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The Department of Computational Biology University of Pittsburgh School of Medicine Hagai Meirovitch

The Department of Computational Biology University of Pittsburgh School of Medicine Hagai Meirovitch. History March 2001 - the Center for Computational Biology and Bioinformatics ( CCBB ) was founded. First location Kaufmann Building

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The Department of Computational Biology University of Pittsburgh School of Medicine Hagai Meirovitch

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  1. The Department of Computational Biology University of Pittsburgh School of Medicine Hagai Meirovitch

  2. History March 2001 - the Center for Computational Biology and Bioinformatics (CCBB) was founded. First location Kaufmann Building Director Dr. Ivet Bahar. Nov. 2002 – CCBB moved to the BST,10th floor. Oct. 2004 - CCBBDepartment of Computational Biology (CB). May-June 2005 – CB will move to BST 3. Faculty and students 7 faculty – 2 Professors, 2 Associate, and 3 Assistant. 6+2 grad. students, 9 Post-docs, 2 rotation students 1 research assistant.

  3. In the future CB is expected to add three more faculty. Administration Executive Administrator, Personnel Administrator, secretary, and 2 System Administrators. Hardware ~40 individual PCs 60 high performance dual processor servers – relatively small number due to limited space. Much larger space in BST3. Printers, copiers etc.

  4. Activities 2003-2006 (NIH, Bahar-PI) Bioengineering and Bioinformatics Summer Institute (BBSI) on Simulation and Computer Visualization of Biological Systems at Multiple Scales. 2003-2007 (NIH, Bahar-PI) Pre-National Program of Excellence in Biomedical Computing (Pre-NPEBC). “Multiscale Dynamics of Cell Cycle Control and Apoptosis”. Both grants with professors from other departments at Pitt, Duquesne, PSC, and CMU. To start in Fall 2005 (?): Pitt-CMU PhD Joint Program in Computational Biology.

  5. From Fall 2002 : a monthly seminar in computational biology of an invited speaker. From Fall 2002: a monthly journal club. From Spring 2005: Biophysical theory club (research activities – Pittsburgh wide) Service The faculty of CB are members in a large number of committees: PhD student committees, admission and curriculum committees, etc.

  6. Teaching Spring terms 2002 & 2003. Drs. Bahar and Meirovitch taught the course: “Introduction to Computational Structural Biology”. Spring 2003 & 2004. Dr. Benos taught the course: “Statistical Methods in Bioinformatics”. Spring term 2004. Dr. Zuckreman has taught the course “Applied Computational Toxicology”. Fall & Spring terms 2005. Dr. Zuckerman is organizing one course and teaching in three of the Molecular Biophysics core courses. Spring term 2005. Dr Bahar is organizing and teaching in “Molecular Biophysics 3”. Drs. Meirovitch and Camacho are teaching parts of this course.

  7. Faculty • 1) Ivet Bahar, PhD, Professor & Chair of CB; joined March 2001. • PhD – Chemistry; was a Professor at Bogazici U., Istanbul. • Was active initially in polymer physics and moved to structural biology through a collaboration with NIH. • Protein function through structure and dynamics; protein-protein interactions; large protein assemblies - viruses, ribosome, etc. • 2)Hagai Meirovitch, PhD, Professor; joined July 2001 from Florida State University. • PhD - chemical physics. Development of simulation methods for complex macromolecule systems. Protein structure; the role of flexibility in protein-protein recognition processes.

  8. 3)Takis Benos, PhD, Assistant Professor; joined Spring 2002 from Washington U., Dept of Genetics, School of Medicine. PhD - Biology. Genome analysis and DNA-protein interactions. Also, he is an experimentalist and a member of the Department of Human Genetics. 4) Daniel M. Zuckerman, PhD, Assistant Professor; joined Oct. 2002 from Johns Hopkins U., Dept of Physiology, School of Medicine. PhD – Physics. Development of models and algorithms for understanding protein behavior and binding, and methods for calculating free energy. He is also a member of the Department of Environmental and Occupational Health.

  9. 5) John Vries,MD, Associate Professor; joined summer 2003. Was the Neurosurgery Chief, Children Hospital. Founded the company, Medical Archival Systems for large scale data base management for medical records. Studying periodic relationships in biological sequences and periodic motions in molecular dynamics simulations. 6)Ivan Maly, PhD, Assistant Professor. Joined August 2003 from MIT, Biological Engineering Division. PhD – Biology. Systems biology – modeling many processes within the cell by differential equations and other techniques – validation by experiments. Dr. Maly is also an experimentalist and a member of Cell Biology and Physiology.

  10. 7) Carlos J. Camacho, PhD, Visiting Associate Professor; joined Sep. 2004 from Boston University. PhD- Physics. Structural genomics, data bases with emphasis on protein interactions.

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