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
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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
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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
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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
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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
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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)