Works by Maranas, Costas

Results: 96

Systems metabolic engineering design: Fatty acid production as an emerging case study.

Published in:

Biotechnology & Bioengineering, 2014, v. 111, n. 5, p. 849, doi. 10.1002/bit.25205

By:

Tee, Ting Wei;
Chowdhury, Anupam;
Maranas, Costas D.;
Shanks, Jacqueline V.

Publication type:

Article

Construction of an E. Coli genome-scale atom mapping model for MFA calculations.

Published in:

Biotechnology & Bioengineering, 2011, v. 108, n. 6, p. 1372, doi. 10.1002/bit.23070

By:

Ravikirthi, Prabhasa;
Suthers, Patrick F.;
Maranas, Costas D.

Publication type:

Article

Analysis of NADPH supply during xylitol production by engineered Escherichia coli.

Published in:

Biotechnology & Bioengineering, 2009, v. 102, n. 1, p. 209, doi. 10.1002/bit.22060

By:

Chin, Jonathan W.;
Khankal, Reza;
Monroe, Caroline A.;
Maranas, Costas D.;
Cirino, Patrick C.

Publication type:

Article

Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments.

Published in:

Biotechnology & Bioengineering, 2008, v. 100, n. 6, p. 1039, doi. 10.1002/bit.21926

By:

Chang, YoungJung;
Suthers, Patrick F.;
Maranas, Costas D.

Publication type:

Article

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

Published in:

Biotechnology & Bioengineering, 2005, v. 91, n. 5, p. 643, doi. 10.1002/bit.20542

By:

Fong, Stephen S.;
Burgard, Anthony P.;
Herring, Christopher D.;
Knight, Eric M.;
Blattner, Frederick R.;
Maranas, Costas D.;
Palsson, Bernhard O.

Publication type:

Article

Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock.

Published in:

Biotechnology & Bioengineering, 2003, v. 84, n. 7, p. 887, doi. 10.1002/bit.10857

By:

Priti Pharkya;
Anthony P. Burgard;
Costas D. Maranas

Publication type:

Article

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.

Published in:

Biotechnology & Bioengineering, 2003, v. 84, n. 6, p. 647, doi. 10.1002/bit.10803

By:

Anthony P. Burgard;
Priti Pharkya;
Costas D. Maranas

Publication type:

Article

Optimization-based framework for inferring and testing hypothesized metabolic objective functions.

Published in:

Biotechnology & Bioengineering, 2003, v. 82, n. 6, p. 670, doi. 10.1002/bit.10617

By:

Anthony P. Burgard;
Costas D. Maranas

Publication type:

Article

Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions.

Published in:

Biotechnology & Bioengineering, 2001, v. 74, n. 5, p. 364, doi. 10.1002/bit.1127

By:

Burgard, Anthony P.;
Maranas, Costas D.

Publication type:

Article

Methane oxidation by anaerobic archaea for conversion to liquid fuels.

Published in:

Journal of Industrial Microbiology & Biotechnology, 2015, v. 42, n. 3, p. 391, doi. 10.1007/s10295-014-1548-7

By:

Mueller, Thomas;
Grisewood, Matthew;
Nazem-Bokaee, Hadi;
Gopalakrishnan, Saratram;
Ferry, James;
Wood, Thomas;
Maranas, Costas

Publication type:

Article

Synthesis of Mixed Refrigerant Cascade Cycles.

Published in:

Chemical Engineering Communications, 2002, v. 189, n. 8, p. 1057, doi. 10.1080/00986440213475

By:

Vaidyaraman, Shankar;
Maranas, Costas D.

Publication type:

Article

SNPeffect: identifying functional roles of SNPs using metabolic networks.

Published in:

Plant Journal, 2020, v. 103, n. 2, p. 512, doi. 10.1111/tpj.14746

By:

Sarkar, Debolina;
Maranas, Costas D.

Publication type:

Article

Little Brown Bats (Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection.

Published in:

Viruses (1999-4915), 2023, v. 15, n. 5, p. 1103, doi. 10.3390/v15051103

By:

Chothe, Shubhada K.;
Jakka, Padmaja;
Boorla, Veda Sheersh;
Ramasamy, Santhamani;
Gontu, Abhinay;
Nissly, Ruth H.;
Brown, Justin;
Turner, Gregory;
Sewall, Brent J.;
Reeder, DeeAnn M.;
Field, Kenneth A.;
Engiles, Julie B.;
Amirthalingam, Saranya;
Ravichandran, Abirami;
LaBella, Lindsey;
Nair, Meera Surendran;
Maranas, Costas D.;
Kuchipudi, Suresh V.

Publication type:

Article

The importance and future of biochemical engineering.

Published in:

Biotechnology & Bioengineering, 2020, v. 117, n. 8, p. 2305, doi. 10.1002/bit.27364

By:

Whitehead, Timothy A.;
Banta, Scott;
Bentley, William E.;
Betenbaugh, Michael J.;
Chan, Christina;
Clark, Douglas S.;
Hoesli, Corinne A.;
Jewett, Michael C.;
Junker, Beth;
Koffas, Mattheos;
Kshirsagar, Rashmi;
Lewis, Amanda;
Li, Chien‐Ting;
Maranas, Costas;
Terry Papoutsakis, E.;
Prather, Kristala L. J.;
Schaffer, Steffen;
Segatori, Laura;
Wheeldon, Ian

Publication type:

Article

Computational de novo design of antibodies binding to a peptide with high affinity.

Published in:

Biotechnology & Bioengineering, 2017, v. 114, n. 6, p. 1331, doi. 10.1002/bit.26244

By:

Poosarla, Venkata Giridhar;
Li, Tong;
Goh, Boon Chong;
Schulten, Klaus;
Wood, Thomas K.;
Maranas, Costas D.

Publication type:

Article

eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 11, p. 2407, doi. 10.1093/nar/30.11.2407

By:

Moore, Gregory L.;
Maranas, Costas D.

Publication type:

Article

Optimal synthesis of refrigeration cycles and selection of refrigerants.

Published in:

AIChE Journal, 1999, v. 45, n. 5, p. 997, doi. 10.1002/aic.690450510

By:

Vaidyaraman, Shankar;
Maranas, Costas D.

Publication type:

Article

Design of single-product campaign batch plants under demand uncertainty.

Published in:

AIChE Journal, 1998, v. 44, n. 4, p. 896, doi. 10.1002/aic.690440415

By:

Petkov, Spas B.;
Maranas, Costas D.

Publication type:

Article

Optimal molecular design under property prediction uncertainty.

Published in:

AIChE Journal, 1997, v. 43, n. 5, p. 1250, doi. 10.1002/aic.690430514

By:

Maranas, Costas D.

Publication type:

Article

Design of combinatorial protein libraries of optimal size.

Published in:

Proteins, 2005, v. 60, n. 4, p. 769, doi. 10.1002/prot.20490

By:

Saraf, Manish C.;
Gupta, Anshuman;
Maranas, Costas D.

Publication type:

Article

SteadyCom: Predicting microbial abundances while ensuring community stability.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 5, p. 1, doi. 10.1371/journal.pcbi.1005539

By:

Chan, Siu Hung Joshua;
Simons, Margaret N.;
Maranas, Costas D.

Publication type:

Article

Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.

Published in:

Bioinformatics, 2006, v. 22, n. 2, p. 209, doi. 10.1093/bioinformatics/bti780

By:

Anshuman Gupta;
Costas D. Maranas;
Réka Albert

Publication type:

Article

A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers.

Published in:

Metabolites (2218-1989), 2021, v. 11, n. 3, p. 168, doi. 10.3390/metabo11030168

By:

Hendry, John I.;
Dinh, Hoang V.;
Sarkar, Debolina;
Wang, Lin;
Bandyopadhyay, Anindita;
Pakrasi, Himadri B.;
Maranas, Costas D.;
Poolman, Mark M. G.

Publication type:

Article

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass.

Published in:

Journal of Experimental Botany, 2023, v. 74, n. 18, p. 5532, doi. 10.1093/jxb/erad255

By:

Choi, Soyeon;
Prabhakar, Pradeep K;
Chowdhury, Ratul;
Pendergast, Thomas H;
Urbanowicz, Breeanna R;
Maranas, Costas;
Devos, Katrien M

Publication type:

Article

Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions.

Published in:

Journal of Experimental Botany, 2022, v. 73, n. 1, p. 275, doi. 10.1093/jxb/erab435

By:

Chowdhury, Niaz Bahar;
Schroeder, Wheaton L;
Sarkar, Debolina;
Amiour, Nardjis;
Quilleré, Isabelle;
Hirel, Bertrand;
Maranas, Costas D;
Saha, Rajib

Publication type:

Article

Nitrogen-use efficiency in maize (Zea mays L.): from ‘omics’ studies to metabolic modelling.

Published in:

Journal of Experimental Botany, 2014, v. 65, n. 19, p. 5657, doi. 10.1093/jxb/eru227

By:

Simons, Margaret;
Saha, Rajib;
Guillard, Lenaïg;
Clément, Gilles;
Armengaud, Patrick;
Cañas, Rafael;
Maranas, Costas D.;
Lea, Peter J.;
Hirel, Bertrand

Publication type:

Article

Challenges of cultivated meat production and applications of genome‐scale metabolic modeling.

Published in:

AIChE Journal, 2020, v. 66, n. 6, p. 1, doi. 10.1002/aic.16235

By:

Suthers, Patrick F.;
Maranas, Costas D.

Publication type:

Article

From directed evolution to computational enzyme engineering—A review.

Published in:

AIChE Journal, 2020, v. 66, n. 3, p. N.PAG, doi. 10.1002/aic.16847

By:

Chowdhury, Ratul;
Maranas, Costas D.

Publication type:

Article

Modeling the effect of chemotaxis on glioblastoma tumor progression.

Published in:

AIChE Journal, 2011, v. 57, n. 3, p. 778, doi. 10.1002/aic.12296

By:

Vital-Lopez, Francisco G.;
Armaou, Antonios;
Hutnik, Michelle;
Maranas, Costas D.

Publication type:

Article

Valuation and Design of Pharmaceutical R&D Licensing Deals.

Published in:

AIChE Journal, 2005, v. 51, n. 1, p. 198, doi. 10.1002/aic.10280

By:

Rogers, Michael J.;
Maranas, Costas D.;
Min Ding

Publication type:

Article

Computational Challenges in Combinatorial Library Design for Protein Engineering.

Published in:

AIChE Journal, 2004, v. 50, n. 2, p. 262, doi. 10.1002/aic.10025

By:

Moore, Gregory L.;
Maranas, Costas D.

Publication type:

Article

Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modeling Approach to Link Leaf Physiology to Kernel Yield.

Published in:

Plant Cell, 2017, v. 29, n. 5, p. 919, doi. 10.1105/tpc.16.00613

By:

Cañas, Rafael A.;
Yesbergenova-Cuny, Zhazira;
Simons, Margaret;
Chardon, Fabien;
Armengaud, Patrick;
Quilleré, Isabelle;
Cukier, Caroline;
Gibon, Yves;
Limami, Anis M.;
Nicolas, Stéphane;
Brulé, Lenaïg;
Lea, Peter J.;
Maranas, Costas D.;
Hirel, Bertrand

Publication type:

Article

Global optimization for molecular conformation problems.

Published in:

Annals of Operations Research, 1993, v. 42, n. 1-4, p. 85, doi. 10.1007/BF02023173

By:

Maranas, Costas D.;
Floudas, Christodoulos A.

Publication type:

Article

Using a residue clash map to functionally characterize protein recombination hybrids.

Published in:

Protein Engineering, 2003, v. 16, n. 12, p. 1025

By:

Costas D. Maranas

Publication type:

Article

Computational design of Candida boidinii xylose reductase for altered cofactor specificity.

Published in:

Protein Science: A Publication of the Protein Society, 2009, v. 18, n. 10, p. 2125, doi. 10.1002/pro.227

By:

Khoury, George A.;
Fazelinia, Hossein;
Chin, Jonathan W.;
Pantazes, Robert J.;
Cirino, Patrick C.;
Maranas, Costas D.

Publication type:

Article

OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.

Published in:

Protein Science: A Publication of the Protein Society, 2009, v. 18, n. 1, p. 180, doi. 10.1002/pro.2

By:

Fazelinia, Hossein;
Cirino, Patrick C.;
Maranas, Costas D.

Publication type:

Article

Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media.

Published in:

Microbial Cell Factories, 2022, v. 21, n. 1, p. 1, doi. 10.1186/s12934-022-01750-3

By:

Schultz, J. Carl;
Mishra, Shekhar;
Gaither, Emily;
Mejia, Andrea;
Dinh, Hoang;
Maranas, Costas;
Zhao, Huimin

Publication type:

Article

Quantitative assessment of uncertainty in the optimization of metabolic pathways.

Published in:

Biotechnology & Bioengineering, 1997, v. 56, n. 2, p. 145, doi. 10.1002/(SICI)1097-0290(19971020)56:2<145::AID-BIT4>3.0.CO;2-P

By:

Petkov, Spas B.;
Maranas, Costas D.

Publication type:

Article

Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints.

Published in:

Bioinformatics, 2018, v. 34, n. 24, p. 4248, doi. 10.1093/bioinformatics/bty446

By:

Chan, Siu H J;
Wang, Lin;
Dash, Satyakam;
Maranas, Costas D

Publication type:

Article

Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models.

Published in:

Bioinformatics, 2017, v. 33, n. 22, p. 3603, doi. 10.1093/bioinformatics/btx453

By:

Chan, Siu H. J.;
Jingyi Cai;
Lin Wang;
Simons-Senftle, Margaret N.;
Maranas, Costas D.

Publication type:

Article

Pareto Optimality Explanation of the Glycolytic Alternatives in Nature.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. 1, doi. 10.1038/s41598-019-38836-9

By:

Ng, Chiam Yu;
Wang, Lin;
Chowdhury, Anupam;
Maranas, Costas D.

Publication type:

Article

Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.

Published in:

BMC Systems Biology, 2017, v. 11, p. 1, doi. 10.1186/s12918-017-0434-0

By:

Serrano-Bermúdez, Luis Miguel;
González Barrios, Andrés Fernando;
Maranas, Costas D.;
Montoya, Dolly

Publication type:

Article

Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 2, doi. 10.1186/1752-0509-7-142

By:

Mueller, Thomas J.;
Berla, Bertram M.;
Pakrasi, Himadri B.;
Maranas, Costas D.

Publication type:

Article

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.

Published in:

BMC Systems Biology, 2011, v. 5, n. 1, p. 28, doi. 10.1186/1752-0509-5-28

By:

Kumar, Vinay Satish;
Ferry, James G.;
Maranas, Costas D.

Publication type:

Article

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.

Published in:

BMC Systems Biology, 2010, v. 4, p. 178, doi. 10.1186/1752-0509-4-178

By:

Zomorrodi, Ali R.;
Maranas, Costas D.

Publication type:

Article

OptCircuit: An optimization based method for computational design of genetic circuits.

Published in:

BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-24

By:

Dasika, Madhukar S.;
Maranas, Costas D.

Publication type:

Article

The Iterative Protein Redesign and Optimization (IPRO) suite of programs.

Published in:

Journal of Computational Chemistry, 2015, v. 36, n. 4, p. 251, doi. 10.1002/jcc.23796

By:

Pantazes, Robert J.;
Grisewood, Matthew J.;
Li, Tong;
Gifford, Nathanael P.;
Maranas, Costas D.

Publication type:

Article

De novo design and Rosetta‐based assessment of high‐affinity antibody variable regions (Fv) against the SARS‐CoV‐2 spike receptor binding domain (RBD).

Published in:

Proteins, 2023, v. 91, n. 2, p. 196, doi. 10.1002/prot.26422

By:

Boorla, Veda Sheersh;
Chowdhury, Ratul;
Ramasubramanian, Ranjani;
Ameglio, Brandon;
Frick, Rahel;
Gray, Jeffrey J.;
Maranas, Costas D.

Publication type:

Article

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 9, p. 1, doi. 10.1371/journal.pcbi.1009448

By:

Wang, Lin;
Upadhyay, Vikas;
Maranas, Costas D.

Publication type:

Article

Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 5, p. 1, doi. 10.1371/journal.pcbi.1008983

By:

Sarkar, Debolina;
Landa, Marine;
Bandyopadhyay, Anindita;
Pakrasi, Himadri B.;
Zehr, Jonathan P.;
Maranas, Costas D.

Publication type:

Article