Welcome to Ron Y. Pinter's website!

I am a Professor of Computer Science and the Ruth Rappaport Medical School (by courtesy)at the Technion-Israel Institute of Technology

        Computer Science Department
        Taub 705
        Haifa 32000, Israel
        Email: pinter@cs.technion.ac.il or: ron.pinter at gmail.com
        Phone: +972-4-829-4955
        Fax: +972-4-829-3900
a picture of(left to right) Prof. Eliezer Shalev Dean of the Ruth Rappaport Medical School, Technion President Prof. Perertz Lavie and myself(in the wheelchair), taken at my 60th birthday symposium (January 2014)by Danny Katz

Professional Interests
Computational Systems Biology, Automated design of integrated circuits, Bioinformatics, Pharmacogenomics,Compiler technology, High Performance Computing, computational geometry Information Integration, Programming Languages, User Interfaces.

Other Interests
history and phylosophy of science, classical music and the plastic arts

Ph.D., Electrical Engineering and Computer Science: Massachusetts Institute of Technology, Cambridge, Mass.; September 1982.
Thesis title: The Impact of Layer Assignment Methods on Layout Algorithms for Integrated Circuits; advisors: Profs. Charles E. Leiserson and Ronald L. Rivest.
M.Sc., Electrical Engineering and Computer Science: Massachusetts Institute of Technology, Cambridge, Mass.; February 1980.
Thesis title: Using Hyperbolic Tangents in Integer Factoring; advisor: Prof. Ronald L. Rivest.
B.Sc., Computer Science, Summa Cum Laude: Technion, Israel Institute of Technology, Haifa, Israel; March 1975.

I am also a proud alumnus of the Hebrew Reali Highschool in Haifa (1971)

Previous Positions
Visiting Scholar inst. for Integrative Genomics Princeton University.Princeton NJ
Vice President, Research and Development, Compugen Ltd., Tel-Aviv, Israel.
Program Manager, Computer Science, IBM Research Lab in Haifa, Israel. and Member, IBM Academy of Technology

visiting Scientist, Dept of Computer Science Yale University New Haven, CT.
Member of Technical Staff, Computing Principles Research Dept., Bell Laboratories, Murray Hill, NJ.


Programming Languages (CS 234319)
Seminar on Data Integration (CS 236806, Spring 2002)
Seminar on Advanced Algorithms in Computational Biology (CS 236806, Spring 2003)
Seminar in Bioinformatics (CS 236818)
Projects in Bioinformatics (CS 236524)
Introduction to Computer Science for Medicine (274121)


Professional Activities
I am in charge of the Bioinformatics Knowledge Unit within the Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering at the Technion, Head of the Bioinformatics Track in the Dept. of Computer Science, and the head of the Department's Computational Biology Lab.

Current Graduate Students (in alphabetic order)

Alon Diament(jointly with Tamir Tuller),Michal Gordon(jointly with Eitan Rubin), Meirav Zehavi (jointly with Hadas Shachnai).

Graduated Students (in reverse chronological order) 1.INoa Tzunz- Henig Ph. D.in Medicine(jointly with Ariel Miller and Nili Avidan): Transcriptional Profiling and pathway analysis of response to Interferon-beta in immune cells and Multiple Sclerosiss 2012. Now with the Lokey Center, Technion

2.Noy Cohen-Ronen (MD thesis) (jointly with Zehava Vadas and Michael Shmoish): bioinformatic analysis of data produced by Flow cytometry in hemato-oncology diseases 2011.
won the 1st prize for MD theses at the Technion 2010-11

3.Itai Sharon Ph. D.in Computer Science(jointly with Oded Beja): Computational Methods for Meagenomic Analysis 2011.
Now at the Banfield Lab UC Berkeley,California

4.Adam Carmi M.Sc.in Computer Science:(jointly with Michael Kaminski): Adaptive Multi-Pass Parsing
Now at Safend Inc.Tel-Aviv, Israel
5.Evgeny (Yuval)Shaphir, M.Sc.in Computer Science(jointly with Shmuel Wimer): Interconnect-driven Cell-based Migration of Integrated Circuit Layout, 2009.
Now at Qualcomm, San Diego.
6. Alexandra Skolozub, M.Sc.in Computer Science: Conditional Integration of Biological Pathways, 2009.
Now at the IBM Research Lab in Haifa.
7. Adi Mano, M.Sc.in Computer Science: Building Phylogenetic Trees Based on Biochemical Pathways, 2008. Now at Google Labs, Haifa.
8. Oleg Rokhlenko, Ph.D.in Computer Science: Algorithms for Labeled Graph Matching with Applications to Systems Biology, 2007. Now at the the Yahoo! Research Labs in Haifa.
9. Yoela Yariv, Ph.D.in Biology (jointly with Nurit Katzir and Gadi Schuster): The Isolation and Characterization of Fruit Ripening-related Genes in Melon (Cucumis melo) – a Genomic Approach, 2007. Now at the Newe-Yaar Research Center.
10. Amir Rubinstein M.Sc.in Computer Science:(jointly with Yona Kassir): Faithful Modeling of Transient Behavior in Developmental Pathways, 2006. Now a graduate student at Tel-Aviv University .
11.Eyal Ackerman, Ph.D.in Computer Science (jointly with Gill Barequet): Counting Problems for Geometric Structures: Rectangulations, Floorplans, and Quasi-Planar Graphs, 2006. Now with Haifa University at Oranim.

12. Shimon Golan, M.Sc.(in ComputerScience) (jointly with Avi Gal): Efficient Algorithms for Computing Resource Availability in Wide Area Application Environments, 2006. Now at the IBM Research Lab in Haifa.
13. Dolev Dotan, M.Sc.(in ComputerScience): HyperFlow: a Visual, Ontology-Based Query and Data-Flow Language for End-User Information Analysis, 2006. Now at the IBM Research Lab in Haifa.
14. Firas Swidan, Ph.D.in Computer Science: Comparative Genomics: from Accurate Mapping to Sorting by Weighted Reversals and Repeat-Annotated Phylogenies, 2006. Now with Biomatters Inc. Auckland New Zealand
15. Haggai Yedidya, M.Sc.(in ComputerScience): Performance Evaluation of Data Cache Organizations for SMT Processors, 2005. Now at Allott Comm.
16. Esti Yeger-Lotem, Ph.D.(in ComputerScience) (jointly with Hanah Margalit of the Hebrew University): Computational Analysis of Integrated Networks of Transcription Regulation and Protein-Protein Interactions, 2005. Now on the faculty of Ben-Gurion Univ. of the Negev Beer Sheva, Israel.
17. Wisam Kadry, M.Sc.(in ComputerScience), Simulation of Metabolic Pathways, 2004. Now at ECI Telecom.
18. Oleg Rokhlenko, M.Sc.,(in ComputerScience)Tree Based Comparison of Metabolic Pathways, 2004.(wqent on for a Ph.D. under my supervision see No.8 above)
19. Joram Pe'er, M.Sc.(in Electrical Engineering): Minimal Multi-level Decomposition of Boolean Functions Using Non-Repeating Literal Trees, 1993.
20. Ilan Levin, M.Sc.(in Electrical Engineering): Realizing Expression Graphs with Xilinx Elements, 1992. Now at GE HealthCare.
21. Shimon Ben-Yehuda, M.Sc.(in Electrical Engineering), Post Generation Symbolic Layout Optimization, 1988. Now at the IBM Research Lab in Haifa.
22. Amnon Joseph, M.Sc.(in Electrical Engineering), Feed-through River Routing, 1987.
23. Joseph Blatman, M.Sc.(in Electrical Engineering), Bus Routing, 1987.
for the official list of the Technion's Graduate School (with links to abstracts and full-text theses see: http://www.graduate.technion.ac.il/Theses/Advisors.asp?Key=19694


  • Noa Henig, Nili Avidan,Ilana Mandel, Elsbeth Taun-Ram, Elizabeta Ginzburg, Tanar Paperna RonY. Pinter, and Ariel Miller: "Interferon-Beta Induces Distinct Gene Expression Response Patterns in Human Monocytes versus T cells", doi:10.1371/ Sharon, I., Battchikova, N., Aro, E.-M., Giglione, C., Meinnel, T., Glaser, F., Pinter, R.Y., Breitbart, M., Rohwer, F., and Beja, O. (2011) "Comparative metagenomics of microbial traits within Oceanic viral Communities. ISME J. advance online
  • F Sharon I, Bercovici S, Pinter RY, and Shlomi T. "Pathway-based functional analysis of metagenomes". Journal of Computational Biology; Vol.18, No.3 (March 2011)pp. 495-505
  • Adi Mano, Tamir Tuller, Oded Beja, and Ron Y. Pinter: "Comparative Classification of Species and the Study of Pathway Evolution based on the Alignment of Metabolic Pathways"; BMC Bioinformatics, Volume 11 Suppl 1 (selected papers from APBC), January 2010.
  • Itai Sharon, Ariella Alperovitch, Forest Rohwer, Matthew Haynes, Fabian Glaser, Nof Atamna-Ismaeel, Ron Y. Pinter, Frederic Partensky, Eugene V. Koonin, Yuri I. Wolf, Nathan Nelson, and Oded Beja: "Photosystem I gene cassettes are present in marine virus genomes"; Nature, Vol. 461, No. 7261 (September 10, 2009), pp. 258-262.
  • Alexandra Skolozub, Ofer Sarig, and Ron Y. Pinter: "Conditional Pathway Integration"; Proceedings of the 8th Annual International Conference on Computational Systems Bioinformatics (CSB), August 2009, pp. 165-176.
  • Itai Sharon, Amrita Pati, Victor M. Markowitz, and Ron Y. Pinter: "A Statistical Framework for the Functional Analysis of Metagenomes"; Proceedings of 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Lecture Notes in Computer Science (LNCS), Vol. 5541, May 2009, pp. 496-511.
  • Martin Akerman, Hilda David-Eden, Ron Y. Pinter, and Yael Mandel-Gutfreund: "A computational approach for genome-wide mapping of splicing factors binding sites"; Genome Biology,, Vol. 10, No. 3 (March 2009).
  • Ariel Miller, Nili Avidan, Noa Tzunz-Henig, Lea Glass-Marmor, Izabella Lejbkowicz, Ron Y. Pinter, and Tamar Paperna: "Translation towards Personalized Medicine in Multiple Sclerosis"; Journal of the Neurological Sciences, Vol. 274 (2008), pp. 68-75.
  • Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, and Michal Ziv-Ukelson: "Seeded Tree Alignment"; IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 4 (October 2008), pp. 503-513 (a preliminary version appeared in the Proceedings of the 7th Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science (LNCS), Vol. 4645, September 2007, pp. 98-110).
  • Ron Y. Pinter, Oleg Rokhlenko, Dekel Tsur, and Michal Ziv-Ukelson:"Approximate labelled Subtree Homeomorphism" Journal of Discrete Algorithms, Vol. 6, No. 3 (September 2008), pp. 480-496.
  • ? Ron Y. Pinter a, Oleg Rokhlenko a,?, Dekel Tsur b, Michal Ziv-Ukelson R. Y. Pinter, O. Rokhlenko, D. Tsur, and M. Ziv-Ukelson: "Approximate Labelled Subtree Homeomorphism"; Journal of Discrete Algorithms, Vol. 6, No. 3 (September 2008), pp. 480-496 (a preliminary version appeared in the Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science (LNCS), Vol. 3109, July 2004, pp. 59-73).
  • M. A. Bender, D. Ge, S. He, H. Hu, R. Y. Pinter, S. Skiena, and F. Swidan: "Improved Bounds on Sorting by Length-Weighted Reversals"; Journal of Computer and System Sciences, Vol, 74, No. 5 (August 2008), pp. 744-774 (a preliminary version appeared in the Proceedings of the 15th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 2004, pp. 912-921).
  • Fanica Gavril, Ron Y. Pinter and Shmuel Zaks: "Intersection Representations of Matrices by Subtrees and Unicycles on Graphs"; Journal of Discrete Algorithms, Vol. 6, No. 2 (2008), pp. 216-228.
  • Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, and Ron Y. Pinter: "Constraint-based Functional Similarity of Metabolic Genes: Going Beyond Network Topology"; Bioinformatics, Vol. 23, No. 16 (August 2007), pp. 2139-2146.
  • Amir Rubinstein, Vyacheslav Gurevich, Zohar Kasulin-Boneh, Lilach Pnueli, Yona Kassir, and Ron Y. Pinter: "Faithful Modeling of Transient Expression and Its Application to Elucidating Negative Feedback Regulation"; Proceedings of the National Academy of Sciences (PNAS), Vol. 104, No. 15 (April 10, 2007), pp. 6241-6246.
  • Firas Swidan, Michal Ziv-Ukelson, and Ron Y. Pinter: "On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem"; Journal of Computational Biology (JCB), Vol. 13, No. 8 (October 2006), pp. 1397-1418.
  • Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, and Ron Y. Pinter: "Flux Based vs. Topology Based Similarity of Metabolic Genes"; Proceedings of the 6th Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science (LNCS), Vol. 4175, September 2006, pp. 274-285.
  • Eyal Ackerman, Gill Barequet, and Ron Y. Pinter: "On the Number of Rectangular Partitions"; Journal of Combinatorial Theory, Series A, Vol. 113, No. 6 (August 2006), pp. 1072-1091.
  • Firas Swidan, Michael Shmoish, Eduardo Rocha, and Ron Y. Pinter: "An Integrative Method for Accurate Comparative Genome Mapping"; PLoS Computational Biology, Vol. 2., No. 8 (August 2006), pp. 870-889.
  • Eyal Ackerman, Gill Barequet, and Ron Y. Pinter: "A bijection between permutations and floorplans, and its applications"; Discrete Applied Mathematics, Vol. 154, No. 12 (July 2006), pp. 1674-1684.
  • Noa Henig, Nili AvidanIlana Mandel Elsbeth Taun-Ran,Elizabeta Ginzburg
  • Yehuda G. Assaraf, Ilan Ifergan, Wisam N. Kadry and Ron Y. Pinter: "Computer Modelling of Antifolate Inhibition of Folate Metabolism using Hybrid Functional Petri Nets"; Journal of Theoretical Biology, Vol. 240, No. 4 (June 2006), pp. 637-647.
  • Eyal Ackerman, Gill Barequet, Ron Y. Pinter, and Dan Romik: "The number of guillotine partitions in d dimensions"; Information Processing Letters (IPL), Vol. 98, No. 4 (May 2006), pp. 162-167.
  • C. Ben-Zaken Zilberstein, M. Ziv-Ukelson, R. Y. Pinter, Z. Yakhini: "A High-Throughput Approach for Associating MicroRNAs with their Activity Conditions"; Journal of Computational Biology (JCB), Vol. 13, No. 2 (March 2006), pp. 245-66 (a preliminary version appeared in the Proceedings of 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), pp. 133-151).
  • Dolev Dotan and Ron Y. Pinter: "HyperFlow: an Integrated Visual Query and Data-Flow Language for End-User Information Analysis"; Proceedings of the IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC'05), September 2005, pp. 27-34.
  • Eyal Ackerman, Gill Barequet, and Ron Y. Pinter: "An Upper Bound on the Number of Rectangulations of a Point Set"; Proceedings of the Eleventh International Computing and Combinatorics Conference (COCOON'05), Lecture Notes in Computer Science (LNCS), Vol. 3595, August 2005, pp. 554-559.
  • R. Y. Pinter, O. Rokhlenko, E. Yeger-Lotem, M. Ziv-Ukelson: "Alignment of Metabolic Pathways"; Bioinformatics, ACM Transactions on Algorithms, (Vol. 8, No. 2), Article 9, April 2012., pp. 3401-3408.
  • Y. Aumann, M. Lewenstein, O. Melamud, R. Y. Pinter, and Z. Yakhini: "Dotted Interval Graphs and High Throughput Genotyping"; ACM Transactions on Algorithms, (Vol. 8, No. 2), Article 9, , April2012, pp. 339-348.
  • F. Swidan, M. A. Bender, D. Ge, S. He, H. Hu, and R. Pinter: "Sorting by length-weighted reversals: Dealing with signs and circularity"; Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science (LNCS), Vol. 3109, July 2004, pp. 32-46.
  • E. Yeger-Lotem, S. Sattath, N. Kashtan, S. Itzkovitz, R. Milo, R. Y. Pinter, U. Alon, and H. Margalit: "Network Motifs in Integrated Cellular Networks of Transcription Regulation and Protein-protein Interaction"; Proceedings of the National Academy of Sciences (PNAS), Vol. 101, No. 16 (April 20, 2004), pp. 5934-5939.
  • Ron Y. Pinter and Oleg Rokhlenko: “New Methods for the Alignment of Complex Structures”; Currents in Computational Molecular Biology, pages 313-314, 2003.
  • Pinter, R.Y., and Skiena, S.: "Sorting with length-weighted reversals"; Proceedings of the 13th International Conference on Genome Informatics (GIW 2002), December 2002, pp. 103-111.
  • Lu, Q., Kraft, R., Eichstaedt, M., Zodik, G., Ford, D.A., Pinter, R.Y., and Nicol, D.: "jCentral: search the web for Java", poster, the 8th International World Wide Web Conference (WWW8), 1999.
  • Joram Pe'er and Ron Y. Pinter: "Minimal Decomposition of Boolean Functions Using Non-Repeating Literal Trees"; Proceedings of the IFIP Workshop on Logic and Architecture Synthesis, IFIP TC10 WD10.5, December 1995, pp. 129-139.
  • David S. Johnson, Andrea S. LaPaugh, and Ron Y. Pinter: "Minimizing Channel Density by Lateral Shifting of Components"; Proceedings of the 5th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA),, January 1994, pp. 122-131.
  • Pinter, S.S., and Pinter, R.Y.: "Parallelizing Programs Using Idioms"; ACM Transactions on Programming Languages and Systems, Vol. 16, No. 3, pp. 305-327, 1994.
  • Ilan Levin and Y. Pinter: "Realizing Expression Graphs using Table-lookup FPGAs"; Proceedings of EuroDAC'93, October 1993, pp. 306-311.
  • Canetti, R., Fertig, P.L., Kravitz, S.A., Malki, D., Pinter, R.Y., Porat, S., and Teperman, A.: "The parallel C (pC) programming language"; IBM Journal on Research and Development, Vol. 35, No. 5/6, pp. 727-741, 1991.
  • Pinter, R.Y., Vortman, P., and Weiss, Z.: "Partial compilation of REXX"; IBM Systems Journal, Vol. 30, No. 3, pp. 312-321, 1991.
  • Luis F. Ortiz, Ron Y. Pinter, and Shlomit S. Pinter: "An Array Language for Data Parallelism: Definition, Compilation, and Applications"; Journal of Supercomputing, Vol. 5, No. 1 (June 1991), pp. 7-29.
  • Andrea S. LaPaugh and Ron Y. Pinter: "Channel Routing for Integrated Circuits"; Annual Reviews of Computer Science, Vol. 4 (1989-1990), pp. 307-363.
  • Amnon Joseph and Ron Y. Pinter: "Feed-Through River Routing"; Integration - the VLSI Journal, Vol. 8 (1989), pp. 41-50.
  • Bernstein, D., Goldin, D.Q., Golumbic, M.C., Krawczyk, H., Mansour, Y., Nahshon, I., and Pinter, R.Y.: "Spill code minimization techniques for optimizing compilers"; Proceedings of the ACM SIGPLAN'89 Conference on Programming Language Design and Implementation, June 1989, pp. 258-263.
  • Shimon Ben-Yehuda and Ron Y. Pinter: "Symbolic Layout Improvement Using String Matching Based Local Transformations"; Proceedings of the Decennial Caltech Conference on VLSI, March 1989, pp. 227-239.
  • Bar-Yehuda, R., Feldman, J.A. Pinter, R.Y., and Wimer S.: "Depth first search and dynamic programming algorithms for efficient CMOS cell generation"; IEEE Transactions on Computer-Aided Design, Vol. CAD-8, No. 7, pp. 737-743, 1989.
  • David Bernstein, Haran Boral, and Ron Y. Pinter: "Optimal Chaining in Expression Trees"; IEEE Transactions on Computers, Vol. 37, No. 11 (November 1988), pp. 1366-1374.
  • Dagan, I., Golumbic, M.C., and Pinter, R.Y.: "Trapezoid graphs and their coloring"; Discrete Applied Mathematics, Vol. 21, pp. 35-46, 1988.
  • Shmuel Wimer, Ron Y. Pinter, and Jack A. Feldman: "Optimal Chaining of CMOS Transistors in a Functional Cell"; IEEE Transactions on Computer-Aided Design, Vol. CAD-6, No. 5 (September 1987), pp. 795-801.
  • Takao Asano, Tetsuo Asano, and Ron Y. Pinter: "Polygon Triangulation: Efficiency and Minimality"; Journal of Algorithms, Vol. 7, No. 2 (June 1986), pp. 221-231.
  • Nissim Francez, Shalom Goldenberg, Ron Y. Pinter, Michael Tiomkin, and Shalom Tsur: "An Environment for Logic Programming"; Proceedings of the ACM SIGPLAN'85 Symposium on Language Issues in Programming Environments, June 1985, pp. 179-190.
  • Ron Y. Pinter: "Efficient String Matching with Don't-Cares"; Combinatorial Algorithms on Words, NATO ASI Series, Vol. F12, Springer-Verlag, 1985, pp. 11-29.
  • Bernstein, D., Pinter, R.Y, and Rodeh, M.: "Optimal scheduling of arithmetic operations in parallel with memory access"; Proceedings of the Twelfth ACM Symposium on Principles of Programming Languages, January 1985, pp. 325-333.
  • Michael R. Garey and Ron Y. Pinter: "Optimum Scan-Width Selection under Containment Constraints"; Bell System Technical Journal, Vol. 63, No. 6 (July-August 1984), pp. 1191-1212.
  • Ron Y. Pinter: "Optimal Layer Assignment for Interconnect"; Journal of VLSI and Computer Systems, Vol. 1, No. 2 (Fall 1984), pp. 123-137.
  • Brenda S. Baker and Ron Y. Pinter: "An Algorithm for the Optimal Placement and Routing of a Circuit within a Ring of Pads"; Proceedings of the Twenty-fourth IEEE Symposium on Foundations of Computer Science, November 1983, pp. 360-370.
  • Charles E. Leiserson and Ron Y. Pinter: "Optimal Placement for River Routing"; SIAM Journal on Computing, Vol. 12, No. 3 (August 1983), pp. 447-462.
  • Ron Y. Pinter: "River Routing: Methodology and Analysis"; Proceedings of the Third Caltech Conference on VLSI, March 1983, pp. 141-163.
  • Andrzej Lingas, Ron Y. Pinter, Ronald L. Rivest, and Adi Shamir: "Minimum Edge Length Partitioning of Rectilinear Polygons"; Proceedings of the Twentieth Annual Allerton Conference on Communication, Control, and Computing, October 1982, pp. 53-63.
  • Ron Y. Pinter: "On Routing Two-point Nets Across a Channel"; Proceedings of the Nineteenth Design Automation Conference, June 1982, pp. 894-902.
  • Ron Y. Pinter: "Optimal Routing in Rectilinear Channels"; Proceedings of the CMU Conference on VLSI Systems and Computations, October 1981, pp. 160-177.
"> href=website and my wife's website href=" daughter's homepage and to my son's Blog!