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Alumni
  Dr. Divesh Bhatt, PhD Chemical Engineering, UC Berkeley
 Email: divesh.bhatt@gmail.com
 Current Affiliation Research Scientist, Kimberly Clark
 Research Interests: Systems modeling of cellular biochemical pathways, conformational transitions in biomolecules.
 Divesh Bhatt
  Lin Liu, PhD student in Mol Biophys & Struct Biology
 Email: lil39@pitt.edu
 Current Affiliation Post Doc, UCSF, Fraser & Kortemme lab
 Research Interests: Investigation of protein dynamics computationally (eg.GNM) and experimentally (eg.NMR).
 Lin Liu
  Ying Liu, MS in Software Engineering, Tsinghua U, China
 Email: yil43@pitt.edu
 Current Affiliation Junior Analytics Manager, Opera Solutions, San Diego, CA
 Research Interests: Combining sequence analysis and structural/dynamical analysis to explore the mechanisms with which proteins interact and perform their functions.
 Ying Liu
  Lidio Meireles, MS in Bioinformatics, Kyoto U, Japan
 Email: lidiomarx@gmail.com
 Current Affiliation Research Scientist, Vertex Pharmaceuticals
 Research Interests: Algorithms for drug design and structural biology.
 Lidio Meireles
  Zheng Yang, PhD in Physics, U of Pittsburgh
 Email: proteinyang@gmail.com
 Current Affiliation Programmer Analyst at iPierian (Drug discovery and development using induced pluripotent stem cells) in San Francisco
 Research Interests: Dynamics of biomolecular systems and supramolecular machinery, effect of inter-residue contact topology and structural symmetry, macromolecular artistic visualization.
 Zheng Yang
  Jason DeChancie, PhD in Chemistry, UCLA
 Email:
 Current Affiliation Biomedical Research Analyst at American Systems, Washington D.C.
 Research Interests: Prediction of protein structure, dynamics, and rates of reactions using molecular dynamics, quantum mechanics, and combined quantum mechanical and molecular mechanical methods.
 Jason DeChancie
  Yan Gu, PhD Cand in Comp Biol,
China U of Sci & Technology
 Email: yan.goo@gmail.com
 Current Affiliation China University of Science and Technology
 Research Interests: Molecular dynamics simulation sampling methods; Free energy calculations; Structures, functions and dynamics of membrane transporter proteins; Elastic network model.
 Yan Gu
  Basak Isin, PhD in Biochem & Mol Genetics,
U of Pittsburgh
 Email: isinbasak@yahoo.com
 Current Affiliation Postdoctoral fellow in Oltvai Lab,
Pathology Department, School of Medicine,
University of Pittsburgh
 Research Interests: My research interests are modeling and simulations of membrane proteins. I also studied the dynamics of influenza virus hemagglutinin and herpes simplex virus glycoprotein gD. Currently, I am developing new models and simulation environments for multiscale study of cell signaling and regulatory processes, and rhodopsin activation.
 Basak Isin
  Enrique Marcos, PhD Student in Comp Chem,
U of Barcelona
 Email: embqtc@cid.csic.es
 Current Affiliation IIQAB (Institut d'Investigacions Químiques i Ambientals de Barcelona), Spain
 Research Interests: Sequence-structure-function of N-acetyl gutamate kinase (NAGK) family of proteins; ANM dynamics; effect of multimerization; allosteric communication.
 Enrique Marcos
  Chakra Chennubhotla, PhD in Comp Sci, U of Toronto
 Email:
 Current Affiliation Computational and Systems Biology
Univ of Pittsburgh
 Research Interests: Signal propagation in allosteric systems and GroEL dynamics and underlying Markov propagation stochastics
 Chakra Chennubhotla
  Eran Eyal , PhD in Bioinformatics, Ben-Gourion U
 Email: eyal.eran@gmail.com
eran.eyal@sheba.health.gov.il
 Current AffiliationHead of Bioinformatics Unit Cancer Research Institute Sheba Medical Center (Tel Hashomer) Ramat Gan 52621, Israel
Eran's home page
 Research Interests: Correlated sites in proteins; correlated substitutions of amino acid pairs (P2P website); anisotropic network model analysis of protein dynamics (ANM website)
 Eran Eyal
  Lee-Wei Yang, PhD in Biochemistry & Mol Genetics
 Email: lwyang@life.nthu.edu.tw
 Current Affiliation Assistant Professor, Institute of Bioinformatics and Structural Biology; National Tsing Hua University 101, Sec 2, Kuang-Fu Rd.; Hsinchu, Taiwan, R.O.C.
 Research Accomplishments: Development of iGNM database and oGNM server for high throughput examination of PDB structures' dynamics using elastic network models normal mode analysis; mechanochemical function of enzymes; see "Investigations: Explorations and revelations taking place in the medical school" in Pitt magazine UPSOM Alumni Interview
 Lee-Wei Yang
  Dror Tobi, PhD in Biochemistry, Hebrew U
 Email: drorto@ariel.ac.il
 Current Affiliation Senior Lecturer, Ariel University Center of Samaria
 Research Interests: Protein docking potentials; n-gram patterns; allosteric transition of hemoglobin from T to R state studied by ANM.
 Dror Tobi
  Zerrin Bagci, PhD in Biochem & Mol Genetics,
U of Pittsburgh
 Email: ebagci@nku.edu.tr
 Current Affiliation Assist Professor, Namik Kemal University, Turkey
School of Arts & Sciences, Biology Department
 Research Interests: Examination of coordination geometry and packing regularities in folded proteins; mathematical modeling of apoptosis by simple mass-action kinetics and examination of effect of nitric oxide on apoptosis Roles of Bax, Bcl-2 and Mitochondrial Permability
 Zerrin Bagci
  Andrew J. Rader, PhD in Physics & Chem,
Michigan State U
 Email: ajrader@iupui.edu
 Current Affiliation Research Scientist, Eli Lilli & Company, Indianapolis
 Research Interests: Computer-aided drug discovery, Pharmaceutical sciences, Protein Folding Cores & Pathways, Biomolecular Dynamics, and Multi-scale Modeling
 Andrew J. Rader
  Ramaswamy Amutha, PhD in Physics, U of Madras
 Email: amutha_ramu@yahoo.com
 Current Affiliation Assistant Professor, Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
 Research Interests: Biomolecular Dynamics Simulations, Drug Design and Ab inito Quantum Calculations.
 Ramaswamy Amutha
  Rajan Munshi, PhD in Biology, U of Mississippi
 Email: Rajan_Munshi@sra.com
 Current Affiliation SRA international - Scientific Review Manager at the Center for Peer Review and Science Management Health and Civil Services Sector, SRA International, Inc. 8490 Progress Drive, Suite 200 Frederick, MD 21701
 Research Interests: Establishment and coordination of the BBSI for simulation and visualization of biological systems
 Rajan Munshi
  Banu Ozkan, Ph.D. in Chem Eng, Bogazici U
 Email: banu.ozkan@asu.edu
 Current Affiliation Asst. Professor, Arizona State University - Department of Physics
Banu Ozkan's Website
 Research Interests: Design of protein structuresusing physical principles;modeling protein folding kinetics using Markov models; understanding the origin of non-classical phi values; computing transition state populations and hidden intermediatesin fast folding proteins
 Banu Ozkan
  Lucy (Chunyan) Xu, PhD in Biol Sci, U of Pittsburgh
 Email: xu_lucy2002@yahoo.com
 Current Affiliation Senior Clinical Research Scientist at Eisai
 Research Interests: Computational Prediction of Allosteric Structural Changes by a Simple Mechanical Model: Application to Hemoglobin T --> R Transition
 Lucy Xu

  Former Students and Theses