Chaim Linhart

Former Ph.D. student under joint supervision of Prof. Ron Shamir (CS school) and Prof. Yossi Shiloh (Medicine School),
School of Computer Science,
Tel Aviv University, Tel Aviv, 69978, ISRAEL.

Email: chaiml @

Pattern Matching (Prof. Ron Shamir)

  • Matching with don't-cares and a small number of mismatches (link to ScienceDirect)
    Paper by C. Linhart and R. Shamir - Information Processing Letters, Vol. 109:5, pp. 273-277, Feb 2009.
  • Faster Pattern Matching with Character Classes using Prime Number Encoding (link to JCSS)
    Paper by C. Linhart and R. Shamir - Journal of Computer and System Sciences, Vol. 75:3, pp. 155-162, May 2009.

  • Computational Biology (Prof. Ron Shamir)

    Promoter & 3' UTR Analysis

  • Software: ALLEGRO and AMADEUS - A motif discovery platform for finding known and novel motifs (e.g., transcription factor or microRNA binding sites) in genomic sequences, given one of the following:
    (a) Large-scale gene expression dataset(s) - Allegro simultaneously searches for cis-regulatory motifs and their associated expression profiles;
    (b) Set(s) of co-regulated genes - Amadeus finds motifs that are over/under-represented in the supplied set(s) with respect to the rest of the genome;
    (c) Only regulatory sequences - Amadeus identifies motifs with global spatial features, i.e., motifs that appear non-uniformly along the promoters, between the two strands, or among the chromosomes.
    Allegro and Amadeus are integrated into a single user-friendly, graphical software package.
  • Software: PRIMA - A software for finding transcription factors whose binding sites are enriched in a given set of promoters.
  • Software: EXPANDER - A gene expression analysis and visualization software.
  • A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans (link to Genome Research)
    Paper by C. Linhart, Y. Halperin, A. Darom, S. Kidron, L. Broday, and R. Shamir - Genome Research, vol. 22, pp. 76-83, 2012.
  • Expander: from expression microarrays to networks and functions (link to Nature Protocols)
    Paper by I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, R. Sharan, Y. Shiloh, and R. Shamir - Nature Protocols, vol. 5, pp. 303-322, February 2010.
  • Allegro: Analyzing expression and sequence in concert to discover regulatory programs (link to NAR)
    Paper by Y. Halperin, C. Linhart, I. Ulitsky, and R. Shamir - Nucleic Acids Research, vol. 37:5, pp. 1566-1579, April 2009.
  • Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets (link to Genome Research)
    Paper by C. Linhart, Y. Halperin, and R. Shamir - Genome Research, Vol. 18:7, pp. 1180-1189, July 2008.
  • Functional genomic delineation of TLR-induced transcriptional networks (link to BMC Genomics)
    Paper by R. Elkon, C. Linhart, Y. Halperin, Y. Shiloh, and R. Shamir - BMC Genomics, Vol. 8:394, Oct 2007.
  • Parallel induction of ATM-dependent pro- and anti-apoptotic signals in response to ionizing radiation in murine lymphoid tissue (link to Oncogene)
    Paper by S. Rashi-Elkeles, R. Elkon, N. Weizman, C. Linhart, N. Amariglio, G. Sternberg, G. Rechavi, A. Barzilai, R. Shamir, and Y. Shiloh - Oncogene, Vol. 25, pp. 1584-1592, Mar 2006.
  • Deciphering Transcriptional Regulatory Elements That Encode Specific Cell-Cycle Phasing by Comparative Genomics Analysis (link to CC)
    Paper by C. Linhart, R. Elkon, Y. Shiloh, and R. Shamir - Cell Cycle, Vol. 4(12), pp. 1788-1797, Dec 2005.
  • EXPANDER - an integrative program suite for microarray data analysis (link to BMC Bioinformatics)
    Paper by R. Shamir, A. Maron-Katz, A. Tanay, C. Linhart, I. Steinfeld, R. Sharan, Y. Shiloh, and R. Elkon - BMC Bioinformatics, Vol. 6:232, Sep 2005.
  • Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis (link to GB)
    Paper by R. Elkon, S. Rashi-Elkeles, Y. Lerenthal, C. Linhart, T. Tenne, N. Amariglio, G. Rechavi, R. Shamir, and Y. Shiloh - Genome Biology, Vol. 6(5):R43, Apr 2005.
  • In Silico Identification of Transcriptional Regulators Associated with c-Myc (link to NAR)
    Paper by R. Elkon, K. Zeller, C. Linhart, C. Dang, R. Shamir, and Y. Shiloh - Nucleic Acids Reserach, Vol. 32(17), pp. 4955-4961, Sep 2004.
  • Genome-wide In-silico Identification of Transcriptional Regulators Controlling Cell Cycle in Human Cells (link to GR)
    Paper by R. Elkon, C. Linhart, R. Sharan, R. Shamir, and Y. Shiloh - Genome Research, Vol. 13(5), pp. 773-780, May 2003.

  • Degenerate Primer Design

  • Degenerate Primer Design: Theoretical analysis and the HYDEN program (link to Humana Press)
    Chapter by C. Linhart and R. Shamir, in PCR primer design, A. Yuryev (editor), Humana Press, July 2007.
  • The degenerate primer design problem: Theory and applications (link to JCB)
    Paper by C. Linhart and R. Shamir - JCB, Vol. 12(4), pp. 431-456, May 2005.
  • M.Sc. thesis: The Degenerate Primer Design Problem (short summary in Hebrew)
    Thesis conducted under the supervision of Prof. Ron Shamir.
  • Software: HYDEN - A software for designing degenerate primers.
  • The Degenerate Primer Design Problem (PDF format)
    Paper by C. Linhart and R. Shamir - Bioinformatics, Vol. 18, Suppl. 1, pp. S172-S180, August 2002 (presented at ISMB '02).
  • DEFOG: A Practical Scheme for Deciphering Families of Genes (PDF format)
    Paper by T. Fuchs, B. Malecova, C. Linhart, R. Sharan, M. Khen, R. Herwig, D. Shmulevich, R. Elkon, M. Steinfath, J.K. O'Brien, U. Radelof, H. Lehrach, D. Lancet, and R. Shamir - Genomics, Vol. 80, No. 3, pp. 295-302, September 2002.
  • The Canine Olfactory Subgenome (link to Genomics)
    Paper by T. Olender, T. Fuchs, C. Linhart, R. Shamir, M. Adams, F. Kalush, M. Khen, and D. Lancet - Genomics, Vol. 83, No. 3, pp. 361-372, March 2004.
  • Related papers:

  • Selecting Degenerate Multiplex PCR Primers (PDF format)
    Paper by R. Souvenir, J. Buhler, G. D. Stormo, and W. Zhang - Proc. of WABI '03, pp. 512-526, September 2003.
  • Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates (HTML format)
    Paper by Y. Gilad, V. Wiebe, M. Przeworski, D. Lancet, and S. Pääbo - PLoS Biology, Volume 2, Issue 1, January 2004.

  • Computational Geometry (Prof. Dan Halperin)

  • On-Line Zone Construction in Arrangements of Lines in the Plane (Postscript format)
    Paper by Y. Aharoni, D. Halperin, I. Hanniel, S. Har-Peled, and C. Linhart - Proc. 3rd International Workshop on Algorithm Engineering, London (WAE '99), Springer LNCS Vol. 1668, 139-153, July 1999.
  • An Experimental Study of On-Line Methods for Zone Construction in Arrangements of Lines in the Plane (link to IJCGA)
    Paper by C. Linhart, D. Halperin, I. Hanniel, and S. Har-Peled - International Journal of Computational Geometry & Applications (IJCGA), Vol. 13, No. 6, pp. 463-485, December 2003.
  • Software: Smallest Enclosing Disc Java applet
  • Software: 1-Disc Cover Java applet - smallest enclosing disc with polygonal obstacles.
  • (zipped Postscript file)
    Proposed API of a new CGAL class - Min_circle_obstacles_2, that approximates the smallest enclosing disc of a set of points in the plane with polygonal obstacles.
  • Computational Geometry, Spring 1999 - final assignment (applied track)

  • Teaching

    Workshop in Computer Science (Bioinformatics focus), Fall 07-08 (lab instructor)


    Data Mining

  • PAKDD Data Mining Competition 2009: New Ways of Using Known Methods
    Paper by C. Linhart, G. Harari, S. Abramovich, and A. Buchris - New Frontiers in Applied Data Mining, Springer LNCS Vol. 5669, 99-105, 2010. This paper describes our model for the 2009 PAKDD competition, which reached 3rd place. We participated in this competition as part of Prof. Yoav Benjamini's Data Mining course.
  • Web-Application Security

  • HTTP Request Smuggling (whitepaper, 2005; Computer Security Journal, Winter 2006)
    A WatchFire whitepaper that describes a novel hacking technique we developed in Sanctum (now WatchFire) that targets HTTP servers (web servers, cache servers, proxies, etc.). HTTP Request Smuggling enables various attacks, such as web cache poisoning, session hijacking, cross-site scripting and most serious the ability to bypass web application firewall protection.

  • Pinzzeta

    Pinzzeta - Unique recruitment for hi-tech
    Pinzzeta is an HR (human resources) company that specializes in placement ("hasama") of very talented and/or experienced personnel in hi-tech companies, with a focus on software engineers and related positions (R&D team leaders, QA, PM, CTO, ...).
    Pinzzeta was founded by Naama Weber-Linhart, who is also its CEO.

    Email: chaiml @