Joint Seminar in Bioinformatics, Tel-Aviv University, Spring 2007.

Instructors: Profs Nir Ben-Tal ( and Benny Chor (

Where : Schreiber 007.
When : Sunday 9:00-11:00, Spring 2007.

The seminar is open to M.Sc. students from the BioInformatics track, Computer Science, and Life Sciences. 3rd year undergraduate students with some relevant background are welcome to participate, provided the M.Sc. students will not fill up the seminar registration.


Each week, one or two students will be assigned a different topic (one or two papers) that will be presented during the weekly, two hours meeting. The talk(s) at the first meeting will be given by the instructors.

Presentation should be prepared specifically for the seminar (not recycled from a different event) in either ppt or pdf format, and distributed (via the seminar site) a few days in advance. We will try (but do not guarantee) to pair
one CS and one biology student for each topic. The main criteria in assigning a grade will be the clarity of presentation. In addition, active participation (on top of the presentation) also carries some weight. Attendance in all meetings is required.

Goals & Scope

The seminar will cover a number of research papers from a variety of current topics in Bioinfrmatics.

Tentative Topics (partial list):

  • Gene expression microarrays.
  • Copy number microarrays.
  • Microarrays for identifying viral strains.
  • Optimal selection of species for genome sequencing or conservation.
  • Multiple sequence alignment.
  • RNA secondary structures.
  • Micro RNAs.
  • Systems biology.
  • Comparative genomics.
  • Issues in protein structures.
  • Protein function.



Time Table (Dynamic)







Benny Chor

Techniques for giving good talks and bad talks.

Genetic code symmetry.

Gavish et al., Genetic code symmetry and efficient design of GC-constrained coding sequences, Bioinformatics 2007 23(2):e57-e63.


Roy Navon

Intro to DNA microarrays; Single Nucleotide Polymorphisms (SNPs); CGH; and CNP (copy number polymorphism)

Conrad et al., A high-resolution survey of deletion polymorphism in the human genome, Nature Genetics 38, 75 - 81 (2006).


Ofir Davidovich

CNV (copy number variation).

Redon et al., Global variation in copy number in the human genome, Nature 444, 444-454 (23 November 2006).


David Burstein

Using DNA microarrays for identifying viruses and other pathogens.

Wang et al., Viral Discovery and Sequence Recovery Using DNA  microarrays. PLoS Biol 1(2): e2 doi:10.1371/journal.pbio.0000002.


Urisman et al., E-Predict: a computational strategy for specie identification based on observed DNA microarray hybridization patterns. Genome Biology, 6:R78,  2005.




Gal Romano


Mapping complex genetic traits: Some genetic background, and employing tiling arrays.


Darvasi A, Pisante-Shalom A (2002) Complexities in the genetic dissection of quantitative trait loci. Trends in Genetics 18, 489–491.

Giora Ben-Ari, Drora Zenvirth, Amir Sherman, Lior David, Michael Klutstein, Uri Lavi, Jossi Hillel, Giora Simchen,
Four linked genes participate in controlling sporulation efficiency in budding yeast. PLoS Genetics Vol. 2, No. 11, e195 doi:10.1371/journal.pgen.0020195

Adam M Deutschbauer, Ronald W Davis,  Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nature Genetics  37, 1333 - 1340 (01 Dec 2005).  


Sharon Bruckner

Algorithms for choosing species in a phylogenetic tree so that the phylogenetic divergence (and related objective functions) is maximized.

Fabio Pardi and Nick Goldman, Species Choice for Comparative Genomics: Being Greedy Works. PLoS Genet 1(6): e71, 2005.

Fabio Pardi and Nick Goldman, Resource Aware Taxon Selection for Maximising Phylogenetic Diversity. Manuscript (2007).








Neta Agmon



Discovery of micro RNAs.

Fire, A, Xu, S, Montgomery, MK, Kostas, SA, Driver, SE, and Mello, CC
(1998). Potent and specific genetic interference by double-stranded RNA in
Caenorhabditis elegans
. Nature 391, 806-811.

(Andrew Fire and Craig Mello won the 2006 Nobel prize in Medicine for this discovery.)





Liron Levkovitz

Computational approaches, employing comparative genomic techniques, for identifying micro RNAs

A. Xie et al., Systematic discovery of regulatory motifs in human  promoters and 3' UTRs by comparison of several mammals. Nature 434,
338-345 (17 March 2005).




Shaul Karni

Clustering and bi-clustering

M. E. J. Newman, Modularity and community structure in networks. PNAS 2006 103: 8577-8582.



Uri David Akavia

Evolution of regulatory motives

A. Tanay, A. Regev, R. Shamir, Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast. Proc. National Academy of Science USA Vol. 102 No. 20, 7203--7208 (2005).



Moran Cabili

Review on metabolic models


Nat. Rev. Microbiol. 2:886–897, Nov. 2004.


Maya Shushan

multiple knockout in silico

D. Deutscher, I. Meilijson, M. Kupiec, E. Ruppin, Multiple knockout analysis of genetic robustness in the yeast metabolic network. NATURE GENETICS, VOL. 38 No 9, SEPTEMBER 2006.


Schragi Schwartz

Codon usage determines efficiency of translation

O. Man and  Y. Pilpel, Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nature Genetics 39, 415 - 421 (2007).


Dorit Guy

RNA editing

1) E. Levanon et al. Evolutionary conserved human targets of Adenosine to Inosine RNA edition. Nucleic Acids Research, 2005, Vol. 33, No. 4, pp. 1162–1168.

2) Y. Neeman et al., Rna editing level in the mouse is determined by the genomic repeat repertoire. RNA (2006), 12:1802-1809.


Efrat Mashiach

Systematic Discovery of New Recognition Peptides Mediating                         Protein Interaction Networks

Neduva et al., 2005.



Boris Broun.

Neighbor joining (x2)



Yifat Felder

Multiple structural alignment by secondary structures

O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson . MASS: Multiple structural alignment by secondary structures. Bioinformatics, 19 Suppl. 1: i95 i104, 2003.

O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson. Multiple structural alignment by secondary structures: algorithm and applications. Protein Science, 12:2492 2507, 2003.



Ariel Ben-Simon

Multiple structural alignment

Anthony D. Hill et al, Comparing programs for Rigid-Body Multiple Structural Superposition of proteins, Proteins 2006


Oranit Dror et al, Multiple structural alignment by secondary structures: algorithm and applications, Protein Science 2003


Allegra Via et al, 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures, Nucleic Acids Research 2007




Oren Golan

Whole genome alignment using suffix arrays

Alignment of whole genomes 

by Delcher, Kasif, Fleischmann,  Peterson,  White and Salzberg

Nucleic Acids Research journal, 1999


The enhanced suffix array and its

applications to genome analysis

by Abouelhoda, Kurtz, and Ohlebusch

Workshop on Algorithms in Bioinformatics, 2002



Last seminar meeting

Nadav Freid

Path blast