David Burstein's Homepage

David Dudu Burstein


Hi, I'm a Ph.D. student under the supervision of Prof. Tal Pupko, in the George S. Wise Faculty of Life Sciences, Tel Aviv University

I'm also a proud fellow of the Edmond J. Safra Bioinformatics Program.

E-mail: davidbur@tau.ac.il

Tel.: (972-3) 6409245
Fax.: (972-3) 6422046
Address: Tel Aviv University, Tel Aviv 69978, Israel


Research interests:

In this early stage of my academic life, I find these topics of great interest:

- Functional genomics
- Machine learning
- Gene targeting
- Molecular evolution and phylogeny
- Whole-genome phylogenies
- Computational complexity



My CV: .doc .pdf

Teaching
Perl programming for biology - autumn 2012

Past teaching
Perl programming for biology:
autumn 2011 , autumn 2010 , spring 2009 , workshop 2010
Introduction to Bioinformatics:
autumn 2007-2008
Biological Sequences Analysis (in MTA):
spring 2008 , spring 2009

My beloved lab members (past and present)

Dr. Adi Stern
Dr. Adi Doron-Faigenboim
Dr. Itay Mayrose
Dr. Eyal Privman
Nimrod Rubinstein
Osnat Penn
Ofir Cohen
Tal Peled
Dayana Alaluf
David Zeevi
Haim Ashkenazy
Yaara Oren

Other dear colleagues

Prof. Gil Segal
Dr. Tal Dagan
Dr. Schraga Schwartz
Dr. Igor Ulitsky
Prof. Chor
Dr. Tamir Tuller
Sahar Gelfman


Publications

Burstein, D.*, Gould, S.B.*, Zimorski, V., Klosges, T., Kiosse, F., Major, P., Martin, W., Pupko, T., Dagan, T. 2011. A machine-learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis. Eukaryotic Cell. accepted.

Gelfman, S., Burstein, D., Penn, O., Schwartz, S., Pupko, T., and Ast, G. 2011. Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Research. accepted.

Barzel, A., Privman, E., Peeri, M., Naor, A., Shachar, E., Burstein, D., Lazary, R., Gophna, U., Pupko, T., and Kupiec, M. 2011. Native homing endonucleases can target conserved genes in humans and in animal models. Nucleic Acids Research. 39(15):6646-6659. [pdf \ abs]

Burstein, D., Zusman, T., Degtyar, E., Viner, R., Segal, G., and Pupko, T. 2009. Genome-scale identification of Legionella pneumophila effectors using a machine learning approach. PLoS Pathog 5(7): e1000508. [pdf \ abs]

Schwartz, S., Silva, J., Burstein, D., Pupko, T., Eyras, E., and Ast, G. 2008. Large scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 18(1):88-103. [pdf \ abs]

Ulitsky, I., Burstein, D., Tuller, T., and Chor, B. 2006. The ACS approach to phylogenomic reconstruction. J. Comput. Biol. 13(2):336-50. [pdf]

Burstein D., Ulitsky I., Tuller T. and Chor B. 2005. Information theoretic approaches to whole genome phylogenomics. Proceedings of the ninth annual international conference on research in computational molecular biology (RECOMB 2005). pp.283-295. [abs]

* These authors contributed equally

Oral presentations and Posters

Igor Ulitsky, David Burstein, Tamir Tuller and Benny Chor. Information Theoretic Approaches to Whole Genome Phylogenies. Israeli Bioinformatics Symposium, IBS 2005, Beer-Sheva, Israel.

Information Theoretic Approaches to Whole Genome Phylogenomics (Oral presentation). International Conference on Research in Computational Molecular Biology (RECOMB 2005), Cambridge, Massachusetts. May 2005.

Some Academic tools I once did
makeCompileFeaturesByPtts.makefile - currently my favorite makefile. It is a makefile I recently wrote that orchestrates exection of numerous perl script files (here is an older version).
Clone Me! little aid for cloning Legionella ORFs
An Eclipse bundle includes also Perl (+ EPIC + BioPerl?) + R (+StatET)

Other useful stuff

Tel Aviv university academic calendar: http://www.google.com/calendar/ical/d5e119e7j819p3k04nvupnpgoo@group.calendar.google.com/public/basic.ics
(iCal format, add to your Google Calendar using add by URL). This is based on
http://www.tau.ac.il/calendar-eng.html

Some personal stuff

My roomate's homepage ^ ^ - Renewed and updated!
My beloved one    + baby turtle    + me
My artist sister Salomé
My baby sister Avigail (aka ZV) and her Michael