• BS, Chemical Engineering, Aristotle University, 1990
• Ph D, Chemical Engineering, Princeton University, 1995

Books

Costas D Maranas and Ali R Zomorrodi, 2016, Optimization Methods in Metabolic Networks, John Wiley & Sons

Journal Articles

Yihui Shen, Hoang V. Dinh, Edward Cruz, Zihong Chen, Caroline R. Bartman, Yasuo Yoshikuni, Huimin Zhao, Costas D Maranas, Martin H. Wühr and Joshua D. Rabinowitz, 2024, "Proteome efficiency of bioenergetic pathways", Biophysical Journal, 123, (3), pp. 248a

Niaz Bahar Chowdhury, Margaret Simons-Senftle, Berengere Decouard, Isabelle Quillere, Martine Rigault, Karuna Anna Sajeevan, Bibek Acharya, Ratul Chowdhury, Bertrand Hirel, Alia Dellagi, Costas D Maranas and Rajib Saha, 2023, "A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation", iScience, 26, (12), pp. 108400

Melanie M. Callaghan, Eashant Thusoo, Bishal D. Sharma, Fitsum Getahun, David M. Stevenson, Costas D Maranas, Daniel G. Olson, Lee R. Lynd and Daniel Amador-Noguez, 2023, "Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism", Metabolic Engineering, 80, pp. 254-266

Soyeon Choi, Pradeep K Prabhakar, Ratul Chowdhury, Thomas H Pendergast, Breeanna R Urbanowicz, Costas D Maranas and Katrien M Devos, 2023, "A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass", Journal of Experimental Botany, 74, (18), pp. 5532-5546

Vikas Upadhyay, Veda Sheersh Boorla and Costas D Maranas, 2023, "Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network", Metabolic Engineering, 78, pp. 171-182

Zong-Yen Wu, Wan Sun, Yihui Shen, Jimmy Pratas, Patrick Suthers, Ping-Hung Hsieh, Sudharsan Dwaraknath, Joshua D. Rabinowitz, Costas D Maranas, Zengyi Shao and Yasuo Yoshikuni, 2023, "Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate", Metabolic Engineering Communications, 16, pp. e00220

Hoang V. Dinh and Costas D Maranas, 2023, "Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis", Metabolic Engineering, 77, pp. 242-255

Wheaton L. Schroeder, Teun Kuil, Antonius J.A. van Maris, Daniel G. Olson, Lee R. Lynd and Costas D Maranas, 2023, "A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis", Metabolic Engineering, 77, pp. 306-322

Mengqi Hu, Hoang V. Dinh, Yihui Shen, Patrick Suthers, Charles J. Foster, Catherine M. Call, Xuanjia Ye, Jimmy Pratas, Zia Fatma, Huimin Zhao, Joshua D. Rabinowitz and Costas D Maranas, 2023, "Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale", Metabolic Engineering, 76, pp. 1-17

Veda Sheersh Boorla, Ratul Chowdhury, Ranjani Ramasubramanian, Brandon Ameglio, Rahel Frick, Jeffrey J. Gray and Costas D Maranas, 2023, "De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)", PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

C Zhuo, Xiande Wang, M Docampo-Palacios, B C Sanders, N L Engle, T J Tschaplinski, J I Hendry, Costas D Maranas, Fang Chen and R A Dixon, 2022, "Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity.", Science advances, 8, (10), pp. eabm8145

T Kuil, S Hon, J Yayo, C Foster, G Ravagnan, Costas D Maranas, L R Lynd, D G Olson and van Maris AJA, 2022, "Functional Analysis of H⁺-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum.", Applied and environmental microbiology, 88, (4), pp. e0185721

Suresh V. Kuchipudi, M Surendran-Nair, R M Ruden, M Yon, R H Nissly, Kurt Vandegrift, R K Nelli, L Li, Bhushan M Jayarao, Costas D Maranas, N Levine, K Willgert, Conlan AJK, R J Olsen, Joshua Davis, J M Musser, Peter J Hudson and Vivek Kapur, 2022, "Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer.", Proceedings of the National Academy of Sciences of the United States of America, 119, (6)

Charles Foster, Veda Sheersh Boorla, Satyakam Dash, Saratram Gopalakrishnan, Tyler B. Jacobson, Daniel G. Olson, Daniel Amador-Noguez, Lee R. Lynd and Costas D Maranas, 2022, "Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model", METABOLIC ENGINEERING, 69, pp. 286-301

Niaz Bahar Chowdhury, Wheaton L. Schroeder, Debolina Sarkar, Nardjis Amiour, Isabelle Quillere, Bertrand Hirel, Costas D Maranas and Rajib Saha, 2022, "Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions", JOURNAL OF EXPERIMENTAL BOTANY, 73, (1), pp. 275-291

Jessica Lynn Schultz, Shekhar Mishra, Emily Gaither, Andrea Mejia, Hoang Dinh, Costas D Maranas and Huimin Zhao, 2022, "Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media", MICROBIAL CELL FACTORIES, 21, (1)

Dinh, Hoang, V, Debolina Sarkar and Costas D Maranas, 2022, "Quantifying the propagation of parametric uncertainty on flux balance analysis", METABOLIC ENGINEERING, 69, pp. 26-39

Abhinay Gontu, Erika A. Marlin, Santhamani Ramasamy, Sabarinath Neerukonda, Gayatri Anil, Jasmine Morgan, Meysoon Quraishi, Chen Chen, Veda Sheersh Boorla, Ruth H. Nissly, Padmaja Jakka, Shubhada K. Chothe, Abirami Ravichandran, Nishitha Kodali, Saranya Amirthalingam, Lindsey LaBella, Kathleen Kelly, Pazhanivel Natesan, Allen M. Minns, Randall M. Rossi, Jacob R Werner, Ernest P Hovingh, Scott Lindner, Deepanker Tewari, Vivek Kapur, Kurt Vandegrift, Costas D Maranas, Meera Surendran Nair, Kuchipudi, Suresh and V, 2022, "Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken", VIRUSES-BASEL, 14, (7)

Deepro Banerjee, Michael A. Jindra, Alec J. Linot, Brian F. Pfleger and Costas D Maranas, 2022, "EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning", CURRENT RESEARCH IN BIOTECHNOLOGY, 4, pp. 1-9

Patrick Suthers and Costas D Maranas, 2022, "Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling", BIOTECHNOLOGY PROGRESS, 38, (5)

Kurt Vandegrift, Michele Yon, Surendran Nair, Meera, Abhinay Gontu, Santhamani Ramasamy, Saranya Amirthalingam, Sabarinath Neerukonda, Ruth H. Nissly, Shubhada K. Chothe, Padmaja Jakka, Lindsey LaBella, Nicole Levine, Sophie Rodriguez, Chen Chen, Sheersh Boorla, Veda, Tod Stuber, Jason R. Boulanger, Nathan Kotschwar, Sarah Grimke Aucoin, Richard Simon, Katrina L. Toal, Randall J. Olsen, James Davis, Dashzeveg Bold, Natasha N. Gaudreault, Dinali Perera, Krishani, Yunjeong Kim, Kyeong-Ok Chang, Costas D Maranas, Juergen A. Richt, James M. Musser, Peter J Hudson, Vivek Kapur and Suresh V. Kuchipudi, 2022, "SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City", VIRUSES-BASEL, 14, (12)

Patrick Suthers, Charles J. Foster, Debolina Sarkar, Lin Wang and Costas D Maranas, 2021, "Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms", Metabolic Engineering, 63, pp. 13-33

Hendry, John, I, Dinh, Hoang, V, Debolina Sarkar, Lin Wang, Anindita Bandyopadhyay, Himadri B. Pakrasi and Costas D Maranas, 2021, "A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers", METABOLITES, 11, (3)

Chen Chen, Veda Sheersh Boorla, Deepro Banerjee, Ratul Chowdhury, Victoria Cavener, Ruth H. Nissly, Abhinay Gontu, Nina R. Boyle, Kurt Vandegrift, Meera Surendran Nair, Kuchipudi, Suresh, V and Costas D Maranas, 2021, "Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118, (42)

Lin Wang and Costas D Maranas, 2021, "Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds", ACS SYNTHETIC BIOLOGY, 10, (5), pp. 1064-1076

Lin Wang, Vikas Upadhyay and Costas D Maranas, 2021, "dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design", PLOS COMPUTATIONAL BIOLOGY, 17, (9)

Debolina Sarkar, Marine Landa, Anindita Bandyopadhyay, Himadri B. Pakrasi, Jonathan P. Zehr and Costas D Maranas, 2021, "Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling", PLOS COMPUTATIONAL BIOLOGY, 17, (5)

Charles Foster, Kamil Charubin, Eleftherios T. Papoutsakis and Costas D Maranas, 2021, "Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture", MSYSTEMS, 6, (1)

Juan Angel Patino-Galindo, Ioan Filip, Ratul Chowdhury, Costas D Maranas, Peter K. Sorger, Mohammed AlQuraishi and Raul Rabadan, 2021, "Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2", GENOME MEDICINE, 13, (1)

Ratul Chowdhury, Matthew J. Grisewood, Veda Sheersh Boorla, Qiang Yan, Brian F. Pfleger and Costas D Maranas, 2020, "IPRO+/-: Computational Protein Design Tool Allowing for Insertions and Deletions", Structure, 28, (12), pp. 1344-1357.e4

Patrick Suthers, Hoang V. Dinh, Zia Fatma, Yihui Shen, Siu Hung Chan, Joshua D. Rabinowitz, Huimin Zhao and Costas D Maranas, 2020, "Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production", Metabolic Engineering Communications, 11

Zhiqing Wang, Aarti Doshi, Ratul Chowdhury, Yixi Wang, Costas D Maranas and Patrick C Cirino, 2020, "Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid", Protein engineering, design & selection : PEDS, 33

Saratram Gopalakrishnan, Satyakam Dash and Costas D Maranas, 2020, "K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data", Metabolic Engineering, 61, pp. 197-205

Sergio Garcia, R. Adam Thompson, Richard J. Giannone, Satyakam Dash, Costas D Maranas and Cong T. Trinh, 2020, "Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design", Frontiers in Bioengineering and Biotechnology, 8

John I. Hendry, Anindita Bandyopadhyay, Shyam Srinivasan, Himadri B. Pakrasi and Costas D Maranas, 2020, "Metabolic model guided strain design of cyanobacteria", Current Opinion in Biotechnology, 64, pp. 17-23

Timothy A. Whitehead, Scott Banta, William E. Bentley, Michael J. Betenbaugh, Christina Chan, Douglas S. Clark, Corinne A. Hoesli, Michael C. Jewett, Beth Junker, Mattheos Koffas, Rashmi Kshirsagar, Amanda Lewis, Chien Ting Li, Costas D Maranas, E. Terry Papoutsakis, Kristala L.J. Prather, Steffen Schaffer, Laura Segatori and Ian Wheeldon, 2020, "The importance and future of biochemical engineering", Biotechnology and Bioengineering, 117, (8), pp. 2305-2318

Debolina Sarkar and Costas D Maranas, 2020, "SNPeffect: identifying functional roles of SNPs using metabolic networks", Plant Journal, 103, (2), pp. 512-531

Kyle Bittinger, Chunyu Zhao, Yun Li, Eileen Ford, Elliot S. Friedman, Josephine Ni, Chiraag V. Kulkarni, Jingwei Cai, Yuan Tian, Qing Liu, Andrew David Patterson, Debolina Sarkar, Siu H.J. Chan, Costas D Maranas, Anumita Saha-Shah, Peder Lund, Benjamin A. Garcia, Lisa M. Mattei, Jeffrey S. Gerber, Michal A. Elovitz, Andrea Kelly, Patricia DeRusso, Dorothy Kim, Casey E. Hofstaedter, Mark Goulian, Hongzhe Li, Frederic D. Bushman, Babette S. Zemel and Gary D. Wu, 2020, "Bacterial colonization reprograms the neonatal gut metabolome", Nature Microbiology, 5, (6), pp. 838-847

Patrick Suthers and Costas D Maranas, 2020, "Challenges of cultivated meat production and applications of genome-scale metabolic modeling", AIChE Journal, 66, (6)

Ratul Chowdhury and Costas D Maranas, 2020, "From directed evolution to computational enzyme engineering—A review", AIChE Journal, 66, (3)

Woochul Song, Himanshu Joshi, Ratul Chowdhury, Joseph Najem, Yue xiao Shen, Chao Lang, Codey B. Henderson, Yu Ming Tu, Megan Farell, Megan E. Pitz, Costas D Maranas, Paul Cremer, Robert Hickey, Stephen A. Sarles, Jun li Hou, Aleksei Aksimentiev and Manish Kumar, 2020, "Artificial water channels enable fast and selective water permeation through water-wire networks", Nature Nanotechnology, 15, (1), pp. 73-79

Woochul Song, Himanshu Joshi, Ratul Chowdhury, Joseph Najem, Yue xiao Shen, Chao Lang, Codey B. Henderson, Yu Ming Tu, Megan Farell, Megan E. Pitz, Costas D Maranas, Paul Cremer, Robert Hickey, Stephen A. Sarles, Jun li Hou, Aleksei Aksimentiev and Manish Kumar, 2020, "Artificial water channels enable fast and selective water permeation through water-wire networks", Nature Nanotechnology, 15, (1), pp. 73-79

Tyler B. Jacobson, Travis K. Korosh, David M. Stevenson, Charles Foster, Costas D Maranas, Daniel G. Olson, Lee R. Lynd and Daniel Amador-Noguez, 2020, "In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using ¹³C and ²H Tracers", mSystems, 5, (2)

Ratul Chowdhury, Veda Sheersh Boorla and Costas D Maranas, 2020, "Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity", Computational and Structural Biotechnology Journal, 18, pp. 2573-2582

Woochul Song, Himanshu Joshi, Ratul Chowdhury, J. Najem, Yue-xiao Shen, Chao Lang, Codey B. Henderson, Yu-Ming Tu, Megan Farell, Megan E. Pitz, Costas D Maranas, Paul Cremer, Robert Hickey, Stephen A. Sarles, Jun-li Hou, Aleksei Aksimentiev and M. Kumar, 2020, "Artificial water channels enable fast and selective water permeation through water-wire networks", NATURE NANOTECHNOLOGY, 15, (1), pp. 73-79

Chiam Yu Ng, Lin Wang, Anupam Chowdhury and Costas D Maranas, 2019, "Pareto Optimality Explanation of the Glycolytic Alternatives in Nature", Scientific Reports, 9, (1)

Hoang V. Dinh, Patrick Suthers, Siu Hung Chan, Yihui Shen, Tianxia Xiao, Anshu Deewan, Sujit S. Jagtap, Huimin Zhao, Christopher V. Rao, Joshua D. Rabinowitz and Costas D Maranas, 2019, "A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data", Metabolic Engineering Communications, 9

Siu H.J. Chan, Elliot S. Friedman, Gary D. Wu and Costas D Maranas, 2019, "Predicting the longitudinally and radially varying gut microbiota composition using multi-scale microbial metabolic modeling", Processes, 7, (7)

Karsten Zengler, Kirsten Hofmockel, Nitin S. Baliga, Scott W. Behie, Hans C. Bernstein, James B. Brown, José R. Dinneny, Sheri A. Floge, Samuel P. Forry, Matthias Hess, Scott A. Jackson, Christer Jansson, Stephen R. Lindemann, Jennifer Pett-Ridge, Costas D Maranas, Ophelia S. Venturelli, Matthew D. Wallenstein, Elizabeth A. Shank and Trent R. Northen, 2019, "EcoFABs: advancing microbiome science through standardized fabricated ecosystems", Nature Methods, 16, (7), pp. 567-571

Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, Sebastián N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdóttir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdóttir, Chiam Yu Ng, German Preciat, Alise Žagare, Siu H.J. Chan, Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto Noronha, Aarash Bordbar, Benjamin Cousins, Diana C. El Assal, Luis V. Valcarcel, Iñigo Apaolaza, Susan Ghaderi, Masoud Ahookhosh, Marouen Ben Guebila, Andrejs Kostromins, Nicolas Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T. Yurkovich, Miguel A.P. Oliveira, Phan T. Vuong, Lemmer P. El Assal, Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A. Bryant, Francisco J. Aragón Artacho, Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard Palsson, Ines Thiele and Ronan M.T. Fleming, 2019, "Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0", Nature Protocols, 14, (3), pp. 639-702

John I. Hendry, Saratram Gopalakrishnan, Justin Ungerer, Himadri B. Pakrasi, Yinjie J. Tang and Costas D Maranas, 2019, "Genome-Scale fluxome of Synechococcus elongatus UTEX 2973 using transient ¹³ C-labeling data", Plant Physiology, 179, (2), pp. 761-769

Justin Ungerer, Kristen E. Wendt, John I. Hendry, Costas D Maranas and Himadri B. Pakrasi, 2019, "Plasticity of the genomic haplotype of Synechococcus elongatus leads to rapid strain adaptation under laboratory conditions", Proceedings of the National Academy of Sciences of the United States of America, 116, (10), pp. 3946-3947

Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi and Costas D Maranas, 2019, "A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism", PLoS Computational Biology, 15, (1)

Laxmicharan Samineni, Boya Xiong, Ratul Chowdhury, Andrew Pei, Louise Kuehster, Huiran Wang, Roman Dickey, Paula Espinoza Soto, Lynnicia Massenburg, Thanh H. Nguyen, Costas D Maranas, Darrell Velegol, Manish Kumar and Stephanie B Velegol, 2019, "7 Log Virus Removal in a Simple Functionalized Sand Filter", ENVIRONMENTAL SCIENCE & TECHNOLOGY, 53, (21), pp. 12706-12714

Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, Sebastian N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdottir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdottir, Chiam Yu Ng, German Preciat, Alise Zagare, Chan, Siu H. J., Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto Noronha, Aarash Bordbar, Benjamin Cousins, El Assal, Diana C., Luis V. Valcarcel, Inigo Apaolaza, Susan Ghaderi, Masoud Ahookhosh, Ben Guebila, Marouen, Andrejs Kostromins, Nicolas Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T. Yurkovich, Oliveira, Miguel A. P., Phan T. Vuong, El Assal, Lemmer P., Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A. Bryant, Aragon Artacho, Francisco J., Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard O. Palsson, Ines Thiele, Fleming and Ronan M. T., 2019, "Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0", NATURE PROTOCOLS, 14, (3), pp. 639-702

Kurt Throckmorton, Vladimir Vinnik, Ratul Chowdhury, Taylor Cook, Marc G. Cheyrette, Costas D Maranas, Brian Pfleger and Michael George Thomas, 2019, "Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code", ACS CHEMICAL BIOLOGY, 14, (9), pp. 2044-2054

Charles J. Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz and Costas D Maranas, 2019, "From Escherichia coli mutant C-13 labeling data to a core kinetic model: A kinetic model parameterization pipeline", PLOS COMPUTATIONAL BIOLOGY, 15, (9)

Satyakam Dash, Daniel G. Olson, Chan, Siu Hung Joshua, Daniel Amador-Noguez, Lee R. Lynd and Costas D Maranas, 2019, "Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum", METABOLIC ENGINEERING, 55, pp. 161-169

Ratul Chowdhury and Costas D Maranas, 2019, "From directed evolution to computational enzyme engineering-A review", AICHE JOURNAL

L Wang and Costas D Maranas, 2018, "MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes.", ACS synthetic biology, 7, (2), pp. 462-473

Hadi Nazem-Bokaee and Costas D Maranas, 2018, "A Prospective Study on the Fermentation Landscape of Gaseous Substrates to Biorenewables Using Methanosarcina acetivorans Metabolic Model", FRONTIERS IN MICROBIOLOGY, 9

Chan, Siu H. J., Lin Wang, Satyakam Dash and Costas D Maranas, 2018, "Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints", BIOINFORMATICS, 34, (24), pp. 4248-4255

Justin Ungerer, Kristen E. Wendt, John I. Hendry, Costas D Maranas and Himadri B. Pakrasi, 2018, "Comparative genomics reveals the molecular determinants of rapid growth of the cyanobacterium Synechococcus elongatus UTEX 2973", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115, (50), pp. E11761-E11770

Matthew J. Grisewood, James G Ferry and Costas D Maranas, 2018, "Computationally Exploring and Alleviating the Kinetic Bottlenecks of Anaerobic Methane Oxidation", FRONTIERS IN ENVIRONMENTAL SCIENCE, 6

Saratram Gopalakrishnan, Himadri B. Pakrasi and Costas D Maranas, 2018, "Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models", METABOLIC ENGINEERING, 47, pp. 190-199

Zaigao Tan, Jong Moon Yoon, Anupam Chowdhury, Kaitlin Burdick, Laura R. Jarboe, Costas D Maranas and Jacqueline V. Shanks, 2018, "Engineering of &ITE. coli &ITinherent fatty acid biosynthesis capacity to increase octanoic acid production", BIOTECHNOLOGY FOR BIOFUELS, 11

Lozada, Nestor J. Hernandez, Rung-Yi Lai, Trevor R. Simmons, Kelsey A. Thomas, Ratul Chowdhury, Costas D Maranas and Brian F. Pfleger, 2018, "Highly Active C-8-AcyI-ACP Thioesterase Variant Isolated by a Synthetic Selection Strategy", ACS SYNTHETIC BIOLOGY, 7, (9), pp. 2205-2215

Lin Wang and Costas D Maranas, 2018, "MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes", ACS SYNTHETIC BIOLOGY, 7, (2), pp. 462-473

Ratul Chowdhury, Matthew F. Allan and Costas D Maranas, 2018, "OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes", ANTIBODIES, 7, (3)

Akhil Kumar, Lin Wang, Chiam Yu Ng and Costas D Maranas, 2018, "Pathway design using de novo steps through uncharted biochemical spaces", NATURE COMMUNICATIONS, 9

Ratul Chowdhury, Tingwei Ren, Manish Shankla, Karl Decker, Matthew Grisewood, Jeevan Prabhakar, Carol S Baker, John H Golbeck, Aleksei Aksimentiev, Manish Kumar and Costas D Maranas, 2018, "PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore", NATURE COMMUNICATIONS, 9

Akhil Kumar, Lin Wang, Chiam Yu Ng and Costas D Maranas, 2018, "Pathway design using de novo steps through uncharted biochemical spaces", NATURE COMMUNICATIONS, 9

S Dash, A Khodayari, J Zhou, E K Holwerda, D G Olson, L R Lynd and Costas D Maranas, 2017, "Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations.", Biotechnology for biofuels, 10, pp. 108

V G Poosarla, T Li, B C Goh, K Schulten, Thomas Wood and Costas D Maranas, 2017, "Computational de novo design of antibodies binding to a peptide with high affinity.", Biotechnology and bioengineering

Miguel Serrano-Bermudez, Luis, Fernando Gonzalez Barrios, Andres, Costas D Maranas and Dolly Montoya, 2017, "Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol", BMC SYSTEMS BIOLOGY, 11

Matthew J. Grisewood, Nestor J. Hernandez-Lozada, James B. Thoden, Nathanael P. Gifford, Daniel Mendez-Perez, Haley A. Schoenberger, Matthew F. Allan, Martha E. Floy, Rung-Yi Lai, Hazel M. Holden, Brian F. Pfleger and Costas D Maranas, 2017, "Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids", ACS CATALYSIS, 7, (6), pp. 3837-3849

Kevin C. Entzminger, Jeong-min Hyun, Robert J. Pantazes, Athena C. Patterson-Orazem, Ahlam N. Qerqez, Zach P. Frye, Randall A. Hughes, Andrew D. Ellington, Raquel L. Lieberman, Costas D Maranas and Jennifer A. Maynard, 2017, "De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide", SCIENTIFIC REPORTS, 7

Mary H. Abernathy, Jingjie Yu, Fangfang Ma, Michelle Liberton, Justin Ungerer, Whitney D. Hollinshead, Saratram Gopalakrishnan, Lian He, Costas D Maranas, Himadri B. Pakrasi, Doug Allen and Yinjie J. Tang, 2017, "Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis", BIOTECHNOLOGY FOR BIOFUELS, 10

Satyakam Dash, Ali Khodayari, Jilai Zhou, Evert K. Holwerda, Daniel G. Olson, Lee R. Lynd and Costas D Maranas, 2017, "Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations", BIOTECHNOLOGY FOR BIOFUELS, 10

Rafael A. Canas, Zhazira Yesbergenova-Cuny, Margaret Simons, Fabien Chardon, Patrick Armengaud, Isabelle Quillere, Caroline Cukier, Yves Gibon, Anis M. Limami, Stphane Nicolas, Lenaig Brule, Peter J. Lea, Costas D Maranas and Bertrand Hirel, 2017, "Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modeling Approach to Link Leaf Physiology to Kernel Yield", PLANT CELL, 29, (5), pp. 919-943

Kathryn E. Tiller, Ratul Chowdhury, Tong Li, Seth D. Ludwig, Sabyasachi Sen, Costas D Maranas and Peter M. Tessier, 2017, "Facile affinity Maturation of antibody Variable Domains Using natural Diversity Mutagenesis", FRONTIERS IN IMMUNOLOGY, 8

Thomas J. Mueller, Justin L. Ungerer, Himadri B. Pakrasi and Costas D Maranas, 2017, "Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973", Scientific Reports, 7

Miguel Suastegui, Chiam Yu Ng, Anupam Chowdhury, Wan Sun, Mingfeng Cao, Emma House, Costas D Maranas and Zengyi Shao, 2017, "Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors", METABOLIC ENGINEERING, 42, pp. 134-144

Chan, Siu H. J., Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle and Costas D Maranas, 2017, "Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models", BIOINFORMATICS, 33, (22), pp. 3603-3609

Chan, Siu Hung Joshua, Margaret N. Simons and Costas D Maranas, 2017, "SteadyCom: Predicting microbial abundances while ensuring community stability", PLOS COMPUTATIONAL BIOLOGY, 13, (5)

A Khodayari and Costas D Maranas, 2016, "A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains.", Nature communications, 7, pp. 13806

Liang Zhang, C Xie, Renea Nichols, S H Chan, C Jiang, R Hao, Patricck Smith, J Cai, M N Simons, E Hatzakis, Costas D Maranas, F J Gonzalez and Andrew David Patterson, 2016, "Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism.", mSystems, 1, (5)

C Y Ng, A Chowdhury and Costas D Maranas, 2016, "A microbial factory for diverse chemicals.", Nature biotechnology, 34, (5), pp. 513-5

R Saha, David X Liu, A Hoynes-O'Connor, M Liberton, Jia Yu, M Bhattacharyya-Pakrasi, A Balassy, Fan Zhang, T S Moon, Costas D Maranas and H B Pakrasi, 2016, "Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses.", mBio, 7, (3)

T J Mueller, E A Welsh, H B Pakrasi and Costas D Maranas, 2016, "Identifying Regulatory Changes to Facilitate Nitrogen Fixation in the Nondiazotroph Synechocystis sp. PCC 6803.", ACS synthetic biology, 5, (3), pp. 250-8

Muyun Lihan, Boon Chong Goh, Tong Li, Costas D Maranas and Klaus Shulten, 2016, "de novo Design and in silico Optimization of Antibody-Like Binders Targeting Ebola Viral Antigen", Biophysical Journal, 110, (3), pp. 537a

Hadi Nazem-Bokaee, Saratram Gopalakrishnan, James G Ferry, Thomas Wood and Costas D Maranas, 2016, "Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans", Microbial cell factories, 15, (1)

V W Soo, M J McAnulty, A Tripathi, F Zhu, Liang Zhang, E Hatzakis, Patricck Smith, S Agrawal, H Nazem-Bokaee, S Gopalakrishnan, Howard M Salis, James G Ferry, Costas D Maranas, Andrew David Patterson and Thomas Wood, 2016, "Reversing methanogenesis to capture methane for liquid biofuel precursors.", Microbial cell factories, 15, pp. 11

Chiam Yu Ng, Satyakam Dash and Costas D Maranas, 2016, "Metabolic modeling of clostridia: current developments and applications", FEMS microbiology letters, 363, (4)

Anupam Chowdhury, Ali Khodayari and Costas D Maranas, 2015, "Improving prediction fidelity of cellular metabolism with kinetic descriptions", Current opinion in biotechnology, 36, pp. 57–64

Thomas J Mueller, Eric A Welsh, Himadri B Pakrasi and Costas D Maranas, 2015, "Identifying regulatory changes to facilitate nitrogen fixation in the non-diazotroph Synechocystis sp. PCC 6803", ACS synthetic Biology, 5, (3), pp. 250–258

Saratram Gopalakrishnan and Costas D Maranas, 2015, "13C metabolic flux analysis at a genome-scale", Metabolic Engineering, 32, pp. 12-22

Anupam Chowdhury and Costas D Maranas, 2015, "Designing overall stoichiometric conversions and intervening metabolic reactions", Scientific reports, 5

Chiam Yu Ng, Ali Khodayari, Anupam Chowdhury and Costas D Maranas, 2015, "Advances in de novo strain design using integrated systems and synthetic biology tools", Current opinion in chemical biology, 28, pp. 105-114

Anupam Chowdhury and Costas D Maranas, 2015, "Personalized Kinetic Models for Predictive Healthcare", Cell Systems, 1, (4), pp. 250-251

Bertram M Berla, Rajib Saha, Costas D Maranas and Himadri B Pakrasi, 2015, "Cyanobacterial Alkanes Modulate Photosynthetic Cyclic Electron Flow to Assist Growth under Cold Stress", Scientific reports, 5

Ratul Chowdhury, Anupam Chowdhury and Costas D Maranas, 2015, "Using gene essentiality and synthetic lethality information to correct yeast and cho cell genome-scale models", Metabolites, 5, (4), pp. 536-570

Saratram Gopalakrishnan and Costas D Maranas, 2015, "Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations", Metabolites, 5, (3), pp. 521-535

Sarah-Maria Fendt and Costas D Maranas, 2015, "Systems biology: Advances diseases understanding and metabolic engineering", Current opinion in biotechnology, 34, pp. v-vi

Chiam Yu Ng, Iman Farasat, Costas D Maranas and Howard M Salis, 2015, "Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration", Metabolic engineering, 29, pp. 86-96

Thomas K Mueller, Matthew J Grisewood, Hadi Nazem-Bokaee, Saratram Gopalakrishnan, James G Ferry, Thomas Wood and Costas D Maranas, 2015, "Methane oxidation by anaerobic archaea for conversion to liquid fuels", Journal of industrial microbiology & biotechnology, 42, (3), pp. 391-401

Robert J Pantazes, Matthew J Grisewood, Tong Li, Nathanael P Gifford and Costas D Maranas, 2015, "The Iterative Protein Redesign and Optimization (IPRO) suite of programs", Journal of computational chemistry, 36, (4), pp. 251-63

Anupam Chowdhury, Ali R Zomorrodi and Costas D Maranas, 2015, "Bilevel optimization techniques in computational strain design", Computers & Chemical Engineering, 72, pp. 363–372

Akhil Kumar and Costas D Maranas, 2014, "CLCA: maximum common molecular substructure queries within the MetRxn database.", Journal of chemical information and modeling, 54, (12), pp. 3417-38

M Simons, R Saha, N Amiour, Akhil Kumar, L Guillard, G Clément, M Miquel, Z Li, G Mouille, P J Lea, B Hirel and Costas D Maranas, 2014, "Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model.", Plant physiology, 166, (3), pp. 1659-74

M Simons, R Saha, L Guillard, G Clément, P Armengaud, R Cañas, Costas D Maranas, P J Lea and B Hirel, 2014, "Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling.", Journal of experimental botany, 65, (19), pp. 5657-71

R Saha, A Chowdhury and Costas D Maranas, 2014, "Recent advances in the reconstruction of metabolic models and integration of omics data.", Current opinion in biotechnology, 29, pp. 39-45

A Khodayari, A R Zomorrodi, Jingang Liao and Costas D Maranas, 2014, "A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.", Metabolic engineering, 25, pp. 50-62

T W Tee, A Chowdhury, Costas D Maranas and J V Shanks, 2014, "Systems metabolic engineering design: fatty acid production as an emerging case study.", Biotechnology and bioengineering, 111, (5), pp. 849-57

A R Zomorrodi, M M Islam and Costas D Maranas, 2014, "d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities.", ACS synthetic biology, 3, (4), pp. 247-57

A Chowdhury, A R Zomorrodi and Costas D Maranas, 2014, "k-OptForce: integrating kinetics with flux balance analysis for strain design.", PLoS computational biology, 10, (2), pp. e1003487

T Li, R J Pantazes and Costas D Maranas, 2014, "OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.", PloS one, 9, (8), pp. e105954

A Khodayari, A Chowdhury and Costas D Maranas, 2014, "Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model.", Frontiers in bioengineering and biotechnology, 2, pp. 76

S Dash, T J Mueller, K P Venkataramanan, E T Papoutsakis and Costas D Maranas, 2014, "Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model.", Biotechnology for biofuels, 7, (1), pp. 144

T J Mueller, M J Grisewood, H Nazem-Bokaee, S Gopalakrishnan, James G Ferry, Thomas Wood and Costas D Maranas, 2014, "Methane oxidation by anaerobic archaea for conversion to liquid fuels.", Journal of industrial microbiology & biotechnology, 42, (3), pp. 391-401

W M Aumiller, B W Davis, N Hashemain, Costas D Maranas, Antonios Armaou and C D Keating, 2014, "Coupled Enzyme Reactions Performed in Heterogeneous Reaction Media: Experiments and Modeling for Glucose Oxidase and Horseradish Peroxidase in PEG/Citrate Aqueous Two-Phase System", J. Phys. Chem. B DOI: 10.1021/jp501126v.

Costas D Maranas, 2014, "Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits", European Journal of Operational Research

Aumiller, William M., Jr., Bradley W. Davis, Negar Hashemian, Costas D Maranas, Antonios Armaou and Christine D Keating, 2014, "Coupled Enzyme Reactions Performed in Heterogeneous Reaction Media: Experiments and Modeling for Glucose Oxidase and Horseradish Peroxidase in a PEG/Citrate Aqueous Two-Phase System", JOURNAL OF PHYSICAL CHEMISTRY B, 118, (9), pp. 2506-2517

T J Mueller, B M Berla, H B Pakrasi and Costas D Maranas, 2013, "Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.", BMC systems biology, 7, pp. 142

A R Zomorrodi, J G Lafontaine Rivera, Jingang Liao and Costas D Maranas, 2013, "Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks.", Biotechnology journal, 8, (9), pp. 1090-104

R J Pantazes and Costas D Maranas, 2013, "MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.", BMC bioinformatics, 14, pp. 168

A R Zomorrodi, P F Suthers, S Ranganathan and Costas D Maranas, 2012, "Mathematical optimization applications in metabolic networks.", Metabolic engineering, 14, (6), pp. 672-86

S Ranganathan, T W Tee, A Chowdhury, A R Zomorrodi, J M Yoon, Y Fu, J V Shanks and Costas D Maranas, 2012, "An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.", Metabolic engineering, 14, (6), pp. 687-704

P F Suthers and Costas D Maranas, 2012, "Orchestrating hi-fi annotations.", Nature chemical biology, 8, (10), pp. 810-1

W B Copeland, B A Bartley, D Chandran, M Galdzicki, K H Kim, S C Sleight, Costas D Maranas and H M Sauro, 2012, "Computational tools for metabolic engineering.", Metabolic engineering, 14, (3), pp. 270-80

A R Zomorrodi and Costas D Maranas, 2012, "OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities.", PLoS computational biology, 8, (2), pp. e1002363

Akhil Kumar, P F Suthers and Costas D Maranas, 2012, "MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.", BMC bioinformatics, 13, pp. 6

R Saha, A T Verseput, B M Berla, T J Mueller, H B Pakrasi and Costas D Maranas, 2012, "Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803.", PloS one, 7, (10), pp. e48285

A R Brochado, S Andrejev, Costas D Maranas and K R Patil, 2012, "Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.", PLoS computational biology, 8, (11), pp. e1002758

N. Wang, K. A. Eckert, A. R. Zomorrodi, P. Xin, W. Pan, D. A. Shearer, J. Weisz, Costas D Maranas and G. A. Clawson, 2012, "Down-Regulation of HtrA1 Activates the Epithelial-Mesenchymal Transition and ATM DNA Damage Response Pathways", PLoS ONE, 7, (6), pp. e39446

Ping Xu, S Ranganathan, Z L Fowler, Costas D Maranas and M A Koffas, 2011, "Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA.", Metabolic engineering, 13, (5), pp. 578-87

R J Pantazes, M J Grisewood and Costas D Maranas, 2011, "Recent advances in computational protein design.", Current opinion in structural biology, 21, (4), pp. 467-72

P Ravikirthi, P F Suthers and Costas D Maranas, 2011, "Construction of an E. Coli genome-scale atom mapping model for MFA calculations.", Biotechnology and bioengineering, 108, (6), pp. 1372-82

V Satish Kumar, James G Ferry and Costas D Maranas, 2011, "Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.", BMC systems biology, 5, pp. 28

R Saha, P F Suthers and Costas D Maranas, 2011, "Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism.", PloS one, 6, (7), pp. e21784

F.-G. Vital-Lopez, A. Armaou, Costas D Maranas and M. Hutnik, 2011, "Modeling the Effect of Chemotaxis In Glioblastoma Tumor Progression", AIChE J., 57, pp. 778-792

P. Khanna, E. Weidert, F. Vital-Lopez, A. Armaou, Costas D Maranas and C. Dong, 2011, "Model Simulations Reveal VCAM-1Augment PAK Activation Rates to Amplify p38 MAPK and VE-Cadherin Phosphorylation", Celular and Molecular Bioengineering, 4, (4), pp. 656-669

A R Zomorrodi and Costas D Maranas, 2010, "Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.", BMC systems biology, 4, pp. 178

R J Pantazes and Costas D Maranas, 2010, "OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding.", Protein engineering, design & selection : PEDS, 23, (11), pp. 849-58

S Ranganathan and Costas D Maranas, 2010, "Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions.", Biotechnology journal, 5, (7), pp. 716-25

S Ranganathan, P F Suthers and Costas D Maranas, 2010, "OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions.", PLoS computational biology, 6, (4), pp. e1000744

P F Suthers, Y J Chang and Costas D Maranas, 2010, "Improved computational performance of MFA using elementary metabolite units and flux coupling.", Metabolic engineering, 12, (2), pp. 123-8

M AbuOun, P F Suthers, G I Jones, B R Carter, M P Saunders, Costas D Maranas, M J Woodward and M F Anjum, 2009, "Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain.", The Journal of biological chemistry, 284, (43), pp. 29480-8

G A Khoury, H Fazelinia, J W Chin, R J Pantazes, Patrick C Cirino and Costas D Maranas, 2009, "Computational design of Candida boidinii xylose reductase for altered cofactor specificity.", Protein science : a publication of the Protein Society, 18, (10), pp. 2125-38

V S Kumar and Costas D Maranas, 2009, "GrowMatch: an automated method for reconciling in silico/in vivo growth predictions.", PLoS computational biology, 5, (3), pp. e1000308

P F Suthers, M S Dasika, V S Kumar, G Denisov, J I Glass and Costas D Maranas, 2009, "A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.", PLoS computational biology, 5, (2), pp. e1000285

J W Chin, R Khankal, C A Monroe, Costas D Maranas and Patrick C Cirino, 2009, "Analysis of NADPH supply during xylitol production by engineered Escherichia coli.", Biotechnology and bioengineering, 102, (1), pp. 209-20

H Fazelinia, Patrick C Cirino and Costas D Maranas, 2009, "OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.", Protein science : a publication of the Protein Society, 18, (1), pp. 180-95

P F Suthers, A Zomorrodi and Costas D Maranas, 2009, "Genome-scale gene/reaction essentiality and synthetic lethality analysis.", Molecular systems biology, 5, pp. 301

S.-C. Lee, Y. J. Chang, D.-M. Shin, J. Han, M.-H. Seo, H. Fazelina, Costas D Maranas and H.-S. Kim, 2009, "Designing the substrate specificity of d-hydantoinase using a rational approach", Enzyme and Microbial Technology, 44, (3), pp. 170-175

Y Chang, P F Suthers and Costas D Maranas, 2008, "Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments.", Biotechnology and bioengineering, 100, (6), pp. 1039-49

M S Dasika and Costas D Maranas, 2008, "OptCircuit: an optimization based method for computational design of genetic circuits.", BMC systems biology, 2, pp. 24

E P Gianchandani, M A Oberhardt, A P Burgard, Costas D Maranas and J A Papin, 2008, "Predicting biological system objectives de novo from internal state measurements.", BMC bioinformatics, 9, pp. 43

F. G. Vital-Lopez, A. Varshney, Costas D Maranas and A. Armaou, 2008, "Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks", Comp. & Chem. Eng., 32, pp. 2065-2071

P F Suthers, A P Burgard, M S Dasika, F Nowroozi, S Van Dien, J D Keasling and Costas D Maranas, 2007, "Metabolic flux elucidation for large-scale models using 13C labeled isotopes.", Metabolic engineering, 9, (5-6), pp. 387-405

R J Pantazes, M C Saraf and Costas D Maranas, 2007, "Optimal protein library design using recombination or point mutations based on sequence-based scoring functions.", Protein engineering, design & selection : PEDS, 20, (8), pp. 361-73

V Satish Kumar, M S Dasika and Costas D Maranas, 2007, "Optimization based automated curation of metabolic reconstructions.", BMC bioinformatics, 8, pp. 212

H Fazelinia, Patrick C Cirino and Costas D Maranas, 2007, "Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity.", Biophysical journal, 92, (6), pp. 2120-30

C. Christensen, A. Gupta, Costas D Maranas and R. Albert, 2007, "Large-scale inference and Graph Theoretical Analysis of Gene-Regulatory Networks", B. Subtilis. Physica A, 373, pp. 796-810

F G Vital-Lopez, Antonios Armaou, E V Nikolaev and Costas D Maranas, 2006, "A computational procedure for optimal engineering interventions using kinetic models of metabolism.", Biotechnology progress, 22, (6), pp. 1507-17

M S Dasika, A Burgard and Costas D Maranas, 2006, "A computational framework for the topological analysis and targeted disruption of signal transduction networks.", Biophysical journal, 91, (1), pp. 382-98

M C Saraf, Gregory Moore, N M Goodey, V Y Cao, Stephen J Benkovic and Costas D Maranas, 2006, "IPRO: an iterative computational protein library redesign and optimization procedure.", Biophysical journal, 90, (11), pp. 4167-80

A Gupta, Costas D Maranas and Reka Albert, 2006, "Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.", Bioinformatics (Oxford, England), 22, (2), pp. 209-14

P Pharkya and Costas D Maranas, 2006, "An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems.", Metabolic engineering, 8, (1), pp. 1-13

S S Fong, A P Burgard, C D Herring, E M Knight, F R Blattner, Costas D Maranas and B O Palsson, 2005, "In silico design and adaptive evolution of Escherichia coli for production of lactic acid.", Biotechnology and bioengineering, 91, (5), pp. 643-8

M C Saraf, A Gupta and Costas D Maranas, 2005, "Design of combinatorial protein libraries of optimal size.", Proteins, 60, (4), pp. 769-77

M S Dasika, A Gupta and Costas D Maranas, 2005, "DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics.", Journal of theoretical biology, 232, (1), pp. 55-69

E V Nikolaev, A P Burgard and Costas D Maranas, 2005, "Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions.", Biophysical journal, 88, (1), pp. 37-49

Costas D Maranas and Min Ding, 2005, "Valuation and Design of Pharmaceutical R&D,", 51, (1), pp. 198-209

M. Rogers, M. Ding and Costas D Maranas, 2005, "Valuation of Pharmaceutical R&D Licensing Deals Using a Real Options Based Approach", AIChE Journal, 51, (1), pp. 198-209

A. Gupta, J. Varner and Costas D Maranas, 2005, "Large-Scale Inference of the Transcriptional Regulation of Bacillus Subtilis", Computers & Chemical Engineering, 29, pp. 565-576

P Pharkya, A P Burgard and Costas D Maranas, 2004, "OptStrain: a computational framework for redesign of microbial production systems.", Genome research, 14, (11), pp. 2367-76

M C Saraf, A R Horswill, Stephen J Benkovic and Costas D Maranas, 2004, "FamClash: a method for ranking the activity of engineered enzymes.", Proceedings of the National Academy of Sciences of the United States of America, 101, (12), pp. 4142-7

A P Burgard, E V Nikolaev, C H Schilling and Costas D Maranas, 2004, "Flux coupling analysis of genome-scale metabolic network reconstructions.", Genome research, 14, (2), pp. 301-12

M S Dasika, A Gupta and Costas D Maranas, 2004, "A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks.", Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 474-85

A. Burgard, P. Pharkya and Costas D Maranas, 2004, "A Computational Procedure for Suggesting Gene Knock-out Strategies for Microbial Strain Optimization", Bioengineering & Biotechnology, 84, pp. 887-899

G. L. Moore and Costas D Maranas, 2004, "Perspectives: Computational Challenges in Combinatorial Library Design for Protein Engineering", AIChE Journal, 50, pp. 262-272

M. Rogers, A. Gupta and Costas D Maranas, 2004, "Real Options Based Approaches to Decision Making Under Uncertainty", Process Systems Engineering Conference Proceedings

A. Lehmann and Costas D Maranas, 2004, "Molecular Design using Quantum Chemical Calculations for Property Estimation", Industrial & Engineering Chemistry Research, 43, pp. 3419-3432

M. J. Rogers, M. Ding and Costas D Maranas, 2004, "A Case Study on the Design of Pharmaceutical R&D Licensing Deals", FOCAPD Conference Proceedings, pp. 475-479

P Pharkya, A P Burgard and Costas D Maranas, 2003, "Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock.", Biotechnology and bioengineering, 84, (7), pp. 887-99

A P Burgard, P Pharkya and Costas D Maranas, 2003, "Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.", Biotechnology and bioengineering, 84, (6), pp. 647-57

M C Saraf and Costas D Maranas, 2003, "Using a residue clash map to functionally characterize protein recombination hybrids.", Protein engineering, 16, (12), pp. 1025-34

A P Burgard and Costas D Maranas, 2003, "Optimization-based framework for inferring and testing hypothesized metabolic objective functions.", Biotechnology and bioengineering, 82, (6), pp. 670-7

M C Saraf, Gregory Moore and Costas D Maranas, 2003, "Using multiple sequence correlation analysis to characterize functionally important protein regions.", Protein engineering, 16, (6), pp. 397-406

Gregory Moore and Costas D Maranas, 2003, "Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.", Proceedings of the National Academy of Sciences of the United States of America, 100, (9), pp. 5091-6

P Pharkya, E V Nikolaev and Costas D Maranas, 2003, "Review of the BRENDA Database.", Metabolic engineering, 5, (2), pp. 71-3

A. Gupta and Costas D Maranas, 2003, "Market -Based Pollution Abatement Strategies: Risk Management Using Emission Option Contracts", Industrial & Engineering Chemistry Research, 42, pp. 802-810

A. P. Burgard and Costas D Maranas, 2003, "An Optimization Based Framework for Inferring and Testing Hypothesized Metabolic Objective Functions", Biotechnology & Bioengineering, 82, pp. 670-670

A. Gupta and Costas D Maranas, 2003, "Managing Uncertainties in Chemical Process Industry (CIP) Supply Chain Planning", Computers & Chemical Engineering, 27, pp. 1219-1227

Gregory Moore and Costas D Maranas, 2002, "Predicting out-of-sequence reassembly in DNA shuffling.", Journal of theoretical biology, 219, (1), pp. 9-17

Gregory Moore and Costas D Maranas, 2002, "eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.", Nucleic acids research, 30, (11), pp. 2407-16

M. J. Rogers, A. Gupta and Costas D Maranas, 2002, "Real Options Based Analysis of Optimal Pharmaceutical R&D Portfolios", Industrial & Engineering Chemistry Research, 41, pp. 6607-6620

S. Vaidyaraman and Costas D Maranas, 2002, "Synthesis of Mixed Refrigerant Cascade Cycles", Chemical Engineering Communications, 189, (8), pp. 1057-1078

A. P. Burgard and Costas D Maranas, 2002, "Review of the Biocatalysis/Biodegradation Database (UM-BBD)", Metabolic Engineering, 4, pp. 111-113

A P Burgard, Gregory Moore and Costas D Maranas, 2001, "Review of the TEIRESIAS-based tools of the IBM Bioinformatics and Pattern Discovery Group.", Metabolic engineering, 3, (4), pp. 285-8

S Lutz, M Ostermeier, Gregory Moore, Costas D Maranas and Stephen J Benkovic, 2001, "Creating multiple-crossover DNA libraries independent of sequence identity.", Proceedings of the National Academy of Sciences of the United States of America, 98, (20), pp. 11248-53

A P Burgard and Costas D Maranas, 2001, "Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions.", Biotechnology and bioengineering, 74, (5), pp. 364-75

A P Burgard, S Vaidyaraman and Costas D Maranas, 2001, "Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments.", Biotechnology progress, 17, (5), pp. 791-7

Gregory Moore, Costas D Maranas, S Lutz and Stephen J Benkovic, 2001, "Predicting crossover generation in DNA shuffling.", Proceedings of the National Academy of Sciences of the United States of America, 98, (6), pp. 3226-31

A. P. Burgard and Costas D Maranas, 2001, "Review of Enzymes and Metabolic Pathways (EMP) database", Metabolic Engineering, 3, pp. 193-194

Costas D Maranas and A. P. Burgard, 2001, "Review of EcoCyc and MetaCyc web databases", Metabolic Engineering, 3, pp. 98-99

Gregory Moore and Costas D Maranas, 2000, "Modeling DNA mutation and recombination for directed evolution experiments.", Journal of theoretical biology, 205, (3), pp. 483-503

A. Gupta, Costas D Maranas and C. M. McDonald, 2000, "Midterm Supply Chain Planning Under Uncertainty: Customer Demand Satisfaction and Inventory Management", Computers & Chemical Engineering, 24, pp. 2613-2621

A. Gupta and Costas D Maranas, 2000, "A Two-Stage Modeling and Solution Framework for Multisite Midterm Planning under Demand Uncertainty", Industrial & Engineering Chemistry Research, 39, pp. 3799-3813

G. L. Moore, Costas D Maranas, K. R. Gutshall and J. E. Brenshley, 2000, "Modeling and Optimization of DNA Recombination", Computers & Chemical Engineering, 24, pp. 693-699

K. V. Camarda, B. W. Bonnell, Costas D Maranas and R. Nagarajan, 1999, "Design of Surfactant Solutions with Optimal Macroscopic Properties", Computers & Chemical Engineering, 23, pp. 467-470

A. Gupta and Costas D Maranas, 1999, "A Hierarchical Lagrangean Relaxation Procedure for Solving Midterm Planning Problems", Industrial & Engineering Chemistry Research, 38, pp. 1937-1947

K. V. Camarda and Costas D Maranas, 1999, "Optimization in Polymer Design using Connectivity Indices", Industrial & Engineering Chemistry Research, 38, pp. 1884-1892

S. Vaidyaraman and Costas D Maranas, 1999, "Optimal Refrigeration Cycle Synthesis and Refrigerant Selection", AIChE Journal, 45, (5), pp. 997-1017

V. S. Raman and Costas D Maranas, 1998, "Optimization in product design with properties correlated with topological indices", Computers & Chemical Engineering, 22, (6), pp. 747-763

S. B. Petkov and Costas D Maranas, 1998, "Design of Multiproduct Batch Plants Under Demand Uncertainty with Staged Capacity Expansions", Computers & Chemical Engineering, 22, pp. 789-792

S. B. Petkov and Costas D Maranas, 1998, "Design of Single-Product Campaign Batch Plants under Demand Uncertainty", AlChE Journal, 44, (4), pp. 896-911

S B Petkov and Costas D Maranas, 1997, "Quantitative assessment of uncertainty in the optimization of metabolic pathways.", Biotechnology and bioengineering, 56, (2), pp. 145-61

S. B. Petkov and Costas D Maranas, 1997, "Multiperiod Planning and Scheduling of Multipurpose Batch Plants Under Demand Uncertainty", Industrial & Engineering Chemistry Research, 36, (11), pp. 4864-4881

I. P. Androulakis, Costas D Maranas and C. A. Floudas, 1997, "Prediction of Oligopeptide Conformations via Deterministic Global Optimization", Journal of Global Optimization, 11, pp. 1-34

Costas D Maranas, 1997, "Optimization Accounting for Property Prediction Uncertainty in Polymer Design", Computers & Chemical Engineering, 21, pp. 1019-1024

Costas D Maranas, 1997, "Optimal Molecular Design Under Property Prediction Uncertainty", AIChE Journal, 43, (5), pp. 1250-1264

Costas D Maranas and C. A. Floudas, 1997, "Global Optimization in Generalized Geometric Programming", Computers & Chemical Engineering, 21, (4), pp. 351-369

S. T. Harding, Costas D Maranas, C. M. McDonald and C. A. Floudas, 1997, "Locating All Homogeneous Azeotropes in Multicomponent Mixtures", Industrial & Engineering Chemistry Research, 36, (1), pp. 160-178

Costas D Maranas, I. P. Androulakis, C. A. Floudas, J. M. Mulvey and A. J. Berger, 1997, "Solving Long-Term Financial Planning Problems via Global Optimization", Journal of Economics Dynamics and Control, 21, (8/9), pp. 1405-1425

Costas D Maranas, 1996, "Optimal Computer-Aided Molecular Design: Application to Polymer Design", Industrial & Engineering Chemistry Research, 35, (10), pp. 3403-3414

C. S. Adjiman, I. P. Androulakis, Costas D Maranas and C. A. Floudas, 1996, "A Global Optimization Method, BB, for Process Design", Computers & Chemical Engineering, 20, pp. S419-S424

Costas D Maranas, C. M. McDonald, S. T. Harding and C. A. Floudas, 1996, "Locating All Azeotropes in Homogeneous Azeotropic Systems", Computers & Chemical Engineering, 20, pp. 413-418

I. P. Androulakis, Costas D Maranas and C. A. Floudas, 1995, "A Global Optimization Method for General Constrained Nonconvex Problems", Journal of Global Optimization, 7, (4), pp. 337-363

Costas D Maranas and C. A. Floudas, 1995, "Finding All Solutions of Nonlinearly Constrained Systems of Equations", Journal of Global Optimization, 7, (2), pp. 143-182

Costas D Maranas, C. A. Floudas and P. N. Pardalos, 1995, "New Results in the Packing of Equal Circles in a Square", Discrete Mathematics, 142, pp. 287-293

Annesha Sengupta, Anindita Bandyopadhyay, Debolina Sarkar, John I. Hendry, Max G. Schubert, Deng Liu, George M. Church, Costas D Maranas and Himadri B. Pakrasi, , "Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973", mBio

Shubhada K. Chothe, Padmaja Jakka, Veda Sheersh Boorla, Santhamani Ramasamy, Abhinay Gontu, Ruth Nissly, Justin Brown, Gregory Turner, Brent J. Sewall, DeeAnn M. Reeder, Kenneth A. Field, Julie B. Engiles, Saranya Amirthalingam, Abirami Ravichandran, Lindsey LaBella, Meera Surendran Nair, Costas D Maranas and Suresh V. Kuchipudi, , "Little Brown Bats (Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection", Viruses, 15, (5), pp. 1103

Conference Proceedings

Michael Jindra, Ratul Chowdhury, Brian Pfleger and Costas D Maranas, 2019, "Computational optimization of a thioesterase for selective chain-length product distribution", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 257

Tingwei Ren, Ratul Chowdhury, Peter J Butler, Costas D Maranas and Manish Kumar, 2018, "Biomimetic Membrane Design Principles for Angstrom Scale Separation", BIOPHYSICAL JOURNAL, 114, (3), pp. 361A-361A

Chan, Siu Hung Joshua and Costas D Maranas, 2018, "Metabolic modeling of microbial communities", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 255

Lin Wang and Costas D Maranas, 2018, "MinGenome: Top-down synthesis of genome minimized strains for bioproduction", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 255

Saratram Gopalakrishnan and Costas D Maranas, 2015, "13C Metabolic flux analysis at the genome-scale", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 249

Ali Khodayari and Costas D Maranas, 2015, "Development of a comprehensive Escherichia coli kinetic metabolic model consistent with multiple genetic and environmental perturbations", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 249

Satyakam Dash and Costas D Maranas, 2015, "Development of regulated metabolic models for anaerobic organisms", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 249

Andrea Balassy, Maitrayee Bhattacharyya, Allison Hoynes-O'Connor, Cheryl Immethun, Michelle Liberton, Deng Liu, Thomas Mueller, Yi Xiao, Jingjie Yu, Tae Seok Moon, Fuzhong Zhang, Costas D Maranas and Himadri Pakrasi, 2015, "Transferring nitrogen fixing capabilities to an oxygenic photosynthetic organism", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 249

Kevin C. Entzminger, Robert J. Pantazes, Costas D Maranas and Jennifer A. Maynard, 2014, "De novo antibody design by complementarity determining region modeling", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 247

F. Vital-Lopez, Costas D Maranas and A. Armaou, 2006, "Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels", Proceedings of the 2006 American Control Conference

E. V. Nikolaev, P. Pharkya, Costas D Maranas and A. Armaou, 2005, "Optimal selection of enzyme levels using large-scale kinetic models", Proceedings of 16th International Federation of Automatic Control World Congress, pp. 6

P. Pharkya and Costas D Maranas, 2005, "A hierarchical framework for metabolic pathway discovery and strain design", FOSBE 2005 Proceedings, pp. 141-144

M. J. Rogers, A. Gupta and Costas D Maranas, 2003, "Risk Management in Options Based Pharmaceutical Portfolio Planning", Proceedings of Foundations of Computer-Aided Process Operations IV, pp. 241-244

Costas D Maranas, G. L. Moore, A. P. Burgard and A. Gupta, 2003, "Systems Engineering Challenges and Opportunities in Computational Biology", Proceedings of Foundations of Computer-Aided Process Operations IV, pp. 13-26

A. Gupta and Costas D Maranas, 2001, "Multiperiod Planning of Multisite Supply Chains Under Demand Uncertainty", European Symposium on Computer-Aided Process Engineering, 11, pp. 871-882

Costas D Maranas, 2001, "Optimization in Molecular Design and Bioinformatics", European Symposium on Computer-Aided Process Engineering, 11, pp. 1157-1164

S. Vaidyaraman and Costas D Maranas, 1999, "Simultaneous Refrigeration Cycle Synthesis and Refrigerant Selection", PRES'99, 2nd Conference on Process Integration, Modeling and Optimisation for Energy Saving and Pollution Reduction

Costas D Maranas, I. P. Androulakis and C. A. Floudas, 1995, "A Deterministic Global Optimization Approach for the Protein Folding Problem", Proc. of DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23, pp. 133-150

Service to Penn State:

Service to External Organizations:

• Administrative Support Work, Chairperson, Domain Lead of Use Inspired Research, Center for Bioenergy Innovation, 2017 - 2023