REU Program 2009

2009 Bio-Grid REU Participants

Lauren Bissett
Affiliation: University of Connecticut
Major: Computer Science

Jared Christopherson
Affiliation: University of Connecticut
Major: Computer Science

Yuran Li
Affiliation: University of Delaware
Major: Biochemistry

Claire Luciano
Affiliation: University of California at San Diego
Major: Computer Science/Bioinformatics

Mathieu Rodrigue
Affiliation: University of Hartford
Major: Computer Science

Nathan Snyder
Affiliation: Carnegie Mellon University
Major: Computer Science

Stephen Tetreault
Affiliation: Rhode Island College
Major: Mathematics and Computer Science

Carol Wong
Affiliation: University of Pennsylvania
Major: Bioengineering

Nicholas Woodfield
Affiliation: University of Connecticut
Major: Computer Science

Michael Zuba
Affiliation: University of Connecticut
Major: Computer Science

BioGrid Poster 2009 — Download

2009 Program Info

** 5/31 (Sun, 1:00PM-6:00PM, Busby) Check-In

** 7/24 (Fri, 8:00AM-12:00PM, Rome Commons) Check-Out

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Week 1
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6/1 (Mon, 10:00-11:00AM, ITE 201A)
Welcome Session and Orientation (Huang, CSE)

6/1 (Mon, 4:30-6:00PM, Swan Lake)
Ice Cream Social, jointly with all UConn REU Sites
(Kimbal, PNB; Bruckner and Peczuh, Chemistry; Washington, MCB)

6/2 (Tue, 10:00-11:00AM, ITE 201A)
Seminar Talk: Grid-Enabled Biomedical Computations (Huang, CSE)

6/3 (Wed, 10:00AM, ITE 201A/BECAT)
Seminar Talk and Tour: BECAT Supercomputing Facilities (Rajasekaran, CSE)

6/4 (Thr, 10:00-11:00AM, ITE 201B)
Seminar Talk: Categorization of Mitochondrial DNA sequences into Haplogroups
(Lee, CSE)

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Week 2
———-
6/8 (Mon, 11:00AM-12:00PM, ITE 201A)
Seminar Talk: TEA & TOAST, Knots & Molecules in Animation, Simulation & Visualization (Peters, CSE)

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Week 3
———-
6/19 (Fri, 12:00PM-1:00PM, BPB 131)
Seminar Talk: Research Ethics Discussion, jointly with all UConn REU Sites
(Dean Robert McCarthy, School of Pharmacy)

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Week 4
———-
6/22 (Mon, 5:00PM-7:00PM, BPB 130)
Seminar Talk: Ethics of Stem Cell Research, hosted by PNB (Pizza Supper)
(Hiskes and Conover, PNB)

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Week 5
———-
6/29 (Mon, 10:00AM-12:00AM, ITE 201A)
Bio-Grid Mini-Symposium: Proposal Presentations (All Bio-Grid Students)

10:00-10:12 Speakers: Bissett, Lauren and Woodfield, Nicholas
Computation of Global Minimum Separation Distance on Bezier Curves and Meshes Using CUDA

10:12-10:24 Speaker: Christopherson, Jared
Optimized Data Migration within a System of Linked Medical Research Databases

10:24-10:36 Speaker: Li, Yuran
Categorization of mtDNA using Support Vector Machines

10:36-10:48 Speaker: Luciano, Claire
Network Motifs and E.coli

10:48-11:00 Speaker: Rodrigue, Mathieu
Analysis of Current Applications of Network Distance Prediction

11:00-11:12 Speaker: Snyder, Nathan
Use of Supervised Learning Methods for Transcription Factor Binding Site Detection

11:12-11:24 Speaker: Tetreault, Stephen
Extracting and Analyzing Information of Single Nucleotide Polymorphisms

11:24-11:36 Speaker: Wong, Carol
Ensemble Learning Algorithms for Classification of Mitochondrial DNA into Haplogroups

11:36-11:48 Speaker: Zuba, Michael
Study of Algorithms and Tools Involving Protein Motifs

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Week 6
———-
7/8 (Wed, 10:00-11:00AM, ITE 201A)
Discussions: Technical Report Writing (Huang, CSE)

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Weeks 7 & 8
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7/20 (Mon, 9:30AM-11:30AM, BPB131)
Diversity Forum: Challenges and Choices in Higher Education

Hosted by:
* Northeast Alliance Summer Research Program for Underrepresented Minorities
* Chemistry NSF Research Experience for Undergraduates
* Physiology and Neurobiology NSF Research Experience for Undergraduates
* Computer Science & Engineering NSF Research Experience for Undergraduates

Moderator:
Lee Aggison, Associate Dean of Graduate School

Panelists:
* Willena Price, Director of African American Cultural Center
* Maria Fernandez, Professor of Nutritional Sciences
* Abdiel Rivera, Graduate Student of Electrical Engineering
* Paul Gaines, Associate Dean of Students, Division of Student Affairs
* Cameron Faustman, Professor of Animal Sciences and Associate Dean of Graduate Programs of College of Agriculture and Natural Resources

7/23 (Thr, 10:00AM-2:30PM, ITEB 336)
Bio-Grid REU Student Symposium

09:55-10:00 Opening Remarks

10:00-10:30 Speakers: Bissett, Lauren and Woodfield, Nicholas
Parallel Computation of the Minimum Separation Distance of Bezier Curves and Surfaces

10:30-11:00 Speaker: Christopherson, Jared
Optimized Data Migration within a System of Linked Medical Research Databases

11:00-11:30 Speakers: Li, Yuran and Wong, Carol
Classification of Mitochondrial DNA SNPs into Haplogroups

11:30-12:00 Speaker: Rodrigue, Mathieu
Analysis of Network Distance Prediction with Global Network Positioning

12:00-13:00 Lunch Break

13:00-13:30 Speaker: Snyder, Nathan
Using Mixed Length Training Sequences in Transcription Factor Binding Site Detection Tools

13:30-14:00 Speaker: Tetreault, Stephen
Extraction of Single Nucleotide Polymorphisms and Use of Current Sequencing Tools

14:00-14:30 Closing Remarks

* Luciano, Claire
* Zuba, Michael
(presentations scheduled on Aug. 6 due to late arrival)

2009 Reports

Bissett, Lauren and Woodfield, Nicholas
Parallel Computation of the Minimum Separation Distance of Bezier Curves and Surfaces

Christopherson, Jared
Optimized Data Migration within a System of Linked Medical Research Databases

Li, Yuran and Wong, Carol
Classification of Mitochondrial DNA SNPs into Haplogroups

Luciano, Claire
Network Motifs and E.coli

Rodrigue, Mathieu
Analysis of Network Distance Prediction with Global Network Positioning

Snyder, Nathan
Use of Supervised Learning Methods for Transcription Factor Binding Site Detection

Tetreault, Stephen
Extraction of Single Nucleotide Polymorphisms and Use of Current Sequencing Tools

Zuba, Michael
A Comparative Study of Network Motif Detection Tools

2009 Student Publications

“Ensemble Learning Algorithms for Classification of mtDNA into Haplogroups”, Briefings in Bioinformatics, 2010, Oxford University Press. (9 pages) (doi: 10.1093/bib/bbq008, Advance Access published on line March 4, 2010, PMID:20203074) (REU students involved: Carol Wong and Yuran Li)

“Structural Motif Enumeration in Transcriptional Regulation Networks”, in Proc. of the first International Conference on Bioinformatics, 131-136, Jan. 20-23, 2010, Valencia, Spain. (REU students involved: Claire Luciano)

“Optimized Data Migration within a Medical Grid”, in Proc. of the 3-rd International Conference on Health Informatics, 117-120, Jan. 20-23, 2010, Valencia, Spain. (REU students involved: Jared Christopherson)