@article{segets2023ideal,
  title={IDEAL COMMUNITIES},
  author={Segets, D and Lin, W and Peukert, W and Lerche, D},
  journal={CEP},
  year={2023}
}

@article{hu2023comparative,
  title={Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale},
  author={Hu, Mengqi and Dinh, Hoang V and Shen, Yihui and Suthers, Patrick F and Foster, Charles J and Call, Catherine M and Ye, Xuanjia and Pratas, Jimmy and Fatma, Zia and Zhao, Huimin and others},
  journal={Metabolic Engineering},
  year={2023},
  publisher={Academic Press}
}

@article{chowdhury2022dissecting,
  title={Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions},
  author={Chowdhury, Niaz Bahar and Schroeder, Wheaton L and Sarkar, Debolina and Amiour, Nardjis and Quiller{\'e}, Isabelle and Hirel, Bertrand and Maranas, Costas D and Saha, Rajib},
  journal={Journal of Experimental Botany},
  volume={73},
  number={1},
  pages={275--291},
  year={2022},
  publisher={Oxford University Press UK}
}

@article{banerjee2022enzymclass,
  title={EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning},
  author={Banerjee, Deepro and Jindra, Michael A and Linot, Alec J and Pfleger, Brian F and Maranas, Costas D},
  journal={Current Research in Biotechnology},
  volume={4},
  pages={1--9},
  year={2022},
  publisher={Elsevier}
}

@article{dinh2022quantifying,
  title={Quantifying the propagation of parametric uncertainty on flux balance analysis},
  author={Dinh, Hoang V and Sarkar, Debolina and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={69},
  pages={26--39},
  year={2022},
  publisher={Academic Press}
}

@article{kuil2022functional,
  title={Functional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum},
  author={Kuil, Teun and Hon, Shuen and Yayo, Johannes and Foster, Charles and Ravagnan, Giulia and Maranas, Costas D and Lynd, Lee R and Olson, Daniel G and van Maris, Antonius JA},
  journal={Applied and environmental microbiology},
  volume={88},
  number={4},
  pages={e01857--21},
  year={2022},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{foster2022assessing,
  title={Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model},
  author={Foster, Charles and Boorla, Veda Sheersh and Dash, Satyakam and Gopalakrishnan, Saratram and Jacobson, Tyler B and Olson, Daniel G and Amador-Noguez, Daniel and Lynd, Lee R and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={69},
  pages={286--301},
  year={2022},
  publisher={Academic Press}
}

@article{rangadurai2022measuring,
  title={Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting},
  author={Rangadurai, Atul and Shi, Honglue and Xu, Yu and Liu, Bei and Abou Assi, Hala and Boom, John D and Zhou, Huiqing and Kimsey, Isaac J and Al-Hashimi, Hashim M},
  journal={Proceedings of the National Academy of Sciences},
  volume={119},
  number={24},
  pages={e2112496119},
  year={2022},
  publisher={National Academy of Sciences}
}

@article{kuchipudi2022multiple,
  title={Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer},
  author={Kuchipudi, Suresh V and Surendran-Nair, Meera and Ruden, Rachel M and Yon, Michele and Nissly, Ruth H and Vandegrift, Kurt J and Nelli, Rahul K and Li, Lingling and Jayarao, Bhushan M and Maranas, Costas D and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={119},
  number={6},
  pages={e2121644119},
  year={2022},
  publisher={National Academy of Sciences}
}

@article{lynd2022toward,
  title={Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels},
  author={Lynd, Lee R and Beckham, Gregg T and Guss, Adam M and Jayakody, Lahiru N and Karp, Eric M and Maranas, Costas and McCormick, Robert L and Amador-Noguez, Daniel and Bomble, Yannick J and Davison, Brian H and others},
  journal={Energy \& Environmental Science},
  volume={15},
  number={3},
  pages={938--990},
  year={2022},
  publisher={Royal Society of Chemistry}
}

@article{schultz2022metabolic,
  title={Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media},
  author={Schultz, J Carl and Mishra, Shekhar and Gaither, Emily and Mejia, Andrea and Dinh, Hoang and Maranas, Costas and Zhao, Huimin},
  journal={Microbial cell factories},
  volume={21},
  number={1},
  pages={1--14},
  year={2022},
  publisher={BioMed Central}
}

@article{zhuo2022developmental,
  title={Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity},
  author={Zhuo, Chunliu and Wang, Xin and Docampo-Palacios, Maite and Sanders, Brian C and Engle, Nancy L and Tschaplinski, Timothy J and Hendry, John I and Maranas, Costas D and Chen, Fang and Dixon, Richard A},
  journal={Science advances},
  volume={8},
  number={10},
  pages={eabm8145},
  year={2022},
  publisher={American Association for the Advancement of Science}
}

@article{chen2022cnn,
  title={A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues},
  author={Chen, Chen and Boorla, Veda Sheersh and Chowdhury, Ratul and Nissly, Ruth H and Gontu, Abhinay and Chothe, Shubhada K and LaBella, Lindsey and Jakka, Padmaja and Ramasamy, Santhamani and Vandegrift, Kurt J and others},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory Preprints}
}

@article{vandegrift2022sars,
  title={SARS-CoV-2 Omicron (B. 1.1. 529) Infection of Wild White-Tailed Deer in New York City},
  author={Vandegrift, Kurt J and Yon, Michele and Surendran Nair, Meera and Gontu, Abhinay and Ramasamy, Santhamani and Amirthalingam, Saranya and Neerukonda, Sabarinath and Nissly, Ruth H and Chothe, Shubhada K and Jakka, Padmaja and others},
  journal={Viruses},
  volume={14},
  number={12},
  pages={2770},
  year={2022},
  publisher={MDPI}
}

@article{chen2022cnn,
  title={A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues (preprint)},
  author={Chen, Chen and Boorla, Veda Sheeresh and Chowdhury, Ratul and Nissly, Ruth and Gontu, Abhinay and Chothe, Shubhada and LaBella, Lindsey and Jakka, Padmaja and Ramasamy, Santhamani and Vandegrift, Kurt and others},
  year={2022}
}

@article{suthers2022examining,
  title={Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling},
  author={Suthers, Patrick F and Maranas, Costas D},
  journal={Biotechnology progress},
  volume={38},
  number={5},
  pages={e3276},
  year={2022},
  publisher={John Wiley \& Sons, Inc. Hoboken, USA}
}

@article{gontu2022development,
  title={Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken},
  author={Gontu, Abhinay and Marlin, Erika A and Ramasamy, Santhamani and Neerukonda, Sabarinath and Anil, Gayatri and Morgan, Jasmine and Quraishi, Meysoon and Chen, Chen and Boorla, Veda Sheersh and Nissly, Ruth H and others},
  journal={Viruses},
  volume={14},
  number={7},
  pages={1358},
  year={2022},
  publisher={MDPI}
}

@article{maranas2022metabolic,
  title={Metabolic modeling for the microbiome},
  author={Maranas, Costas and Sarkar, Debolina and Chan, Joshua},
  year={2022}
}

@article{shen2022proteome,
  title={Proteome capacity constraints favor respiratory ATP generation},
  author={Shen, Yihui and Dinh, Hoang V and Cruz, Edward and Call, Catherine M and Baron, Heide and Ryseck, Rolf-Peter and Pratas, Jimmy and Subramanian, Arjuna and Fatma, Zia and Weilandt, Daniel and others},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{boorla2022ml,
  title={ML helps predict enzyme turnover rates},
  author={Boorla, Veda Sheersh and Upadhyay, Vikas and Maranas, Costas D},
  journal={Nature Catalysis},
  volume={5},
  number={8},
  pages={655--657},
  year={2022},
  publisher={Nature Publishing Group}
}

@article{boorla2022novo,
  title={De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)},
  author={Boorla, Veda Sheersh and Chowdhury, Ratul and Ramasubramanian, Ranjani and Ameglio, Brandon and Frick, Rahel and Gray, Jeffrey J and Maranas, Costas D},
  journal={Proteins: Structure, Function, and Bioinformatics},
  year={2022},
  publisher={John Wiley \& Sons, Inc. Hoboken, USA}
}

@article{dinh2022evaluating,
  title={Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis},
  author={Dinh, Hoang V and Maranas, Costas D},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@inproceedings{schroeder2022building,
  title={Building Bottom-up Kinetic Models for Optimizing Cell-Free Lignocellulose Degradation Systems},
  author={Schroeder, Wheaton and Olson, Daniel and Maranas, Costas D},
  booktitle={2022 AIChE Annual Meeting},
  year={2022},
  organization={AIChE}
}

@inproceedings{schroeder2022tracking,
  title={Tracking Pyrophosphate Metabolism and Evaluating Its Significance in the Bioprocessing of Lignocellulosic Biomass By Clostridium Thermocellum},
  author={Schroeder, Wheaton and Kuil, Tuen and Olson, Daniel and Maranas, Costas D},
  booktitle={2022 AIChE Annual Meeting},
  year={2022},
  organization={AIChE}
}

@article{liu2021engineering,
  title={Engineering biology approaches for food and nutrient production by cyanobacteria},
  author={Liu, Deng and Liberton, Michelle and Hendry, John I and Aminian-Dehkordi, Javad and Maranas, Costas D and Pakrasi, Himadri B},
  journal={Current Opinion in Biotechnology},
  volume={67},
  pages={1--6},
  year={2021},
  publisher={Elsevier Current Trends}
}

@misc{pfleger2021gene,
  title={Gene construct encoding mutant thioesterase, mutant thioesterase encoded thereby, transformed host cell containing the gene construct, and method of using them to produce medium-chain fatty acids},
  author={Pfleger, Brian F and Hernandez-Lozada, Nestor Jose and Maranas, Costas and Grisewood, Matthew},
  year={2021},
  month=jul # "~6",
  note={US Patent 11,053,480}
}

@article{suthers2021recent,
  title={Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms},
  author={Suthers, Patrick F and Foster, Charles J and Sarkar, Debolina and Wang, Lin and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={63},
  pages={13--33},
  year={2021},
  publisher={Academic Press}
}

@article{foster2021building,
  title={Building kinetic models for metabolic engineering},
  author={Foster, Charles J and Wang, Lin and Dinh, Hoang V and Suthers, Patrick F and Maranas, Costas D},
  journal={Current Opinion in Biotechnology},
  volume={67},
  pages={35--41},
  year={2021},
  publisher={Elsevier Current Trends}
}

@article{foster2021modeling,
  title={Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture},
  author={Foster, Charles and Charubin, Kamil and Papoutsakis, Eleftherios T and Maranas, Costas D},
  journal={Msystems},
  volume={6},
  number={1},
  pages={e01325--20},
  year={2021},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{hendry2021genome,
  title={A genome-scale metabolic model of Anabaena 33047 to guide genetic modifications to overproduce nylon monomers},
  author={Hendry, John I and Dinh, Hoang V and Sarkar, Debolina and Wang, Lin and Bandyopadhyay, Anindita and Pakrasi, Himadri B and Maranas, Costas D},
  journal={Metabolites},
  volume={11},
  number={3},
  pages={168},
  year={2021},
  publisher={MDPI}
}

@article{wang2021dgpredictor,
  title={dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design},
  author={Wang, Lin and Upadhyay, Vikas and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={17},
  number={9},
  pages={e1009448},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{chen2021computational,
  title={Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2},
  author={Chen, Chen and Boorla, Veda Sheersh and Banerjee, Deepro and Chowdhury, Ratul and Cavener, Victoria S and Nissly, Ruth H and Gontu, Abhinay and Boyle, Nina R and Vandegrift, Kurt and Nair, Meera Surendran and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={118},
  number={42},
  pages={e2106480118},
  year={2021},
  publisher={National Academy of Sciences}
}

@misc{hendry2021genome,
  title={A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers. Metabolites 2021, 11, 168},
  author={Hendry, JI and Dinh, HV and Sarkar, D and Wang, L and Bandyopadhyay, A and Pakrasi, HB and Maranas, CD},
  year={2021},
  publisher={s Note: MDPI stays neutral with regard to jurisdictional claims in published~…}
}

@article{wang2021computationally,
  title={Computationally prospecting potential pathways from lignin monomers and dimers toward aromatic compounds},
  author={Wang, Lin and Maranas, Costas D},
  journal={ACS Synthetic Biology},
  volume={10},
  number={5},
  pages={1064--1076},
  year={2021},
  publisher={American Chemical Society}
}

@article{sarkar2021elucidation,
  title={Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling},
  author={Sarkar, Debolina and Landa, Marine and Bandyopadhyay, Anindita and Pakrasi, Himadri B and Zehr, Jonathan P and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={17},
  number={5},
  pages={e1008983},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{patino2021recombination,
  title={Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2},
  author={Pati{\~n}o-Galindo, Juan {\'A}ngel and Filip, Ioan and Chowdhury, Ratul and Maranas, Costas D and Sorger, Peter K and AlQuraishi, Mohammed and Rabadan, Raul},
  journal={Genome Medicine},
  volume={13},
  number={1},
  pages={1--14},
  year={2021},
  publisher={BioMed Central}
}

@misc{pfleger2021gene,
  title={Gene construct encoding mutant thioesterase, mutant thioesterase encoded thereby, transformed host cell containing the gene construct, and method of using them to produce medium-chain fatty acids},
  author={Pfleger, Brian F and Hernandez-Lozada, Nestor Jose and Maranas, Costas and Grisewood, Matthew},
  year={2021},
  month=sep # "~23",
  note={US Patent App. 17/332,186}
}

@article{kuchipudi2021multiple,
  title={Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer},
  author={Kuchipudi, Suresh V and Surendran-Nair, Meera and Ruden, Rachel M and Yon, Michelle and Nissly, Ruth H and Nelli, Rahul K and Li, Lingling and Jayarao, Bhushan M and Vandegrift, Kurt J and Maranas, Costas D and others},
  journal={BioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

@article{ghaffari2021computational,
  title={Computational redesign of trans-enoyl-CoA reductase from Treponema denticola (tdTER) to generate focused C8-CoA and C10-CoA library},
  author={Ghaffari, Soodabeh and Chowdhury, Ratul and Maranas, Costas D and Maranas, Costas},
  journal={COMPUTATIONAL REDESIGN OF ENZYMES AND CHANNEL PROTEINS},
  pages={1},
  year={2021},
  publisher={The Pennsylvania State University}
}

@article{ghaffari2021incorporating,
  title={Incorporating Stability Score into Iterative Protein Redesign and Optimization Suite of Programs (IPRO)},
  author={Ghaffari, Soodabeh and Sarkar, Debolina and Chowdhury, Ratul and Maranas, Costas D},
  journal={COMPUTATIONAL REDESIGN OF ENZYMES AND CHANNEL PROTEINS},
  pages={42},
  year={2021},
  publisher={The Pennsylvania State University}
}

@article{boorla2021computational,
  title={Computational redesign of Outer membrane protein F (OmpF) for capturing chemical warfare agent molecules},
  author={Boorla, Veda Sheersh and Sarkar, Debolina and Ghaffari, Soodabeh and Chowdhury, Ratul and Maranas, Costas D},
  journal={COMPUTATIONAL REDESIGN OF ENZYMES AND CHANNEL PROTEINS},
  pages={27},
  year={2021},
  publisher={The Pennsylvania State University}
}

@inproceedings{chowdhury2021integrated,
  title={Integrated Computational and Experimental Study to Dissect the Stress Response of Maize Root},
  author={Chowdhury, Niaz and Schroeder, Wheaton and Zhang, Dongdong and Simons, Margaret N and Hirel, Bertrand and Cahoon, Edgar and Maranas, Costas D and Saha, Rajib},
  booktitle={2021 AIChE Annual Meeting},
  year={2021},
  organization={AIChE}
}

@article{hendry2020metabolic,
  title={Metabolic model guided strain design of cyanobacteria},
  author={Hendry, John I and Bandyopadhyay, Anindita and Srinivasan, Shyam and Pakrasi, Himadri B and Maranas, Costas D},
  journal={Current opinion in biotechnology},
  volume={64},
  pages={17--23},
  year={2020},
  publisher={Elsevier}
}

@article{chowdhury2020directed,
  title={From directed evolution to computational enzyme engineering—a review},
  author={Chowdhury, Ratul and Maranas, Costas D},
  journal={AIChE Journal},
  volume={66},
  number={3},
  pages={e16847},
  year={2020},
  publisher={John Wiley \& Sons, Inc. Hoboken, USA}
}

@article{gopalakrishnan2020k,
  title={K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data},
  author={Gopalakrishnan, Saratram and Dash, Satyakam and Maranas, Costas},
  journal={Metabolic engineering},
  volume={61},
  pages={197--205},
  year={2020},
  publisher={Academic Press}
}

@article{song2020artificial,
  title={Artificial water channels enable fast and selective water permeation through water-wire networks},
  author={Song, Woochul and Joshi, Himanshu and Chowdhury, Ratul and Najem, Joseph S and Shen, Yue-xiao and Lang, Chao and Henderson, Codey B and Tu, Yu-Ming and Farell, Megan and Pitz, Megan E and others},
  journal={Nature nanotechnology},
  volume={15},
  number={1},
  pages={73--79},
  year={2020},
  publisher={Nature Publishing Group}
}

@misc{pfleger2020gene,
  title={Gene construct encoding mutant thioesterase, mutant thioesterase encoded thereby, transformed host cell containing the gene construct, and method of using them to produce medium-chain fatty acids},
  author={Pfleger, Brian F and Hernandez-Lozada, Nestor Jose and Maranas, Costas and Grisewood, Matthew},
  year={2020},
  month=jun # "~23",
  note={US Patent 10,689,631}
}

@article{sarkar2020snpeffect,
  title={SNPeffect: identifying functional roles of SNPs using metabolic networks},
  author={Sarkar, Debolina and Maranas, Costas D},
  journal={The Plant Journal},
  volume={103},
  number={2},
  pages={512--531},
  year={2020}
}

@article{jacobson2020vivo,
  title={In vivo thermodynamic analysis of glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum using 13C and 2H tracers},
  author={Jacobson, Tyler B and Korosh, Travis K and Stevenson, David M and Foster, Charles and Maranas, Costas and Olson, Daniel G and Lynd, Lee R and Amador-Noguez, Daniel},
  journal={Msystems},
  volume={5},
  number={2},
  pages={e00736--19},
  year={2020},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{suthers2020challenges,
  title={Challenges of cultivated meat production and applications of genome-scale metabolic modeling},
  author={Suthers, Patrick F and Maranas, Costas D},
  journal={AIChE Journal},
  volume={66},
  number={6},
  year={2020},
  publisher={Univ. of Illinois at Urbana-Champaign, IL (United States)}
}

@article{chowdhuri2020flood,
  title={Flood susceptibility mapping by ensemble evidential belief function and binomial logistic regression model on river basin of eastern India},
  author={Chowdhuri, Indrajit and Pal, Subodh Chandra and Chakrabortty, Rabin},
  journal={Advances in Space Research},
  volume={65},
  number={5},
  pages={1466--1489},
  year={2020},
  publisher={Pergamon}
}

@article{chowdhury2020biophysical,
  title={Biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity},
  author={Chowdhury, Ratul and Maranas, Costas D},
  journal={bioRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}

@inproceedings{lynd2020lignocellulose,
  title={Lignocellulose-to-Ethanol via Consolidated Bioprocessing with Cotreatment},
  author={Lynd, Lee and Holwerda, Evert and Olson, Daniel G and Hon, Shuen and Herring, CHris and Kubis, Matthew and Ghosh, Sanchari and Moynihan, Galen and Foster, Charles and Maranas, Costas and others},
  booktitle={SBFC2020 Symposium on Biomaterials, Fuels and Chemicals},
  year={2020},
  organization={SIMB}
}

@article{garcia2020development,
  title={Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and computational strain design},
  author={Garcia, Sergio and Thompson, R Adam and Giannone, Richard J and Dash, Satyakam and Maranas, Costas D and Trinh, Cong T},
  journal={Frontiers in bioengineering and biotechnology},
  volume={8},
  pages={772},
  year={2020},
  publisher={Frontiers Media SA}
}

@article{suthers2020genome,
  title={Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production},
  author={Suthers, Patrick F and Dinh, Hoang V and Fatma, Zia and Shen, Yihui and Chan, Siu Hung Joshua and Rabinowitz, Joshua D and Zhao, Huimin and Maranas, Costas D},
  journal={Metabolic engineering communications},
  volume={11},
  pages={e00148},
  year={2020},
  publisher={Elsevier}
}

@article{boorla2020novo,
  title={De novo design of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike protein},
  author={Boorla, Veda Sheersh and Chowdhury, Ratul and Maranas, Costas D},
  journal={BioRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}

@article{wang2020engineering,
  title={Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid},
  author={Wang, Zhiqing and Doshi, Aarti and Chowdhury, Ratul and Wang, Yixi and Maranas, Costas D and Cirino, Patrick C},
  journal={Protein Engineering, Design and Selection},
  volume={33},
  year={2020},
  publisher={Oxford Academic}
}

@article{chowdhury2020computational,
  title={Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity},
  author={Chowdhury, Ratul and Boorla, Veda Sheersh and Maranas, Costas D},
  journal={Computational and structural biotechnology journal},
  volume={18},
  pages={2573--2582},
  year={2020},
  publisher={Elsevier}
}

@article{chowdhury2020ipro+,
  title={IPRO+/-: Computational protein design tool allowing for insertions and deletions},
  author={Chowdhury, Ratul and Grisewood, Matthew J and Boorla, Veda Sheersh and Yan, Qiang and Pfleger, Brian F and Maranas, Costas D},
  journal={Structure},
  volume={28},
  number={12},
  pages={1344--1357},
  year={2020},
  publisher={Cell Press}
}

@article{hendry2020metabolic,
  title={Metabolic flux analysis reaching genome wide coverage: lessons learned and future perspectives},
  author={Hendry, John I and Dinh, Hoang V and Foster, Charles and Gopalakrishnan, Saratram and Wang, Lin and Maranas, Costas D},
  journal={Current Opinion in Chemical Engineering},
  volume={30},
  pages={17--25},
  year={2020},
  publisher={Elsevier}
}

@article{whitehead2020importance,
  title={The importance and future of biochemical engineering},
  author={Whitehead, Timothy A and Banta, Scott and Bentley, William E and Betenbaugh, Michael J and Chan, Christina and Clark, Douglas S and Hoesli, Corinne A and Jewett, Michael C and Junker, Beth and Koffas, Mattheos and others},
  journal={Biotechnology and bioengineering},
  volume={117},
  number={8},
  pages={2305--2318},
  year={2020}
}

@article{bittinger2020bacterial,
  title={Bacterial colonization reprograms the neonatal gut metabolome},
  author={Bittinger, Kyle and Zhao, Chunyu and Li, Yun and Ford, Eileen and Friedman, Elliot S and Ni, Josephine and Kulkarni, Chiraag V and Cai, Jingwei and Tian, Yuan and Liu, Qing and others},
  journal={Nature microbiology},
  volume={5},
  number={6},
  pages={838--847},
  year={2020},
  publisher={Nature Publishing Group}
}

@inproceedings{foster2020assessing,
  title={Assessing the Impact of Allosteric Enzyme Regulations Limiting Ethanol Titer in Clostridium Thermocellum Using a Core Kinetic Model},
  author={Foster, Charles and Boorla, Veda Sheersh and Jacobson, Tyler and Chowdhury, Ratul and Gopalakrishnan, Saratram and Dash, Satyakam and Olson, Daniel and Amador-Noguez, Daniel and Lynd, Lee R and Maranas, Costas D},
  booktitle={2020 Virtual AIChE Annual Meeting},
  year={2020},
  organization={AIChE}
}

@article{chowdhury2020biophysical,
  title={Biophysical characterization of the SARS-CoV2 spike protein binding with the ACE2 receptor explains increased COVID-19 pathogenesis},
  author={Chowdhury, Ratul and Maranas, Costas D},
  year={2020}
}

@article{song2020artificial,
  title={Artificial water channels enable fast and selective water permeation through water-wire networks (vol 135, pg 2152, 2013)},
  author={Song, Woochul and Joshi, Himanshu and Chowdhury, Ratul and Najem, Joseph S and Shen, Yue-xiao and Lang, Chao and Henderson, Codey B and Tu, Yu-Ming and Farell, Megan and Pitz, Megan E and others},
  journal={NATURE NANOTECHNOLOGY},
  volume={15},
  number={2},
  pages={162--162},
  year={2020},
  publisher={NATURE PUBLISHING GROUP MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}
}

@article{ungerer2019reply,
  title={Reply to Zhou and Li: Plasticity of the genomic haplotype of Synechococcus elongatus leads to rapid strain adaptation under laboratory conditions},
  author={Ungerer, Justin and Wendt, Kristen E and Hendry, John I and Maranas, Costas D and Pakrasi, Himadri B},
  journal={Proceedings of the National Academy of Sciences},
  volume={116},
  number={10},
  pages={3946--3947},
  year={2019},
  publisher={National Acad Sciences}
}

@article{dash2019thermodynamic,
  title={Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum},
  author={Dash, Satyakam and Olson, Daniel G and Chan, Siu Hung Joshua and Amador-Noguez, Daniel and Lynd, Lee R and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={55},
  pages={161--169},
  year={2019},
  publisher={Elsevier}
}

@inproceedings{foster201913,
  title={From 13 c Labeling Data to a Core Metabolism Kinetic Model: A Kinetic Model Parameterization Pipeline},
  author={Foster, Charles and Gopalakrishnan, Saratram and Srinivasan, Shyam and Dash, Satyakam and Antoniewicz, Maciek and Maranas, Costas D},
  booktitle={2019 AIChE Annual Meeting},
  year={2019},
  organization={AIChE}
}

@article{foster2019escherichia,
  title={From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline},
  author={Foster, Charles J and Gopalakrishnan, Saratram and Antoniewicz, Maciek R and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={15},
  number={9},
  pages={e1007319},
  year={2019},
  publisher={Public Library of Science}
}

@inproceedings{sarkar2019looking,
  title={Looking Beyond GWAS: Identifying Functional Roles of SNPs Using Metabolic Networks in Arabidopsis and Populus},
  author={Sarkar, Debolina and Maranas, Costas},
  booktitle={2019 AIChE Annual Meeting},
  year={2019},
  organization={AIChE}
}

@article{throckmorton2019directed,
  title={Directed evolution reveals the functional sequence space of an adenylation domain specificity code},
  author={Throckmorton, Kurt and Vinnik, Vladimir and Chowdhury, Ratul and Cook, Taylor and Chevrette, Marc G and Maranas, Costas and Pfleger, Brian and Thomas, Michael George},
  journal={ACS chemical biology},
  volume={14},
  number={9},
  pages={2044--2054},
  year={2019},
  publisher={ACS Publications}
}

@inproceedings{chowdhury2019ipro+,
  title={Ipro+/-Computational Protein Design Tool for Predicting Indels Along with Substitutions for Redesign of Channel Proteins and Enzymes Alike},
  author={Chowdhury, Ratul and Maranas, Costas},
  booktitle={2019 AIChE Annual Meeting},
  year={2019},
  organization={AIChE}
}

@article{ng2019pareto,
  title={Pareto optimality explanation of the glycolytic alternatives in nature},
  author={Ng, Chiam Yu and Wang, Lin and Chowdhury, Anupam and Maranas, Costas D},
  journal={Scientific reports},
  volume={9},
  number={1},
  pages={1--15},
  year={2019},
  publisher={Nature Publishing Group}
}

@misc{maranas2019angstrom,
  title={Angstrom-scale separations by design using precision biomimetic membrane},
  author={Maranas, Costas D and Kumar, Manish and Chowdhury, Ratul and Ren, Tingwei},
  year={2019},
  month=oct # "~31",
  publisher={Google Patents},
  note={US Patent App. 16/397,416}
}

@article{zengler2019ecofabs,
  title={EcoFABs: advancing microbiome science through standardized fabricated ecosystems},
  author={Zengler, Karsten and Hofmockel, Kirsten and Baliga, Nitin S and Behie, Scott W and Bernstein, Hans C and Brown, James B and Dinneny, Jos{\'e} R and Floge, Sheri A and Forry, Samuel P and Hess, Matthias and others},
  journal={Nature methods},
  volume={16},
  number={7},
  pages={567--571},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{heirendt2019creation,
  title={Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0},
  author={Heirendt, Laurent and Arreckx, Sylvain and Pfau, Thomas and Mendoza, Sebasti{\'a}n N and Richelle, Anne and Heinken, Almut and Haraldsd{\'o}ttir, Hulda S and Wachowiak, Jacek and Keating, Sarah M and Vlasov, Vanja and others},
  journal={Nature protocols},
  volume={14},
  number={3},
  pages={639--702},
  year={2019},
  publisher={Nature Publishing Group}
}

@misc{pfleger2019gene,
  title={Gene construct encoding mutant thioesterase, mutant thioesterase encoded thereby, transformed host cell containing the gene construct, and method of using them to produce medium-chain fatty acids},
  author={Pfleger, Brian F and Hernandez-Lozada, Nestor Jose and Maranas, Costas and Grisewood, Matthew},
  year={2019},
  month=sep # "~24",
  publisher={Google Patents},
  note={US Patent 10,421,951}
}

@article{hendry2019genome,
  title={Genome-scale fluxome of Synechococcus elongatus UTEX 2973 using transient 13C-labeling data},
  author={Hendry, John I and Gopalakrishnan, Saratram and Ungerer, Justin and Pakrasi, Himadri B and Tang, Yinjie J and Maranas, Costas D},
  journal={Plant physiology},
  volume={179},
  number={2},
  pages={761--769},
  year={2019},
  publisher={American Society of Plant Biologists}
}

@article{chan2019predicting,
  title={Predicting the longitudinally and radially varying gut microbiota composition using multi-scale microbial metabolic modeling},
  author={Chan, Siu HJ and Friedman, Elliot S and Wu, Gary D and Maranas, Costas D},
  journal={Processes},
  volume={7},
  number={7},
  pages={394},
  year={2019},
  publisher={MDPI}
}

@inproceedings{jindra2019computational,
  title={Computational optimization of a thioesterase for selective chain-length product distribution},
  author={Jindra, Michael and Chowdhury, Ratul and Pfleger, Brian and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={257},
  year={2019},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{sarkar2019engineering,
  title={Engineering microbial chemical factories using metabolic models},
  author={Sarkar, Debolina and Maranas, Costas D},
  journal={BMC Chemical Engineering},
  volume={1},
  number={1},
  pages={1--11},
  year={2019},
  publisher={BioMed Central}
}

@article{sarkar2019diurnal,
  title={A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism},
  author={Sarkar, Debolina and Mueller, Thomas J and Liu, Deng and Pakrasi, Himadri B and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={15},
  number={1},
  pages={e1006692},
  year={2019},
  publisher={Public Library of Science}
}

@article{maranas2019identifying,
  title={Identifying functional roles of SNPs using metabolic networks for improved plant breeding},
  author={Maranas, Costas and Sarkar, Debolina},
  year={2019}
}

@article{samineni20197,
  title={7 log virus removal in a simple functionalized sand filter},
  author={Samineni, Laxmicharan and Xiong, Boya and Chowdhury, Ratul and Pei, Andrew and Kuehster, Louise and Wang, Huiran and Dickey, Roman and Soto, Paula Espinoza and Massenburg, Lynnicia and Nguyen, Thanh H and others},
  journal={Environmental Science \& Technology},
  volume={53},
  number={21},
  pages={12706--12714},
  year={2019},
  publisher={American Chemical Society}
}

@article{maranas2019poredesigner,
  title={PoreDesigner: A computational tool for the design of membrane pores for separations},
  author={Maranas, Costas and Chowdhury, Ratul and Kumar, Manish},
  year={2019}
}

@inproceedings{chowdhury2019ipro+,
  title={Ipro+/-: A Computational Protein Design Tool Allowing NOT ONLY for Amino Acid Changes but Also Insertions and Deletions},
  author={Chowdhury, Ratul and Maranas, Costas D},
  booktitle={2019 AIChE Annual Meeting},
  year={2019},
  organization={AIChE}
}

@article{dinh2019comprehensive,
  title={A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data},
  author={Dinh, Hoang V and Suthers, Patrick F and Chan, Siu Hung Joshua and Shen, Yihui and Xiao, Tianxia and Deewan, Anshu and Jagtap, Sujit S and Zhao, Huimin and Rao, Christopher V and Rabinowitz, Joshua D and others},
  journal={Metabolic engineering communications},
  volume={9},
  pages={e00101},
  year={2019},
  publisher={Elsevier}
}

@inproceedings{johnson2019metabolism,
  title={Metabolism of S-lignin by Pseudomonas putida KT2440},
  author={Johnson, Christopher W and Notonier, Sandra and Dumalo, Linda and Abraham, Paul E and Hatmaker, Elizabeth A and Werner, Allison and Amore, Antonella and Wang, Lin and Giannone, Richard J and Guss, Adam M and others},
  booktitle={SIMB Annual Meeting and Exhibition 2019},
  year={2019},
  organization={SIMB}
}

@inproceedings{wang2019computational,
  title={Computational Pathway Design for Funneling Lignin Intermediates to Aromatic Products},
  author={Wang, Lin and Maranas, Costas},
  booktitle={2019 AIChE Annual Meeting},
  year={2019},
  organization={AIChE}
}

@inproceedings{samineni2019enhanced,
  title={Enhanced virus removal in a practical sand filter},
  author={Samineni, Laxmicharan and Xiong, Boya and Chowdhury, Ratul and Nguyen, Thanh and Maranas, Costas and Velegol, Darrell and Kumar, Manish and Velegol, Stephanie},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={258},
  year={2019},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{chowdhury2019computational,
  title={Computational Protein Design Using Optimization Programs and Force-Field Calculations},
  author={Chowdhury, Ratul and Maranas, Costas and Kumar, Manish},
  booktitle={2019 AIChE Annual Meeting},
  year={2019},
  organization={AIChE}
}

@inproceedings{suthers2019assessing,
  title={Assessing the Metabolic Capabilities of the Yeast Issatchenkia Orientalis SD108 and Its Application to Biochemical Production},
  author={Suthers, Patrick and Fatma, Zia and Shen, Yihui and Chan, Siu Hung Joshua and Dinh, Hoang and Rabinowitz, Joshua D and Zhao, Huimin and Maranas, Costas},
  booktitle={2019 AIChE Annual Meeting},
  year={2019},
  organization={AIChE}
}

@techreport{maranas2018ensemble,
  title={Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production},
  author={Maranas, Costas D},
  year={2018},
  institution={Pennsylvania State Univ., University Park, PA (United States)}
}

@article{tan2018engineering,
  title={Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production},
  author={Tan, Zaigao and Yoon, Jong Moon and Chowdhury, Anupam and Burdick, Kaitlin and Jarboe, Laura R and Maranas, Costas D and Shanks, Jacqueline V},
  journal={Biotechnology for biofuels},
  volume={11},
  number={1},
  pages={1--15},
  year={2018},
  publisher={BioMed Central}
}

@article{chowdhury2018poredesigner,
  title={PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore},
  author={Chowdhury, Ratul and Ren, Tingwei and Shankla, Manish and Decker, Karl and Grisewood, Matthew and Prabhakar, Jeevan and Baker, Carol and Golbeck, John H and Aksimentiev, Aleksei and Kumar, Manish and others},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={1--10},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{grisewood2018computationally,
  title={Computationally exploring and alleviating the kinetic bottlenecks of anaerobic methane oxidation},
  author={Grisewood, Matthew J and Ferry, James G and Maranas, Costas D},
  journal={Frontiers in Environmental Science},
  volume={6},
  pages={84},
  year={2018},
  publisher={Frontiers Media SA}
}

@article{ren2018biomimetic,
  title={Biomimetic Membrane Design Principles for Angstrom Scale Separation},
  author={Ren, Tingwei and Chowdhury, Ratul and Butler, Peter and Maranas, Costas and Kumar, Manish},
  journal={Biophysical Journal},
  volume={114},
  number={3},
  pages={361a},
  year={2018},
  publisher={Elsevier}
}

@article{gopalakrishnan2018elucidation,
  title={Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models},
  author={Gopalakrishnan, Saratram and Pakrasi, Himadri B and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={47},
  pages={190--199},
  year={2018},
  publisher={Elsevier}
}

@incollection{nazem2018biochemistry,
  title={The biochemistry and physiology of respiratory-driven reversed methanogenesis},
  author={Nazem-Bokaee, Hadi and Yan, Zhen and Maranas, Costas D and Ferry, James G},
  booktitle={Methane Biocatalysis: Paving the Way to Sustainability},
  pages={183--197},
  year={2018},
  publisher={Springer}
}

@article{kumar2018pathway,
  title={Pathway design using de novo steps through uncharted biochemical spaces},
  author={Kumar, Akhil and Wang, Lin and Ng, Chiam Yu and Maranas, Costas D},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={1--15},
  year={2018},
  publisher={Nature Publishing Group}
}

@inproceedings{wang2018mingenome,
  title={MinGenome: Top-down synthesis of genome minimized strains for bioproduction},
  author={Wang, Lin and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={255},
  year={2018},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{dinh2018identification,
  title={Identification of growth-coupled production strains considering protein costs and kinetic variability},
  author={Dinh, Hoang V and King, Zachary A and Palsson, Bernhard O and Feist, Adam M},
  journal={Metabolic engineering communications},
  volume={7},
  pages={e00080},
  year={2018},
  publisher={Elsevier}
}

@article{chowdhury2018optmaven,
  title={OptMAVEn-2.0: de novo design of variable antibody regions against targeted antigen epitopes},
  author={Chowdhury, Ratul and Allan, Matthew F and Maranas, Costas D},
  journal={Antibodies},
  volume={7},
  number={3},
  pages={23},
  year={2018},
  publisher={MDPI}
}

@inproceedings{chan2018metabolic,
  title={Metabolic modeling of microbial communities},
  author={Chan, Siu Hung Joshua and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={255},
  year={2018},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@incollection{simons2018modeling,
  title={Modeling plant metabolism: advancements and future capabilities},
  author={Simons-Senftle, Margaret N and Sarkar, Debolina and Maranas, Costas D},
  booktitle={Engineering Nitrogen Utilization in Crop Plants},
  pages={57--76},
  year={2018},
  publisher={Springer}
}

@article{chan2018accelerating,
  title={Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints},
  author={Chan, Siu HJ and Wang, Lin and Dash, Satyakam and Maranas, Costas D},
  journal={Bioinformatics},
  volume={34},
  number={24},
  pages={4248--4255},
  year={2018},
  publisher={Oxford University Press}
}

@article{nazem2018prospective,
  title={A prospective study on the fermentation landscape of gaseous substrates to biorenewables using Methanosarcina acetivorans metabolic model},
  author={Nazem-Bokaee, Hadi and Maranas, Costas D},
  journal={Frontiers in microbiology},
  volume={9},
  pages={1855},
  year={2018},
  publisher={Frontiers Media SA}
}

@article{canas2018correction,
  title={CORRECTION: Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modelling Approach to Link Leaf Physiology to Kernel Yield.},
  author={Canas, Rafael and Yesbergenova-Cuny, Zhazira and Simons, Margaret and Chardon, Fabien and Armengaud, Patrick and Quillere, Isabelle and Cukier, Caroline and Gibon, Yves and Limami, Anis-Mohamed and Nicolas, Stephane and others},
  journal={The Plant cell},
  volume={30},
  pages={946},
  year={2018}
}

@article{ungerer2018comparative,
  title={Comparative genomics reveals the molecular determinants of rapid growth of the cyanobacterium Synechococcus elongatus UTEX 2973},
  author={Ungerer, Justin and Wendt, Kristen E and Hendry, John I and Maranas, Costas D and Pakrasi, Himadri B},
  journal={Proceedings of the National Academy of Sciences},
  volume={115},
  number={50},
  pages={E11761--E11770},
  year={2018},
  publisher={National Acad Sciences}
}

@article{wang2018mingenome,
  title={MinGenome: an in silico top-down approach for the synthesis of minimized genomes},
  author={Wang, Lin and Maranas, Costas D},
  journal={ACS synthetic biology},
  volume={7},
  number={2},
  pages={462--473},
  year={2018},
  publisher={American Chemical Society}
}

@article{wang2018exploring,
  title={Exploring the combinatorial space of complete pathways to chemicals},
  author={Wang, Lin and Ng, Chiam Yu and Dash, Satyakam and Maranas, Costas D},
  journal={Biochemical Society Transactions},
  volume={46},
  number={3},
  pages={513--522},
  year={2018},
  publisher={Portland Press Ltd.}
}

@inproceedings{chowdhury2018optmaven,
  title={Optmaven-2.0: A Fast Protocol for de novo Design of Antibody Variable Region Against Aspecific Antigen Epitope},
  author={Chowdhury, Ratul and Allan, Matthew F and Maranas, Costas},
  booktitle={2018 AIChE Annual Meeting},
  year={2018},
  organization={AIChE}
}

@inproceedings{chan2018predicting,
  title={Predicting the Spatially Differential Gut Microbiota Composition Using Genome-Scale Metabolic Modeling},
  author={Chan, Siu Hung Joshua and Senftle, Margaret and Maranas, Costas},
  booktitle={2018 AIChE Annual Meeting},
  year={2018},
  organization={AIChE}
}

@inproceedings{suthers2018developing,
  title={Developing Genome-Scale Whole-Plant Models for Poplar (Populus deltoides) and Switchgrass (Panicum virgatum)},
  author={Suthers, Patrick and Sarkar, Debolina and Maranas, Costas},
  booktitle={2018 AIChE Annual Meeting},
  year={2018},
  organization={AIChE}
}

@article{jarboe2018engineering,
  title={Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production},
  author={Jarboe, Laura and Tan, Zaigao and Yoon, Jong Moon and Chowdhury, Anupam and Shanks, Jacqueline and Burdick, Kaitlin and Maranas, Costas},
  year={2018}
}

@article{evangelisti2018therapeutic,
  title={Therapeutic targeting of mTOR in T-cell acute lymphoblastic leukemia: an update},
  author={Evangelisti, Camilla and Chiarini, Francesca and McCubrey, James A and Martelli, Alberto M},
  journal={International journal of molecular sciences},
  volume={19},
  number={7},
  pages={1878},
  year={2018},
  publisher={MDPI}
}

@article{mueller2017identifying,
  title={Identifying the metabolic differences of a fast-growth phenotype in Synechococcus UTEX 2973},
  author={Mueller, Thomas J and Ungerer, Justin L and Pakrasi, Himadri B and Maranas, Costas D},
  journal={Scientific reports},
  volume={7},
  number={1},
  pages={1--8},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{dash2017development,
  title={Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations},
  author={Dash, Satyakam and Khodayari, Ali and Zhou, Jilai and Holwerda, Evert K and Olson, Daniel G and Lynd, Lee R and Maranas, Costas D},
  journal={Biotechnology for biofuels},
  volume={10},
  number={1},
  pages={1--16},
  year={2017},
  publisher={BioMed Central}
}

@phdthesis{dinh2017identification,
  title={Identification of growth-coupled and kinetically robust production in strain designs using genome-scale models},
  author={Dinh, Hoang Viet},
  year={2017},
  school={University of California, San Diego}
}

@article{suastegui2017multilevel,
  title={Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors},
  author={Su{\'a}stegui, Miguel and Ng, Chiam Yu and Chowdhury, Anupam and Sun, Wan and Cao, Mingfeng and House, Emma and Maranas, Costas D and Shao, Zengyi},
  journal={Metabolic engineering},
  volume={42},
  pages={134--144},
  year={2017},
  publisher={Elsevier}
}

@article{tessier2017nature,
  title={Nature inspired antibody design and optimization},
  author={Tessier, Peter and Tiller, Kathryn and Rabia, Lilia and Julian, Mark and Li, Lijuan and Ludwig, Seth and Garde, Shekhar and Chowdhury, Ratul and Maranas, Costas and Kumar, Sandeep},
  year={2017}
}

@inproceedings{gopalakrishnan2017cyanobacterial,
  title={Cyanobacterial genome-scale carbon mapping models for genome-scale 13C-metabolic flux elucidation},
  author={Gopalakrishnan, Saratram and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={253},
  year={2017},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{chowdhury2017systematic,
  title={Systematic Redesigning of E. coli water Channel Porin, Ompf, for Desired Pore Size Using Iterative Protein Redesign and Optimization (IPRO) Suite},
  author={Chowdhury, Ratul and Ren, Tingwei and Decker, Karl and Aksimentiev, Aleksei and Kumar, Manish and Maranas, Costas},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@article{wang2017review,
  title={A review of computational tools for design and reconstruction of metabolic pathways},
  author={Wang, Lin and Dash, Satyakam and Ng, Chiam Yu and Maranas, Costas D},
  journal={Synthetic and systems biotechnology},
  volume={2},
  number={4},
  pages={243--252},
  year={2017},
  publisher={Elsevier}
}

@inproceedings{chan2017steadycom,
  title={Steadycom: Modeling Microbial Communities Under Steady-State Growth},
  author={Chan, Siu Hung Joshua and Simons-Senftle, Margaret and Maranas, Costas D},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@inproceedings{wang2017optimization,
  title={Optimization Driven Top-Down Synthesis of Genome Minimized Strains for Bioproduction},
  author={Wang, Lin and Maranas, Costas D},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@article{maranas2017computational,
  title={Computational redesign of acyl-ACP thioesterase with improved selectivity towards medium chain fatty acids at high production levels},
  author={Maranas, Costas D and Grisewood, Matthew J and Hernandez Lozada, N{\'e}stor J and Pfleger, Brian F},
  year={2017}
}

@article{serrano2017clostridium,
  title={Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol},
  author={Serrano-Berm{\'u}dez, Luis Miguel and Gonz{\'a}lez Barrios, Andr{\'e}s Fernando and Maranas, Costas D and Montoya, Dolly},
  journal={BMC systems biology},
  volume={11},
  number={1},
  pages={1--13},
  year={2017},
  publisher={BioMed Central}
}

@misc{chowdhury2017method,
  title={Method for designing overall stoichiometric conversions and intervening metabolic reactions},
  author={Chowdhury, Anupam and Maranas, Costas D},
  year={2017},
  month=apr # "~27",
  publisher={Google Patents},
  note={US Patent App. 15/146,602}
}

@inproceedings{dash2017constructing,
  title={Constructing Predictive Kinetic Models of Metabolism with Transcriptional Regulation},
  author={Dash, Satyakam and Gopalakrishnan, Saratram and Foster, Charles and Maranas, Costas D},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@inproceedings{maranas2017metabolic,
  title={Metabolic Modeling of Microbial Communities},
  author={Maranas, Costas D},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@article{canas2017exploiting,
  title={Exploiting the genetic diversity of maize using a combined metabolomic, enzyme activity profiling, and metabolic modeling approach to link leaf physiology to kernel yield},
  author={Ca{\~n}as, Rafael A and Yesbergenova-Cuny, Zhazira and Simons, Margaret and Chardon, Fabien and Armengaud, Patrick and Quiller{\'e}, Isabelle and Cukier, Caroline and Gibon, Yves and Limami, Anis M and Nicolas, St{\'e}phane and others},
  journal={The Plant Cell},
  volume={29},
  number={5},
  pages={919--943},
  year={2017},
  publisher={American Society of Plant Biologists}
}

@article{entzminger2017novo,
  title={De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide},
  author={Entzminger, Kevin C and Hyun, Jeong-min and Pantazes, Robert J and Patterson-Orazem, Athena C and Qerqez, Ahlam N and Frye, Zach P and Hughes, Randall A and Ellington, Andrew D and Lieberman, Raquel L and Maranas, Costas D and others},
  journal={Scientific reports},
  volume={7},
  number={1},
  pages={1--11},
  year={2017},
  publisher={Nature Publishing Group}
}

@inproceedings{suastegui2017multilevel,
  title={Multilevel engineering of the upstream aromatic module in Saccharomyces cerevisiae for high production of polymer and drug precursors},
  author={Suastegui, Miguel and Shao, Zengyi and Ng, Chiam and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={253},
  year={2017},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{chan2017uncovering,
  title={Uncovering and Correcting the Effect of Biomass Molecular Weight Discrepancies in FBA Calculations},
  author={Chan, Siu Hung Joshua and Cai, Jingyi and Wang, Lin and Simons-Senftle, Margaret and Maranas, Costas D},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@techreport{maranas2017development,
  title={Development of a Knowledgebase (MetRxn) of Metabolites, Reactions and Atom Mappings to Accelerate Discovery and Redesign},
  author={Maranas, Costas D},
  year={2017},
  institution={Pennsylvania State Univ., University Park, PA (United States)}
}

@article{grisewood2017computational,
  title={Computational redesign of acyl-ACP thioesterase with improved selectivity toward medium-chain-length fatty acids},
  author={Grisewood, Matthew J and Hern{\'a}ndez-Lozada, N{\'e}stor J and Thoden, James B and Gifford, Nathanael P and Mendez-Perez, Daniel and Schoenberger, Haley A and Allan, Matthew F and Floy, Martha E and Lai, Rung-Yi and Holden, Hazel M and others},
  journal={ACS catalysis},
  volume={7},
  number={6},
  pages={3837--3849},
  year={2017},
  publisher={ACS Publications}
}

@inproceedings{hernandez2017metabolic,
  title={Metabolic engineering of bacteria for production of oleochemicals},
  author={Hernandez, Nestor and Grisewood, Matthew and Maranas, Costas and Pfleger, Brian},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={253},
  year={2017},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{chan2017standardizing,
  title={Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models},
  author={Chan, Siu HJ and Cai, Jingyi and Wang, Lin and Simons-Senftle, Margaret N and Maranas, Costas D},
  journal={Bioinformatics},
  volume={33},
  number={22},
  pages={3603--3609},
  year={2017},
  publisher={Oxford University Press}
}

@inproceedings{abernathy2017deciphering,
  title={Deciphering Cyanobacterial Phenotypes for Fast Photoautotrophic Growth},
  author={Abernathy, Mary and Yu, Jingjie and Ma, Fangfang and Liberton, Michelle and Ungerer, Justin and Hollinshead, Whitney D and Gopalakrishnan, Saratram and He, Lian and Maranas, Costas D and Pakrasi, Himadri B and others},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@inproceedings{gopalakrishnan2017elucidation,
  title={Elucidation of Carbon Flux Topology Representing Photoautotrophic Growth in Synechocystis PCC 6803 Using Genome-Scale Isotopic Instationary Metabolic Flux Analysis},
  author={Gopalakrishnan, Saratram and Pakrasi, Himadri B and Maranas, Costas D},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@article{chan2017steadycom,
  title={SteadyCom: predicting microbial abundances while ensuring community stability},
  author={Chan, Siu Hung Joshua and Simons, Margaret N and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={13},
  number={5},
  pages={e1005539},
  year={2017},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{tiller2017facile,
  title={Facile affinity maturation of antibody variable domains using natural diversity mutagenesis},
  author={Tiller, Kathryn E and Chowdhury, Ratul and Li, Tong and Ludwig, Seth D and Sen, Sabyasachi and Maranas, Costas D and Tessier, Peter M},
  journal={Frontiers in immunology},
  volume={8},
  pages={986},
  year={2017},
  publisher={Frontiers Media SA}
}

@article{gopalakrishnan2017genome,
  title={Genome-scale mapping models and algorithms for stationary and instationary MFA-based metabolic flux elucidation},
  author={Gopalakrishnan, Saratram and Maranas, Costas D},
  year={2017}
}

@article{abernathy2017deciphering,
  title={Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis},
  author={Abernathy, Mary H and Yu, Jingjie and Ma, Fangfang and Liberton, Michelle and Ungerer, Justin and Hollinshead, Whitney D and Gopalakrishnan, Saratram and He, Lian and Maranas, Costas D and Pakrasi, Himadri B and others},
  journal={Biotechnology for biofuels},
  volume={10},
  number={1},
  pages={1--13},
  year={2017},
  publisher={BioMed Central}
}

@article{chan2017computational,
  title={Computational modeling of microbial communities},
  author={Chan, Siu HJ and Simons, Margaret and Maranas, Costas D},
  journal={Systems Biology},
  pages={163--189},
  year={2017},
  publisher={Wiley-VCH Verlag GmbH \& Co. KGaA Weinheim, Germany}
}

@article{poosarla2017computational,
  title={Computational de novo design of antibodies binding to a peptide with high affinity},
  author={Poosarla, Venkata Giridhar and Li, Tong and Goh, Boon Chong and Schulten, Klaus and Wood, Thomas K and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={114},
  number={6},
  pages={1331--1342},
  year={2017},
  publisher={Wiley Online Library}
}

@inproceedings{dash2017kinetic,
  title={Kinetic modeling of metabolism in clostridia},
  author={Dash, Satyakam and Khodayari, Ali and Stephanopoulos, Gregory and Lynd, Lee and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={253},
  year={2017},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{pistikopoulos2017multiscale,
  title={Multiscale Systems Engineering II-In Honor of Professor Christodoulos A. Floudas (Invited Talks)},
  author={Pistikopoulos, Efstratios N and Ierapetritou, Marianthi and Maranas, Costas D},
  booktitle={2017 AIChE Annual Meeting},
  year={2017},
  organization={AIChE}
}

@inproceedings{grisewood2016computational,
  title={Computational redesign of acyl-ACP thioesterase for medium-chain fatty acid production},
  author={Grisewood, Matthew and Hernandez-Lozada, Nestor and Pfleger, Brian and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={251},
  year={2016},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{dash2016metabolic,
  title={Metabolic modeling of clostridia: current developments and applications},
  author={Dash, Satyakam and Ng, Chiam Yu and Maranas, Costas D},
  journal={FEMS microbiology letters},
  volume={363},
  number={4},
  pages={fnw004},
  year={2016},
  publisher={Oxford University Press}
}

@article{ng2016microbial,
  title={A microbial factory for diverse chemicals},
  author={Ng, Chiam Yu and Chowdhury, Anupam and Maranas, Costas D},
  journal={Nature Biotechnology},
  volume={34},
  number={5},
  pages={513--515},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{soo2016reversing,
  title={Reversing methanogenesis to capture methane for liquid biofuel precursors},
  author={Soo, Valerie WC and McAnulty, Michael J and Tripathi, Arti and Zhu, Fayin and Zhang, Limin and Hatzakis, Emmanuel and Smith, Philip B and Agrawal, Saumya and Nazem-Bokaee, Hadi and Gopalakrishnan, Saratram and others},
  journal={Microbial cell factories},
  volume={15},
  number={1},
  pages={1--14},
  year={2016},
  publisher={BioMed Central}
}

@article{lihan2016novo,
  title={de novo Design and in silico Optimization of Antibody-Like Binders Targeting Ebola Viral Antigen},
  author={Lihan, Muyun and Goh, Boon Chong and Li, Tong and Maranas, Costas D and Shulten, Klaus},
  journal={Biophysical Journal},
  volume={110},
  number={3},
  pages={537a},
  year={2016},
  publisher={Elsevier}
}

@misc{zomorrodi2016optimization,
  title={Optimization methods in metabolic networks},
  author={Zomorrodi, Ali R and Maranas, Costas D},
  year={2016},
  publisher={John Wiley \& Sons}
}

@inproceedings{dash2016kinetic,
  title={Kinetic modeling of metabolism in obligatory anaerobes},
  author={Dash, S and Khodayari, A and Holwerda, EK and Olson, P and Theisen, M and Liao, JC and Stephanopoulos, G and Lynd, LR and Maranas, C},
  booktitle={11th Metabolic Engineering Conference 2016},
  pages={600--601},
  year={2016},
  organization={AIChE}
}

@article{mueller2016identifying,
  title={Identifying regulatory changes to facilitate nitrogen fixation in the nondiazotroph Synechocystis sp. PCC 6803},
  author={Mueller, Thomas J and Welsh, Eric A and Pakrasi, Himadri B and Maranas, Costas D},
  journal={ACS synthetic biology},
  volume={5},
  number={3},
  pages={250--258},
  year={2016},
  publisher={American Chemical Society}
}

@article{nazem2016assessing,
  title={Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans},
  author={Nazem-Bokaee, Hadi and Gopalakrishnan, Saratram and Ferry, James G and Wood, Thomas K and Maranas, Costas D},
  journal={Microbial cell factories},
  volume={15},
  number={1},
  pages={1--13},
  year={2016},
  publisher={BioMed Central}
}

@article{saha2016diurnal,
  title={Diurnal regulation of cellular processes in the cyanobacterium Synechocystis sp. strain PCC 6803: Insights from transcriptomic, fluxomic, and physiological analyses},
  author={Saha, Rajib and Liu, Deng and Hoynes-O’Connor, Allison and Liberton, Michelle and Yu, Jingjie and Bhattacharyya-Pakrasi, Maitrayee and Balassy, Andrea and Zhang, Fuzhong and Moon, Tae Seok and Maranas, Costas D and others},
  journal={MBio},
  volume={7},
  number={3},
  pages={e00464--16},
  year={2016},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@inproceedings{li2016development,
  title={Development and validation of computational methods for de novo design of antibody variable regions},
  author={Li, Tong and Poosarla, Venkata and Wood, Thomas and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={251},
  year={2016},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{khodayari2016genome,
  title={A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains},
  author={Khodayari, Ali and Maranas, Costas D},
  journal={Nature communications},
  volume={7},
  number={1},
  pages={1--12},
  year={2016},
  publisher={Nature Publishing Group}
}

@inproceedings{mueller2016hierarchy,
  title={A hierarchy of modeling frameworks for cyanobacterial metabolism: From gsms to ME models},
  author={Mueller, T and Simons, M and Maranas, CD and Gopalakrishnan, S and Pakrasi, HB},
  booktitle={Metabolic Engineering 11},
  pages={549--550},
  year={2016}
}

@article{zhang2016farnesoid,
  title={Farnesoid X receptor signaling shapes the gut microbiota and controls hepatic lipid metabolism},
  author={Zhang, Limin and Xie, Cen and Nichols, Robert G and Chan, Siu HJ and Jiang, Changtao and Hao, Ruixin and Smith, Philip B and Cai, Jingwei and Simons, Margaret N and Hatzakis, Emmanuel and others},
  journal={MSystems},
  volume={1},
  number={5},
  pages={e00070--16},
  year={2016},
  publisher={American Society for Microbiology 1752 N St., NW, Washington, DC}
}

@article{mueller2016metabolic,
  title={METABOLIC ENGINEERING 11},
  author={Mueller, T and Simons, M and Maranas, CD and Gopalakrishnan, S and Pakrasi, HB},
  journal={METABOLIC ENGINEERING},
  volume={11},
  pages={11},
  year={2016}
}

@inproceedings{dash2015development,
  title={Development of regulated metabolic models for anaerobic organisms},
  author={Dash, Satyakam and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={249},
  year={2015},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{gopalakrishnan2015achieving,
  title={Achieving metabolic flux analysis for S. cerevisiae at a genome-scale: challenges, requirements, and considerations},
  author={Gopalakrishnan, Saratram and Maranas, Costas D},
  journal={Metabolites},
  volume={5},
  number={3},
  pages={521--535},
  year={2015},
  publisher={MDPI}
}

@article{khodayari2015succinate,
  title={Succinate overproduction: a case study of computational strain design using a comprehensive Escherichia coli kinetic model},
  author={Khodayari, Ali and Chowdhury, Anupam and Maranas, Costas D},
  journal={Frontiers in bioengineering and biotechnology},
  volume={2},
  pages={76},
  year={2015},
  publisher={Frontiers Media SA}
}

@misc{ferry2015methane,
  title={Methane-to-acetate pathway for producing liquid biofuels and biorenewables},
  author={Ferry, James Gregory and Maranas, Costas D and Wood, Thomas Keith},
  year={2015},
  month=may # "~28",
  publisher={Google Patents},
  note={US Patent App. 14/550,547}
}

@article{ng2015advances,
  title={Advances in de novo strain design using integrated systems and synthetic biology tools},
  author={Ng, Chiam Yu and Khodayari, Ali and Chowdhury, Anupam and Maranas, Costas D},
  journal={Current opinion in chemical biology},
  volume={28},
  pages={105--114},
  year={2015},
  publisher={Elsevier}
}

@inproceedings{balassy2015transferring,
  title={Transferring nitrogen fixing capabilities to an oxygenic photosynthetic organism},
  author={Balassy, Andrea and Bhattacharyya, Maitrayee and Hoynes-O'Connor, Allison and Immethun, Cheryl and Liberton, Michelle and Liu, Deng and Mueller, Thomas and Xiao, Yi and Yu, Jingjie and Moon, Tae Seok and others},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={249},
  year={2015},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{gopalakrishnan201513c,
  title={13C metabolic flux analysis at a genome-scale},
  author={Gopalakrishnan, Saratram and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={32},
  pages={12--22},
  year={2015},
  publisher={Elsevier}
}

@article{pantazes2015iterative,
  title={The iterative protein redesign and optimization (IPRO) suite of programs},
  author={Pantazes, Robert J and Grisewood, Matthew J and Li, Tong and Gifford, Nathanael P and Maranas, Costas D},
  journal={Journal of computational chemistry},
  volume={36},
  number={4},
  pages={251--263},
  year={2015},
  publisher={Wiley Online Library}
}

@inproceedings{khodayari2015160,
  title={160. Improving computational strain design strategies by incorporation of kinetic information},
  author={Khodayari, Ali and Chowdhury, Anupam and Maranas, Costas D},
  booktitle={Genomic Science Contractors--Grantees Meeting XIII},
  pages={228},
  year={2015}
}

@article{ng2015rational,
  title={Rational design of a synthetic Entner--Doudoroff pathway for improved and controllable NADPH regeneration},
  author={Ng, Chiam Yu and Farasat, Iman and Maranas, Costas D and Salis, Howard M},
  journal={Metabolic engineering},
  volume={29},
  pages={86--96},
  year={2015},
  publisher={Elsevier}
}

@article{berla2015cyanobacterial,
  title={Cyanobacterial alkanes modulate photosynthetic cyclic electron flow to assist growth under cold stress},
  author={Berla, Bertram M and Saha, Rajib and Maranas, Costas D and Pakrasi, Himadri B},
  journal={Scientific reports},
  volume={5},
  number={1},
  pages={1--12},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{chowdhury2015bilevel,
  title={Bilevel optimization techniques in computational strain design},
  author={Chowdhury, Anupam and Zomorrodi, Ali R and Maranas, Costas D},
  journal={Computers \& Chemical Engineering},
  volume={72},
  pages={363--372},
  year={2015},
  publisher={Elsevier}
}

@article{ebrahim2015genome,
  title={Do genome-scale models need exact solvers or clearer standards?},
  author={Ebrahim, Ali and Almaas, Eivind and Bauer, Eugen and Bordbar, Aarash and Burgard, Anthony P and Chang, Roger L and Dr{\"a}ger, Andreas and Famili, Iman and Feist, Adam M and Fleming, Ronan MT and others},
  journal={Molecular systems biology},
  volume={11},
  number={10},
  pages={831},
  year={2015}
}

@article{chowdhury2015using,
  title={Using gene essentiality and synthetic lethality information to correct yeast and CHO cell genome-scale models},
  author={Chowdhury, Ratul and Chowdhury, Anupam and Maranas, Costas D},
  journal={Metabolites},
  volume={5},
  number={4},
  pages={536--570},
  year={2015},
  publisher={MDPI}
}

@misc{fendt2015editorial,
  title={Editorial overview: Systems biology: Advances diseases understanding and metabolic engineering},
  author={Fendt, Sarah-Maria and Maranas, Costas D},
  journal={Current opinion in biotechnology},
  volume={34},
  pages={v--vi},
  year={2015}
}

@article{chowdhury2015designing,
  title={Designing overall stoichiometric conversions and intervening metabolic reactions},
  author={Chowdhury, Anupam and Maranas, Costas D},
  journal={Scientific reports},
  volume={5},
  number={1},
  pages={1--20},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{mueller2015methane,
  title={Methane oxidation by anaerobic archaea for conversion to liquid fuels},
  author={Mueller, Thomas J and Grisewood, Matthew J and Nazem-Bokaee, Hadi and Gopalakrishnan, Saratram and Ferry, James G and Wood, Thomas K and Maranas, Costas D},
  journal={Journal of Industrial Microbiology and Biotechnology},
  volume={42},
  number={3},
  pages={391--401},
  year={2015},
  publisher={Oxford University Press}
}

@article{chowdhury2015personalized,
  title={Personalized Kinetic Models for Predictive Healthcare},
  author={Chowdhury, Anupam and Maranas, Costas D},
  journal={Cell systems},
  volume={1},
  number={4},
  pages={250--251},
  year={2015},
  publisher={Cell Press}
}

@inproceedings{khodayari2015development,
  title={Development of a comprehensive Escherichia coli kinetic metabolic model consistent with multiple genetic and environmental perturbations},
  author={Khodayari, Ali and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={249},
  year={2015},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{chowdhury2015improving,
  title={Improving prediction fidelity of cellular metabolism with kinetic descriptions},
  author={Chowdhury, Anupam and Khodayari, Ali and Maranas, Costas D},
  journal={Current opinion in biotechnology},
  volume={36},
  pages={57--64},
  year={2015},
  publisher={Elsevier}
}

@article{dash2014capturing,
  title={Capturing the response of Clostridium acetobutylicumto chemical stressors using a regulated genome-scale metabolic model},
  author={Dash, Satyakam and Mueller, Thomas J and Venkataramanan, Keerthi P and Papoutsakis, Eleftherios T and Maranas, Costas D},
  journal={Biotechnology for biofuels},
  volume={7},
  number={1},
  pages={1--16},
  year={2014},
  publisher={BioMed Central}
}

@inproceedings{li2014optmaven,
  title={OptMAVEn: De novo design of antibody variable regions},
  author={Li, Tong and Pantazes, Robert and Maranas, Costas D},
  booktitle={Food, Pharmaceutical and Bioengineering Division 2014-Core Programming Area at the 2014 AIChE Annual Meeting},
  pages={406--413},
  year={2014},
  organization={AIChE}
}

@article{tee2014systems,
  title={Systems metabolic engineering design: fatty acid production as an emerging case study},
  author={Tee, Ting Wei and Chowdhury, Anupam and Maranas, Costas D and Shanks, Jacqueline V},
  journal={Biotechnology and Bioengineering},
  volume={111},
  number={5},
  pages={849--857},
  year={2014}
}

@article{simons2014nitrogen,
  title={Nitrogen-use efficiency in maize (Zea mays L.): from ‘omics’ studies to metabolic modelling},
  author={Simons, Margaret and Saha, Rajib and Guillard, Lena{\"\i}g and Cl{\'e}ment, Gilles and Armengaud, Patrick and Ca{\~n}as, Rafael and Maranas, Costas D and Lea, Peter J and Hirel, Bertrand},
  journal={Journal of experimental botany},
  volume={65},
  number={19},
  pages={5657--5671},
  year={2014},
  publisher={Oxford University Press}
}

@article{khodayari2014kinetic,
  title={A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data},
  author={Khodayari, Ali and Zomorrodi, Ali R and Liao, James C and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={25},
  pages={50--62},
  year={2014},
  publisher={Elsevier}
}

@article{kumar2014clca,
  title={CLCA: maximum common molecular substructure queries within the MetRxn database},
  author={Kumar, Akhil and Maranas, Costas D},
  journal={Journal of chemical information and modeling},
  volume={54},
  number={12},
  pages={3417--3438},
  year={2014},
  publisher={ACS Publications}
}

@article{zomorrodi2014coarse,
  title={Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits},
  author={Zomorrodi, Ali R and Maranas, Costas D},
  journal={European Journal of Operational Research},
  volume={237},
  number={2},
  pages={665--676},
  year={2014},
  publisher={Elsevier}
}

@article{saha2014recent,
  title={Recent advances in the reconstruction of metabolic models and integration of omics data},
  author={Saha, Rajib and Chowdhury, Anupam and Maranas, Costas D},
  journal={Current opinion in biotechnology},
  volume={29},
  pages={39--45},
  year={2014},
  publisher={Elsevier}
}

@article{zomorrodi2014d,
  title={d-OptCom: dynamic multi-level and multi-objective metabolic modeling of microbial communities},
  author={Zomorrodi, Ali R and Islam, Mohammad Mazharul and Maranas, Costas D},
  journal={ACS synthetic biology},
  volume={3},
  number={4},
  pages={247--257},
  year={2014},
  publisher={ACS Publications}
}

@article{aumiller2014coupled,
  title={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},
  author={Aumiller Jr, William M and Davis, Bradley W and Hashemian, Negar and Maranas, Costas and Armaou, Antonios and Keating, Christine D},
  journal={The Journal of Physical Chemistry B},
  volume={118},
  number={9},
  pages={2506--2517},
  year={2014},
  publisher={ACS Publications}
}

@article{simons2014assessing,
  title={Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model},
  author={Simons, Margaret and Saha, Rajib and Amiour, Nardjis and Kumar, Akhil and Guillard, Lena{\"\i}g and Cl{\'e}ment, Gilles and Miquel, Martine and Li, Zhenni and Mouille, Gregory and Lea, Peter J and others},
  journal={Plant Physiology},
  volume={166},
  number={3},
  pages={1659--1674},
  year={2014},
  publisher={American Society of Plant Biologists}
}

@article{li2014optmaven,
  title={OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes},
  author={Li, Tong and Pantazes, Robert J and Maranas, Costas D},
  journal={PloS one},
  volume={9},
  number={8},
  pages={e105954},
  year={2014},
  publisher={Public Library of Science}
}

@article{chowdhury2014k,
  title={k-OptForce: integrating kinetics with flux balance analysis for strain design},
  author={Chowdhury, Anupam and Zomorrodi, Ali R and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={10},
  number={2},
  pages={e1003487},
  year={2014},
  publisher={Public Library of Science San Francisco, USA}
}

@inproceedings{entzminger2014novo,
  title={De novo antibody design by complementarity determining region modeling},
  author={Entzminger, Kevin C and Pantazes, Robert J and Maranas, Costas D and Maynard, Jennifer A},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={247},
  year={2014},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{simons2014assessing,
  title={Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model1 [C][W][OPEN]},
  author={Simons, Margaret and Saha, Rajib and Amiour, Nardjis and Kumar, Akhil and Guillard, Lena{\"\i}g and Cl{\'e}ment, Gilles and Miquel, Martine and Li, Zhenni and Mouille, Gregory and Lea, Peter J and others},
  year={2014}
}

@article{bates2014biotechnology,
  title={www. biotechnology-journal. com},
  author={Bates, Ron and Baneyx, Fran{\c{c}}ois and Borth, Nicole and Cabral, Joaquim and Canovas, Manuel and Chang, Jo-Shu and Chang, Matthew and Chen, Wen-Yih and Choo, Andre and Cirino, Patrick C and others},
  year={2014}
}

@article{grisewood2013optzyme,
  title={OptZyme: computational enzyme redesign using transition state analogues},
  author={Grisewood, Matthew J and Gifford, Nathanael P and Pantazes, Robert J and Li, Ye and Cirino, Patrick C and Janik, Michael J and Maranas, Costas D},
  journal={PloS one},
  volume={8},
  number={10},
  pages={e75358},
  year={2013},
  publisher={Public Library of Science}
}

@article{berla2013synthetic,
  title={Synthetic biology of cyanobacteria: unique challenges and opportunities},
  author={Berla, Bertram M and Saha, Rajib and Immethun, Cheryl M and Maranas, Costas D and Moon, Tae Seok and Pakrasi, Himadri B},
  journal={Frontiers in microbiology},
  volume={4},
  pages={246},
  year={2013},
  publisher={Frontiers Media SA}
}

@article{pantazes2013maps,
  title={MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies},
  author={Pantazes, Robert J and Maranas, Costas D},
  journal={BMC bioinformatics},
  volume={14},
  number={1},
  pages={1--13},
  year={2013},
  publisher={BioMed Central}
}

@inproceedings{grisewood2013transition,
  title={Transition state analogue-based computational enzyme design},
  author={Grisewood, M and Gifford, N and Janik, MJ and Maranas, CD},
  booktitle={Food, Pharmaceutical and Bioengineering Division 2013-Core Programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future},
  year={2013},
  organization={AIChE}
}

@article{mueller2013rapid,
  title={Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow},
  author={Mueller, Thomas J and Berla, Bertram M and Pakrasi, Himadri B and Maranas, Costas D},
  journal={BMC systems biology},
  volume={7},
  number={1},
  pages={1--12},
  year={2013},
  publisher={BioMed Central}
}

@misc{maranas2013method,
  title={Method for determining gene knockouts},
  author={Maranas, Costas D and Burgard, Anthony R and Pharkya, Priti},
  year={2013},
  month=jun # "~4",
  publisher={Google Patents},
  note={US Patent 8,457,941}
}

@article{zomorrodi2013optimization,
  title={Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks},
  author={Zomorrodi, Ali R and Lafontaine Rivera, Jimmy G and Liao, James C and Maranas, Costas D},
  journal={Biotechnology journal},
  volume={8},
  number={9},
  pages={1090--1104},
  year={2013},
  publisher={Wiley Online Library}
}

@article{maranas2013rapid,
  title={Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow},
  author={Maranas, Costas D and Pakrasi, Himadri B and Berla, Bertram M and Mueller, Thomas J},
  year={2013}
}

@article{saha2012reconstruction,
  title={Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803},
  author={Saha, Rajib and Verseput, Alex T and Berla, Bertram M and Mueller, Thomas J and Pakrasi, Himadri B and Maranas, Costas D},
  journal={PloS one},
  volume={7},
  number={10},
  pages={e48285},
  year={2012},
  publisher={Public Library of Science}
}

@article{zomorrodi2012optcom,
  title={OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities},
  author={Zomorrodi, Ali R and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={8},
  number={2},
  pages={e1002363},
  year={2012},
  publisher={Public Library of Science San Francisco, USA}
}

@techreport{maranas2012development,
  title={Development of Computational Tools for Metabolic Model Curation, Flux Elucidation and Strain Design},
  author={Maranas, Costas D},
  year={2012},
  institution={Pennsylvania State Univ., University Park, PA (United States)}
}

@misc{maranas2012method,
  title={Method for redesign of microbial production systems},
  author={Maranas, Costas D and Burgard, Anthony P and Pharkya, Priti},
  year={2012},
  month=jan # "~31",
  publisher={Google Patents},
  note={US Patent 8,108,152}
}

@article{zomorrodi2012mathematical,
  title={Mathematical optimization applications in metabolic networks},
  author={Zomorrodi, Ali R and Suthers, Patrick F and Ranganathan, Sridhar and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={14},
  number={6},
  pages={672--686},
  year={2012},
  publisher={Academic Press}
}

@article{kumar2012metrxn,
  title={MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases},
  author={Kumar, Akhil and Suthers, Patrick F and Maranas, Costas D},
  journal={BMC bioinformatics},
  volume={13},
  number={1},
  pages={1--13},
  year={2012},
  publisher={BioMed Central}
}

@article{ranganathan2012pubmed,
  title={PubMed ID 23036703},
  author={Ranganathan, Sridhar and Teeb, Ting Wei and Chowdhuryc, Anupam and Zomorrodic, Ali R and Yoon, Jong Moon and Fu, Yanfen and Shanksb, Jacqueline V and Maranas, Costas D},
  journal={Metabolic Engineering},
  year={2012}
}

@article{copeland2012computational,
  title={Computational tools for metabolic engineering},
  author={Copeland, Wilbert B and Bartley, Bryan A and Chandran, Deepak and Galdzicki, Michal and Kim, Kyung H and Sleight, Sean C and Maranas, Costas D and Sauro, Herbert M},
  journal={Metabolic engineering},
  volume={14},
  number={3},
  pages={270--280},
  year={2012},
  publisher={Academic Press}
}

@inproceedings{pantazes2012computational,
  title={Computational model of VDJ recombination for antibody design},
  author={Pantazes, Robert J and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={243},
  year={2012},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{brochado2012impact,
  title={Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks},
  author={Brochado, Ana Rita and Andrejev, Sergej and Maranas, Costas D and Patil, Kiran R},
  journal={PLoS computational biology},
  volume={8},
  number={11},
  pages={e1002758},
  year={2012},
  publisher={Public Library of Science San Francisco, USA}
}

@article{suthers2012orchestrating,
  title={Orchestrating hi-fi annotations},
  author={Suthers, Patrick F and Maranas, Costas D},
  journal={Nature Chemical Biology},
  volume={8},
  number={10},
  pages={810--811},
  year={2012},
  publisher={Nature Publishing Group}
}

@inproceedings{ranganathan2012using,
  title={Using OptForce to customize metabolic interventions for the overproduction of fatty acids C6 through C16 in Escherichia coli},
  author={Ranganathan, Sridhar and Wang, Ting Wei and Welsh, Jesse and Yoon, Jong Moon and Shanks, Jacqueline V and San, Ka-Yiu and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={243},
  year={2012},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{saha2012contrasting,
  title={Contrasting the metabolic capabilities of cyanobacterial species for assessing bio-production platform selection},
  author={Saha, Rajib and Berla, Bertram M and Mueller, Thomas and Elvitigala, Thanura and Page, Lawrence E and Pakrasi, Himadri B and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={243},
  year={2012},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{ranganathan2012integrated,
  title={An integrated computational and experimental study for overproducing fatty acids in Escherichia coli},
  author={Ranganathan, Sridhar and Tee, Ting Wei and Chowdhury, Anupam and Zomorrodi, Ali R and Yoon, Jong Moon and Fu, Yanfen and Shanks, Jacqueline V and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={14},
  number={6},
  pages={687--704},
  year={2012},
  publisher={Elsevier}
}

@article{pantazes2011recent,
  title={Recent advances in computational protein design},
  author={Pantazes, Robert J and Grisewood, Matthew J and Maranas, Costas D},
  journal={Current opinion in structural biology},
  volume={21},
  number={4},
  pages={467--472},
  year={2011},
  publisher={Elsevier}
}

@article{vital2011modeling,
  title={Modeling the effect of chemotaxis on glioblastoma tumor progression},
  author={Vital-Lopez, Francisco G and Armaou, Antonios and Hutnik, Michelle and Maranas, Costas D},
  journal={AIChE journal},
  volume={57},
  number={3},
  pages={778--792},
  year={2011},
  publisher={Wiley Online Library}
}

@article{xu2011genome,
  title={Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA},
  author={Xu, Peng and Ranganathan, Sridhar and Fowler, Zachary L and Maranas, Costas D and Koffas, Mattheos AG},
  journal={Metabolic engineering},
  volume={13},
  number={5},
  pages={578--587},
  year={2011},
  publisher={Elsevier}
}

@inproceedings{vital2011modeling,
  title={Modeling the effect of temozolomide treatment on orthotopic models of glioma},
  author={Vital-Lopez, Francisco G and Maranas, Costas D and Armaou, Antonios},
  booktitle={Proceedings of the 2011 American Control Conference},
  pages={2969--2974},
  year={2011},
  organization={IEEE}
}

@article{satish2011metabolic,
  title={Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans},
  author={Satish Kumar, Vinay and Ferry, James G and Maranas, Costas D},
  journal={BMC systems biology},
  volume={5},
  number={1},
  pages={1--10},
  year={2011},
  publisher={BioMed Central}
}

@inproceedings{kumar2011metrxn,
  title={MetRxn\&: reaction and metabolite standardization and congruency across databases and genome-scale metabolic models},
  author={Kumar, Akhil and Suthers, P and Maranas, CD},
  booktitle={GTL Conference},
  pages={1--2},
  year={2011}
}

@inproceedings{koffas2011rational,
  title={Rational design of recombinant phytochemical microbial producers},
  author={Koffas, Mattheos and Maranas, Costas},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={241},
  year={2011},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{saha2011zea,
  title={Zea mays i RS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism},
  author={Saha, Rajib and Suthers, Patrick F and Maranas, Costas D},
  journal={PloS one},
  volume={6},
  number={7},
  pages={e21784},
  year={2011},
  publisher={Public Library of Science}
}

@inproceedings{xu2011integrated,
  title={An integrated computational and experimental study to increase the intra-cellular malonyl-CoA: application to flavanone synthesis},
  author={Xu, Peng and Ranganathan, Sridhar and Maranas, Costas D and Koffas, Mattheos},
  booktitle={2011 IEEE 37th Annual Northeast Bioengineering Conference (NEBEC)},
  pages={1--2},
  year={2011},
  organization={IEEE}
}

@techreport{maranas2011method,
  title={Method for determining gene knockouts},
  author={Maranas, Costas D and Burgard, Anthony R and Pharkya, Priti},
  year={2011},
  institution={Genomatica Inc}
}

@article{khanna2011model,
  title={Model simulations reveal VCAM-1 augment PAK activation rates to amplify p38 MAPK and VE-cadherin phosphorylation},
  author={Khanna, Payal and Weidert, Eric and Vital-Lopez, Francisco and Armaou, Antonios and Maranas, Costas D and Dong, Cheng},
  journal={Cellular and Molecular Bioengineering},
  volume={4},
  number={4},
  pages={656--669},
  year={2011},
  publisher={Springer US}
}

@misc{maranas2011method,
  title={Method for determining gene knockouts},
  author={Maranas, Costas D and Burgard, Anthony R and Pharkya, Priti},
  year={2011},
  month=sep # "~27",
  publisher={Google Patents},
  note={US Patent 8,027,821}
}

@article{ravikirthi2011construction,
  title={Construction of an E. Coli genome-scale atom mapping model for MFA calculations},
  author={Ravikirthi, Prabhasa and Suthers, Patrick F and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={108},
  number={6},
  pages={1372--1382},
  year={2011},
  publisher={Wiley Online Library}
}

@misc{maranas2011method,
  title={Method and system for modeling cellular metabolism},
  author={Maranas, Costas D and Burgard, Anthony P},
  year={2011},
  month=dec # "~27",
  publisher={Google Patents},
  note={US Patent 8,086,414}
}

@article{maranas2011metabolic,
  title={Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans},
  author={Maranas, Costas D and Ferry, James G and Kumar, Vinay Satish},
  year={2011}
}

@article{antoniewicz2011biotechnology,
  title={www. biotechnology-journal. com},
  author={Antoniewicz, Maciek R and Bates, Ron and Cabral, Joaquim and Canovas, Manuel and Chang, Jo-Shu and Chang, Matthew and Chen, Wen-Yih and Choo, Andre and Cirino, Patrick C and Cowan, Don and others},
  year={2011}
}

@misc{maranas2010method,
  title={Method and system for modeling cellular metabolism},
  author={Maranas, Costas D and Burgard, Anthony P},
  year={2010},
  month=may # "~4",
  publisher={Google Patents},
  note={US Patent 7,711,490}
}

@article{dash2010ensemble,
  title={Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production},
  author={Dash, Satyakam and Khodayari, Ali and Holwerda, Evert K and Olson, Daniel G and Islam, M Ahsanul and Theisen, Matthew and Liao, James C and Stephanopoulos, Gregory and Lynd, Lee R and Maranas, Costas D},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  volume={107},
  number={29},
  pages={13087--92},
  year={2010}
}

@article{suthers2010improved,
  title={Improved computational performance of MFA using elementary metabolite units and flux coupling},
  author={Suthers, Patrick F and Chang, Young J and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={12},
  number={2},
  pages={123--128},
  year={2010},
  publisher={Elsevier}
}

@article{ranganathan2010optforce,
  title={OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions},
  author={Ranganathan, Sridhar and Suthers, Patrick F and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={6},
  number={4},
  pages={e1000744},
  year={2010},
  publisher={Public Library of Science San Francisco, USA}
}

@inproceedings{ranganathan2010identification,
  title={Identification of non-native routes and engineering interventions for the microbial production of long-chain alcohols},
  author={Ranganathan, Sridhar and Suthers, Patrick F and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={239},
  year={2010},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{zomorrodi2010improving,
  title={Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data},
  author={Zomorrodi, Ali R and Maranas, Costas D},
  journal={BMC systems biology},
  volume={4},
  number={1},
  pages={1--15},
  year={2010},
  publisher={BioMed Central}
}

@article{ranganathan2010microbial,
  title={Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions},
  author={Ranganathan, Sridhar and Maranas, Costas D},
  journal={Biotechnology journal},
  volume={5},
  number={7},
  pages={716--725},
  year={2010},
  publisher={Wiley Online Library}
}

@misc{maranas2010method,
  title={Method for redesign of microbial production systems},
  author={Maranas, Costas D and Burgard, Anthony P and Pharkya, Priti},
  year={2010},
  month=nov # "~2",
  publisher={Google Patents},
  note={US Patent 7,826,975}
}

@article{pantazes2010optcdr,
  title={OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding},
  author={Pantazes, RJ and Maranas, Costas D},
  journal={Protein Engineering, Design \& Selection},
  volume={23},
  number={11},
  pages={849--858},
  year={2010},
  publisher={Oxford University Press}
}

@article{maranas2009modeling,
  title={Modeling Tools for Metabolic Engineering},
  author={Maranas, Costas D},
  journal={The Metabolic Pathway Engineering Handbook: Fundamentals},
  volume={1},
  year={2009},
  publisher={CRC Press}
}

@inproceedings{suthers2009biot,
  title={BIOT 200-Using computations to reconstruct, analyze, and redesign metabolism},
  author={Suthers, Patrick F and Zomorrodi, Alireza and Ranganathan, Sridhar and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={238},
  year={2009},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{suthers2009genome,
  title={A genome-scale metabolic reconstruction of Mycoplasma genitalium, i PS189},
  author={Suthers, Patrick F and Dasika, Madhukar S and Kumar, Vinay Satish and Denisov, Gennady and Glass, John I and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={5},
  number={2},
  pages={e1000285},
  year={2009},
  publisher={Public Library of Science San Francisco, USA}
}

@article{kumar2009growmatch,
  title={GrowMatch: an automated method for reconciling in silico/in vivo growth predictions},
  author={Kumar, Vinay Satish and Maranas, Costas D},
  journal={PLoS computational biology},
  volume={5},
  number={3},
  pages={e1000308},
  year={2009},
  publisher={Public Library of Science San Francisco, USA}
}

@article{abuoun2009genome,
  title={Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain},
  author={AbuOun, Manal and Suthers, Patrick F and Jones, Gareth I and Carter, Ben R and Saunders, Mark P and Maranas, Costas D and Woodward, Martin J and Anjum, Muna F},
  journal={Journal of Biological Chemistry},
  volume={284},
  number={43},
  pages={29480--29488},
  year={2009},
  publisher={Elsevier}
}

@article{fazelinia2009optgraft,
  title={OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold},
  author={Fazelinia, Hossein and Cirino, Patrick C and Maranas, Costas D},
  journal={Protein Science},
  volume={18},
  number={1},
  pages={180--195},
  year={2009},
  publisher={Wiley Online Library}
}

@article{khoury2009computational,
  title={Computational design of Candida boidinii xylose reductase for altered cofactor specificity},
  author={Khoury, George A and Fazelinia, Hossein and Chin, Jonathan W and Pantazes, Robert J and Cirino, Patrick C and Maranas, Costas D},
  journal={Protein Science},
  volume={18},
  number={10},
  pages={2125--2138},
  year={2009},
  publisher={Wiley Online Library}
}

@article{suthers2009genome,
  title={Genome-scale gene/reaction essentiality and synthetic lethality analysis},
  author={Suthers, Patrick F and Zomorrodi, Alireza and Maranas, Costas D},
  journal={Molecular systems biology},
  volume={5},
  number={1},
  pages={301},
  year={2009},
  publisher={John Wiley \& Sons, Ltd Chichester, UK}
}

@inproceedings{fazelinia2009biot,
  title={BIOT 94-Computational enzyme redesign for cofactor/substrate specificity},
  author={Fazelinia, Hossein and Khoury, George A and Cirino, Patrick C and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={238},
  year={2009},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{chin2009analysis,
  title={Analysis of NADPH supply during xylitol production by engineered Escherichia coli},
  author={Chin, Jonathan W and Khankal, Reza and Monroe, Caroline A and Maranas, Costas D and Cirino, Patrick C},
  journal={Biotechnology and bioengineering},
  volume={102},
  number={1},
  pages={209--220},
  year={2009},
  publisher={Wiley Online Library}
}

@incollection{suthers2009using,
  title={Using Systems Engineering to Reconstruct, Analyze and Redesign Metabolism},
  author={Suthers, Patrick F and Kumar, Vinay Satish and Zomorrodi, Alireza and Ranganathan, Sridhar and Maranas, Costas D},
  booktitle={Computer Aided Chemical Engineering},
  volume={27},
  pages={113--115},
  year={2009},
  publisher={Elsevier}
}

@article{lee2009designing,
  title={Designing the substrate specificity of D-hydantoinase using a rational approach},
  author={Lee, Sang-Chul and Chang, YoungJung and Shin, Dong-Min and Han, Jieun and Seo, Moon-Hyeong and Fazelinia, Hossein and Maranas, Costas D and Kim, Hak-Sung},
  journal={Enzyme and Microbial Technology},
  volume={44},
  number={3},
  pages={170--175},
  year={2009},
  publisher={Elsevier}
}

@inproceedings{fazelinia2008biot,
  title={BIOT 73-Experimental characterization of a de novo designed calcium binding site},
  author={Fazelinia, Hossein and Cinno, Patrick C and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={236},
  year={2008},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{maranas2008using,
  title={Using Computations to Reconstruct, Analyze and Redesign Metabolic Systems},
  author={Maranas, Costas},
  booktitle={The 2008 Annual Meeting},
  year={2008}
}

@article{chang2008identification,
  title={Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments},
  author={Chang, YoungJung and Suthers, Patrick F and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={100},
  number={6},
  pages={1039--1049},
  year={2008},
  publisher={Wiley Online Library}
}

@inproceedings{chang2008complete,
  title={Complete Flux Elucidation Using Metabolic Flux Analysis},
  author={Chang, Young Jung and Suthers, Patrick F and Maranas, Costas D},
  booktitle={2008 AIChE Annual Meeting, AIChE 100},
  year={2008}
}

@inproceedings{vital2008modeling,
  title={Modeling the Effect of a Crowding Agent on the Activity of Enzyme-Au Bioconjugates},
  author={Vital-Lopez, Francisco G and Keighron, Jacqueline and Keating, Christine D and Maranas, Costas D and Armaou, Antonios},
  booktitle={2008 AIChE Annual Meeting, AIChE 100},
  year={2008}
}

@inproceedings{suthers2008biot,
  title={BIOT 293-Genome-scale model of a minimal organism: Mycoplasma genitalium},
  author={Suthers, Patrick F and Dasika, Madhukar S and Kumar, Vinay Satish and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={236},
  year={2008},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{ranganathan2008exhaustive,
  title={Exhaustive Identification of All Engineering Interventions Leading to Targeted Overproductions},
  author={Ranganathan, Sridhar and Suthers, Patrick F and Maranas, Costas D},
  booktitle={The 2008 Annual Meeting},
  year={2008}
}

@inproceedings{chang2008identification,
  title={Identification of Optimal Measurement Sets for Isotopically Non-Stationary Mfa Experiments},
  author={Chang, Young Jung and Suthers, Patrick and Maranas, Costas D},
  booktitle={2008 AIChE Annual Meeting, AIChE 100},
  year={2008}
}

@inproceedings{khoury2008computational,
  title={Computational Analysis and Design for Altered Cofactor Specificity},
  author={Khoury, George A and Fazelinia, Hossein Z and Maranas, Costas D},
  booktitle={2008 AIChE Annual Meeting, AIChE 100},
  year={2008}
}

@inproceedings{tang2008biot,
  title={BIOT 12-AraC regulatory protein mutants with altered effector specificity},
  author={Tang, Shuang-Yan and Fazelinia, Hossein and Maranas, Costas D and Cirino, Patrick C},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={236},
  year={2008},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{dasika2008optcircuit,
  title={OptCircuit: an optimization based method for computational design of genetic circuits},
  author={Dasika, Madhukar S and Maranas, Costas D},
  journal={BMC systems biology},
  volume={2},
  number={1},
  pages={1--19},
  year={2008},
  publisher={BioMed Central}
}

@article{vital2008implication,
  title={Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks},
  author={Vital-Lopez, Francisco G and Varshney, Amit and Maranas, Costas D and Armaou, Antonios},
  journal={Computers \& Chemical Engineering},
  volume={32},
  number={9},
  pages={2065--2071},
  year={2008},
  publisher={Elsevier}
}

@article{vital2008hybrid,
  title={Hybrid multi-scale modeling of brain tumor progression},
  author={Vital-Lopez, Francisco G and Maranas, Costas D and Armaou, Antonios},
  year={2008}
}

@inproceedings{zomorrodi2008computational,
  title={Computational Analysis of Synthetic Gene/reaction Lethality In E. coli},
  author={Zomorrodi, Alireza and Suthers, Patrick F and Maranas, Costas D},
  booktitle={The 2008 Annual Meeting},
  year={2008}
}

@article{gianchandani2008predicting,
  title={Predicting biological system objectives de novo from internal state measurements},
  author={Gianchandani, Erwin P and Oberhardt, Matthew A and Burgard, Anthony P and Maranas, Costas D and Papin, Jason A},
  journal={BMC bioinformatics},
  volume={9},
  number={1},
  pages={1--13},
  year={2008},
  publisher={BioMed Central}
}

@inproceedings{suthers2007metabolic,
  title={Metabolic Map Of Metabolism For Mycoplasma genitalium},
  author={Suthers, Patrick F and Dasika, Madhukar S and Maranas, Costas D},
  booktitle={The 2007 Annual Meeting},
  year={2007}
}

@inproceedings{fazelinia2007biot,
  title={BIOT 429-Computational procedure for transferring new binding sites into existing protein scaffolds},
  author={Fazelinia, Hossein and Cirino, Patrick C and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={234},
  year={2007},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{suthers2007metabolic,
  title={Metabolic flux elucidation for large-scale models using 13C labeled isotopes},
  author={Suthers, Patrick F and Burgard, Anthony P and Dasika, Madhukar S and Nowroozi, Farnaz and Van Dien, Stephen and Keasling, Jay D and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={9},
  number={5-6},
  pages={387--405},
  year={2007},
  publisher={Elsevier}
}

@inproceedings{fazelinia2007computational,
  title={Computational procedure for transferring binding site into a protein scaffold},
  author={Fazelinia, Hossein and Maranas, Costas D},
  booktitle={BIOPHYSICAL JOURNAL},
  pages={203A--203A},
  year={2007},
  organization={BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998 USA}
}

@inproceedings{chang2007integer,
  title={An Integer Programming Approach For The Measurement Set Identifiability Problem In Metabolic Flux Analysis},
  author={Chang, YoungJung and Suthers, Patrick F and Maranas, Costas D},
  booktitle={The 2007 Annual Meeting},
  year={2007}
}

@article{satish2007optimization,
  title={Optimization based automated curation of metabolic reconstructions},
  author={Satish Kumar, Vinay and Dasika, Madhukar S and Maranas, Costas D},
  journal={BMC bioinformatics},
  volume={8},
  number={1},
  pages={1--16},
  year={2007},
  publisher={BioMed Central}
}

@inproceedings{kumar2007biot,
  title={BIOT 181-Elucidating and filling gaps in genome-scale metabolic networks},
  author={Kumar, Vinay Satish and Dasika, Madhukar S and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={234},
  year={2007},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{cirino2007biot,
  title={BIOT 343-Designing AraC effector specificity through modeling and dual selection},
  author={Cirino, Patrick C and Tang, Shuang-Yan and Fazelinia, Hossein and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={234},
  year={2007},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{fazelinia2007extending,
  title={Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity},
  author={Fazelinia, Hossein and Cirino, Patrick C and Maranas, Costas D},
  journal={Biophysical journal},
  volume={92},
  number={6},
  pages={2120--2130},
  year={2007},
  publisher={Elsevier}
}

@inproceedings{fazelinia2007introducing,
  title={Introducing A Systematic Computational Approach To Graft A Novel Binding Site Into A Protein With A Known Scaffold},
  author={Fazelinia, Hossein and Cirino, Patrick C and Maranas, Costas D},
  booktitle={The 2007 Annual Meeting},
  year={2007}
}

@inproceedings{suthers2007biot,
  title={BIOT 172-Metabolic flux elucidation for large-scale models: 13C labeled isotope experiments and experimental design},
  author={Suthers, Patrick F and Burgard, Anthony P and Dasika, Madhukar S and Nowroozi, Farnaz and Van Dien, Stephen and Keasling, Jay D and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={234},
  year={2007},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{maranas2007computational,
  title={Computational Protein Engineering},
  author={Maranas, Costas},
  journal={한국생물공학회 학술대회},
  pages={40--40},
  year={2007}
}

@article{pantazes2007optimal,
  title={Optimal protein library design using recombination or point mutations based on sequence-based scoring functions},
  author={Pantazes, Robert J and Saraf, Manish C and Maranas, Costas D},
  journal={Protein Engineering, Design \& Selection},
  volume={20},
  number={8},
  pages={361--373},
  year={2007},
  publisher={Oxford University Press}
}

@article{christensen2007large,
  title={Large-scale inference and graph-theoretical analysis of gene-regulatory networks in B. Subtilis},
  author={Christensen, Claire and Gupta, Anshuman and Maranas, Costas D and Albert, R{\'e}ka},
  journal={Physica A: Statistical Mechanics and its Applications},
  volume={373},
  pages={796--810},
  year={2007},
  publisher={Elsevier}
}

@inproceedings{suthers2007metabolic,
  title={Metabolic Flux Elucidation For Large-Scale Models: 13 C Labeled Isotope Analysis Of A Strain Of Escherichia coli Producing Amorphadiene},
  author={Suthers, Patrick F and Burgard, Anthony and Nowroozi, Farnaz and Van Dien, Stephen and Keasling, Jay D and Maranas, Costas D},
  booktitle={The 2007 Annual Meeting},
  year={2007}
}

@inproceedings{vital2007signal,
  title={Signal Transduction and Targeted Disruption Analyses Using Kinetic Models of Signaling Networks},
  author={Vital-Lopez, Francisco G and Varshney, Amit and Maranas, Costas D and Armaou, Antonios},
  booktitle={The 2007 Annual Meeting},
  year={2007}
}

@inproceedings{kumar2007optimization,
  title={An Optimization Based Method To Automatically Reconcile In Silico/in Vivo Growth Predictions},
  author={Kumar, Vinay S and Maranas, Costas D},
  booktitle={The 2007 Annual Meeting},
  year={2007}
}

@article{dasika2006edited,
  title={This un-edited manuscript has been accepted for publication in Biophysical Journal and is freely available on BioFast at http://www. biophysj. org. The final copyedited version of the paper may be found at http://www. biophysj. org.},
  author={Dasika, Madhukar S and Burgard, Anthony and Maranas, Costas D},
  year={2006},
  publisher={Citeseer}
}

@article{pharkya2006optimization,
  title={An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems},
  author={Pharkya, Priti and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={8},
  number={1},
  pages={1--13},
  year={2006},
  publisher={Elsevier}
}

@inproceedings{suthers2006metabolic,
  title={Metabolic Flux Elucidation for Genome-Scale Models Using 13 C Labeled Isotopes},
  author={Suthers, Patrick F and Burgard, Anthony and Dasika, Madhukar S and Nowroozi, Farnaz and Van Dien, Stephen and Keasling, Jay D and Maranas, Costas D},
  booktitle={The 2006 Annual Meeting},
  year={2006}
}

@article{vital2006computational,
  title={A computational procedure for optimal engineering interventions using kinetic models of metabolism},
  author={Vital-Lopez, Francisco G and Armaou, Antonios and Nikolaev, Evgeni V and Maranas, Costas D},
  journal={Biotechnology progress},
  volume={22},
  number={6},
  pages={1507--1517},
  year={2006},
  publisher={Wiley Online Library}
}

@inproceedings{fazelinia2006computation,
  title={Computation-Guided Design of Arac Regulatory Protein Effector Specificity},
  author={Fazelinia, Hossein and Cirino, Patrick C and Maranas, Costas D},
  booktitle={The 2006 Annual Meeting},
  year={2006}
}

@inproceedings{vital2006bifurcation,
  title={Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels},
  author={Vital-Lopez, Francisco G and Maranas, Costas D and Armaou, Antonios},
  booktitle={2006 American Control Conference},
  pages={6--pp},
  year={2006},
  organization={IEEE}
}

@inproceedings{dasika2006biot,
  title={BIOT 93-Computational design of synthetic biological circuits},
  author={Dasika, Madhukar S and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={232},
  year={2006},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{chin2006understanding,
  title={Understanding Cofactor Partitioning in Xylitol-Producing Escherichia Coli Expressing Xylose Reductase},
  author={Chin, Jonathan W and Maranas, Costas D and Cirino, Patrick C},
  booktitle={The 2006 Annual Meeting},
  year={2006}
}

@inproceedings{christensen2006inference,
  title={Inference and analysis of gene-regulatory networks in the bacterium B. subtilis},
  author={Christensen, Claire and Gupta, Anshuman and Albert, Reka and Maranas, Costas},
  booktitle={APS March Meeting Abstracts},
  pages={W29--009},
  year={2006}
}

@article{gupta2006elucidation,
  title={Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites},
  author={Gupta, Anshuman and Maranas, Costas D and Albert, R{\'e}ka},
  journal={Bioinformatics},
  volume={22},
  number={2},
  pages={209--214},
  year={2006},
  publisher={Oxford University Press}
}

@inproceedings{fazelinia2006biot,
  title={BIOT 50-Computational design and experimental characterization of AraC regulatory protein with novel effector specificity},
  author={Fazelinia, Hossein and Cirino, Patrick C and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={232},
  year={2006},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{saraf2006ipro,
  title={IPRO: an iterative computational protein library redesign and optimization procedure},
  author={Saraf, Manish C and Moore, Gregory L and Goodey, Nina M and Cao, Vania Y and Benkovic, Stephen J and Maranas, Costas D},
  journal={Biophysical journal},
  volume={90},
  number={11},
  pages={4167--4180},
  year={2006},
  publisher={Elsevier}
}

@article{dasika2006computational,
  title={A computational framework for the topological analysis and targeted disruption of signal transduction networks},
  author={Dasika, Madhukar S and Burgard, Anthony and Maranas, Costas D},
  journal={Biophysical journal},
  volume={91},
  number={1},
  pages={382--398},
  year={2006},
  publisher={Elsevier}
}

@inproceedings{chin2006biot,
  title={BIOT 185-Understanding cofactor partitioning in xylitol-producing Escherichia coli expressing xylose reductase},
  author={Chin, Jonathan W and Maranas, Costas D and Cirino, Patrick C},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={232},
  year={2006},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{pharkya2006development,
  title={Development of Computational tools for Analyzing and Redesigning Biological Networks},
  author={Pharkya, Priti and Dasika, Madhukar and Kumar, Vinay Satish and Veeraghavan, Narayanan and Suthers, Patrick and Burgard, Anthony and Maranas, Costas D},
  booktitle={Proc. of Genomics: GTL Contractor-Grantee Workshop IV},
  pages={125--126},
  year={2006}
}

@inproceedings{suthers2006biot,
  title={BIOT 7-Metabolic flux elucidation using 13C labeled isotopes for genome-scale models},
  author={Suthers, Patrick F and Burgard, Anthony P and Dasika, Madhukar S and Nowroozi, Farnaz and Van Dien, Stephen and Keasling, Jay D and Maranas, Costas D},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={232},
  year={2006},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{gupta2005large,
  title={Large-scale inference of the transcriptional regulation of Bacillus subtilis},
  author={Gupta, Anshuman and Varner, Jeffrey D and Maranas, Costas D},
  journal={Computers \& chemical engineering},
  volume={29},
  number={3},
  pages={565--576},
  year={2005},
  publisher={Elsevier}
}

@article{fong2005silico,
  title={In silico design and adaptive evolution of Escherichia coli for production of lactic acid},
  author={Fong, Stephen S and Burgard, Anthony P and Herring, Christopher D and Knight, Eric M and Blattner, Frederick R and Maranas, Costas D and Palsson, Bernhard O},
  journal={Biotechnology and bioengineering},
  volume={91},
  number={5},
  pages={643--648},
  year={2005},
  publisher={Wiley Online Library}
}

@inproceedings{maranas2005hierarchical,
  title={Hierarchical" top-down" and" bottom-up" framework for regulatory network elucidation and verification.},
  author={Maranas, CD and Dasika, MS and Gupta, A},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={229},
  pages={U195--U195},
  year={2005},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@article{gabbar2005frewen,
  title={Frewen, TA, 713 Friehs, K., 1113 Froment, G., 2265},
  author={Gabbar, HA and Gallivan, MA and Gesthuisen, R and Ghaeli, M and Ghosh, S and Gill, RT and Gilles, ED and Glasser, D and Gombert, AK and Gonye, GE and others},
  journal={Computers and Chemical Engineering},
  volume={29},
  pages={2494--2496},
  year={2005}
}

@inproceedings{fong2005metabolic,
  title={Metabolic engineering of Escherichia coli through in silico design and experimental evolution},
  author={Fong, Stephen S and Burgard, Anthony and Maranas, Costas D and Palsson, Bernhard O},
  booktitle={05AIChE: 2005 AIChE Annual Meeting and Fall Showcase},
  year={2005}
}

@inproceedings{vital2005sensitivity,
  title={Sensitivity and bifurcation analysis of the metabolism of escherichia coli at optimal enzyme levels},
  author={Vital-Lopez, Francisco G and Maranas, Costas D and Armaou, Antonios},
  booktitle={05AIChE: 2005 AIChE Annual Meeting and Fall Showcase},
  year={2005}
}

@inproceedings{nikolaev2005general,
  title={A general hybrid optimization framework for the optimal modulation of enzyme levels using large-scale kinetic models of bacterial metabolism},
  author={Nikolaev, Evgeni and Pharkya, Priti and Armaou, Antonios and Maranas, Costas D},
  booktitle={05AIChE: 2005 AIChE Annual Meeting and Fall Showcase},
  year={2005}
}

@article{rogers2005valuation,
  title={Valuation and design of pharmaceutical R\&D licensing deals},
  author={Rogers, Michael J and Maranas, Costas D and Ding, Min},
  journal={AIChE Journal},
  volume={51},
  number={1},
  pages={198--209},
  year={2005},
  publisher={Wiley Online Library}
}

@article{saraf2005456b,
  title={456b Ipro: Iterative Protein Redesign and Optimization Procedure: Application to Three Case-Studies},
  author={Saraf, Manish C and Brian, A and Maranas, Costas D},
  year={2005}
}

@article{dasika2005demsim,
  title={DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics},
  author={Dasika, Madhukar S and Gupta, Anshuman and Maranas, Costas D},
  journal={Journal of theoretical biology},
  volume={232},
  number={1},
  pages={55--69},
  year={2005},
  publisher={Elsevier}
}

@inproceedings{dasika2005optimization,
  title={Optimization-based strategies for the systematic analysis and therapeutic disruption of signal transduction networks},
  author={Dasika, Madhukar S and Burgard, Anthony P and Maranas, Costas D},
  booktitle={05AIChE: 2005 AIChE Annual Meeting and Fall Showcase},
  year={2005}
}

@article{maranas2005systems,
  title={Systems Engineering Challenges and Opportunities in Biology-Preface},
  author={Maranas, C and Hatzimanikatis, V},
  journal={Computers \& Chemical Engineering},
  volume={29},
  number={3},
  pages={405--406},
  year={2005},
  publisher={Elsevier Science}
}

@article{maranas2005computers,
  title={Computers and Chemical Engineering: Preface},
  author={Maranas, C and Hatzimanikatis, V},
  journal={Computers and Chemical Engineering},
  volume={29},
  number={3},
  pages={405--406},
  year={2005},
  publisher={Elsevier BV}
}

@article{gupta2005department,
  title={Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA},
  author={Gupta, Anshuman and Varner, Jeffrey D and Maranas, Costas D},
  journal={Computers and Chemical Engineering},
  volume={29},
  number={3},
  pages={565--576},
  year={2005},
  publisher={Oxford; New York: Pergamon Press, 1977-}
}

@article{saraf2005design,
  title={Design of combinatorial protein libraries of optimal size},
  author={Saraf, Manish C and Gupta, Anshuman and Maranas, Costas D},
  journal={Proteins: Structure, function, and bioinformatics},
  volume={60},
  number={4},
  pages={769--777},
  year={2005},
  publisher={Wiley Online Library}
}

@article{nikolaev2005optimal,
  title={Optimal selection of enzyme levels using large-scale kinetic models},
  author={Nikolaev, Evgeni V and Pharkya, Priti and Maranas, Costas D and Armaou, Antonios},
  journal={IFAC Proceedings Volumes},
  volume={38},
  number={1},
  pages={25--30},
  year={2005},
  publisher={Elsevier}
}

@inproceedings{pharkya2005optimization,
  title={An optimization framework for elucidating maximization hypotheses in metabolic network flux distribution},
  author={Pharkya, Priti and Burgard, Anthony P and Maranas, Costas D},
  booktitle={05AIChE: 2005 AIChE Annual Meeting and Fall Showcase},
  year={2005}
}

@article{nikolaev2005elucidation,
  title={Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions},
  author={Nikolaev, Evgeni V and Burgard, Anthony P and Maranas, Costas D},
  journal={Biophysical journal},
  volume={88},
  number={1},
  pages={37--49},
  year={2005},
  publisher={Elsevier}
}

@inproceedings{maranas2005computational,
  title={Computational approaches to combinatorial protein library design.},
  author={Maranas, CD and Saraf, MC and Moore, GL},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={229},
  pages={U213--U213},
  year={2005},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@inproceedings{fazelinia2005computational,
  title={Computational design of arac protein with novel effector specificity},
  author={Fazelinia, Hossein and Cirino, Patrick C and Maranas, Costas D},
  booktitle={05AIChE: 2005 AIChE Annual Meeting and Fall Showcase},
  year={2005}
}

@article{pharkya2004optstrain,
  title={OptStrain: a computational framework for redesign of microbial production systems},
  author={Pharkya, Priti and Burgard, Anthony P and Maranas, Costas D},
  journal={Genome research},
  volume={14},
  number={11},
  pages={2367--2376},
  year={2004},
  publisher={Cold Spring Harbor Lab}
}

@article{saraf2004famclash,
  title={FamClash: a method for ranking the activity of engineered enzymes},
  author={Saraf, Manish C and Horswill, Alexander R and Benkovic, Stephen J and Maranas, Costas D},
  journal={Proceedings of the National Academy of Sciences},
  volume={101},
  number={12},
  pages={4142--4147},
  year={2004},
  publisher={National Acad Sciences}
}

@article{burgard2004flux,
  title={Flux coupling analysis of genome-scale metabolic network reconstructions},
  author={Burgard, Anthony P and Nikolaev, Evgeni V and Schilling, Christophe H and Maranas, Costas D},
  journal={Genome research},
  volume={14},
  number={2},
  pages={301--312},
  year={2004},
  publisher={Cold Spring Harbor Lab}
}

@article{lehmann2004molecular,
  title={Molecular design using quantum chemical calculations for property estimation},
  author={Lehmann, Andreas and Maranas, Costas D},
  journal={Industrial \& engineering chemistry research},
  volume={43},
  number={13},
  pages={3419--3432},
  year={2004},
  publisher={ACS Publications}
}

@article{moore2004computational,
  title={Computational challenges in combinatorial library design for protein engineering},
  author={Moore, Gregory L and Maranas, Costas D},
  journal={AIChE Journal},
  volume={50},
  number={2},
  pages={262--272},
  year={2004},
  publisher={Wiley Subscription Services, Inc., A Wiley Company Hoboken}
}

@article{gupta2004real,
  title={Real-options-based planning strategies under uncertainty},
  author={Gupta, Anshuman and Maranas, Costas D},
  journal={Industrial \& engineering chemistry research},
  volume={43},
  number={14},
  pages={3870--3878},
  year={2004},
  publisher={ACS Publications}
}

@misc{maranas2004method,
  title={Method for determining gene knockout strategies},
  author={Maranas, Costas D and Burgard, Anthony R and Pharkya, Priti},
  year={2004}
}

@article{burgard2003optknock,
  title={Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization},
  author={Burgard, Anthony P and Pharkya, Priti and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={84},
  number={6},
  pages={647--657},
  year={2003},
  publisher={Wiley Online Library}
}

@article{rogers2003risk,
  title={Risk management in real options based pharmaceutical portfolio planning},
  author={Rogers, Michael J and Gupta, Anshuman and Maranas, Costas D},
  journal={Proceeding Foundations of Computer-Aided Process Operation (FOCAPO)},
  pages={12--15},
  year={2003}
}

@incollection{dasika2003mixed,
  title={A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks},
  author={Dasika, Madhukar S and Gupta, Anshuman and Maranas, Costas D},
  booktitle={Biocomputing 2004},
  pages={474--485},
  year={2003},
  publisher={World Scientific}
}

@article{moore2003identifying,
  title={Identifying residue--residue clashes in protein hybrids by using a second-order mean-field approach},
  author={Moore, Gregory L and Maranas, Costas D},
  journal={Proceedings of the National Academy of Sciences},
  volume={100},
  number={9},
  pages={5091--5096},
  year={2003},
  publisher={The National Academy of Sciences}
}

@inproceedings{maranas2003systems,
  title={Systems engineering challenges and opportunities in computational biology},
  author={Maranas, Costas D and Moore, Gregory L and Burgard, Anthony P and Gupta, Anshuman},
  booktitle={Proceedings FOCAPO},
  pages={13--26},
  year={2003}
}

@article{pharkya2003review,
  title={Review of the BRENDA Database},
  author={Pharkya, Priti and Nikolaev, Evgeni V and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={5},
  number={2},
  pages={71--73},
  year={2003},
  publisher={Orlando, FL: Academic Press, c1999-}
}

@article{pharkya2003exploring,
  title={Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock},
  author={Pharkya, Priti and Burgard, Anthony P and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={84},
  number={7},
  pages={887--899},
  year={2003},
  publisher={Wiley Online Library}
}

@article{saraf2003using,
  title={Using multiple sequence correlation analysis to characterize functionally important protein regions},
  author={Saraf, Manish C and Moore, Gregory L and Maranas, Costas D},
  journal={Protein Engineering},
  volume={16},
  number={6},
  pages={397--406},
  year={2003},
  publisher={Oxford University Press}
}

@article{gupta2003market,
  title={Market-based pollution abatement strategies: Risk management using emission option contracts},
  author={Gupta, Anshuman and Maranas, Costas D},
  journal={Industrial \& engineering chemistry research},
  volume={42},
  number={4},
  pages={802--810},
  year={2003},
  publisher={ACS Publications}
}

@inproceedings{maranas2003computational,
  title={Computational approaches for combinatorial protein library prescreening and optimization.},
  author={Maranas, CD and Moore, GL and Saraf, MC and Lee, S},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={226},
  pages={U275--U275},
  year={2003},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA}
}

@incollection{rogers2003real,
  title={Real options based approaches to decision making under uncertainty},
  author={Rogers, Michael J and Gupta, Anshuman and Maranas, Costas D},
  booktitle={Computer Aided Chemical Engineering},
  volume={15},
  pages={310--315},
  year={2003},
  publisher={Elsevier}
}

@article{pharkya2003metabol,
  title={METABOL},
  author={Pharkya, Priti and Nikolaev, Evgeni V and Maranas, Costas D and Zhu, T and Phalakornkule, C and Ghosh, S and Grossmann, IE and Koepsel, RR and Ataai, MM and Domach, MM and others},
  journal={Metabolic Engineering},
  volume={5},
  number={2},
  year={2003}
}

@article{saraf2003using,
  title={Using a residue clash map to functionally characterize protein recombination hybrids},
  author={Saraf, Manish C and Maranas, Costas D},
  journal={Protein engineering},
  volume={16},
  number={12},
  pages={1025--1034},
  year={2003},
  publisher={Oxford University Press}
}

@misc{maranas2003modeling,
  title={Modeling framework for predicting the number, type, and distribution of crossovers in directed evolution experiments},
  author={Maranas, Costas and Moore, Gregory},
  year={2003},
  month=apr # "~17",
  publisher={Google Patents},
  note={US Patent App. 10/037,572}
}

@article{burgard2003optimization,
  title={Optimization-based framework for inferring and testing hypothesized metabolic objective functions},
  author={Burgard, Anthony P and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={82},
  number={6},
  pages={670--677},
  year={2003},
  publisher={Wiley Online Library}
}

@incollection{moore2003modeling,
  title={Modeling and optimization of directed evolution protocols},
  author={Moore, Gregory L and Maranas, Costas D},
  booktitle={Enzyme Functionality},
  pages={188--213},
  year={2003},
  publisher={CRC Press}
}

@article{gupta2003managing,
  title={Managing demand uncertainty in supply chain planning},
  author={Gupta, Anshuman and Maranas, Costas D},
  journal={Computers \& chemical engineering},
  volume={27},
  number={8-9},
  pages={1219--1227},
  year={2003},
  publisher={Elsevier}
}

@article{moore2003pennsylvania,
  title={Pennsylvania State University University Park, Pennsylvania, USA},
  author={Moore, Gregory L and Maranas, Costas D},
  journal={Enzyme Functionality: Design: Engineering, and Screening},
  pages={171},
  year={2003},
  publisher={CRC Press}
}

@article{moore2003modeling,
  title={Modeling and Optimization of},
  author={Moore, Gregory L and Maranas, Costas D},
  journal={Enzyme Functionality: Design: Engineering, and Screening},
  pages={185},
  year={2003},
  publisher={CRC Press}
}

@article{vaidyaraman2002synthesis,
  title={Synthesis of mixed refrigerant cascade cycles},
  author={Vaidyaraman, Shankar and Maranas, Costas D},
  journal={Chemical Engineering Communications},
  volume={189},
  number={8},
  pages={1057--1078},
  year={2002},
  publisher={Taylor \& Francis}
}

@article{pharkya2002optstrain,
  title={Optstrain: a Hierarchical Metabolic Pathway Discovery and Design Framework for Microbial Production Systems},
  author={Pharkya, Priti and Maranas, C},
  journal={Projects. Csail. Mit. Edu},
  year={2002}
}

@article{moore2002predicting,
  title={Predicting out-of-sequence reassembly in DNA shuffling},
  author={Moore, Gregory L and Maranas, Costas D},
  journal={Journal of theoretical biology},
  volume={219},
  number={1},
  pages={9--17},
  year={2002},
  publisher={Elsevier}
}

@article{rogers2002real,
  title={Real options based analysis of optimal pharmaceutical research and development portfolios},
  author={Rogers, Michael J and Gupta, Anshuman and Maranas, Costas D},
  journal={Industrial \& engineering chemistry research},
  volume={41},
  number={25},
  pages={6607--6620},
  year={2002},
  publisher={ACS Publications}
}

@article{moore2002codonopt,
  title={e CodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments},
  author={Moore, Gregory L and Maranas, Costas D},
  journal={Nucleic acids research},
  volume={30},
  number={11},
  pages={2407--2416},
  year={2002},
  publisher={Oxford University Press}
}

@article{burgard2002review,
  title={Review of the biocatalysis/biodegradation database (UM-BBD)},
  author={Burgard, Anthony P and Maranas, Costas D},
  journal={Metabolic Engineering},
  volume={4},
  number={2},
  pages={111--113},
  year={2002},
  publisher={Academic Press}
}

@article{maranas2001review,
  title={Review of EcoCyc and MetaCyc databases},
  author={Maranas, Costas D and Burgard, Anthony P},
  journal={Metabolic Engineering},
  volume={3},
  number={2},
  pages={98--99},
  year={2001},
  publisher={Academic Press}
}

@incollection{maranas2001optimization,
  title={Optimization in molecular design and bioinformatics},
  author={Maranas, Costas D},
  booktitle={Computer Aided Chemical Engineering},
  volume={9},
  pages={1157--1164},
  year={2001},
  publisher={Elsevier}
}

@article{burgard2001review,
  title={Review of the enzymes and metabolic pathways (EMP) database},
  author={Burgard, Anthony P and Maranas, Costas D},
  journal={Metabolic Engineering},
  volume={3},
  number={3},
  pages={193--194},
  year={2001},
  publisher={Academic Press}
}

@article{burgard2001review,
  title={Review of the TEIRESIAS-based tools of the IBM Bioinformatics and Pattern Discovery Group},
  author={Burgard, Anthony P and Moore, Gregory L and Maranas, Costas D},
  journal={Metabolic engineering},
  volume={3},
  number={4},
  pages={285--288},
  year={2001},
  publisher={Academic Press}
}

@incollection{gupta2001multiperiod,
  title={Multiperiod planning of multisite supply chains under demand uncertainty},
  author={Gupta, Anshuman and Maranas, Costas D},
  booktitle={Computer Aided Chemical Engineering},
  volume={9},
  pages={871--876},
  year={2001},
  publisher={Elsevier}
}

@article{burgard2001minimal,
  title={Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments},
  author={Burgard, Anthony P and Vaidyaraman, Shankar and Maranas, Costas D},
  journal={Biotechnology progress},
  volume={17},
  number={5},
  pages={791--797},
  year={2001},
  publisher={Wiley Online Library}
}

@article{lutz2001creating,
  title={Creating multiple-crossover DNA libraries independent of sequence identity},
  author={Lutz, Stefan and Ostermeier, Marc and Moore, Gregory L and Maranas, Costas D and Benkovic, Stephen J},
  journal={Proceedings of the National Academy of Sciences},
  volume={98},
  number={20},
  pages={11248--11253},
  year={2001},
  publisher={The National Academy of Sciences}
}

@article{burgard2001probing,
  title={Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions},
  author={Burgard, Anthony P and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={74},
  number={5},
  pages={364--375},
  year={2001},
  publisher={Wiley Online Library}
}

@article{anderlund2001doi,
  title={doi: 10.1006 {\^A}mben. 2001.0202, available online at http: {\^A}{\^A}www. idealibrary. com},
  author={Anderlund, Mikael and Aon, Juan C and Aristidou, Aristos and Ataai, MM and Bailey, James E and Barkovich, Robert and Barnavon, L and Bennett, George N and Bettenbrock, K and Bongaerts, Johannes and others},
  journal={Metabolic Engineering},
  volume={3},
  pages={395},
  year={2001}
}

@article{moore2001predicting,
  title={Predicting crossover generation in DNA shuffling},
  author={Moore, Gregory L and Maranas, Costas D and Lutz, Stefan and Benkovic, Stephen J},
  journal={Proceedings of the National Academy of Sciences},
  volume={98},
  number={6},
  pages={3226--3231},
  year={2001},
  publisher={The National Academy of Sciences}
}

@article{moore2000modeling,
  title={Modeling and optimization of DNA recombination},
  author={Moore, Gregory L and Maranas, Costas D and Gutshall, Kevin R and Brenchley, Jean E},
  journal={Computers \& Chemical Engineering},
  volume={24},
  number={2-7},
  pages={693--699},
  year={2000},
  publisher={Elsevier}
}

@article{gupta2000mid,
  title={Mid-term supply chain planning under demand uncertainty: customer demand satisfaction and inventory management},
  author={Gupta, Anshuman and Maranas, Costas D and McDonald, Conor M},
  journal={Computers \& Chemical Engineering},
  volume={24},
  number={12},
  pages={2613--2621},
  year={2000},
  publisher={Elsevier}
}

@article{gupta2000two,
  title={A two-stage modeling and solution framework for multisite midterm planning under demand uncertainty},
  author={Gupta, Anshuman and Maranas, Costas D},
  journal={Industrial \& Engineering Chemistry Research},
  volume={39},
  number={10},
  pages={3799--3813},
  year={2000},
  publisher={ACS Publications}
}

@article{camarda1999optimization,
  title={Optimization in polymer design using connectivity indices},
  author={Camarda, Kyle V and Maranas, Costas D},
  journal={Industrial \& Engineering Chemistry Research},
  volume={38},
  number={5},
  pages={1884--1892},
  year={1999},
  publisher={ACS Publications}
}

@article{camarda1999design,
  title={Design of surfactant solutions with optimal macroscopic properties},
  author={Camarda, Kyle V and Bonnell, Brian W and Maranas, Costas D and Nagarajan, Ramanathan},
  journal={Computers \& Chemical Engineering},
  volume={23},
  pages={S467--S470},
  year={1999},
  publisher={Elsevier}
}

@article{vaidyaraman1999optimal,
  title={Optimal synthesis of refrigeration cycles and selection of refrigerants},
  author={Vaidyaraman, Shankar and Maranas, Costas D},
  journal={AIChE Journal},
  volume={45},
  number={5},
  pages={997--1017},
  year={1999},
  publisher={Wiley Online Library}
}

@article{gupta1999hierarchical,
  title={A hierarchical Lagrangean relaxation procedure for solving midterm planning problems},
  author={Gupta, Anshuman and Maranas, Costas D},
  journal={Industrial \& Engineering Chemistry Research},
  volume={38},
  number={5},
  pages={1937--1947},
  year={1999},
  publisher={ACS Publications}
}

@article{petkov1998design,
  title={Design of multiproduct batch plants under demand uncertainty with staged capacity expansions},
  author={Petkov, Spas B and Maranas, Costas D},
  journal={Computers \& chemical engineering},
  volume={22},
  pages={S789--S792},
  year={1998},
  publisher={Elsevier}
}

@article{petkov1998design,
  title={Design of single-product campaign batch plants under demand uncertainty},
  author={Petkov, Spas B and Maranas, Costas D},
  journal={AIChE Journal},
  volume={44},
  number={4},
  pages={896--911},
  year={1998},
  publisher={Wiley Online Library}
}

@article{raman1998optimization,
  title={Optimization in product design with properties correlated with topological indices},
  author={Raman, V Shankar and Maranas, Costas D},
  journal={Computers \& Chemical Engineering},
  volume={22},
  number={6},
  pages={747--763},
  year={1998},
  publisher={Elsevier}
}

@article{maranas1997solving,
  title={Solving long-term financial planning problems via global optimization},
  author={Maranas, CD and Androulakis, IP and Floudas, CA and Berger, AJ and Mulvey, JM},
  journal={Journal of Economic Dynamics and Control},
  volume={21},
  number={8-9},
  pages={1405--1425},
  year={1997},
  publisher={North-Holland}
}

@article{harding1997locating,
  title={Locating all homogeneous azeotropes in multicomponent mixtures},
  author={Harding, ST and Maranas, CD and McDonald, CM and Floudas, CA},
  journal={Industrial \& engineering chemistry research},
  volume={36},
  number={1},
  pages={160--178},
  year={1997},
  publisher={American Chemical Society}
}

@article{petkov1997multiperiod,
  title={Multiperiod planning and scheduling of multiproduct batch plants under demand uncertainty},
  author={Petkov, Spas B and Maranas, Costas D},
  journal={Industrial \& engineering chemistry research},
  volume={36},
  number={11},
  pages={4864--4881},
  year={1997},
  publisher={ACS Publications}
}

@article{maranas1997optimal,
  title={Optimal molecular design under property prediction uncertainty},
  author={Maranas, Costas D},
  journal={AIChE Journal},
  volume={43},
  number={5},
  pages={1250--1264},
  year={1997},
  publisher={Wiley Online Library}
}

@article{maranas1997optimization,
  title={Optimization accounting for property prediction uncertainty in polymer design},
  author={Maranas, Costas D},
  journal={Computers \& chemical engineering},
  volume={21},
  pages={S1019--S1024},
  year={1997},
  publisher={Elsevier}
}

@article{maranas1997global,
  title={Global optimization in generalized geometric programming},
  author={Maranas, Costas D and Floudas, Christodoulos A},
  journal={Computers \& Chemical Engineering},
  volume={21},
  number={4},
  pages={351--369},
  year={1997},
  publisher={Elsevier}
}

@article{petkov1997quantitative,
  title={Quantitative assessment of uncertainty in the optimization of metabolic pathways},
  author={Petkov, Spas B and Maranas, Costas D},
  journal={Biotechnology and bioengineering},
  volume={56},
  number={2},
  pages={145--161},
  year={1997},
  publisher={Wiley Online Library}
}

@article{androulakis1997prediction,
  title={Prediction of oligopeptide conformations via deterministic global optimization},
  author={Androulakis, Ioannis P and Maranas, Costas D and Floudas, Christodoulos A},
  journal={Journal of Global Optimization},
  volume={11},
  number={1},
  pages={1--34},
  year={1997},
  publisher={Kluwer Academic Publishers}
}

@article{adjiman1996global,
  title={A global optimization method, $\alpha$BB, for process design},
  author={Adjiman, Claire S and Androulakis, Ioannis P and Maranas, Costas D and Floudas, Christodoulos A},
  journal={Computers \& Chemical Engineering},
  volume={20},
  pages={S419--S424},
  year={1996},
  publisher={Elsevier}
}

@inproceedings{floudas1996prediction,
  title={Prediction of oligopeptide conformations via deterministic global optimization.},
  author={Floudas, CA and Androulakis, IP and Maranas, CD},
  booktitle={ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
  volume={212},
  pages={49--COMP},
  year={1996},
  organization={AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036}
}

@article{maranas1996locating,
  title={Locating all azeotropes in homogeneous azeotropic systems},
  author={Maranas, CD and McDonald, CM and Harding, ST and Floudas, CA},
  journal={Computers \& chemical engineering},
  volume={20},
  pages={S413--S418},
  year={1996},
  publisher={Pergamon}
}

@article{maranas1996optimal,
  title={Optimal computer-aided molecular design: A polymer design case study},
  author={Maranas, Costas D},
  journal={Industrial \& engineering chemistry research},
  volume={35},
  number={10},
  pages={3403--3414},
  year={1996},
  publisher={ACS Publications}
}

@article{maranas1995new,
  title={New results in the packing of equal circles in a square},
  author={Maranas, Costas D and Floudas, Christodoulos A and Pardalos, Panos M},
  journal={Discrete Mathematics},
  volume={142},
  number={1-3},
  pages={287--293},
  year={1995},
  publisher={Elsevier}
}

@phdthesis{maranas1995global,
  title={Global optimization in computational chemistry and process systems engineering},
  author={Maranas, Costas D},
  year={1995},
  school={Princeton University}
}

@article{maranas1995deterministic,
  title={A deterministic global optimization approach for the protein folding problem.},
  author={Maranas, Costas D and Androulakis, Ioannis P and Floudas, Christodoulos A},
  journal={Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
  volume={23},
  pages={133--150},
  year={1995}
}

@article{maranas1995finding,
  title={Finding all solutions of nonlinearly constrained systems of equations},
  author={Maranas, Costas D and Floudas, Christodoulos A},
  journal={Journal of Global Optimization},
  volume={7},
  number={2},
  pages={143--182},
  year={1995},
  publisher={Kluwer Academic Publishers}
}

@article{androulakis1995alphabb,
  title={$\alpha$BB: A global optimization method for general constrained nonconvex problems},
  author={Androulakis, Ioannis P and Maranas, Costas D and Floudas, Christodoulos A},
  journal={Journal of Global Optimization},
  volume={7},
  number={4},
  pages={337--363},
  year={1995},
  publisher={Kluwer Academic Publishers}
}

@incollection{maranas1994global,
  title={A global optimization method for Weber’s problem with attraction and repulsion},
  author={Maranas, Costas D and Floudas, Christodoulos A},
  booktitle={Large Scale Optimization},
  pages={259--285},
  year={1994},
  publisher={Springer}
}

@article{maranas1994global,
  title={Global minimum potential energy conformations of small molecules},
  author={Maranas, Costas D and Floudas, Christodoulos A},
  journal={Journal of Global Optimization},
  volume={4},
  number={2},
  pages={135--170},
  year={1994},
  publisher={Kluwer Academic Publishers}
}

@techreport{floudas1994deterministic,
  title={A deterministic global optimization approach for molecular structure determination},
  author={Floudas, CA and Maranas, CD},
  year={1994},
  institution={Univ. of Michigan, Ann Arbor, MI (United States)}
}

@techreport{mulvey1994solving,
  title={Solving dynamic control problems via deterministic global optimization},
  author={Mulvey, J and Maranas, C and Androulakis, IP and Floudas, C and Berger, A},
  year={1994},
  institution={Univ. of Michigan, Ann Arbor, MI (United States)}
}

@article{maranas1994deterministic,
  title={A deterministic global optimization approach for molecular structure determination},
  author={Maranas, Costas D and Floudas, Christodoulos A},
  journal={The Journal of chemical physics},
  volume={100},
  number={2},
  pages={1247--1261},
  year={1994},
  publisher={American Institute of Physics}
}

@article{maranas1993global,
  title={Global optimization for molecular conformation problems},
  author={Maranas, Costas D and Floudas, Christodoulos A},
  journal={Annals of Operations Research},
  volume={42},
  number={1},
  pages={85--117},
  year={1993},
  publisher={Baltzer Science Publishers, Baarn/Kluwer Academic Publishers}
}

@article{maranas1992global,
  title={A global optimization approach for Lennard-Jones microclusters},
  author={Maranas, Costas D and Floudas, Christodoulos A},
  journal={The Journal of chemical physics},
  volume={97},
  number={10},
  pages={7667--7678},
  year={1992},
  publisher={American Institute of Physics}
}

@article{salisreversing,
  title={Reversing Methanogenesis to Capture Methane for Liquid Biofuel Precursors},
  author={Salis, M and Ferry, James G and Maranas, Costas D and Patterson, Andrew D and Wood, Thomas K}
}

@article{entzmingersupplementary,
  title={Supplementary data for},
  author={Entzminger, Kevin C and Hyun, Jeong-min and Pantazes, Robert J and Patterson-Orazem, Athena C and Qerqez, Ahlam N and Frye, Zach P and Hughes, Randall A and Ellington, Andrew D and Lieberman, Raquel L and Maranas, Costas D and others}
}

@article{khodayarik,
  title={k-ecoli457: A genome-scale Escherichia coli kinetic metabolic model satisfying flux data for multiple mutant strains},
  author={Khodayari, Ali and Maranas, Costas D}
}

@article{sinskeygregory,
  title={Gregory N. Stephanopoulos},
  author={Sinskey, Anthony J and Hatzimanikatis, Vassily and Yarmush, Martin and Buckland, Barry C and Nielsen, Jens and Kelleher, Joanne and Maranas, Costas and Sahm, Hermann}
}

@article{maranassynechococcus,
  title={SYNECHOCOCCUS ELONGATUS UTEX 2973, A NEW CYANOBACTERIAL STRAIN THAT EXHIBITS RAPID AUTOTROPHIC GROWTH},
  author={Maranas, Costas D and Pakrasi, B}
}

@article{sinskeyvassily,
  title={Vassily Hatzimanikatis},
  author={Sinskey, Anthony J and Nielsen, Jens and Kelleher, Joanne and Maranas, Costas and Sahm, Hermann}
}

@article{cirinodesigning,
  title={Designing Arac Effector Specificity through Modeling and Dual Selection},
  author={Cirino, Patrick C and Fazelinia, Hossein and Tang, Shuang-Yan and Maranas, Costas}
}

@article{sinskeygregory,
  title={Gregory N. Stephanopoulos},
  author={Sinskey, Anthony J and Hatzimanikatis, Vassily and Yarmush, Martin and Buckland, Barry C and Nielsen, Jens and Kelleher, Joanne and Maranas, Costas and Sahm, Hermann}
}

@article{hatzimanikatisgregory,
  title={Gregory N. Stephanopoulos},
  author={Hatzimanikatis, Vassily and Lee, Sang Yup and Kelleher, Joanne and Maranas, Costas and Nielsen, Jens and Liao, James}
}

@article{cirinodesign,
  title={Design and Analysis of AraC Regulatory Protein Mutants with Altered Effector Specificity},
  author={Cirino, Patrick C and Maranas, Costas D and Tang, Shuang-Yan and Fazelinia, Hossein Z}
}

@article{sinskeygregory,
  title={Gregory N. Stephanopoulos},
  author={Sinskey, Anthony J and Hatzimanikatis, Vassily and Yarmush, Martin and Buckland, Barry C and Nielsen, Jens and Kelleher, Joanne and Maranas, Costas and Sahm, Hermann}
}

@article{vitalcomputational,
  title={A Computational Approach to Identify Optimal Interventions to Bacterial Metabolism},
  author={Vital-Lopez, Francisco G and Maranas, Costas D and Armaou, Antonios}
}

@article{dasikacomputational,
  title={Computational Design of Synthetic Biological Circuits},
  author={Dasika, Madhukar S and Maranas, Costas D}
}

@article{pitkanenchristina,
  title={Christina Chan, Fran-cois Berthiaume, Kyongbum Lee, and Martin L. Yarmush},
  author={Pitkanen, Juha-Pekka and Aristidou, Aristos and Salusjarvi, Laura and Ruohonen, Laura and Penttila, Merja and Koffas, Mattheos AG and Jung, Gyoo Yeol and Stephanopoulos, Gregory and Robin, J and Bonneau, S and others}
}

@article{chanconstruction,
  title={Construction of genome-scale metabolic models for non-model yeast organisms for biofuel and bioproduct engineering},
  author={Chan, Siu HJ and Dinh, Hoang and Gopalakrishnan, Saratram and Maranas, Costas D}
}

@article{honimproving,
  title={Improving Clostridium thermocellum Product Titers by Increasing the Thermodynamic Driving Force of its Glycolytic Pathway},
  author={Hon, Shuen and Dash, Satyakam and Jacobson, Tyler and Cui, Jingxuan and Stevenson, David M and Kuil, Teun and van Maris, Antonius and Amador-Noguez, Daniel and Maranas, Costas D and Olson, Daniel G and others}
}

@article{pantazes14maps,
  title={MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured},
  author={Pantazes, RJ and Maranas, CD},
  journal={BMC bioinformatics},
  volume={14},
  publisher={on AntibodyChain (http://www. antibodychain. com) Ho me> Pub licatio ns~…}
}

@article{maranascomputational,
  title={Computational Design of Synthetic Biological Circuits},
  author={Maranas, Costas D and Park, Univeristy}
}

@article{sinskeygregory,
  title={Gregory N. Stephanopoulos},
  author={Sinskey, Anthony J and Hatzimanikatis, Vassily and Yarmush, Martin and Buckland, Barry C and Nielsen, Jens and Kelleher, Joanne and Maranas, Costas and Sahm, Hermann}
}

@article{hendrygenome,
  title={Genome-scale fluxome of the fast-growing cyanobacterium Synechococcus elongatus UTEX},
  author={Hendry, John I and Gopalakrishnan, Saratram and Ungerer, Justin and Tang, Yinjie J and Maranas, Costas D and Pakrasi, Himadri B}
}

@article{antonczaknext,
  title={The next issue of this journal},
  author={Antonczak, Alicja K and Morris, Josephine and Tippmann, Eric M and Pantazes, Robert J and Grisewood, Matthew J and Maranas, Costas and Verschueren, Erik and Vanhee, Peter and van der Sloot, Almer and Serrano, Luis and others}
}

@article{alpergregory,
  title={Gregory N. Stephanopoulos},
  author={Alper, Hal and Hatzimanikatis, Vassily and Lee, Sang Yup and Kelleher, Joanne and Maranas, Costas and Nielsen, Jens and Liao, James}
}

@article{rogerscase,
  title={A CASE STUDY ON THE DESIGN OF PHARMACEUTICAL R\&D LICENSING DEALS},
  author={Rogers, Michael J and Ding, Min and Maranas, Costas D}
}

@article{guptasupplementary,
  title={Supplementary Information Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination sites},
  author={Gupta, Anshuman and Maranas, Costas D and Albert, R{\'e}ka},
  publisher={Citeseer}
}

@article{hosseincomputation,
  title={Computation Guided Protein Design for Altered Cofactor Specificity and Introduction of a New Binding Site},
  author={Hossein, Z Fazelinia and Khoury, George A and Cirino, Patrick C and Maranas, Costas D}
}

@article{maranasnon,
  title={Non-Confidential Description-PSU No. 4315 “Method for Designing Overall Stoichiometric Conversions and Intervening Metabolic Reactions”},
  author={Maranas, Costas and Chowdhury, Anupam}
}

@article{fendtsystems,
  title={Systems biology-Advances in disease understanding and in metabolic engineering},
  author={Fendt, Sarah-Maria and Maranas, Costas D}
}

@article{gongrsc,
  title={rsc. li/ees},
  author={Gong, Eunhee and Ali, Shahzad and Hiragond, Chaitanya B and Kim, Hong Soo and Powar, Niket S and Kim, Dongyun and Kim, Hwapyong and In, Su-Il and Lynd, LR and Beckham, GT and others}
}

@article{banerjeedevelopment,
  title={Development of Anabaena 33047, a fast-growing N2-fixing cyanobacterium, as a carbon neutral bioproduction platform},
  author={Banerjee, Anindita and Liu, Deng and Hendry, John I and Maranas, Costas D and Antoniewicz3 andHimadri, Maciek R and Pakrasi, B}
}

@article{chothesars,
  title={SARS-CoV-2 Compatible ACE2 Receptors in Little Brown Bats (Myotis lucifugus)},
  author={Chothe, Shubhada K and Jakka, Padmaja and Boorla, Veda Sheersh and Ramasamy, Santhamani and Gontu, Abhinay and Nissly, Ruth H and Brown, Justin and Turner, Gregory and Sewall, Brent J and Reeder, DeeAnn and others}
}