CSE 5097 Sec. 003: Algorithms and Applications Seminar

Fall 2010

Intructor: Yufeng Wu

Time and Location: Wednesdays 4:00-5:00 pm. ITEB 201. We expect to meet for one hour weekly. This is tentative: if there is conflicts, we will try to find another time.

Description: The seminar is devoted to the presentation and discussion of current research in algorithms and their applications in areas such as bioinformatics, systems, etc. 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 and hone your presentation skills!

Requirements: Students are required to attend weekly seminar meetings. Each student will be responsible for presenting one research paper. The students can either pick a paper from the some suggested paper by the instructor or choose a paper on algorithms and applications. In the latter case, the students should consult the instructor for their choice of paper.
The presentation is usually informal (i.e. present on white board), which allows more interactions.

Schedule:

Time
Title
Speaker
12/1
Probabilistic heuristic for a computationally difficult set covering problem, by GC Feo Mauricio, A Thomas - Operations research letters, 1989 (link)
B. Hou
11/24
Thanksgiving break

11/17
No meeting (attend CSE colloquium)

11/10
Faster algorithms for string matching with k mismatches, J. of Algorithms, 2004. (link)
C. Li
11/3
RAPID detection of gene-gene interactions in genome-wide association studies (link), Bioinformatics, 2010
J. Wang
10/27
A Bayesian Approach to Protein Model Quality Assessment (link), ICML 2009
M. Nicolae
10/20
TEAM: efficient two-locus epistasis tests in human genome-wide association study (link), ISMB 2010. And if time permits, also: Effective Algorithms for Fusion Gene Detection (link), WABI 2010
J. Zhang
10/13
No meeting (attend CSE colloquium).

10/6
De Novo Peptide Sequencing via Tandem Mass Spectrometry (link), JCB 1999
Hang He
9/29
A spectral method to separate disconnected and nearly-disconnected web graph components (link), KDD 2001
James Lindsay
9/22
ReFHap: A Reliable and Fast Algorithm for Single Individual Haplotyping by J. Duitama, et al. (PDF) Jorge Duitama
9//15
Haplotype Inference on Pedigrees with Recombinations and Mutations (PDF)
Ion Mandoiu
9/8
No meetings (meet at the CSE colloquium instead).

9/1
Alignment-Free Phylogenetic Reconstruction, Constantinos Daskalakis and Sebastien Roch, RECOMB 2010 (Link)
Yufeng Wu