Research Workshop in Bioinformatics 2006


Instructor :  Prof. Benny Chor (, Schreiber 329.
Teaching Assistant : Tamir Tuller (, Schreiber 223.
Where : Kaplun-Physics, Room 319.
When : Wednesday 15:00-17:00, Spring 2006.

The workshop is open is open to all 3rd year Computer Science students, but students of the bioinformatics track will have higher priority in registering.


Goals & scope

The goal of this workshop is to provide experience with small scale, supervised research projects in bioinformatics. In the past, some of these projects have led to publication in conferences and journals. However this is obviously not a necessary for attaining a good grade.



  1. Analysis, design and implementation of combinatorial optimization algorithms with bioinformatics relevance.
  2. Investigate contemporary problems in comparative genomics, DNA chips analysis, phylogenetic analysis, and more.
  3. Getting acquainted with publicly available Bioinformatics databases and using them.
  4. Conducting supervised research in computational biology.
  5. Efficient implementation of algorithms in C, C++, Java or Matlab.


The workshop will provide hands on experience in implementing various optimization techniques, developing statistical tools for analyzing biological data, and using public biological databases. Most (but not all)  projects have both research and implementation aspects. We offer projects in various current subjects in computational biology, including analysis of gene expression data and DNA microarrays, analysis of gene structure, understanding genomic pathways, construction of phylogenetic trees and networks, etc.

Unlike other workshops, there will be about seven meetings with required participation by all students. These include (1) an introductory lecture, (2) proposed projects' descriptions, (3) brief description, by the students, of their chosen projects, (4) a lecture by the system staff, (5) mid-semester progress reports, by the students, (6-7) final report on the projects, , by the students.

The workshop also includes a lecture on topics in software engineering, given by the Computer Science system staff, that are relevant for medium to large scale software projects. Students are expected to utilize these tools and techniques in the final projects and documentation.

An integral part of the workshop is presenting an outline of the project, as well as the completed project, to all participants (not just the course staff). It is mandatory to physically attend class during these entire parts of the workshop, which are expected to take place on March 29th (outlines presentation) and during the last three meetings (final projects presentation).  Naturally, your projects should be completed by then, and submitted no later than the last day of the semester.

Projects will be performed in groups consisting of at most two students (if the number of students is odd, one triplet may be allowed).

In the first two weeks, each group must choose two preferred projects and send them to Tamir (
We will try to match choices with availability, but in case of collisions, assignments will be based on the time at which the request reaches Tamir's mailbox.

Tentative Timetable  (subject to changes)


March. 8

Introduction to BioInformatics. Administratrivia.

March. 15

Overview of  Proposed Projects



















Suggested Workshop Topics (Incomplete List, Subject to Change)


  1. Modeling and inferring genetic networks, using DNA microarrays data.
  2. Finding meaningful signals in disease gene expression datasets.
  3. Analyzing probabilistic models for genes networks.
  4. Methods for gene finding.
  5. Large-scale detection of conserved genomic regions.
  6. Network based phylogenies.
  7. Algorithms for inferring phylogenetic networks.
  8. Relations between gene interaction and chromosomal location.
  9. Inferring phylogenetic relationships based on a variety of biological data.