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Feb 17, 2019 (from left to right: standing: Anna L Reinhard, Yan Zhang, Hongchun Li, Luca Ponzoni, Ivet Bahar, Ana Ligia Scott, Fangyuan (Chelsea) Chen, James Krieger, Pemra Doruker, Stephanie Aldrich; sitting: Augustin Cruz, Jiyoung Lee and kids, Fen Pei)
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PhD Alumni |
Dr. Yan Zhang, PhD in Comp Biol, Pitt/CMU, 2022
| | Email: | yzhang12@illumina.com
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| | Current Affiliation | Computational Biologist at Illumina, California, USA
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| | PhD Research Area: Mesoscale modeling
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Dr. Bentley Wingert, PhD in Comp Biol, Pitt/CMU, 2021
| | Email: | bwingert89@gmail.com
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| | Current Affiliation |
Scientist at New Equilibrium Biosciences, Massachusetts, USA |
| | PhD Research Area:
Drug discovery and dynamics of intrinsically disordered protein domains. |
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Dr. Fen Pei, PhD in Comp Biol, Pitt/CMU, 2020
| | Email: |
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| | Current Affiliation |
Machine Learning Scientist at TANDEM AI, Boston, Massachusetts |
| | PhD Research Area:
Quantitative Systems Pharmacology. |
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Dr. She "John" Zhang, PhD in Comp Biol, Pitt/CMU, 2020
| | Email: |
shezhang620@gmail.com |
| | Current Affiliation |
Scientific Developer at OpenEye Scientific, Santa Fe, New Mexico |
| | PhD Research Area:
Macrocycle permeability, weighted ensemble simulations, and other aspects of software toolkit development |
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Dr. Cihan Kaya, PhD in Comp Biol, Pitt/CMU, 2018
| | Email: |
kayac@upmc.edu |
| | Current Affiliation |
Director, Informatics & Scientific Computing, Sonic Healthcare, Pennsylvania, USA |
| | PhD Research Area:
Multiscale modeling of biological sys. |
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Dr. Murat Can Cobanoglu, PhD in Comp Biol, Pitt/CMU, 2015
| | Email: |
mcancobanoglu@gmail.com |
| | Current Affiliation |
Principal Computational Biologist, Exact Sciences, Houston, Texas.
Murat Can Cobanoglu's Website |
| | PhD Research Area:
Polypharmacology methods and models. Drug-target interaction. |
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Dr. Anindita Dutta, PhD in Comp Biol, Pitt/CMU, 2013
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Dr. Lin Liu, PhD in Mol Biophys & Struct Biol, Pitt/CMU, 2011
| | Email: |
lil39@pitt.edu |
| | Current Affiliation |
Senior Scientist, RemeGen Biosciences, California, USA |
| | PhD Research Area:
Investigation of protein dynamics computationally (eg.GNM) and experimentally (eg.NMR). |
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Dr. Ying Liu, PhD in Comp Biol, Pitt/CMU, 2011
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Dr. Lidio Meireles, PhD in Comp Biol, Pitt/CMU, 2011
| | Email: |
lidiomarx@gmail.com |
| | Current Affiliation |
Lead Analytic Scientist, FICO, San Diego, California |
| | PhD Research Area:
Algorithms for drug design and structural biology. |
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Dr. Ahmet Bakan, PhD in Comp Biol, Pitt/CMU, 2009
| | Email: |
ahb12@pitt.edu |
| | Current Affiliation |
Senior Software Engineer, Google, San Francisco, California |
| | PhD Research Area:
computer-aided drug discovery, development of ProDy for protein (families) dynamics based on PCA of experimental structural datasets and ENM calculations. |
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Dr. Zheng Yang, PhD in Physics, U of Pittsburgh, 2008
| | Email: |
zheng.yang@miracare.com |
| | Current Affiliation |
Co-Founder & CTO at Mira, San Francisco, California |
| | PhD Research Area:
Dynamics of biomolecular systems and supramolecular machinery, effect of inter-residue contact topology and icosahedral symmetry, allosteric transitions and signal transduction mechanisms of GroEL, viral capsids dynamics, macromolecular artistic visualization. |
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Dr. Basak Isin, PhD in Biochem & Mol Genetics, Pitt, 2008
| | Email: |
isinbasak@yahoo.com |
| | Current Affiliation |
Lead Product Manager, CDK Global, Portland, Oregon |
| | PhD Research Area:
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. |
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Dr. E. Zerrin Bagci, PhD in Biochem & Mol Genetics, Pitt, 2007
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Dr. Lee-Wei Yang, PhD in Biochemistry & Mol Genetics, Pitt, 2005
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Dr. Banu Ozkan, Ph.D. in Chem Eng, Bogazici U, 2001
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Dr. Ozlem Keskin, PhD in Chem Eng, Bogazici U, 1999
| | Email: |
okeskin@ku.edu.tr |
| | Current Affiliation |
Associate Dean of College of Engineering for Research & Development, Koc University, Turkey |
| | PhD Research Area:
Computational Biology, bioinformatics, protein-protein interactions and protein dynamics |
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Dr. Canan Atilgan, PhD in Chemical Engineering, Bogazici U, 1996
| | Email: |
canan@sabanciuniv.edu |
| | Current Affiliation |
Professor, Materials Science and Nano Engineering, Sabanci University, Turkey; President of the Sciences Academy Society in Turkey (recognized by ALLEA - All European Academies of Sciences and Humanities) |
| | PhD Research Area:
Polymer and protein dynamics, theoretical and computational investigation of complex molecular systems |
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Dr. Pemra Doruker, PhD in Chemical Engineering, Bogazici U, 1995
| | Email: |
doruker@boun.edu.tr |
| | Current Affiliation |
Professor, Chemical Engineering, Bogazici University, Turkey; Principal Investigator, U of Pittsburgh, Department of Computational and Systems Biology, School of Medicine, Pennsylvania |
| | PhD Research Area:
Computational structural biology, Protein dynamics and interactions, Multi-scale modeling and simulation |
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Dr. Turkan Haliloglu, PhD in Chemical Engineering, Bogazici U, 1992
| | Email: |
halilogt@boun.edu.tr |
| | Current Affiliation |
Professor, Chemical Engineering, and Director of the Polymer Research Center (PRC) at Bogazici University, Istanbul, Turkey |
| | PhD Research Area:
Biopolymers, Computational Structural Biology, Protein dynamics, Binding and Folding of Proteins, Protein Interactions |
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Former Students and Theses |
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