RNA Structure Prediction
RNA Structural Alignment
Constrained Sequence Alignment
RNA Structural Search


Eran's paper accepted for publication in Bioinformatics

E. Barash, N. Sal-Man, S. Sabato and M. Ziv-Ukelson, "BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM." Bioinformatics(2018)

Dina's poster received Best Poster Award at the IBS-2018

Dina's poster, "CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes", received a Best Poster Award at the Israel Bioinfomatics Symposium 2018.

Dina's paper accepted for publication in Bioinformatics

D. Svetlitsky, T. Dagan, V. Chalifa-Caspi and Michal Ziv-Ukelson. "CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes." Bioinformatics (2018). link

Amir's paper published in Algorithmica

Carmel, A., Tsur, D. and Ziv-Ukelson, M. "On Almost Monge All Scores Matrices". Algorithmica(2018) link

Arnon's RAGB Monitor included in Omic Tools

Arnon's RAGB Monitor (Synteny Block Detection) included in Omic Tools Link to Omic Tools

Our paper in WABI 2016

A. Benshahar, V. Caspi, D. Hermelin and M. Ziv-Ukelson, "A Biclique Approach to Reference Anchored Gene Blocks and its Applications to Pathogenicity Islands", Proc. WABI 2016(The 16th International Workshop on Algorithms in Bioinformatics), Aarhus (2016) Link to a recording of the presentation

Our paper in CPM 2016

Carmel, Amir, Dekel Tsur, and Michal Ziv-Ukelson. "On Almost Monge All Scores Matrices." LIPIcs-Leibniz International Proceedings in Informatics. Vol. 54. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 2016.‏ Link to a recording of the presentation

Our paper in WABI 2015

I. Y. Smoly, A. Carmel, Y. Shemer-Avni, E. Yeger Lotem, and M. Ziv-Ukelson, Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns. it Proc The 15th Workshop on Algorithms in Bioinformatics (WABI2015), Lecture Notes in Computer Science, LNBI 9289, pp:53-65, Atlanta, Georgia, USA (2015). Link to a recording of the presentation

Hosting Stringology 2015

In Stringology 2015 we celebrated Gadi Landua's Birthday. Link to Conference Site

Our paper in CPM 2014

A. Carmel, N. Musa-Lempel, D. Tsur and M. Ziv-Ukelson, The Worst Case Complexity of Maximum Parsimony. Proc. CPM 2014 (The 25th Annual Symposium on Combinatorial Pattern Matching), Moscow, Russia, June 16-18, 2014.

Our paper in BIBM 2013

A. Yogev, N. Milo and M. Ziv-Ukelson, StemSearch: RNA Search Tool Based on Stem Identification and Indexing, Proc. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013), Shanghai, China, December 18-21, 2013.

Our paper in ISMB 2013

ismb2013ISMB 2013 - 21th Annual International Conference on Intelligent Systems for Molecular Biology, Berlin, July 19 - 23, 2013. Alex Lan, Michal Ziv-Ukelson and Esti Yeger-Lotem, A Context-Sensitive Framework for the Analysis of Human Signalling Pathways in Molecular Interaction Networks. link to citation

ContextFold praised by comparative analysis of RNA folders (NAR 2013)

"... rankings based on the RNAstrand data set were dominated by single-sequence methods: in 7 of 10 rankings, ContextFold was the best performing method..." CompaRNA paper in NAR: CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction, by Puton, Kozlowski, Rother, and Bujnicki, Nucleic Acids Research (2013).

Our paper in CPM 2013

cpmCPM 2013 - The 24th Annual Symposium on Combinatorial Pattern Matching, Bad Herrenalb, Germany, June 17–19, 2013: "Efficient All Path Score Computations on Grid Graphs", by Ury Metarrazo, Dekel Tsur and Michal Ziv-Ukelson link to citation

Hosting IBS-2013 in BGU

alonWe are happy to announce the 15th Israeli Bioinformatics Symposium, which will take place on June 27th 2013 at Ben-Gurion University of the Negev.

Context Fold Server update

Context Fold server has a new and improved interactive web interface, thanks to Elad Levi

Our paper in WABI 2012

algo2012WABI 2012 - September 2012 - Ljubljana, Slovenia: "RNA Tree Comparisons Via Unrooted Unordered Alignments". by Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz and Michal Ziv-Ukelson. link

EMC Teaching and Research award - 2012

emc Congratulations to Isana Veksler-Lublinsky for winning EMC award for Teaching and Research for 2012

RECOMB 2011 Best Paper Award

rna We were very happy to hear that our paper, "Rich Parameterization Improves RNA Structure Prediction", by Shay Zakov, Yoav Goldberg, Michael Elhadad and Michal Ziv-Ukelson, has received the RECOMB 2011 Best Paper Award. Thanks !

Our paper in CPM 2011

Palermo in June for CPM 2011: "Edit Distance with Duplications and Contractions Revisited". by Tamar Pinhas, Dekel Tsur, Shay Zakov, and Michal Ziv-Ukelson. link