Costas D. Maranas (b. 1967), Robert V. & Gloria H. Waltemeyer Chair,Donald B. Broughton Professor, Department of Chemical Engineering, The Pennsylvania State University
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.
Ph.D. Chemical Engineering, University of Wisconsin–Madison, 2005
Ph.D. Genome Sciences, University of Tennessee, Knoxville, 2019
B.S. Chemical Engineering, UC San Diego, 2017
B.Tech Chemical Engineering,
Indian Institute of Technology Delhi, 2022
B.S. Molecular Biology and Biochemistry, Rutgers University-New Brunswick, 2022
A.A. General Studies, Lake-Sumter State College, 2019
B.S. Chemical Engineering, Miami University of Ohio, 2023
B.S. Chemical Engineering, Sharif University of Technology, 2021
M.Tech Chemical Engineering, Indian Institute of Technology Madras, 2024
B.S. Chemical Engineering, Penn State, 2025
Dr. Wheaton L. Schroeder, 2021-2024. Email: wheaton.schroeder[at]wsu.edu
PhD: University of Nebraska – Lincoln
Current position: Assistant Professor, Voiland School of Chemical Engineering and Bioengineering, Washington State University
Dr. John Irudaya Hendry, 2019-2022. Email: jih11[at]psu.edu
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]gmail.com
PhD: Wuhan University
Current position: Advanced Chemist, Eastman Chemical Company
Dr. Siu Hung Joshua Chan, 2015-2018. Email: joshua.chan[at]colostate.edu
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]csiro.au
PhD: Virginia Tech
Current position: Research Fellow, The Australian National University, Canberra, Australia
Dr. Tong Li, 2013-2016. Email: tong.li[at]basf.com
PhD: University of Leuven, Belgium
Current position: Data Scientist, BASF, San Diego.
Dr. Ali R. Zomorrodi, 2012-2013. Email: azomorrodi[at]mgh.harvard.edu
PhD: Pennsylvania State University
Current position: Computational & Systems Biology Lead at Mass General Hospital.
Dr. Young Jung Chang, 2007-2008. Email: yjchang[at]andrew.cmu.edu
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]gmail.com
PhD: Lobachevsky Nizhegorod State University, Russia
Current position: Machine Learning Stylus Medicine, Cambridge, MA.
Dr. Anshuman Gupta, 2002-2005. Email: anshumanxgupta[at]gmail.com
PhD: Pennsylvania State University
Current position: Chief Data Officer at Futurense Technologies, India.
Dr. Kyle Camarda, 1998-2000. Email: camarda[at]ku.edu
PhD: University of Illinois at Urbana-Champaign
Current position: Associate Professor, Department of Chemical and Petroleum Engineering, University of Kansas.
Dr. Vikas Upadhyay, 2025. Email: vuu10[at]psu.edu
Thesis: "A systems approach to advancing computational biosynthesis planning with machine learning"
Current position: Post-doctoral Scholar with Dr. Huimin Zhao, UIUC.
Dr. Debolina Sarkar, 2021. Email: sarkardebolina27[at]gmail.com
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]gmail.com
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]gmail.com
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]gmail.com
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]zymergen.com
Thesis: "Metabolic modeling of Clostridia for biofuel production."
Current position: Senior Biological Data Scientist at Gingko Bioworks, Inc., El Cerrito, CA.
Dr. Chiam Yu Ng, 2017. Email: ngchiamyu[at]gmail.com
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]exxonmobil.com
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]genomatica.com
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]gmail.com
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]mpgis.net
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]zymergen.com
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]unl.edu
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]auburn.edu
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]mgh.harvard.edu
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]thermofisher.com
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]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. Vinay Satish Kumar, 2010. Email: vinay[at]fb.com
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]cornell.edu
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]email.chop.edu
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]gmail.com
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]citi.com
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]xencor.com
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]genomatica.com
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]biogen.com
Thesis: "Molecular design in chemical and biological systems"
Current position: Senior Scientist at Biogen, Cambridge, MA.
Dr. Anthony Burgard, 2004. Email: Anthony.Burgard[at]netl.doe.gov
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]gmail.com
Thesis: "Supply chain management under uncertainty".
Current position: Chief Data Officer at Futurense Technologies, India.
Dr. Shankar Vaidyaraman, August 2001. Email: shankarraman_vaidyaraman[at]lilly.com
Thesis: "Optimization based methodology for refrigeration system synthesis and molecular design"
Current position: Research scientist at Eli Lilly and Company, Indianapolis, IN.
Soodabeh Ghaffari, 2022. Email: soodabehghaffari[at]gmail.com
Thesis: "Computational Redesign of Enzymes and Channel Proteins"
Current position: Research Specialist II, Princeton University.
Mohammad Mazharul Islam, 2014. Email: mislam[at]virginia.edu
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]exxonmobil.com
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]usa.dupont.com
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.
Matthew Allan, 2017. Email: mfallan[at]mit.edu
Current position: PhD Candidate at MIT.
Stephen Spagnol, 2010. Email: SSpagnol[at]ITS.JNJ.com
Current position: Associate Principal Scientist at Merck.
