Joint Seminar in
Bioinformatics,
Instructors: Profs Nir Ben-Tal (NirB@tauex.tau.ac.il) and Benny Chor (benny@cs.tau.ac.il).
Where : Schreiber 007.
When : Sunday
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.
Administratrivia
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):
Time Table (Dynamic)
|
Date |
Lecturer |
Topic |
Paper(s) |
|
|
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. |
|
11/3 |
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). |
|
18/3 |
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). |
|
18/3 |
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. |
|
25/3 |
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. |
|
25/3 |
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. |
|
|
|
|
|
|
15/4 |
Neta Agmon |
Discovery of micro RNAs. |
Fire, A, Xu, S, Montgomery, MK,
Kostas, SA, Driver, SE, and Mello, CC (Andrew Fire and Craig Mello won the 2006 Nobel prize in Medicine for this discovery.)
|
|
15/4 |
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,
|
|
22/4 |
Shaul Karni |
Clustering and bi-clustering |
M. E. J. Newman, Modularity and community structure in networks. PNAS 2006 103: 8577-8582. |
|
22/4 |
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). |
|
29/4 |
Moran Cabili |
Review on metabolic models |
N. Price,J.Reed and B.Palsson, GENOME-SCALE MODELS OF MICROBIAL CELLS:EVALUATING THE CONSEQUENCES OF CONSTRAINTS. Nat. Rev. Microbiol. 2:886–897, Nov. 2004. |
|
29/4 |
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. |
|
6/5 |
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). |
|
6/5 |
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. |
|
3/6 |
Efrat Mashiach |
Systematic Discovery of New Recognition Peptides
Mediating
Protein Interaction Networks |
Neduva et al., 2005. |
|
3/6 |
Boris Broun. |
Neighbor joining (x2) |
|
|
10/6 |
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. |
|
10/6 |
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 |
|
17/6 |
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 |
|
17/6 Last seminar meeting |
Nadav Freid |
Path blast |
|