089/cmb.2007.0061}
}
@article{pinter2008approximate,
title = {{Approximate labelled subtree homeomorphism}},
author = {Pinter, R.Y. and Rokhlenko, O. and Tsur, D. and Ziv-Ukelson, M.},
journal = {Journal of Discrete Algorithms},
volume = {6},
number = {3},
pages = {480--496},
issn = {1570-8667},
year = {2008},
publisher = {Elsevier}
}
@article{loya20083,
title = {{The 3′-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein}},
author = {Loya, A. and Pnueli, L. and Yosefzon, Y. and Wexler, Y. and Ziv-Ukelson, M. and Arava, Y.},
journal = {Rna},
volume = {14},
number = {7},
pages = {1352},
issn = {1355-8382},
year = {2008},
publisher = {Cold Spring Harbor Lab}
}
@article{lozano2008seeded,
title = {{Seeded tree alignment}},
author = {Lozano, A. and Pinter, R.Y. and Rokhlenko, O. and Valiente, G. and Ziv-Ukelson, M.},
journal = {IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics},
pages = {503--513},
issn = {1545-5963},
year = {2008},
publisher = {Published by the IEEE CS, CI, and EMB Societies \& the ACM}
}
@article{mozes2009fast,
title = {{Fast algorithms for computing tree LCS}},
author = {Mozes, S. and Tsur, D. and Weimann, O. and Ziv-Ukelson, M.},
journal = {Theoretical Computer Science},
volume = {410},
number = {43},
pages = {4303--4314},
issn = {0304-3975},
year = {2009},
publisher = {Elsevier}
}
@article{horesh2009rnaslider,
title = {{RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry}},
author = {Horesh, Y. and Wexler, Y. and Lebenthal, I. and Ziv-Ukelson, M. and Unger, R.},
journal = {BMC bioinformatics},
volume = {10},
number = {1},
pages = {76},
issn = {1471-2105},
year = {2009},
publisher = {BioMed Central Ltd}
}
@article{veksler2010gene,
title = {{Gene bi-targeting by viral and human miRNAs}},
author = {Veksler-Lublinsky, I. and Shemer-Avni, Y. and Kedem, K. and Ziv-Ukelson, M.},
journal = {BMC bioinformatics},
volume = {11},
number = {1},
pages = {249},
issn = {1471-2105},
year = {2010},
publisher = {BioMed Central Ltd},
url = {http://www.biomedcentral.com/1471-2105/11/249/abstract/}
}
@article{ziv2010faster,
title = {{A faster algorithm for simultaneous alignment and folding of RNA}},
author = {Ziv-Ukelson, M. and Gat-Viks, I. and Wexler, Y. and Shamir, R.},
journal = {Journal of Computational Biology},
volume = {17},
number = {8},
pages = {1051--1065},
issn = {1066-5277},
year = {2010},
publisher = {Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}
@article{wolfsonhave,
title = {{Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis}},
author = {Wolfson, K. and Zakov, S. and Sipper, M. and Ziv-Ukelson, M.},
journal = {Genetic Programming and Evolvable Machines},
pages = {1--40},
issn = {1389-2576},
publisher = {Springer},
year = {2010},
url = {http://www.springerlink.com/index/JG7217823027K847.pdf}
}
@article{milo2012rna,
title = {{RNA Tree Comparisons via Unrooted Unordered Alignments}},
author = {Milo, N. and Zakov, S. and Katzenelson, E. and Bachmat, E. and Dinitz, Y. and Ziv-Ukelson, M.},
journal = {Algorithms in Bioinformatics},
pages = {135--148},
year = {2012},
url = {http://www.springerlink.com/content/2n7152748231l874/},
publisher = {Springer}
}
@article{meshesha2012microrna,
title = {The microRNA Transcriptome of Human Cytomegalovirus (HCMV)},
author = {Meshesha, M.K. and Veksler-Lublinsky, I. and Isakov, O. and Reichenstein, I. and Shomron, N. and Kedem, K. and Ziv-Ukelson, M. and Bentwich, Z. and Avni, Y.S.},
journal = {The Open Virology Journal},
volume = {6},
pages = {38},
year = {2012},
publisher = {Bentham Science Publishers}
}
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