CSE 5097 Sec. 003: Bioinformatics Seminar

Spring 2009



Intructors: Ion Mandoiu and Yufeng Wu

Time and Location: Wednesdays 2:30-3:30 pm. ITEB 201. We expect to meet for one hour weekly.

Description: The seminar is devoted to the presentation and discussion of current research in bioinformatics and computational biology. Students will read and present research papers selected based on their own research interests and instructors' suggestions.  This is a great opportunity to learn about recent developments in these dynamic fields and hone your presentation skills!

Requirements: Students are expected to attend weekly seminar meetings. Each student will be responsible for presenting one research paper. The students can either pick a paper from the following suggested paper or choose a paper on Bioinformatics. In the latter case, the students should consult the instructors for their choice of paper. The presentation can be either in power point or white board based. If power points are to be used, we recommend the slides to be prepared several days in advanced and sent to the instructors so that feedbacks can be given.

Schedule:

Time
 Title
 Speaker
4/22
 Discovery of biological networks from diverse functional genomic data (link), Genome Biology, 2005. B. Pei
4/15
 A robust framework for detecting structural variations in a genome (link), ISMB 2008.
 J. Zhang
4/8
 Imputation-based local ancestry inference in admixed populations (paper)
 J. Kennedy
4/3
 Attend bioinformatics talk by Iuliana Ionita at 2 pm (ITEB 336)
3/25
 Statistical Inference for Isoform Expression in RNA-seq (link).
 J. Lindsay
3/18
 Optimal pooling for genome re-sequencing with ultra-high-throughput short reads technology (link), ISMB 2008.
 Xinyu Que
3/11
 Spring recess
3/4
 No meeting
2/25
 Discovery of microRNA-mRNA modules via population-based probabilistic learning (link),  J.G. Joung, Bioinformatics, 2007. Chih Lee
2/18
 Regulatory Networks Define Phenotypic Classes of Human Stem Cell Lines (link), F. J. Muller, et al., 2008.
 Jin Jun
2/11
 Transcriptome sequencing to detect gene fusions in cancer (link),  C. Maher, et al., Nature, 2009. Jorge Duitama
2/4
 Paul Medvedev, Michael Brudno: Ab Initio Whole Genome Shotgun Assembly
with Mated Short Reads. RECOMB 2008: 50-64 (paper)
 Ion Mandoiu
1/28
 Cancelled (snow day)
1/21
 Stem Cell Genealogy: An Overview (paper 1, paper 2)
 Yufeng Wu


List of suggested paper:

* Gene expression and network analysis:

Regulatory Networks Define Phenotypic Classes of Human Stem Cell Lines (link), F. J. Muller, et al., Nature, 2008.
Using Bayesian Networks to Analyze Expression Data (link), N. Friedman, et al., JCB, 2000.  This is a widely cited paper.
Fast and Accurate Alignment of Multiple Protein Networks (link), M. Kalaev, et al., RECOMB 2008. This is a more algorithmic paper.


* Other topics

Transcriptome sequencing to detect gene fusions in cancer (link),  C. Maher, et al., Nature, 2009. This paper is on an important applicaton of NGS.
Discovery of microRNA-mRNA modules via population-based probabilistic learning (link),  J.G. Joung, Bioinformatics, 2007.
Computational Epigenetics (link), C. Bock and T. Lengauer, Bioinformatics,  2007. This is an overview, and more papers cited by this one may need be read when presented.