BBSI @ Pitt 2006 Schedule
(click
here for the 2006
Participants)
This page contains the coursework schedule, class and
computer laboratory notes, ethics groups, schedule, and presentations, and the
schedules of the seminar speakers for the 2006 program.
Hold mouse over lecture links for description of class notes files.
Coursework Schedule
(pdf)
(3073
BST-3) (Note
Exceptions *)
top
*Computer
Traning Center, Pittsburgh Supercomputing Center, 300 South Craig
|
Week |
Day, Date |
Session I 9-10.30 am |
Session II 10.45 am-12.15 pm |
Lab 1.30-4.30 pm |
|
1 |
Mon, 5/22 | No class | No class | |
| Tue, 5/23 | Linear Algebra (RC) | Biochemistry Review I (RM) | ||
| Wed, 5/24 | Linear Algebra (RC) | Biochemistry Review II (RM) | Primer | Lab (RC) | |
| Thu, 5/25 | Differential Equations (GBE) | Biochemistry Review III (RM) | Computing Primer (JB) | |
| Fri, 5/26 | Differential Equations (GBE) | Sequence Analysis (TB) | ||
| 2 | Mon, 5/29 | No class | No class | |
| Tue, 5/30 | Probability & Statistics (HM) | Sequence Analysis (TB) | (GBE) | |
| Wed, 5/31 | Probability & Statistics (HM) | Sequence Analysis (TB) | (HM) | |
| Thu, 6/1 | Data Visualization (JS) | High-Throughput Data Analysis (TB) | ||
| Fri, 6/2 | Data Visualization (JS) | Thermodynamics & Statistical Mechanics (HM) | (JS)* | |
| 3 | Mon, 6/5 | Molecular Visualization (JM) | Thermodynamics & Statistical Mechanics (HM) | Lab (JM) |
| Tue, 6/6 | Molecular Visualization (JM) | Overview of Comp Struct Biol in the Post-Genomic Era (IB) | ||
| Wed, 6/7 | Molecular Visualization (JM) | Sequence-Structure-Function Relations (IB) | Theory | Lab (IB) | |
| Thu, 6/8 | Protein Structure and Dynamics (IB) | Folding Kinetics & Molecular Dynamics Simulations (IB) | (IB) | |
| Fri, 6/9 | Molecular Simulations (JM) | Molecular Simulations (JM) | (JM) | |
|
4 |
Mon, 6/12 | Kinetics (JS) | Kinetics (JS) | (JS)* |
| Tue, 6/13 | Cellular Simulations (JS) | Cellular Simulations (JS) | ||
| Wed, 6/14 | Subcellular Simulations (GBE) | Subcellular Simulations (GBE) | ||
| Thu, 6/15 | Subcellular Simulations (RC) | Subcellular Simulations (RC) | (RC) | |
| Fri, 6/16 | No class | No class | ||
All lectures and lab
sessions will be held in 3073
BST-3, except where noted (*)
*Computer Training Center, Pittsburgh Supercomputing Center, 300 South Craig
IB,
Ivet Bahar; TB, Takis Benos; JB, Jason Boles; RC, Rob Coalson; GBE, G. Bard Ermentrout;
JM, Jeffry Madura; HM, Hagai Meirovitch; RM, Rajan
Munshi; JS, Joel Stiles
|
|
Seminar Schedule
| Number |
Date |
Speaker |
Affiliation |
Type |
| 1 | May 23 | Bino John, PhD |
Assistant Professor Department of Computational Biology University of Pittsburgh School of Medicine |
Research |
| 2 | May 30 | Robert Murphy, PhD |
Professor Departments of Biological Sciences and Biomedical Engineering Director, Center for Bioimage Informatics Carnegie Mellon University |
Research |
| 3 | June 6 | Alan Seadler, PhD |
Chair, Biotechnology
Leadership Director, Center for Biotechnology Duquesne University |
Career |
| 4 | June 13 | Igor Kurnikov, PhD |
Assistant Professor Department of Environmental and Occupational Health University of Pittsburgh |
Research |
| 5 | June 23* | Student Participation |
Ethics Forum for all REU
students at the University of Pittsburgh and Duquesne University |
Ethics |
| 6 | June 30 | Zoltan Oltvai, MD |
Associate Professor, Department of Pathology Assistant Director, Division of Molecular Diagnostics University of Pittsburgh School of Medicine |
Research |
| 7 | July 5† | Yoram Vodovotz, PhD |
Director, Center for
Inflammation and Regenerative Modeling
Associate Professor, Departments of Surgery and Immunology University of Pittsburgh School of Medicine |
Career |
| 8 | July 11 | Naftali Kaminski, MD |
Director, Simmons Center for
Interstitial Lung Diseases Division of Pulmonary, Allergy, and Critical Care Medicine University of Pittsburgh School of Medicine |
Career |
| 9 | July 18 | Student Participation |
Career Workshop for BBSI @ Pitt students (panel discussion and Q&A with individuals representing a variety of career paths) |
Career |
*
Friday, June 23, 9 am-2 pm,
Pittsburgh Athletic Association (Pennsylvania Room)
†
Wednesday, July 5
Journal Club Schedule
(pdf) (Thursday, 4-5 pm, 3073 BST-3) top| Number | Date |
Student
Presenter (Faculty Mentor) |
Paper Title |
| 1 | Jun 1 |
Nicole Kennerly (Sholmo Ta'asan) |
Strategies for
containing an emerging influenza pandemic in Southeast Asia. Ferguson et al., Nature, 437: 209-214 (2005) (paper | presentation) |
| 2 | Jun 1 |
Chi Zheng (Michael Sacks) |
Defining
biomechanical endpoints for tissue engineered heart valve leaflets
from native leaflet properties. Merryman et al., Prog. Pediatr.
Cardiol., 21: 153–160 (2006) (paper | presentation) |
| 3 | Jun 8 |
Ryan Cheng (Ken Jordan) |
Optimization by
simulated annealing. Kirkpatrick et al., Nature, 220: 671-680 (1983) (paper | presentation) |
| 4 | Jun 8 |
Christopher
Hackmeyer (Billy Day) |
The T-Taxol
conformation. Alcaraz et al., J. Med. Chem., 49: 2478-2488 (2006) (paper | presentation) |
| 5 | Jun 15 |
Abderrahmane
Benghanem (Maria Kurnikova) |
The essential dynamics of
Thermolysin: conformation of hinge-bending motion and comparison of
simulations in vacuum and water. Van Aalten et al., Proteins: Struct. Funct. Genet., 22: 45-54 (1995) (paper | presentation) |
| 6 | Jun 15 |
Marie Wilkening (Joel Stiles) |
Regulation of the
eukaryotic cell cycle: molecular antagonism, hysteresis, and
irreversible transitions. Tyson & Novak, J. Theor. Biol., 210: 249-263 (2001) (paper | presentation) |
| 7 | Jun 22 |
Megan Jeans (G. Bard Ermentrout) |
Beyond a pacemaker's
entrainment limit: phase walk-through. Ermentrout & Riznel, Am. J. Physiol., 246: 102-106 (1984) (paper | presentation) |
| 8 | Jun 22 |
Amanda McCoy (Dan Zuckerman) |
Weighted-ensemble
Brownian dynamics simulations for protein associated reactions. Huber & Kim, Biophysical J., 70: 97-110 (1996) (paper | presentation) |
| 9 | Jun 29 |
Stephanie Lucas (Takis Benos) |
Evolutionary analysis of the well
characterized endo16 promoter reveals substantial variation within functional sites Balhoff & Wray, PNAS, 102: 8591-8596 (2005) (paper | presentation) |
| 10 | Jun 29 |
Jieming Shen (Hugh Nicholas) |
M-Coffee: combining multiple sequence alignment methods with T-Coffee Wallace et al., Nucleic Acids Res., 34: 1692–1699 (2006) (paper | presentation) |
| 11 | Jul 6 |
Angelo Kontgas (Bino John) |
Identification of
microRNAs of the herpesvirus family Pfeffer et al., Nature Methods, 2: 269-276 (2005) (paper | presentation) |
| 12 | Jul 6 |
Ji Lee (Bino John) |
Using hexamers to
predict cis-regulatory motifs in Drosophila, Chan & Kibler, BMC Bioinformatics, 6: 262-270 (2005) (paper | presentation) |
| 13 | Jul 6 |
Zofia Koscielniak (G. Bard Ermentrout) |
Spiral waves in
disinhibited mammalian neocortex Huang et al., J. Neurosci., 24: 9897-9902 (2004) (paper | presentation) |