CSE 5097 Sec. 003: Algorithms and Applications Seminar

Fall 2009

Intructor: Yufeng Wu

Time and Location: Wednesdays 4:00-5:00 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 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 following suggested paper or choose a paper on algorithms and applications. 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.


A New Approach to Incremental Topological Ordering (link), from SODA 2009.
A. Turlington
A Universally Fastest Algorithms for Max 2-Sat, Max 2-CSP, and Everything in Between (link) from SODA 2009.
C. Li
Multiple intents re-ranking (link). This is a paper from STOC 2009, about internet searching.
Y. Wang
Opportunistic Data Structures with Applications (link). This paper is related to Burrows-Wheeler transformation in string matching.
M. Nicolae
Sorting by Placement and Shift (link), SODA 2009.
J. Wang
Graph Theoretic Approaches to RECOMBINOMICS (also CSE colloquium link). Location: ITEB 336. Note it is a Monday.
L. Parida
Virus Quasispecies Assembly using Network Flows (also CSE colloquium link). Location:  ITEB 336
A. Zelikovsky
Sorting Cancer Karyotypes by Elementary Operations (link)
H. He
Algorithm Engineering for Color-Coding with Applications to Signaling Pathway Detection, by Falk Huffner, Sebastian Wernicke, and Thomas Zichner (link)
I. Mandoiu
SHREC: a short-read error correction method (link)
J. Duitama
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs (link) V. Kundeti
Global alignment of protein-protein interaction networks by graph matching methods, by M. Zaslavskiy et al.  (link)
Yufeng Wu