Doron Lipson's Homepage

Who am I? 

I completed a PhD at the Computer Science department of the Technion, in the field of Computational Biology, under the supervision of Dr. Zohar Yakhini. I am a part of the Laboratory of Computational Biology.

My primary research area is combinatorial methods for analysis of microarray data and design of hybridization-based methods. I am currently working on methods for analysis of DNA copy number data from tumor samples, and would like to learn about recurring patterns of genomic instability in different types of cancer. My work focuses on defining biologically-motivated statistical models and efficient algorithmics for discovering such patterns; and understanding the results of the application of these methods to biological data.

Education 
2003-2007 Technion Ph.D., Computer Science
"Computational Aspects of DNA Copy Number Measurement" [Thesis]

Advisor: Dr. Zohar Yakhini
2000-2002 Technion M.Sc., Computer Science, Cum Laude
"
Optimization Problems in Design of Olinucleotides for Hybridization-based Methods" [Thesis]

Advisors: Dr. Zohar Yakhini and Prof. Uri Sivan
1998-2000 Hebrew University B.Sc., Computer Science and Biology, Cum Laude
Research Interests 
  • Combinatorial methods for analysis of microarray data, and specifically - DNA copy number data from aCGH.

  • Optimization problems in design of oligonucleotides for hybridization-based methods such as microarrays and qPCR.

  • Genetic algorithms and similar biologically inspired algorithms.

Previous research projects 
  • Study of emergence of spontaneous beating patterns in self-assembled networks of heart cells. Project included development of novel computer-aided technique for visual recording and analysis of physical movement of cultured cells. [Abstract]
    Project was done under the supervision of Prof. E. Braun of the Physics department, Technion, Haifa, Israel.

  • Biological simulation programming projects:

    • Design and development of SONN - Simulator of Neural Networks. Used for simulating neural computations of small neural networks.

    • Design and development of BIOQ - Simulator of Biological Equations. Used for simulating biochemical reactions, and ion channel behavior.

  • Study of protein interaction in the neuronal exocytic machinery, using mathematical models and computer simulation.
    Project was done under the supervision of Prof. H. Parnas of the Neurobiology department, Hebrew Univesity, Jeruslaem, Israel.

  • Analysis of protein structure and dynamics using NMR measurements:
    NtrC (bacterial response regulator) - Analysis of kinetic activation using NMR relaxation experiments. [Abstract]
    Project was done under the supervision of Dr. D. Kern of the Biochemistry department, Brandeis Univesity, Waltham, MA.

  • A simulation study of the performance of SBH (sequencing by hybridization) on genomic sequences. [Report] [Poster]
    Project was done under the supervision of Dr. Zohar Yakhini of the CS department, Technion, Haifa, Israel.

  • Design of oligonucleotide array for aCGH (array-based Comparative Genomic Hybridization). [Abstract]
    Project was done during internship at Agilent Laboratories, Palo-Alto, CA. 

Teaching 
2004 Advanced Topics in Bioinformatics Teaching Assistant and co-Lecturer
2003 Digital Image Processing Teaching Assistant
2002-2006 Projects in Bioinformatics Project Advisor (5 semesters)
2001 Introduction to Bioinformatics Teaching Assistant
2000-2002 Algorithms in Graph Theory Teaching Assistant (4 semesters)
Awards
  • Agilent LSCA Innovation Merit Award, 2006

  • Agilent Fellowship, 2005-2006.

  • Barney Oliver Award for Innovation, 2005

  • "Amirim" honors program, Faculty of Sciences, Hebrew University, 1999-2000.

  • "Etgar" honors program, School of Life Sciences, Hebrew University, 1998-2000. 

Publications 
Contact Information 

Email: dlipson@cs.technion.ac.il

Telephones:
  • Office: +972 (4) 829-5529/4937
Mailing Address:
  • Doron Lipson,
    Department of Computer Science,
    Technion, Haifa 32000
    Israel

Office: Taub 595/615