Group Director
 |
Prof. Costas D. Maranas E-mail: costas[at]psu.edu PhD, Chemical Engineering, Princeton University, 1995. |
Postdoctoral Scholars
|
Tong Li E-mail: tul12[at]psu.edu PhD, Computational Medicinal Chemistry, University of Leuven, Belgium, 2009. MS, Bioinformatics, University of Leuven, Belgium, 2005. MS, Pharmacology, Ocean University of China, China, 2004. BS, Pharmaceutical Chemistry, Ocean University of China, China, 2001. |
|
Hadi Nazem-Bokaee E-mail: hnbokaee[at]psu.edu Ph.D., Biological Systems Engineering, Virginia Tech, 2014 M.Sc., Chemical Engineering, Sharif University of Technology, Iran, 2005 B.Sc., Chemical Engineering, Iran University of Science and Technology, Iran, 2001 |
Graduate Students (in order of seniority)
 |
Akhil Kumar E-mail: azk172[at]psu.edu BTech, Computer Science, MD University, ROHTAK, India 2006 |
 |
Matt Grisewood E-mail: mjg5185[at]psu.edu MS, Chemical Engineering, Penn State, 2013 BS, Chemical Engineering, Penn State, 2011 |
 |
Anupam Chowdhury E-mail: axc1028[at]psu.edu BE, Chemical Engineering, Jadavpur University, India, 2011 |
|
Ali Khodayari E-mail: auk241[at]psu.edu MS, Chemical Engineering, Sharif University of Technology, Iran, 2010 BS, Chemical Engineering, The University of Kashan, Iran, 2007 |
 |
Chiam Yu Ng E-mail: cun121[at]psu.edu MS, Chemical and Biological Engineering, Korea University, South Korea, 2012 BE, Chemical and Biological Engineering, Korea University, South Korea, 2010 |
 |
Margaret Simons E-mail: mns157[at]psu.edu BS, Chemical Engineering, University of Maryland, College Park, 2012 |
 |
Thomas Mueller E-mail: tjm5293[at]psu.edu BS, Chemical Engineering, Penn State, 2012 |
 |
Saratram Gopalakrishnan E-mail: sxg375[at]psu.edu B.E. Biotechnology, Manipal University, 2011 M.S.E. Chemical and Biomolecular Engineering, Johns Hopkins University, 2013 |
|
Ratul Chowdhury E-mail: rzc158[at]psu.edu B.E., Chemical Engineering, Jadavpur University, India, 2013 |
 |
Satyakam Dash E-mail: sud25[at]psu.edu MS, Chemical and Biomolecular Engineering, Rice University, 2013. MTech, Biotechnology and Biochemical Engineering, IIT Kharagpur, India, 2011. BTech, Biotechnology and Biochemical Engineering, IIT Kharagpur, India, 2011. |
 |
Nathan Esperon E-mail: nge103[at]psu.edu M.S.E., Chemical Engineering, University of Michigan, 2013. B.S.E., Bioengineering, University of Pittsburgh, 2012. |
Undergraduate Students
 |
Brandon Nicklas E-mail: bzn5041[at]psu.edu |
Group Alumni
Postdoctoral Scholars
Dr. Ali Reza Zomorrodi, 2012-2013. Email: alirzomorrodi[at]gmail.com
PhD: Pennsylvania State University
Current position: Postdoctoral Research Associate, Bioinformatics Program & Biomedical Engineering Department, Boston University.
Dr. Patrick Suthers, 2005-2013. Email: suthers@engr.psu.edu
PhD: University of Wisconsin-Madison
Dr. YoungJung Chang, 2007-2008. Email: yjchang[at]andrew.cmu.edu
PhD: University of Illinois at Urbana-Champaign
Current position: Research Associate, Merck Sharp & Dohme Corp.
Dr. Evgeni Nikolaev, 2002-2005. Email: en46[at]cornell.edu
PhD: Lobachevsky Nizhegorod State University, Russia
Current position: Instructor of Mathematics, New Jersey State University (Rutgers).
Dr. Anshuman Gupta, 2002-2005. Email: anshumanxgupta[at]gmail.com
PhD: Pennsylvania State University
Current position: Vice President-Analytics, Indicus Analytics, India.
Dr. Kyle Camarda, 1998-2000. Email: camarda[at]ku.edu
PhD: University of Illinois at Urbana-Champaign
Current position: Associate Processor, Department of Chemical and Petroleum Engineering, University of Kansas.
PhD Theses Supervised
Dr. Rajib Saha, 2014. Email: rajibsaha[at]wustl.edu,
rajibsaha11[at]gmail.com
Thesis: "Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms"
Current position: Postdoctoral Research Associate, Department of Biology, Washington University in St. Louis.
Dr. Robert Pantazes, 2014.
Email: pantazes[at]engineering.ucsb.edu
Thesis: "Computational methods for the de novo design of antibodies"
Current position: Postdoctoral Research Associate, Department of Chemical Engineering, UC Santa Barbara.
Dr. Ali Reza Zomorrodi, 2012.
Email: alirzomorrodi[at]gmail.com
Thesis: "Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities"
Current position: Postdoctoral Research Associate, Bioinformatics Program & Biomedical Engineering Department, Boston University.
Dr. Sridhar Ranganathan, 2012. Email: sridhar.ranganathan[at]lifetech.com
Thesis: "Using computations to analyze and redesign metabolism"
Current position: Staff Scientist, Synthetic Biology, Life Technologies.
Dr. Francisco Vital-Lopez, 2011. Email: fvitallopez[at]bioanalysis.org
Thesis: "Development of hybrid intracellular/extracellular models of brain tumor progression and medication strategies"
Current position: Research scientist, Biotechnology High Performance Computing Software Applications Institute (BHSAI).
Dr. Prabhasa Ravikirthi, 2010. Email: prabhasarao@gmail.com
Thesis: "Construction of a genome-scale atom mapping model of E.coli for metabolic flux analysis"
Dr. Vinay Satish Kumar, 2010. Email: vinay[at]fb.com
Thesis: "Systems based optimization approaches to analyze and improve metabolic networks"
Current position: Data Scientist, Facebook.
Dr. Jonathan Chin, 2010. Email: jwc25[at]cornell.edu
Thesis: "Engineering and analysis of cofactor partitioning for NADPH-dependent xylitol production in Escherichia coli"
Current position: Scientist, Algenol Biofuels.
Dr. Hossein Fazelinia, 2009. Email: Hossein.Fazelinia[at]fccc.edu
Thesis: "Computational design and experimental characterization of proteins with novel functions"
Current position: Postdoctoral research fellow, Fox Chase Cancer Center.
Dr. Madhukar Dasika, 2007. Email: dasika[at]amyris.com
Thesis: "Systems engineering based approaches for biological network, inference, analysis and redesign"
Current position: Scientist, DuPont.
Dr. Manish Saraf, 2006. Email: manish.saraf[at]citi.com
Thesis: "Development of computational tools for the design and optimization of combinatorial protein libraries"
Current position: Vice President, Citigroup.
Dr. Gregory Moore, May 2005. Email: gmoore[at]xencor.com
Thesis: "Modeling and optimization in directed evolution protocols and protein engineering"
Current position: Senior Scientist, Protein Engineering, Xencor.
Dr. Priti Pharkya, December 2005. Email: ppharkya[at]genomatica.com
Thesis: "Optimization based redesign of microbial production systems"
Current position: Senior Research Scientist II, Genomatica.
Dr. Andreas Lehmann, December 2004. Email: Andreas.Lehmann[at]fccc.edu
Thesis: "Molecular design in chemical and biological systems"
Current position: Postdoctoral Associate, Fox Chase Cancer Center.
Dr. Anthony Burgard, 2004. Email: aburgard[at]genomatica.com
Thesis: "Optimization-based frameworks for the analysis and redesign of metabolic networks"
Current position: Associate Director, Computational Technologies, Genomatica.
Dr. Anshuman Gupta, August 2002. Email: anshumanxgupta[at]gmail.com
Thesis: "Supply chain management under uncertainty".
Current position: Vice President-Analytics, Indicus Analytics, India.
Dr. Shankar Vaidyaraman, August 2001. Email: shankar.vaidyaraman[at]zsassociates.com
Thesis: "Optimization based methodology for refrigeration system synthesis and molecular design"
Current position: Marketing Associate, Eli Lily and Company.
M.S. Student Theses/Projects Supervised
M. Mazharul Islam, 2014.
Thesis: "Dynamic multi-level and multi-objective metabolic modeling of microbial communities"
Current position: PhD Candidate (under the supervision of Dr. Armaou and Dr. Rioux) at Pennsylvania State University.
N. Gifford, 2014.
M. Grisewood, 2013.
Thesis: "OptZyme: A Computational Tool for Altering Enzymatic Specificity"
Current position: Doctoral Student, Department of Chemical Engineering, Pennsylvania State University.
A. Kumar, 2013.
Thesis: "MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases"
Current position: Doctoral student, Department of Bioinformatics and Genomics, Pennsylvania State University.
A. R. Zomorrodi, 2011.
Thesis: "Optimization-driven design of synthetic genetic circuits using biobricks"
Current position: Postdoctoral Research Associate, Bioinformatics Program & Biomedical Engineering Department, Boston University.
R. Saha, 2011.
Thesis: "Reconstruction of a genome-scale metabolic model of maize metabolism"
Current position: Postdoctoral Research Associate, Department of Chemical Engineering, University of Washington.
P. Ravikirthi, 2010.
Thesis: "Construction of a genome-scale atom mapping model of E.coli for metabolic flux analysis"
Current position: Bioinformatician, Positive Bioscience, India.
G. Khoury, 2010.
Thesis: "Computational design to switch protein cofactor specificity and create enzymatic activity"
Current position: Doctoral Student, Department of Chemical and Biological Engineering, Princeton University.
V. S. Kumar, 2008.
Thesis: "Optimization methods to compare strain design strategies in metabolic networks using different cellular objectives"
Current position: Data Scientist, Facebook.
S. Ranganathan, 2008.
Thesis: "Metabolic Engineering and Strain Design procedures for valuable chemical synthesis"
Current position: Staff Scientist, Synthetic Biology, Life Technologies.
M. Rogers, 2004.
Thesis: "Real options based planning of pharmaceutical product pipelines"
Current position: Business Development Manager, DuPont.
M. Kalp, 1999
Thesis: "Development of process design case studies for the capstone design course"
Current position: Project Engineer, Croda.
S. Petkov, August 1997
Thesis: "Analysis and optimization of chemical process systems under uncertainty"
Current position: Director Business Development, Huvepharma, Bulgaria.