REU Program 2008

Participants

(Right to Left):
Yozen Hernandez (CUNY-Hunter), Clifford Locke (UConn), Bardiya Vaziri (U. Texas Dallas), Wade Gobel (Carleton College), Michael Smith (UConn), Andrew Peters (UConn), Carl Bergenhem (UConn), Sanjiv Dinakar (UConn), Nikoletta DiGirolamo (CUNY-Hunter), Roman Ciloci (VC/ECPI).

2008 Program Info

** 6/8 (Sun, 2:00PM-9:00PM, Rome Commons) Check-In

** 8/1 (Fri, 8:00AM-11:00AM, Rome Commons) Check-Out

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Week 1
———-
6/9 (Mon, 10:00AM, ITE 201)
Welcome Session and Orientation
(by Prof. Chun-Hsi Huang and other Participating CSE Faculty: J. Cui, A. Kiayias, I. Mandoiu, S. Rajasekaran, B. Wang and Y. Wu)

6/11 (Wed, 10:00AM, ITE 201)
Seminar Talk: Introduction to Bio-Grid
(by Prof. Chun-Hsi Huang, CSE)

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Week 2
———-
6/16 (Mon, 3:00PM-4:00PM, ITE 201)
Seminar Talk: Supercomputing Facilities at BECAT
(by Prof. Sanguthevar Rajasekaran, CSE)

6/18 (Wed, 10:00AM-11:00AM, ITE 201)
Seminar Talk: Motif Search and Protein Function Studies
(by Prof. Sanguthevar Rajasekaran, CSE)

6/18 (Wed, 12:00PM-1:00PM, CHM A203)
Joint Seminar Talk with All UConn REU Sites
Ethics in Science
(by Dean Robert McCarthy, School of Pharmacy)

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Week 3
———-
6/23 (Mon, 10:00AM-11:00AM, ITE 201)
Seminar Talk: Computational Approaches for Haplotype Analysis (I)
(by Prof. Ion Mandoiu, CSE)

6/25 (Wed, 10:00AM-11:00AM
Seminar Talk: Computational Approaches for Haplotype Analysis (II)
(by Prof. Ion Mandoiu, CSE)

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Week 4
———-
6/30 (Mon, 10:00AM-11:00AM, ITE 201)
Seminar Talk: Suffix Trees and Biological Pattern Matching (I)
(by Prof. Yufeng Wu, CSE)

7/2 (Wed, 10:00AM-11:00AM, ITE 201)
Seminar Talk: Suffix Trees and Biological Pattern Matching (II)
(by Prof. Yufeng Wu, CSE)

———-
Week 5
———-
7/9 (Wed, 10:00AM-11:00AM, ITE 201)
Seminar Talk: Technical Report Writing and Presentation
(by Prof. Chun-Hsi Huang, CSE)

7/11 (Fri, 6:35PM, Norwich, CT)
Joint Recreational Activities with All UConn REU Sites
CT Minor League Baseball Game
(by Prof. Mark Peczuh, Chemistry)

———-
Week 6
———-
7/16 (Wed, 2:30PM-3:30PM, ITE 201)
Seminar Talk: Graduate Studies of CSE: From Application to Degree Completion
(by Prof. Steve Demurjian, Director of Graduate Studies, CSE)

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Week 7
———-
7/23 (Wed, 10:00AM-11:00AM, ITE 201)
Seminar Talk: Getting Research Work Published
(by Prof. Chun-Hsi Huang, CSE)

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Week 8
———-
7/31 (Thr, 9:00AM-1:30PM, ITEB 336)
Bio-Grid REU Student Symposium


2008 Reports

Ciloci, Roman
Path Optimization in Computer Networks

DiGirolamo, Nikoletta
Algorithms for the Multiple Degenerate Primer Selection Problem

Dinakar, Sanjiv and Hernandez, Yozen
SNP Individual Genotyping from Low-Coverage Sequencing Data

Gobel, Wade
Detecting Botnets Using Hidden Markov Models on Network Traces

Locke, Clifford
Implementation of Planted Motif Search Algorithms PMS1 and PMS2

Peters, Andrew
Building The Efficient Site: Planning, Organizing & Integrating a Modular Design

Smith, Mike and Bergenhem, Carl
Study of Data Localities in Suffix-Tree Based Genetic Algorithms

Vaziri, Bardiya
Study with Regards to the Legal Requirements for a Health Grid in the United States

2008 Student Publications

Carl Bergenhem, Chih Lee and Chun-Hsi Huang, On the Cache-Awareness in DNA Probe Selection, Proceedings of the 2008 Rocky Mountain Bioinformatics Conference, pp. 16-17, Dec. 4-7, 2008, Aspen/Snowmass, CO.

B. Vaziri, V. Lanza and C.-H. Huang, Semantic Integration in Biomedical Networks, Poster at the ISCB Conference on Semantics in Healthcare and Life Sciences (C-SHALS), Feb. 25-27, 2009, Boston, MA.

D. Sharma, S. Balla, S. Rajasekaran and N. DiGirolamo, Degenerate Primer Selection Algorithms, Proceedings of the 6-th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology, pp. 155-162, Mar. 30 – Apr. 2, 2009, Nashville, TN.

S. Dinakar, J. Duitama, Y. Hernandez, J. Kennedy, I.I. Mandoiu and Y. Wu, Linkage Disequilibrium Based Single Individual Genotyping from Low-Coverage Short Sequencing Reads, Poster at 2008 Personal Genomes Meeting, Cold Spring Harbor Laboratory, Oct. 9-12, 2008, Cold Spring Harbor, NY.

S. Dinakar, Y. Hernandez, J. Kennedy, I.I. Mandoiu and Y. Wu, Linkage Disequilibrium Based Single Individual Genotyping from Low-Coverage Short Sequencing Reads, Poster at 2008 Meeting on Genomics of Common Diseases, Sep. 6-9, 2008, The Broad Institute of MIT and Harvard, Cambridge, MA.