Seminar in Bioinformatics 2005



Instructors:  Prof. Benny Chor ( and Dr. Tal Pupko (
Where : Britain Building (Life Science, north of Schreiber Building), Room 222.
When : Thursday 12:00-14:00, Fall 2005.

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




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.


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.




  • Evolutionary trees based on whole genomes
  • Genome Alignment
  • Finding ultraconservative regions between genomes
  • The chimpanzee’s genome
  • Molecular dating
  • Coalescence
  • Model selection in phylogeny
  • Prediction of secondary structures in proteins
  • Prediction of RNA structures
  • Haplotypes


Students can approach the instructors as of mid October for inquiries and papers assignment.



Tentative Timetable (subject to changes)


Nov. 3

"Informational theoretical methods for constructing whole genome phylogies" by Burstein et al.  (Lecturer: Benny Chor).

Nov 10


Nov 17


Nov 24


Dec 1


Dec 8


Dec 15


Dec 22


Dec 29




Jan 5


Jan 12


Jan 19


Jan 26


Feb 2




Suggested Seminar Papers (List Subject to Change)


·        M. Blanchette et al., Aligning multiple genomic sequences with the Threaded Blockset Aligner, Genome Res. 2004 14: 708-715.   [Abstract]  [Full Text]

·        G. Bejerano et al., Into the Heart of Darkness: Large Scale Clustering of Human Non-Coding DNA. Bioinformatics, 20:I40-I48, 2004 (presented at ISMB/ECCB-2004)  [preprint]  [website]

·        G. Bejerano et al., Science, 304:1321-1325, 2004. [download] [website]

·        K. Hellmann, et al., Why do human diversity levels vary at a megabase scale?

     Genome Res.,  2005;  15(9):  1222 - 1231. [Abstract]  [Full Text] [PDF]

·        V. B. Yap and L. Pachter, Identification of evolutionary hotspots in the rodent genomes. Genome Res. 2004 14: 574-579.   [Abstract]  [Full Text]

·        G. Bourque, P. Pevzner, and G. Tesler, Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons from Human, Mouse, and Rat Genomes. Genome Res. 2004 14: 507-516.   [Abstract]  [Full Text]   

·        D. Penny, Relativity of molecular clocks. 2005. Nature 436: 183-184.

·        Elhaik E, Sabath N, Graur D. The "Inverse Relationship Between Evolutionary Rate and age of Mammalian Genes" is an Artifact of Increased Genetic Distance with Rate of Evolution and Time of Divergence. Mol Biol Evol. 2005 Sep 8; [Epub ahead of print]

·        Siepel A, Haussler D. 2004. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 11(2-3):413-428.

·        Shulman-Peleg A, Nussinov R, Wolfson HJ. 2004. Recognition of functional sites in protein structures. J Mol Biol. 339(3):607-633.  

·        Carmel I, Tal S, Vig I, Ast G. 2004. Comparative analysis detects dependencies among the 5' splice-site positions. RNA. 10(5):828-840

·        Kaplan T, Friedman N, Margalit H. 2005. Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol. 2005 Jun;1(1):e1. Epub 2005 Jun 24.

·        Felsenstein J. “Brownian motion and gene frequencies”. Chapter 23 in Felsenstein’s book “Inferring Phylogenies”. Sinauer press, 2004.

·        Fisher J, Piterman N, Hubbard EJ, Stern MJ, Harel D. 2005. Computational insights into Caenorhabditis elegans vulval development. Proc Natl Acad Sci U S A. 102(6):1951-1956.

·        Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong P, Wilson RK, Paabo S, Rocchi M, Eichler EE. 2005. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature. 437(7055):88-93. 



Assigned Papers