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.

• 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.

• 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. 

• 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. 

• D.T. Ting, D. Lipson, S. Paul, B.W. Brannigan, S. Akhavanfard, E.J. Coffman, G. Contino, V. Deshpande, A.J. Iafrate, S. Letovsky, M.N. Rivera, N. Bardeesy, S. Maheswaran, D.A. Haber, " Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers" , Science, published online 13 January 2011.

• P. Kapranov, F. Ozsolak , S.W. Kim, S. Foissac, D. Lipson, C. Hart, S. Roels, C. Borel, S.E. Antonarakis, A.P. Monaghan, B. John, P.M. Milos, " New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism" , Nature, 466(7306):642-6, 2010.
  Reviewed by: M. Swami, "Small RNAs: A novel class", Nature Reviews Genetics 11(9):594, 2010.

• E. Giladi, J. Healy, G. Myers, C. Hart, P. Kapranov, D. Lipson, S. Roels, E. Thayer, S. Letovsky, " Error tolerant indexing and alignment of short reads with covering template families" , J. Computational Biology, 17(10):1279-1293, 2010.

• C. Hart, D. Lipson, F. Ozsolak, T. Raz, K. Steinmann, J.F. Thompson, P.M. Milos, " Single Molecule Tools: Fluorescence Based Approaches " , Methods in Enzymology, 472:407-430, 2010.

• Y. Buganim, I. Goldstein, D. Lipson, M. Milyavsky, S. Polak-Charcon, C. Mardoukh, H. Solomon, E. Kalo, S. Madar, R. Brosh, M. Perelman, R. Navon, N. Goldfinger, I. Barshack, Z. Yakhini, V. Rotter, " A Novel Translocation Breakpoint within the BPTF Gene Is Associated with a Pre-Malignant Phenotype" , PLoS ONE, 5(3): e9657, 2010.

• D. Lipson, T. Raz, A. Kieu, D.R. Jones, E. Giladi, E. Thayer, J.F. Thompson, S. Letovsky, P.M. Milos, M. Causey, "Quantification of the Yeast Transcriptome by Single-molecule Sequencing" , Nature Biotechnology, 27(7):652-8, 2009.

• J. Bowers, J. Mitchell, E. Beer, P.R. Buzby, M. Causey, J.W. Efcavitch, M. Jarosz, E. Krzymanska-Olejnik, L. Kung, D. Lipson, G.M. Lowman, S. Marappan, P. McInerney, A. Platt, A. Roy, S.M. Siddiqi, K. Steinmann, J.F. Thompson, "Virtual terminator nucleotides for next-generation DNA sequencing" , Nature Methods, 6, 593-595 (2009).

• Margaret Taub, Doron Lipson and Terence P. Speed, "Methods for Allocating Ambiguous Short-reads", Communications in Information and Systems, 10(2):69-82, 2010.

• Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson and Zohar Yakhini, "GOrilla: a Tool for Discovery and Visualization of Enriched GO Terms in Ranked Gene Lists", BMC Bioinformatics, 10(48) 2009.

• S. Farkash-Amar, D. Lipson, A. Polten, A. Goren, C. Helmstetter, Z. Yakhini and I. Simon, "Global Organization of Replication Time Zones of the Mouse Genome", Genome Research, 18(10):1562-70, 2008.

• Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael T. Barrett, John N. Weinstein, Anne-Lise Borresen-Dale, Zohar Yakhini, "Framework for Identifying Common Aberrations in DNA Copy Number Data". Proceedings of RECOMB '07, LNCS 4453, 122-136, Springer, 2007.

• Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini. "Discovering Motifs in Ranked Lists of DNA",  PLoS Computational Biology, 3(3):e39, 2007.

• E. Dehan, A. Ben-Dor, W. Liao, D. Lipson, H. Frimer, S. Rienstein, D. Simansky, M. Krupsky, P. Yaron, E. Friedman, G. Rechavi, M. Perlman, A. Aviram-Goldring, S. Izraeli, M. Bittner, Z. Yakhini, N. Kaminski, "Chromosomal aberrations and gene expression profiles in non-small cell lung cancer", Lung Cancer, 56(2):175-184, 2007.

• Doron Lipson, Zohar Yakhini, Yonatan Aumann, "Optimization of Probe Coverage for High-Resolution Oligonucleotide aCGH".
  Bioinformatics 23(2):e77-e83, 2007.

• Ilya Baskin, Stav Zaitsev, Doron Lipson, Rachel Gilad, Kinneret Keren, Gidi Ben-Yoseph, Uri Sivan, "A Molecular Shift Register and its Utilization as an Autonomous DNA Synthesizer". Physical Review Letters 97, 208103, 2006.

• Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini, "Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis". Proceedings of RECOMB '05, LNCS 3500, p. 83, Springer-Verlag, 2005.
  Also in Journal of Computational Biology, Vol. 13, No. 2: 215-228, 2006.

• Michael T. Barrett, Alicia Scheffer, Amir Ben-Dor, Nick Sampas, Doron Lipson, Robert Kincaid, Peter Tsang, Bo Curry, Kristin Baird, Paul S. Meltzer, Zohar Yakhini, Laurakay Bruhn, Stephen Laderman, "Comparative Genomic Hybridization using Oligonucleotide Microarrays and Total Genomic DNA", PNAS, Vol. 101, No. 51, 21 December 2004, pp. 17765-17770.

• Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini (2004) "Joint Analysis of DNA Copy Numbers and Gene Expression Levels", Proceedings of WABI 2004, LNCS 3240, p. 135, Springer-Verlag, 2004.

• Doron Lipson, Peter Web, Zohar Yakhini (2002) "Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome", Proceedings of WABI 2002, LNCS 2452, pp. 491-505, Springer-Verlag, 2002.

• Brian F. Volkman, Doron Lipson, David E Wemmer, Dorothee Kern (2001) "Two-State Allosteric Behavior in a Single-Domain Signaling Protein", Science Vol. 291, 23 March 2001, pp. 2429-2433.
  Reviewed in: Matthias Buck and Michael K. Rosen (2001), "Flipping a Switch", Science Vol. 291, pp. 2329-2330.

• N.J. Turton, D.J. Judah, J. Riley, R. Davies, D. Lipson, J.A. Styles, A.G. Smith, T.W. Gant, "Gene expression and amplification in breast carcinoma cells with intrinsic and acquired doxorubicin resistance", Oncogene, March 2001, Vol. 20, No. 11 pp.1300-1306.

• Yoav Soen, Netta Cohen, Doron Lipson, and Erez Braun (1999), "Emergence of spontaneous rhythm disorders in self-assembled networks of heart cells", Physical Review Letters, Vol. 82, Num. 17 , 26 April 1999, pp. 3556-3559.
  Reviewed by the American Institute of Physics. 

• Office: +972 (4) 829-5529/4937

• Doron Lipson,
  Department of Computer Science,
  Technion, Haifa 32000
  Israel

Office: Taub 595/615