Seminar in Bioinformatics 2005



Instructors :  Prof. Benny Chor ( and Dr. Tal Pupko (
Where : Britain Building (Life Science, north of Schreiber Building), Room 222.
When : Wednesdays 9:00-11:00, Spring 2005.

The seminar is open is open to 3rd year and M.Sc. Computer Science and BioInformatics students.




The seminar is taken by Computer Science and Biology students. Each week, a pair of students will be assigned a different topic (one or two papers) that will be presented during the weekly, two hours meeting. (If the number of students is odd, one triplet may be allowed.).


Presentation should be prepared in either ppt or pdf format, and distributed (via the seminar site) a few days in advance. We will try to pair one CS and one biology student for each paper.  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 topics in bioinfrmatics. These topics will include (but are not limited to) molecular evolution, phylogenetic reconstruction and complexity, comparative genomics, DNA chips and gene expression analysis, finding regulatory motives, finding micro RNA structures in large genomes.


The lectureres will distribute a list of proposed topics/papers.


Tentative Timetable (subject to changes)


Feb. 23

"Maximum likelihood of evolutionary trees is hard", by Benny Chor

March 2

"Combining genes in phylogeny", by Tal Pupko

March 9

 "RNAi", by Ofir Cohen, and RNAi movie

March 16

 Cancelled due to students’ strike

March 23

 "Computational Aspects of microRNAs", by Yaron Levy

March 30

 "Evolution of the Genetic Codes", by Adi Stern

April  4

 “Protein-Protein Interactions”, by Israel Steinfeld

April 13

 “Surface Accessibility”, by Nimrod Rubinstein and Yaacov Lifshits:
  part1, part2

April 20, 27

 Happy and Kosher break, by Passover

May 4

 DNA microarrays, SNPs, and pharmacogenomics , by Guy Nimrod and Alina Starovolsky: part1, part2

May 11

 Memorial day, no classes

May 18

 Evolution of phosphorylation  sites, by Eyal Privman and Igor Makarov

part1, part2

May 25

 Bayesian reconstruction of evolutionary trees, by  Amir Hadadi

(see also paper)

 Genetic linkage analysis, by  Dotan Schreiber


 Grand Finale: A MeX session  by Vered and Yaron