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ORCIDMichal Ziv-Ukelson
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2020 – today
- 2023
[j43]Eden Ozeri, Meirav Zehavi, Michal Ziv-Ukelson:
New algorithms for structure informed genome rearrangement. Algorithms Mol. Biol. 18(1): 17 (2023)- [j42]Dana Fisman, Dolav Nitay, Michal Ziv-Ukelson:
Learning of Structurally Unambiguous Probabilistic Grammars. Log. Methods Comput. Sci. 19(1) (2023) - 2022
- [j41]Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein, Michal Ziv-Ukelson:
Predicting the pathogenicity of bacterial genomes using widely spread protein families. BMC Bioinform. 23(1): 253 (2022) - [c35]Eden Ozery, Meirav Zehavi, Michal Ziv-Ukelson:
New Algorithms for Structure Informed Genome Rearrangement. WABI 2022: 11:1-11:19 - [i5]Dana Fisman, Dolav Nitay, Michal Ziv-Ukelson:
Learning of Structurally Unambiguous Probabilistic Grammars. CoRR abs/2203.09441 (2022) - 2021
- [j40]Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson:
Approximate search for known gene clusters in new genomes using PQ-trees. Algorithms Mol. Biol. 16(1): 16 (2021) - [c34]Dolav Nitay, Dana Fisman, Michal Ziv-Ukelson:
Learning of Structurally Unambiguous Probabilistic Grammars. AAAI 2021: 9170-9178 - 2020
- [j39]Dina Svetlitsky, Tal Dagan
, Michal Ziv-Ukelson:
Discovery of multi-operon colinear syntenic blocks in microbial genomes. Bioinform. 36(Supplement-1): i21-i29 (2020) - [j38]Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson:
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. J. Comput. Biol. 27(11): 1561-1580 (2020) - [c33]Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson:
Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees. WABI 2020: 1:1-1:24 - [i4]Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, Michal Ziv-Ukelson:
Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees. CoRR abs/2007.03589 (2020) - [i3]Dolav Nitay, Dana Fisman, Michal Ziv-Ukelson:
Learning of Structurally Unambiguous Probabilistic Grammars. CoRR abs/2011.07472 (2020)
2010 – 2019
- 2019
- [j37]Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson:
On Almost Monge All Scores Matrices. Algorithmica 81(1): 47-68 (2019) - [j36]Dina Svetlitsky, Tal Dagan, Vered Chalifa-Caspi, Michal Ziv-Ukelson:
CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes. Bioinform. 35(10): 1634-1643 (2019) - [j35]Eran Barash, Neta Sal-Man, Sivan Sabato, Michal Ziv-Ukelson:
BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM. Bioinform. 35(12): 2001-2008 (2019) - [j34]Jonathan Engel, Isana Veksler-Lublinsky, Michal Ziv-Ukelson:
Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes. J. Comput. Biol. 26(7): 745-766 (2019) - [c32]Michal Ziv-Ukelson:
Stringology Combats Microbiological Threats (Invited Talk). CPM 2019: 3:1-3:1 - [c31]Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson:
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. WABI 2019: 9:1-9:13 - [i2]Roni Zoller, Meirav Zehavi, Michal Ziv-Ukelson:
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. CoRR abs/1912.01934 (2019) - 2018
- [j33]Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson:
A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands. J. Comput. Biol. 25(2): 214-235 (2018) - [i1]Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson:
Dynamic all scores matrices for LCS score. CoRR abs/1808.03553 (2018) - 2017
- [j32]Ilan Y. Smoly, Eugene Lerman, Michal Ziv-Ukelson, Esti Yeger Lotem:
MotifNet: a web-server for network motif analysis. Bioinform. 33(12): 1907-1909 (2017) - [j31]Ilan Y. Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger Lotem:
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. PLoS Comput. Biol. 13(1) (2017) - 2016
- [j30]Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson:
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns. J. Comput. Biol. 23(3): 165-179 (2016) - [c30]Amir Carmel, Dekel Tsur, Michal Ziv-Ukelson:
On Almost Monge All Scores Matrices. CPM 2016: 17:1-17:12 - [c29]Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson:
A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands. WABI 2016: 14-26 - 2015
- [c28]Achiya Elyasaf, Pavel Vaks, Nimrod Milo, Moshe Sipper, Michal Ziv-Ukelson:
Learning Heuristics for Mining RNA Sequence-Structure Motifs. GPTP 2015: 21-38 - [c27]Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson:
Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns. WABI 2015: 53-65 - 2014
- [j29]Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson:
The Worst Case Complexity of Maximum Parsimony. J. Comput. Biol. 21(11): 799-808 (2014) - [j28]Tamar Pinhas, Nimrod Milo, Gregory Kucherov, Michal Ziv-Ukelson:
Algorithms for path-constrained sequence alignment. J. Discrete Algorithms 24: 48-58 (2014) - [j27]Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson:
Efficient all path score computations on grid graphs. Theor. Comput. Sci. 525: 138-149 (2014) - [c26]Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson:
The Worst Case Complexity of Maximum Parsimony. CPM 2014: 79-88 - [c25]Shay Zakov, Nimrod Milo, Tamar Pinhas, Sivan Yogev, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Dekel Tsur, Michal Ziv-Ukelson:
Recent Results on Three Problems in Comparative Structural RNAomics. CMSR@ECCB 2014: 58-58 - 2013
- [j26]Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson:
Unrooted unordered homeomorphic subtree alignment of RNA trees. Algorithms Mol. Biol. 8: 13 (2013) - [j25]Tamar Pinhas, Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson:
Efficient edit distance with duplications and contractions. Algorithms Mol. Biol. 8: 27 (2013) - [j24]Alexander Lan, Michal Ziv-Ukelson, Esti Yeger Lotem:
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. Bioinform. 29(13): 210-216 (2013) - [c24]Sivan Yogev, Nimrod Milo, Michal Ziv-Ukelson:
StemSearch: RNA search tool based on stem identification and indexing. BIBM 2013: 145-152 - [c23]Ury Matarazzo, Dekel Tsur, Michal Ziv-Ukelson:
Efficient All Path Score Computations on Grid Graphs. CPM 2013: 211-222 - 2012
- [j23]Isana Veksler-Lublinsky, Yonat Shemer-Avni, Eti Meiri, Zvi Bentwich, Klara Kedem, Michal Ziv-Ukelson:
Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV). BMC Bioinform. 13: 322 (2012) - [c22]Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson:
RNA Tree Comparisons via Unrooted Unordered Alignments. WABI 2012: 135-148 - 2011
- [j22]Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson:
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach. Algorithms Mol. Biol. 6: 20 (2011) - [j21]Kfir Wolfson, Shay Zakov, Moshe Sipper, Michal Ziv-Ukelson:
Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis. Genet. Program. Evolvable Mach. 12(2): 121-160 (2011) - [j20]Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson:
Regular Language Constrained Sequence Alignment Revisited. J. Comput. Biol. 18(5): 771-781 (2011) - [j19]Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson:
Rich Parameterization Improves RNA Structure Prediction. J. Comput. Biol. 18(11): 1525-1542 (2011) - [j18]Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson:
Sparse RNA folding: Time and space efficient algorithms. J. Discrete Algorithms 9(1): 12-31 (2011) - [c21]Tamar Pinhas, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson:
Edit Distance with Duplications and Contractions Revisited. CPM 2011: 441-454 - [c20]Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson:
Rich Parameterization Improves RNA Structure Prediction. RECOMB 2011: 546-562 - 2010
- [j17]Isana Veksler-Lublinsky, Yonat Shemer-Avni, Klara Kedem, Michal Ziv-Ukelson:
Gene bi-targeting by viral and human miRNAs. BMC Bioinform. 11: 249 (2010) - [j16]Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir:
A Faster Algorithm for Simultaneous Alignment and Folding of RNA. J. Comput. Biol. 17(8): 1051-1065 (2010) - [c19]Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson:
Regular Language Constrained Sequence Alignment Revisited. IWOCA 2010: 404-415 - [c18]Nimrod Milo, Tamar Pinhas, Michal Ziv-Ukelson:
SA-REPC - Sequence Alignment with Regular Expression Path Constraint. LATA 2010: 451-462 - [c17]Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson:
Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant's Approach. WABI 2010: 65-77
2000 – 2009
- 2009
- [j15]Yury Lifshits, Shay Mozes, Oren Weimann, Michal Ziv-Ukelson:
Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions. Algorithmica 54(3): 379-399 (2009) - [j14]Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, Ron Unger:
RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry. BMC Bioinform. 10 (2009) - [j13]Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson:
Fast algorithms for computing tree LCS. Theor. Comput. Sci. 410(43): 4303-4314 (2009) - [c16]Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson:
Sparse RNA Folding: Time and Space Efficient Algorithms. CPM 2009: 249-262 - 2008
- [j12]Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson:
Approximate labelled subtree homeomorphism. J. Discrete Algorithms 6(3): 480-496 (2008) - [j11]Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson:
Seeded Tree Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 5(4): 503-513 (2008) - [c15]Shay Mozes, Dekel Tsur, Oren Weimann, Michal Ziv-Ukelson:
Fast Algorithms for Computing Tree LCS. CPM 2008: 230-243 - [c14]Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir:
A Faster Algorithm for RNA Co-folding. WABI 2008: 174-185 - 2007
- [j10]Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
A Study of Accessible Motifs and RNA Folding Complexity. J. Comput. Biol. 14(6): 856-872 (2007) - [j9]Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem:
A Structure-Based Flexible Search Method for Motifs in RNA. J. Comput. Biol. 14(7): 908-926 (2007) - [j8]Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson:
Two algorithms for LCS Consecutive Suffix Alignment. J. Comput. Syst. Sci. 73(7): 1095-1117 (2007) - [c13]Shay Mozes, Oren Weimann, Michal Ziv-Ukelson:
Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions. CPM 2007: 4-15 - [c12]Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson:
Seeded Tree Alignment and Planar Tanglegram Layout. WABI 2007: 98-110 - 2006
- [j7]Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini:
A High-Throughput Approach for Associating MicroRNAs with Their Activity Conditions. J. Comput. Biol. 13(2): 245-266 (2006) - [j6]Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson:
On the Complexity of Sparse Exon Assembly. J. Comput. Biol. 13(5): 1013-1027 (2006) - [j5]Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter:
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. J. Comput. Biol. 13(8): 1397-1418 (2006) - [c11]Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter:
On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. CPM 2006: 141-152 - [c10]Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
A Study of Accessible Motifs and RNA Folding Complexity. RECOMB 2006: 473-487 - 2005
- [j4]Ron Y. Pinter, Oleg Rokhlenko, Esti Yeger Lotem, Michal Ziv-Ukelson:
Alignment of metabolic pathways. Bioinform. 21(16): 3401-3408 (2005) - [c9]Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson:
On the Complexity of Sparse Exon Assembly. CPM 2005: 201-218 - [c8]Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini:
A High-Throughput Approach for Associating microRNAs with Their Activity Conditions. RECOMB 2005: 133-151 - [c7]Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression. WABI 2005: 13-26 - 2004
- [c6]Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, Michal Ziv-Ukelson:
Approximate Labelled Subtree Homeomorphism. CPM 2004: 59-73 - [c5]Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson:
Two Algorithms for LCS Consecutive Suffix Alignment. CPM 2004: 173-193 - 2003
- [j3]Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson:
Sparse LCS Common Substring Alignment. Inf. Process. Lett. 88(6): 259-270 (2003) - [j2]Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson:
A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices. SIAM J. Comput. 32(6): 1654-1673 (2003) - [c4]Gad M. Landau, Baruch Schieber, Michal Ziv-Ukelson:
Sparse LCS Common Substring Alignment. CPM 2003: 225-236 - 2002
- [c3]Maxime Crochemore, Gad M. Landau, Michal Ziv-Ukelson:
A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. SODA 2002: 679-688 - 2001
- [j1]Gad M. Landau, Michal Ziv-Ukelson:
On the Common Substring Alignment Problem. J. Algorithms 41(2): 338-359 (2001) - 2000
- [c2]Gad M. Landau, Michal Ziv-Ukelson:
On the shared substring alignment problem. SODA 2000: 804-814
1990 – 1999
- 1998
- [c1]Michal Ziv-Ukelson, Aaron Kershenbaum:
A Dictionary Matching Algorithm Fast on the Average for Terms of Varying Length. CPM 1998: 34-54
Coauthor Index
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