@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}
}