REU Program 2012

2012 Bio-Grid REU Participants

Briere, Emily
Affiliation: Duke University
Major: Mechanical Engineering

Dhanaraj, Dhinakaran
Affiliation: University of Connecticut
Major: Electrical and Computer Engineering

Espinoza, Max
Affiliation: Fairfield University
Major: Computer Science

Hocum, Jonah
Affiliation: Lewis-Clark State College
Major: Computer Science

Knowlton, Stephanie
Affiliation: University of Connecticut
Major: Biomedical Engineering

Mulhall, Brian
Affiliation: University of Connecticut
Major: Computer Science and Engineering

2012 Program Info

** 5/20 (Sun, 7:00AM-11:00PM, Rome Commons) Check-In

** 7/27 (Fri, 7:00AM-11:00PM, Rome Commons) Check-Out

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Week 1
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Orientation (BioGrid)
5/21 (Mon, 10:00AM, ITE 201)
Orientation and Program Overview

Social Activities (BioGrid+CAS+Trustable)
5/21 (Mon, 6:00PM, ITE 301)
Pizza Get-Together

Research Seminars (BioGrid)
5/21 (Mon, 11:00AM-12:00PM, ITE 201)
Network Motif Detection: Principles and Practice
Speaker: Saad Quader (UConn)
5/22 (Tue, 10:00AM-11:00AM, ITE 201)
Investigation of RNA Metabolism: Modeling with Petri Nets
Speaker: Therese Smith (UConn)
5/22 (Tue, 11:00AM-12:00PM, ITE 201)
Transcription Factor Binding Site Search and Visualization
Speaker: Chih Lee (UConn)
5/23 (Wed, 10:00AM)
Project Discussions and Assignment

5/24 (Thr, 3:00PM-4:30PM, UTEB 150)
Special Bioinformatics Seminar
Translating Genomes to Metabolic Networks and Pathway-Based Omics Data Analysis
Speaker: Peter Karp (SRI International)

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Week 2
———-
Responsible Conduct of Research (RCR) Seminar Series (PNB+BioGrid)
* The Basis of Research Ethics
* Scientific Record Keeping
* Ethics in the Use of Humans/Animals in Research
* Conflict of Interest
* Ethics in Mentoring and Training Relationship
* Misconduct of Research
* Ethics in Publications and Authorship

5/30 (Wed, 6:30PM-7:30PM, BPB 130)
5/31 (Thr, 6:30PM-7:30PM, BPB 130)
6/01 (Fri, 6:30PM-7:30PM, BPB 130)

Social Activities (All UConn REU Sites)
5/29 (Tue, 4:30PM, Swan Lake)
Ice Cream Social

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Week 3
———-
6/06 (Wed, 12:30PM, TLS 153)
Invited Talk on Graduate Study, Programs and Applications (hosted by PNB)
Speaker: Alan Hein (MIT)
Pizza Lunch at noon

6/07 (Thr, 9:00AM, UTEB 150)
Engineering Ethics Seminar (Engineering Sites)
Speaker: Dan Vallero (Duke)

6/08 (Fri, 11:00AM, ITE 125)
Seminar on Technical Presentations (Trustable+CAS+BioGrid)
Speaker: John Chandy (UConn)

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Week 4
———-
6/13 (Wed, 10:00AM, ITE 201)
Informational Session on Proposal Preparation
Speaker: Chun-Hsi Huang (UConn)

6/15 (Fri, 4:30PM, UTEB Courtyard)
BBQ (hosted by CMBE)

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Week 5
———-
6/18 (Mon, 1:00PM-2:00PM, Homer Babbidge Library)
Primary Literature Search
Speaker: Carolyn Mills (UConn)

6/21 (Thr, 10:00AM-11:30AM, ITE 301)
Bio-Grid Mini-Symposium: Proposal Presentations (All Bio-Grid Students)

10:00AM-10:15AM Speaker: Jonah Hocum
Downstream Applications of Transcription Factor Binding Site Search Tools

10:15AM-10:30AM Speaker: Max Espinoza
On Network Randomization Methods: A Negative Control Study

10:30AM-10:45AM Speaker: Emily Briere
Design and Build of Calibration Device for Scintillating Fibers of Tagger Microscope

10:45AM-11:00AM Speaker: Dhinakaran Dhanaraj
Study of the Statistical Significance of Large(r) Network Motifs

11:00AM-11:15AM Speaker: Stephanie Knowlton
Petri Net Modeling and Analysis of Biological Processes Implicated in Amyotrophic Lateral Sclerosis

11:15AM-11:30AM Speaker: Brian Mulhall
Creating Benchmark Biological Networks

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Week 6
———-
6/26 (Tue, 10:00AM-11:30AM, UTEB 150)
Special Bioinformatics Seminar
Development of Pathway Tools: Past, Present, Future
Speaker: Peter Karp (SRI International)

6/28 (Thr, 10:00AM-11:30AM, UTEB 150)
Special Bioinformatics Seminar
Computational Discovery of Novel Pathways: Pathway Tools Omics Data Analysis
Speaker: Peter Karp (SRI International)

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Week 7
———-
7/03 (Tue, 10:00AM-11:30AM, UTEB 150)
Special Bioinformatics Seminar
Synthetic Biology and Metabolic Engineering with Pathway/Genome Databases
Speaker: Peter Karp (SRI International)

7/05 (Thr, 10:00AM-11:30AM, UTEB 150)
Special Bioinformatics Seminar
Recent Developments in the HumanCyc and EcoCyc Metabolic Databases for Humans and E.coli
Speaker: Peter Karp (SRI International)

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Week 8
———-
7/12 (Thr, 10:00AM-11:00AM, ITEB 201)
Informational Session on Technical Report Writing
Speaker: Chun-Hsi Huang (UConn)

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Week 9
———-
7/20 (Fri, 9:00AM-11:00AM, MSB P38)
Panel Discussions on Diversity in STEM Field (All UConn REU Sites)
Panel Moderators: Mark Peczuh and Charmane Thurmand (UConn)

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Week 10
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7/27 (Fri, 11:10AM-2:00PM, ITE 119)
Bio-Grid REU Student Presentations

11:10AM-11:30AM Speaker: Jonah Hocum
Downstream Applications of Transcription Factor Binding Site Search Tools

11:30AM-11:50AM Speaker: Emily Briere
Design and Build of Calibration Device for Scintillating Fibers of Tagger Microscope

11:50AM-12:10PM Speaker: Stephanie Knowlton
Petri Net Modeling and Analysis of Biological Processes Implicated in Amyotrophic Lateral Sclerosis

12:10PM-1:00PM Lunch Break

1:00PM-1:20PM Speaker: Max Espinoza
On Network Randomization Methods: A Negative Control Study

1:20PM-1:40PM Speaker: Dhinakaran Dhanaraj
Study of the Statistical Significance of Large(r) Network Motifs

1:40PM-2:00PM Speaker: Brian Mulhall
Creating Benchmark Biological Networks

2012 Reports

Briere, Emily
Design and Fabrication of Calibration Device for Scintillating Fibers of Tagger Microscope: For use in GlueX’s QCD Experiment

Dhanaraj, Dhinakaran
Study of the Statistical Significance of Large(r) Network Motifs

Espinoza, Max
On Network Randomization Methods: A Negative Control Study

Hocum, Jonah
Downstream Applications of Transcription Factor Binding Site Search Tools

Knowlton, Stephanie
Petri Net Modeling and Analysis of Biological Processes Implicated in Amyotrophic Lateral Sclerosis

Mulhall, Brian
Creating Benchmark Biological Networks