Principal investigator

Prof. Costas D. Maranas


Costas D. Maranas (b. 1967), Donald B. Broughton Professor, Department of Chemical Engineering, The Pennsylvania State University

BS, Chemical Engineering, Aristotle University, Greece, (1990)
MA, Chemical Engineering, Princeton University (1992)
Ph.D. in Chemical Engineering, Princeton University (1995)

Allan P. Colburn Award for Excellence in Publications by a Young Member of AIChE (2002), Outstanding Young Investigator Award of the Computing and Systems Technology AIChE Division (2006), S.V. Sotirchos Lectureship at 6th Panhellenic Chemical Engineering Conference (2007), Penn State Engineering Alumni Society (PSEAS) Outstanding Research Award (2012) Penn State Engineering Alumni Society (PSEAS) Premier Research Award (2016)

Editorial Boards for PLoS Computational Biology, BMC Systems Biology, IEEE Life Sciences, Biotechnology Journal and Metabolic Engineering

Fellow of the American Institute of Medical and Biological Engineering (AIMBE).

Reviewer for NSF, NIH and DOE.

Research interests: Computational protein, enzyme and antibody engineering; reconstruction, curation and analysis of metabolic networks; computational strain design and synthetic biology; metabolism of photosynthetic organisms; metabolism of obligatory anaerobes; modeling of microbial communities; optimization theory and algorithms.

Detailed CV (as of Feb 2024)

Short bio

Postdoctoral Scholars

Patrick F. Suthers


Ph.D. Chemical Engineering, University of Wisconsin–Madison, 2005

M.S. Chemical Engineering, University of Wisconsin–Madison, 2000
B.S. Chemical Engineering, Tennessee Technological University, 1997

Wheaton L. Schroeder


Ph.D. Chemical Engineering, University of Nebraska - Lincoln, 2021

B.S. Chemical Engineering and Liberal Arts and Sciences (Mathematics), Iowa State University, 2015

Graduate Students

Veda Sheersh Boorla


M.Tech and B.Tech Chemical Engineering, Indian Institute of Technology Kharagpur, 2019

Vikas Upadhyay


B.Tech Chemical Engineering,
Indian Institute of Technology Hyderabad, 2018

Mengqi Hu


B.S. Chemical Engineering, UC San Diego, 2017

Juliana Simas

[email protected]

Master's in Computational Modeling, Laboratório Nacional de Computação Científica, 2020

Bachelor's in Biotechnology, University of Brasília, 2017

Mohit Anand

[email protected]

B.Tech Chemical Engineering,
Indian Institute of Technology Delhi, 2022

Eric Mooney

[email protected]

B.S. Molecular Biology and Biochemistry, Rutgers University-New Brunswick, 2022

Austin Delanau Hartley

[email protected]

A.A. General Studies, Lake-Sumter State College, 2019

B.S. Chemical Engineering, University of South Florida, 2023

Tommy Willis

[email protected]

B.S. Chemical Engineering, Miami University of Ohio, 2023

Roghaye Mohammadbeygi

[email protected]

B.S. Chemical Engineering, Sharif University of Technology, 2021

Group Alumni

Postdoctoral Scholars

Dr. John Irudaya Hendry, 2019-2022. Email: jih11[at]
PhD: India Institute of Technology Bombay
Current position: Research scientist at Biotechnology High Performance Computing Software Applications Institute (BHSAI), Frederick, MD

Dr. Chen Chen, 2020-2022. Email: cchen5891[at]
PhD: Wuhan University
Current position: Advanced Chemist, Eastman Chemical Company

Dr. Siu Hung Joshua Chan, 2015-2018. Email: joshua.chan[at]
PhD: Technical University of Denmark
Current position: Assistant Professor, Department of Chemical and Biological Engineering, Colorado State University

Dr. Hadi Nazem-Bokaee, 2014-2017. Email: Hadi.NazemBokaee[at]
PhD: Virginia Tech
Current position: Research Fellow, The Australian National University, Canberra, Australia

Dr. Tong Li, 2013-2016. Email:[at]
PhD: University of Leuven, Belgium
Current position: Data Scientist, BASF, San Diego.

Dr. Ali R. Zomorrodi, 2012-2013. Email: azomorrodi[at]
PhD: Pennsylvania State University
Current position: Computational & Systems Biology Lead at Mass General Hospital.

Dr. Young Jung Chang, 2007-2008. Email: yjchang[at]
PhD: University of Illinois at Urbana-Champaign
Current position: Associate Principal Scientist, Merck Sharp & Dohme Corp.

Dr. Evgeni Nikolaev, 2002-2005. Email: evgeni.nikolaev[at]
PhD: Lobachevsky Nizhegorod State University, Russia
Current position: Machine Learning Stylus Medicine, Cambridge, MA.

Dr. Anshuman Gupta, 2002-2005. Email: anshumanxgupta[at]
PhD: Pennsylvania State University
Current position: Chief Data Officer at Futurense Technologies, India.

Dr. Kyle Camarda, 1998-2000. Email: camarda[at]
PhD: University of Illinois at Urbana-Champaign
Current position: Associate Professor, Department of Chemical and Petroleum Engineering, University of Kansas.

PhD Theses Supervised

Dr. Hoang Dinh, 2023. Email: hvdinh16[at]
Thesis: "Data-integrated amd model-driven analysis of yeast metabolism and resource allocation at genome-scale"
Current position: TBD.

Dr. Debolina Sarkar, 2021. Email: sarkardebolina27[at]
Thesis: "Integrating modeling of phototrophic metabolism leveraging multi-omics datasets"
Current position: Scientist at International Flavors and Fragrances, Inc (IFF), Palo Alto, CA.

Dr. Charles Foster, 2021. Email: charlesfoster1766[at]
Thesis: "Leveraging the kinetics of metabolism and microbial growth for metabolic engineering and scientific discovery in Clostridia."
Current position: Scientist IV, Applied Microbial Physiology at dsm-firmenich, Washington DC-Baltimore area.

Dr. Lin Wang, 2020. Email: wanglin44[at]
Thesis: "Computational methods for designing de novo metabolic pathways and genome-minimized chassis strains."
Current position: Computational scientist at Google X.

Dr. Ratul Chowdhury, 2019. Email: r.chowdhury.024[at]
Thesis: "Computational redesign of protein channels, enzymes, and antibodies."
Current position: Assistant Professor, Chemical and Biological Engineering, Iowa State University, Ames IA.

Dr. Satyakam Dash, 2019. Email: sdash[at]
Thesis: "Metabolic modeling of Clostridia for biofuel production."
Current position: Senior Biological Data Scientist at Gingko Bioworks, Inc., El Cerrito, CA.

Dr. Saratram Gopalakrishnan, 2019. Email: s1gopalakrishnan[at]
Thesis: "Nonlinear optimization techniques for genome-scale flux elucidation and kinetic parameterization."
Current position: Post-doctoral associate, dept. of Pediatrics, School of Health Sciences, UCSD, La Jolla, CA.

Dr. Matthew Grisewood, 2018. Email: Matthew.Grisewood[at]
Thesis: "Development and Applications of Computational Enzyme Engineering Tools."
Current position: Principal Scientist II at Schodinger, Inc.

Dr. Chiam Yu Ng, 2017. Email: ngchiamyu[at]
Thesis: "Computational Design and Optimization of Metabolic Pathways."
Current position: Computational scientist at Google X.

Dr. Margaret (Simons) Senftle, 2017. Email: Margaret.n.senftle[at]
Thesis: "Development and Application of Metabolic Models for Determining the Effect of Genetic and Environmental Perturbations on Maize."
Current position: Process engineer Exxon, Inc.

Dr. Ali Khodayari, 2017. Email: akhodayari[at]
Thesis: "Kinetic Modeling in Genome-scale Metabolic Models: Parameterization and Strain Design"
Current position: Associate Director, Systems Bioengineering at Genomatica, Inc., San Diego, CA.

Dr. Akhil Kumar, 2017. Email: kmr.akhil[at]
Thesis: "Elucidation and Synthetic Design of Biochemical Pathways Using novoStoic"
Current position: Machine Learning Scientist at Upside, Greater Seattle Area

Dr. Thomas Mueller, 2016. Email: tmueller[at]
Thesis: "Modeling Metabolism and Regulation to Facilitate Strain Characterization and Design"
Current position: VP, Analytics and Data Strategy, Inizio Engage, Fort Washington, PA.

Dr. Anupam Chowdhury, 2016. Email: achowdhury[at]
Thesis: "Developing optimization-based algorithms for rational engineering of microbial strains"
Current position: Associate Director, Head of Technology at Andes, Oakland, CA.

Dr. Rajib Saha, 2014. Email: rsaha2[at]
Thesis: "Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms"
Current position: Associate Professor, Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE.

Dr. Robert Pantazes, 2014. Email: rjp0029[at]
Thesis: "Computational methods for the de novo design of antibodies"
Current position: Assistant Professor, Chemical Engineering, Auburn University, Auburn, AL.

Dr. Ali R. Zomorrodi, 2012. Email: azomorrodi[at]
Thesis: "Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities"
Current position: Computational & Systems Biology Lead at Mass General Hospital.

Dr. Sridhar Ranganathan, 2012. Email: sridhar.ranganathan[at]
Thesis: "Using computations to analyze and redesign metabolism"
Current position: Director of R & D Computational Biology at Jumpcode Genomics, San Franciso, CA.

Dr. Francisco Vital-Lopez, 2011. Email: fvitallopez[at]
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. Vinay Satish Kumar, 2010. Email: vinay[at]
Thesis: "Systems based optimization approaches to analyze and improve metabolic networks"
Current position: Senior Staff Software Engineer, Generative AI at Meta AI, New York, NY.

Dr. Jonathan Chin, 2010. Email: jwc25[at]
Thesis: "Engineering and analysis of cofactor partitioning for NADPH-dependent xylitol production in Escherichia coli"
Current position: Scientist at Seqirus, Fort Myers, FL.

Dr. Hossein Fazelinia, 2009. Email: fazeliniah[at]
Thesis: "Computational design and experimental characterization of proteins with novel functions"
Current position: Principle Bioinformatics Scientist at CHOP-Penn Proteomics

Dr. Madhukar Dasika, 2007. Email: msd179[at]
Thesis: "Systems engineering based approaches for biological network, inference, analysis and redesign"
Current position: Data Scientist at Amgen, Los Angeles Metro Area.

Dr. Manish Saraf, 2006. Email: manish.saraf[at]
Thesis: "Development of computational tools for the design and optimization of combinatorial protein libraries"
Current position: Director at Citi, New York, NY.

Dr. Gregory Moore, May 2005. Email: gmoore[at]
Thesis: "Modeling and optimization in directed evolution protocols and protein engineering"
Current position: Sr. Director, Protein Engineering at Xencor, Monrovia, CA.

Dr. Priti Pharkya, December 2005. Email: ppharkya[at]
Thesis: "Optimization based redesign of microbial production systems"
Current position: Vice President and Head, Strategy and Corporate Development

Dr. Andreas Lehmann, December 2004. Email: andreas.lehmann[at]
Thesis: "Molecular design in chemical and biological systems"
Current position: Senior Scientist at Biogen, Cambridge, MA.

Dr. Anthony Burgard, 2004. Email: Anthony.Burgard[at]
Thesis: "Optimization-based frameworks for the analysis and redesign of metabolic networks"
Current position: Research General Engineer at National Energy Technology Laboratory, Greater Pittsburgh Region.

Dr. Anshuman Gupta, August 2002. Email: anshumanxgupta[at]
Thesis: "Supply chain management under uncertainty".
Current position: Chief Data Officer at Futurense Technologies, India.

Dr. Shankar Vaidyaraman, August 2001. Email: shankarraman_vaidyaraman[at]
Thesis: "Optimization based methodology for refrigeration system synthesis and molecular design"
Current position: Research scientist at Eli Lilly and Company, Indianapolis, IN.

M.S. Student Theses/Projects Supervised

Soodabeh Ghaffari, 2022. Email: soodabehghaffari[at]
Thesis: "Computational Redesign of Enzymes and Channel Proteins"
Current position: Research Specialist II, Princeton University.

Mohammad Mazharul Islam, 2014. Email: mislam[at]
Thesis: "Dynamic multi-level and multi-objective metabolic modeling of microbial communities"
Current position: Research Associate (under the supervision of Dr. Jason Papin) at the University of Virgina.

Nathan Gifford, 2014.
Thesis: "Computational Redesign of Acyl-acp Thioesterases for Increased Substrate Specificity"
Current position: Applications Engineer at Harper International, Buffalo-Niagara Falls Area, NY.

Prabhasa Ravikirthi, 2010.
Thesis: "Construction of a genome-scale atom mapping model of E.coli for metabolic flux analysis"
Current position: Bioinformatics Developer at PierianDx, Greater Hyderabad Area, India.

George Khoury, 2010. Email: george.a.khoury[at]
Thesis: "Computational design to switch protein cofactor specificity and create enzymatic activity"
Current position: Business Team Leader at ExxonMobil, Greater Houston Area.

Michael Rogers, 2004. Email: Michael.J.Rogers[at]
Thesis: "Real options based planning of pharmaceutical product pipelines"
Current position: Senior Director Corporate Strategy at The Chemours Company, Wilmington, DE.

M. Kalp, 1999
Thesis: "Development of process design case studies for the capstone design course"
Current position: Project Engineer at Croda, State College, PA.

Spas Petkov, August 1997
Thesis: "Analysis and optimization of chemical process systems under uncertainty"
Current position: Director of Business Development, Huvepharma, Bulgaria.

Honor Undergraduate Student Theses/Projects Supervised

Matthew Allan, 2017. Email: mfallan[at]
Current position: PhD Candidate at MIT.

Stephen Spagnol, 2010. Email: SSpagnol[at]
Current position: Associate Principal Scientist at Merck.