Participants of the BBSI @ Pitt 2008
(under construction)
(click here for the 2008 Educational schedule)


The academic backgrounds of the students admitted to the 2008 program are:

 

Click here for students' research and their comments on the program.
To see photographs taken by the students during the program, click here.
 



The 2008 BBSI class

(L to R, back) Jessie Wehner, Yan Gu, John Schmidt, Katie Kinzler, Davis Buenger, Bill Glassford, Arti Khana, Brian Chen, Arif Harmanci
(L to R, front) Jess Wagner, Anna Kirk, Jackie Barnes, Abdallah Bukari, Shiksha Mantri, Nilgun Yilmaz, Edwin Kamau

 

Anita Anburajan (e-mail)
Junior, Biochemistry / Economics, New York University

Mentor: John Rosenberg / Biological Sciences, University of Pittsburgh
 Project: First Order Corrections of pKa Values for Crystallization Optimization Trials
 Research Proposal  |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Statistical methods for the objective design of screening procedures for macromolecular crystallization (2000) D. Hennessy et al., Acta Cryst. D56, 817–827
 paper | presentation
Click here for Anita's comments on the BBSI @ Pitt 2008



 

Jacqueline Barnes (e-mail)
Senior, Neurophysics, University of Pittsburgh

Mentor: Joel Stiles / Pittsburgh Supercomputing Company
 Project: Computational Investigation of a Kai-Protein Circadian Oscillator
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for Jackie's comments on the BBSI @ Pitt 2008



Davis Buenger (e-mail)
Junior, Mathematics, Rice University

Mentor: Jim Faeder / Computational Biology, University of Pittsburgh
 Project: Discovering nontermination in rule based modeling
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Abstract interpretation of cellular signaling networks (2008) V. Danos et al. Lecture Notes in Computer Science, 4905, 83-97
 paper | presentation
Click here for Davis's comments on the BBSI @ Pitt 2008



 

Abdallah Bukari (e-mail)
Junior, Chemical Engineering, Princeton University

Mentor: Jeffry Madura / Chemistry & Biochemistry and Center for Computational Sciences, Duquesne University
 Project: Molecular Dynamics Simulations of LeuT Transport Restrained by Normal Modes
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity, D.A. Doyle, et al. (1998) Science 280, 69-77
 paper | presentation
Click here for Abdallah's comments on the BBSI @ Pitt 2008



 


Brian Chen (e-mail)
Senior, Biological Sciences / Religious Studies, University of Pittsburgh
Mentor: Hugh Nicholas / Pittsburgh Supercomputing Center
Project: Functional Classification of Inositol-5-Monophosphate Dehydrogenase (IMPDH)
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Genome Landscapes and Bacteriophage Codon Usage (2008) J.B. Lucks et al., PLoS Comput Biol 4, e1000001
 paper | presentation
Click here for Brian's comments on the BBSI @ Pitt 2008



William Glassford (e-mail)
Senior, Biology, Indiana University of Pennsylvania

Mentor: Chakra Chennubhotla / Computational Biology, University of Pittsburgh
 Project: Robustness and Statistical Significance of Allosteric Communication Pathways Derived from Conservation Scores and Markov Propagation Models
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES (2006) C. Chennubhotla and I. Bahar, Molecular Systems Biology, 2, 36
 paper | presentation
Click here for Bill's comments on the BBSI @ Pitt 2008



 

Edwin Kamau (e-mail)
1st year graduate school, Biochemistry, Kennesaw State University

Mentor: Gabriela Mustata / Computational Biology, University of Pittsburgh
 Project: Pharmacophore Model Development for the Identification of Novel Acetylcholinesterase Inhibitors
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design (2008) Y. Xu, et al. Protein Sci. 17, 601-605
 paper | presentation
Click here for Edwin's comments on the BBSI @ Pitt 2008



 

Arti Khana (e-mail)
Senior, Biomedical Engineering, The George Washington University

Mentor: Takis Benos / Computational Biology, University of Pittsburgh
 Project: Designing an algorithm to study flu viruses
 Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution (2005) E. Ghedin et al., Nature, 437, 1162-1166
 paper | presentation
Click here for Arti's comments on the BBSI @ Pitt 2008


 

Kathryn Kinzler (e-mail)
Senior, Biochemistry / Molecular Biology and Math, Gettsburg College

Mentor: G. Bard Ermentrout / Mathematics, University of Pittsburgh
Project: Mathematical Modeling of Ant Pheromones: Determination of Optimum Pheromone Evaporation Rate and Simulation of Pheromone Tracking Abilities
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
From nonlinearity to optimality: pheromone trail foraging by ants (2003) D.J.T. Sumpter and M. Beekman, Animal Behaviour, 66, 273–280
 paper | presentation
Click here for Katie's comments on the BBSI @ Pitt 2008

Anna Kirk (e-mail)
Senior, Mathematics and Chemistry / Whitworth University

Mentor: Carlos Camacho / Computational Biology, University of Pittsburgh
 Project: Rigid-body Docking of Mdm2 Antagonists
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Rajamani D, Thiel S, Vajda S, Camacho C. (2004) Anchor residues in protein-protein interactions. PNAS 101, 11287- 11292
 paper | presentation
Click here for Anna's comments on the BBSI @ Pitt 2008



 

John Schmidt (e-mail)
Senior, Biological Sciences / Chemistry, University of Pittsburgh

Mentor: Judith Klein-Seetharaman / Structural Biology, University of Pittsburgh
 Project: Interactions Between HIV Proteins GP160, Nef, and the Human Body
 Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for John's comments on the BBSI @ Pitt 2008



Jessica Wagner (e-mail)
Senior, Biochemistry / Molecular Biology and Math, Gettysburg College

Mentor: Silvia Wognum and Michael Sacks / Bioengineering, University of Pittsburgh
 Project: Three-dimensional visualization of the orientation of the extracellular matrix fibers of rat urinary bladder wall tissues
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Contribution of the extracellular matrix to the viscoelastic behavior of the urinary bladder wall (2007) J. Nagatomi et al., Biomechan Model Mechanobiol, (Online) 1617-7940
 paper | presentation
Click here for Jess's comments on the BBSI @ Pitt 2008



 

Jessica Wehner (e-mail)
1st year graduate school, Mathematics, Georgia College and State University

Mentor: Madhavi Ganapathiraju / Biomedical Informatics, University of Pittsburgh
 Project: Developing an Active Learning Framework for Transmembrane Helix Prediction
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
Comparison of probabilistic combination methods for protein secondary structure prediction (2004) Y. Liu et al., Bioinformatics, 20, 3099–3107
 paper | presentation
Click here for Jessie's comments on the BBSI @ Pitt 2008

Guest Students of the BBSI @ Pitt 2008

Yan Gu (e-mail)
2nd year graduate school, Computational Biology, University of Science and Technology of China (USTC)

Mentor: Ivet Bahar / Computational Biology, University of Pittsburgh
 Project: Project title
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for Yan's comments on the BBSI @ Pitt 2008

Arif Harmanci (e-mail)
2nd year graduate school, Electrical and Computer Engineering, University of Rochester

Mentor: Judith Klein-Seetharaman / Structural Biology, University of Pittsburgh, Chakra Chennubhotla / Computational Biology, University of Pittsburgh
 Project: Identifying Unfolding Pathways of G Protein-Coupled Receptor Protein Structures
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for Arif's comments on the BBSI @ Pitt 2008

Shiksha Mantri (e-mail)
Senior, Chemistry, Indian Institute of Technology, Bombay

Mentor: Bino John / Computational Biology, University of Pittsburgh
 Project: Project title
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for Shiksha's comments on the BBSI @ Pitt 2008

Matthew Rockar (e-mail)
Seneca Valley High School

Mentor: Jeffry Madura / Chemistry & Biochemistry and Center for Computational Sciences, Duquesne University
 Project: Project title
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for Matthew's comments on the BBSI @ Pitt 2008

Anthony Sosso (e-mail)
Hampton High School

Mentor: Jeffry Madura / Chemistry & Biochemistry and Center for Computational Sciences, Duquesne University
 Project: Project title
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for Anthony's comments on the BBSI @ Pitt 2008

Nilgun Yilmaz (e-mail)
Junior, Molecular Biology & Genetics, Bilkent University

Mentor: Jim Faeder / Computational Biology, University of Pittsburgh
 Project: Development of VEGF signaling pathway model by using BioNetGen
Research Proposal |  Research Abstract  |  Research Presentation  |  Poster Presentation 

Journal Club:
 Title of Journal Club paper
 paper | presentation
Click here for Nilgun's comments on the BBSI @ Pitt 2008

 

     Program Photographs (taken by students during the program)
 

     

    Program participants wearing their BBSI t-shirts (click to see the design on front and back of the t-shirts)