Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, Jan, Que, Richard, Fleming, Ronan M T, Thiele, Ines, Orth, Jeffrey D, Feist, Adam M, Zielinski, Daniel C, Bordbar, Aarash +5 more·2011·Nature Protocols
Cited by (1,002)
Items 101–200 of 1,002
- Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast MetabolismAung, Hnin W., Henry, Susan A., Walker, Larry P. · 2013 · Industrial Biotechnology
- Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahliiNagarajan, Harish, Sahin, Merve, Nogales, Juan, Latif, Haythem, Lovley, Derek R, Ebrahim, Ali, Zengler, Karsten · 2013 · Microbial Cell Factories
- Constrained Allocation Flux Balance AnalysisMatteo Mori, Terence Hwa B, Olivier Martin, Andrea De Martino, Enzo Marinari · 2016 · PLoS Computational Biology
- Towards systems metabolic engineering in Pichia pastorisJan-Philipp Schwarzhans, Tobias Luttermann, Martina Geier, Jörn Kalinowski, Karl Friehs · 2017 · Biotechnology Advances
- Systematic Analysis of Gut Microbiome Reveals the Role of Bacterial Folate and Homocysteine Metabolism in Parkinson’s DiseaseRosario, Dorines, Bidkhori, Gholamreza, Lee, Sunjae, Bedarf, Janis, Hildebrand, Falk, Le Chatelier, Emmanuelle, Uhlen, Mathias, Ehrlich, Stanislav Dusko, Proctor, Gordon, Wüllner, Ullrich et al. · 2021 · Cell Reports
- COBRAme: A computational framework for genome-scale models of metabolism and gene expressionLloyd, Colton J., Ebrahim, Ali, Yang, Laurence, King, Zachary A., Catoiu, Edward, O’Brien, Edward J., Liu, Joanne K., Palsson, Bernhard O. · 2018 · PLOS Computational Biology
- Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting AcetogensKaspar Valgepea, Renato de Souza Pinto Lemgruber, Kieran Meaghan, Robin William Palfreyman, Tanus Abdalla, Björn D. Heijstra, James B. Y. H. Behrendorff, Ryan C. Tappel, Michael Köpke, Séan Dennis Simpson et al. · 2017 · Cell Systems
- Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway ModelingMiroslava Čuperlović‐Culf · 2018 · Metabolites
- Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-PathMiguel A. Campodonico, Bárbara A. Andrews, Juan A. Asenjo, Bernhard Ørn Palsson, Adam M. Feist · 2014 · Metabolic Engineering
- Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogenMarcellin, Esteban, Behrendorff, James B., Nagaraju, Shilpa, DeTissera, Sashini, Segovia, Simon, Palfreyman, Robin W., Daniell, James, Licona-Cassani, Cuauhtemoc, Quek, Lake-ee, Speight, Robert et al. · 2016 · Green Chemistry
- Evolutionary adaptations to new environments generally reverse plastic phenotypic changesWei-Chin Ho, Jianzhi Zhang · 2018 · Nature Communications
- Flux Balance Analysis of Barley Seeds: A Computational Approach to Study Systemic Properties of Central MetabolismEva Grafahrend‐Belau, Falk Schreiber, Dirk Koschützki A, Björn H. Junker · 2008 · PLANT PHYSIOLOGY
- Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineeringChiam Yu Ng, Moo-Young Jung, Jinwon Lee, Min‐Kyu Oh · 2012 · Microbial Cell Factories
- Systematic phenome analysis of Escherichia coli multiple‐knockout mutants reveals hidden reactions in central carbon metabolismKenji Nakahigashi, Yoshihiro Toya, Nobuyoshi Ishii, Tomoyoshi Soga, Miki Launois Hasegawa, Hisami Watanabe, Yuki Takai, Masayuki Honma, Hirotada Mori, Masaru Tomita · 2009 · Molecular Systems Biology
- A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applicationsMaciek R. Antoniewicz · 2020 · Metabolic Engineering
- Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State DataLuca Gerosa, Bart Rudolf Boudewijn Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas Schmidt, Εlad Noor, Uwe Sauer · 2015 · Cell Systems
- Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakeiYoseb Song, Jin Soo Lee, Jongoh Shin, Gyu Min Lee, Sangrak Jin, Seulgi Kang, Jung-Kul Lee, Dong Rip Kim, Eun Yeol Lee, Sun Chang Kim et al. · 2020 · Proceedings of the National Academy of Sciences
- AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genomeCristiana Gomes de Oliveira Dal’Molin, Lake‐Ee Quek, Robin William Palfreyman, Lars Keld Nielsen · 2011 · BMC Genomics
- A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1Sigurdsson, Martin I, Jamshidi, Neema, Steingrimsson, Eirikur, Thiele, Ines, Palsson, Bernhard Ø · 2010 · BMC Systems Biology
- Elucidation of complexity and prediction of interactions in microbial communitiesCristal Zúñiga, Livia Soares Zaramela, Karsten Zengler · 2017 · Microbial Biotechnology
- Biotechnological potential of microbial consortia and future perspectivesShashi Kant Bhatia, Ravi Kant Bhatia, Yong‐Keun Choi, Eunsung Kan, Yun‐Gon Kim, Yung‐Hun Yang · 2018 · Critical Reviews in Biotechnology
- Redox balance is key to explaining full vs. partial switching to low-yield metabolismvan Hoek, Milan JA, Merks, Roeland MH · 2012 · BMC Systems Biology
- Towards kinetic modeling of genome‐scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraintsAnirikh Chakrabarti, Ljubiša Mišković, Keng Cher Soh, Vassily Hatzimanikatis A · 2013 · Biotechnology Journal
- Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic modelsAite, Méziane, Chevallier, Marie, Frioux, Clémence, Trottier, Camille, Got, Jeanne, Cortés, María Paz, Mendoza, Sebastián N., Carrier, Grégory, Dameron, Olivier, Guillaudeux, Nicolas et al. · 2018 · PLOS Computational Biology
- Metabolic pathway engineering towards enhancing microalgal lipid biosynthesis for biofuel application—A reviewGoldy De Bhowmick, Lokanand Koduru, Ramkrishna Sen · 2015 · Renewable and Sustainable Energy Reviews
- Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory networkTige R. Rustad, Kyle J. Minch, Shuyi Ma, Jessica K. Winkler, Samuel J. Hobbs, Mark J. Hickey, William H. Brabant, Serdar Turkarslan, Nathan D. Price, Nitin S. Baliga et al. · 2014 · Genome biology
- Improving metabolic flux predictions using absolute gene expression dataDave Chi Hoo Lee, Kieran Smallbone A B, Warwick B. Dunn, Ettore Murabito, Catherine L. Winder, Douglas Bruce Kell, Pedro Mendes, Neil Swainston · 2012 · BMC Systems Biology
- Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver StageRebecca R. Stanway, Ellen Bushell, Anush Chiappino-Pepe, Magali Roques, Theo Sanderson, Blandine M. D. Franke-Fayard, Reto Caldelari, Murielle Golomingi, Mary Akinyi Nyonda, Vikash Pandey et al. · 2019 · Cell
- Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico OptimisationTeusink, Bas, Wiersma, Anne, Jacobs, Leo, Notebaart, Richard A., Smid, Eddy J. · 2009 · PLoS Computational Biology
- DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysisJose Alberto Gomez, Kai Höffner, Paul I. Barton · 2014 · BMC Bioinformatics
- The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do soDouglas Bruce Kell, Paul D. Dobson, Elizabeth Bilsland, Stephen G. Oliver · 2012 · Drug Discovery Today
- Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic networkBen Heavner, Kieran Smallbone A B, Brandon Barker, Pedro Mendes, Larry P. Walker · 2012 · BMC Systems Biology
- Extracellular Microbial Metabolomics: The State of the ArtFarhana R. Pinu, Silas Granato Villas-Bôas · 2017 · Metabolites
- Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic associationHarish Nagarajan, Mallory Embree, Amelia‐Elena Rotaru, Pravin Malla Shrestha, Adam M. Feist, Bernhard Ørn Palsson, Derek R. Lovley, Karsten Zengler · 2013 · Nature Communications
- A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer BiologyArturo Casini, Fangyuan Chang, Raïssa Eluère, Andrew M. King, Eric M. Young, Quentin M. Dudley, Ashty S. Karim, Katelin Pratt, Cassandra Bristol, Anthony L. Forget et al. · 2018 · Journal of the American Chemical Society
- A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2Ines Thiele, Daniel R. Hyduke, Benjamin Steeb, Guy Fankam, Doug K. Allen, Susanna Bazzani, Pep Charusanti, Feng‐Chi Chen, Ronan M. T. Fleming, Chao Agnes Hsiung et al. · 2011 · BMC Systems Biology
- Optimization of lipid production with a genome-scale model of Yarrowia lipolyticaMartin Kavšček, Govindprasad Bhutada, Tobias Madl, Klaus Natter · 2015 · BMC Systems Biology
- Reconstruction of Tissue-Specific Metabolic Networks Using CORDAAndré Schultz, Amina Ann Qutub · 2016 · PLoS Computational Biology
- Designing Metabolic Division of Labor in Microbial CommunitiesMeghan Thommes, Taiyao Wang, Qi Zhao, Ioannis Ch. Paschalidis, Daniel Segrè · 2019 · mSystems
- Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysisJacqueline E. Gonzalez, Christopher P. Long, Maciek R. Antoniewicz · 2016 · Metabolic Engineering
- Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEEDScott Devoid, Ross Overbeek, Matthew DeJongh, Veronika Vonstein, Aaron A. Best, Christopher S. Henry · 2013 · Methods in molecular biology
- Metabolic characterization of a CHO cell size increase phase in fed-batch culturesXiao Pan, Ciska Dalm, René H. Wijffels, Dirk E. Martens · 2017 · Applied Microbiology and Biotechnology
- MetExplore: collaborative edition and exploration of metabolic networksLudovic Cottret, Clément Frainay, Maxime Chazalviel, Floréal Cabanettes, Yoann Gloaguen, Etienne Camenen, Benjamin Merlet, Stéphanie Heux, Jean‐Charles Portais, Nathalie Poupin et al. · 2018 · Nucleic Acids Research
- Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretionJahir M. Gutierrez, Amir Feizi, Shangzhong Li, Thomas Beuchert Kallehauge, Hooman Hefzi, Lise Marie Grav, Daniel Ley, Deniz Baycın Hızal, Michael J. Betenbaugh, Bjørn Gunnar Rude Voldborg et al. · 2020 · Nature Communications
- Metabolic Associations of Reduced Proliferation and Oxidative Stress in Advanced Breast CancerLivnat Jerby‐Arnon, Lior Wolf, Carsten Denkert, Gideon Y. Stein, Mika Hilvo, Matej Orešič, Tamar Geiger, Eytan Ruppin · 2012 · Cancer Research
- Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesisJennifer A. Bartell, Anna S. Blazier, Phillip Yen, Juliane Charlotte Thøgersen, Lars Jelsbak, Joanna B. Goldberg, Jason A. Papin · 2017 · Nature Communications
- Systems metabolic engineering: Genome‐scale models and beyondJohn Blazeck, Hal S. Alper · 2010 · Biotechnology Journal
- Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic PathwaysYusuke Minato, Daryl M. Gohl, Joshua M. Thiede, Jeremy M. Chacón, William R. Harcombe, Fumito Maruyama, Anthony D. Baughn · 2019 · mSystems
- Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coliXuewen Chen, Ana Paula Alonso, Doug K. Allen, Jennifer L. Reed, Yair Shachar‐Hill · 2010 · Metabolic Engineering
- A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolyticaNicolás Loira, Thierry Dulermo, Jean‐Marc Nicaud, David James Sherman · 2012 · BMC Systems Biology
- Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomicsNicholas D. Gold, Christopher M. Gowen, François-Xavier Lussier, Sarat C. Cautha, Radhakrishnan Mahadevan, Vincent J. J. Martin · 2015 · Microbial Cell Factories
- Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems AnalysisMatthew Oberhardt, Jacek Puchałka, Vítor A. P. Martins dos Santos, Jason A. Papin · 2011 · PLoS Computational Biology
- sybil – Efficient constraint-based modelling in RGabriel Gelius‐Dietrich, Abdelmoneim Amer Desouki, Claus Jonathan Fritzemeier, Martin J. Lercher · 2013 · BMC Systems Biology
- Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communitiesAli R. Zomorrodi, Daniel Segrè · 2017 · Nature Communications
- Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approachIlya R. Akberdin, Merlin Thompson, Richard Hamilton, Nalini Desai, Danny C. Alexander, Calvin A. Henard, Michael Thomas Guarnieri, Marina Kalyuzhnaya · 2018 · Scientific Reports
- Genome-resolved metagenomics: a game changer for microbiome medicineNayeon Kim, Junyeong Ma, Wonjong Kim, Jungyeon Kim, P. Belenky, Insuk Lee · 2024 · Experimental and Molecular Medicine
- ITEP: An integrated toolkit for exploration of microbial pan-genomesMatthew N. Benedict, James R. Henriksen, William W. Metcalf, Rachel J. Whitaker, Nathan D. Price · 2014 · BMC Genomics
- Experimental methods and modeling techniques for description of cell population heterogeneityR. Lencastre Fernandes, Marta Nierychlo, Luisa Lundin, A.E. Pedersen, Pilar Eliana Puentes‐Téllez, Abhishek Dutta, Magnus Carlquist, Andrijana Bolic, Daniel Schäpper, A.C. Brunetti et al. · 2011 · Biotechnology Advances
- Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formationN.A.L. Flahaut, Anne Wiersma, Bert van de Bunt, Dirk E. Martens, Peter J. Schaap, Lolke Sijtsma, Vítor A. P. Martins dos Santos, Willem M. de Vos · 2013 · Applied Microbiology and Biotechnology
- Mathematical optimization applications in metabolic networksAli R. Zomorrodi, Patrick F. Suthers, Sridhar Ranganathan, Costas D. Maranas · 2012 · Metabolic Engineering
- Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomicsAarash Bordbar, James T. Yurkovich, Giuseppe Paglia, Óttar Rolfsson, Ólafur E. Sigurjónsson, Bernhard Ørn Palsson · 2017 · Scientific Reports
- Reconstruction and flux‐balance analysis of the Plasmodium falciparum metabolic networkGermán Plata, Tzu‐Lin Hsiao, Kellen L. Olszewski, Manuel Llinás, Dennis Vitkup · 2010 · Molecular Systems Biology
- Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth ConditionsCristal Zúñiga, Chien‐Ting Li, Tyler Huelsman, Jennifer Levering, Daniel Craig Zielinski, Brian O. McConnell, Christopher P. Long, Eric P. Knoshaug, Michael Thomas Guarnieri, Maciek R. Antoniewicz et al. · 2016 · PLANT PHYSIOLOGY
- Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysisJared T. Broddrick, Benjamin E. Rubin, David G. Welkie, Niu Du, Nathan Mih, Spencer Diamond, Jenny J. Lee, Susan S. Golden, Bernhard Ørn Palsson · 2016 · Proceedings of the National Academy of Sciences
- Automatic construction of metabolic models with enzyme constraintsBekiaris, Pavlos Stephanos, Klamt, Steffen · 2020 · BMC Bioinformatics
- The genome of Onchocerca volvulus, agent of river blindnessJames Anthony Cotton, Sasisekhar Bennuru, Alexandra Grote, Bhavana Harsha, Alan Tracey, Robin N. Beech, Stephen R. Doyle, Matthew Dunn, Julie C. Dunning Hotopp, Nancy E. Holroyd et al. · 2016 · Nature Microbiology
- Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear CellsPartho Sen, Esko Kemppainen, Matej Orešič · 2018 · Frontiers in Molecular Biosciences
- Flux sampling is a powerful tool to study metabolism under changing environmental conditionsHelena A. Herrmann, Beth C. Dyson, Lucy Vass, Giles N. Johnson, Jean‐Marc Schwartz · 2019 · npj Systems Biology and Applications
- Systems biology for crop improvementLekha T. Pazhamala, Himabindu Kudapa, Wolfram Weckwerth, A. Harvey Millar, Rajeev Kumar Varshney · 2021 · The Plant Genome
- Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes
<i>In Silico</i>Heinken, Almut, Thiele, Ines · 2015 · Applied and Environmental Microbiology
- Metabolic network modeling of microbial communitiesBiggs, Matthew B., Medlock, Gregory L., Kolling, Glynis L., Papin, Jason A. · 2015 · WIREs Systems Biology and Medicine
- Adder and a coarse-grained approach to cell size homeostasis in bacteriaJohn T. Sauls, Dongyang Li, Suckjoon Jun · 2016 · Current Opinion in Cell Biology
- Mitochondrial Regulation of the Hippocampal Firing Rate Set Point and Seizure SusceptibilityBoaz Styr, Nir Gonen, Daniel Zarhin, Antonella Ruggiero, Refaela Atsmon, Neta Gazit, Gabriella Braun, Samuel G. A. Frère, Irena Vertkin, Ilana Shapira et al. · 2019 · Neuron
- Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model DiatomJennifer Levering, Jared T. Broddrick, Christopher L. Dupont, Graham Peers, Karen Beeri, Joshua J. Mayers, Alessandra A. Gallina, Andrew Ellis Allen, Bernhard Ørn Palsson, Karsten Zengler · 2016 · PLoS ONE
- fast G ap F ill : efficient gap filling in metabolic networksInes Thiele, Nikos A. Vlassis, Ronan M. T. Fleming · 2014 · Bioinformatics
- Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix itDouglas Bruce Kell · 2013 · FEBS Journal
- The Emerging Facets of Non-Cancerous Warburg EffectAlyaa M. Abdel‐Haleem, Nathan E. Lewis, Neema Jamshidi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori · 2017 · Frontiers in Endocrinology
- An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, i YL1228Yu-Chieh Liao, Tzu‐Wen Huang, Feng-Chi Chen, Pep Charusanti, Jay Sung-Joong Hong, Hwan‐You Chang, Shih‐Feng Tsai, Bernhard Ørn Palsson, Chao Agnes Hsiung · 2011 · Journal of Bacteriology
- Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model ValidationCatherine Bjerre Collin, Tom Gebhardt, Martin Golebiewski, Tugce Karaderi, Maximilian Hillemanns, Faiz M. Khan, Ali Salehzadeh‐Yazdi, Marc W. Kirschner, Sylvia Krobitsch, Lars Kuepfer · 2022 · Journal of Personalized Medicine
- Beyond growth rate 0.6: What drives Corynebacterium glutamicum to higher growth rates in defined mediumSimon Unthan, Alexander Grünberger, Jan van Ooyen, Jochem Gätgens, Johanna Heinrich, Nicole Paczia, Wolfgang Wiechert, Dietrich Kohlheyer, Stephan Noack · 2013 · Biotechnology and Bioengineering
- A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicolaGavin H. Thomas, Jeremy Zucker, Sandy J. Macdonald, Anatoly Sorokin, Igor Goryanin, Angela E. Douglas · 2009 · BMC Systems Biology
- Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic modelsNeelakantan Thulasi Devika, Karthik Raman · 2019 · Scientific Reports
- Using the reconstructed genome-scale human metabolic network to study physiology and pathologyBordbar, A., Palsson, B. O. · 2012 · Journal of Internal Medicine
- Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coliRoger L. Chang, Kathleen A. Andrews, Donghyuk Kim, Zhanwen Li, Adam Godzik, Bernhard Ørn Palsson · 2013 · Science
- A metabolic network approach for the identification and prioritization of antimicrobial drug targetsArvind K. Chavali, Kevin M. D’Auria, Erik L. Hewlett, Richard D. Pearson, Jason A. Papin · 2012 · Trends in Microbiology
- Origins and Evolution of MicroRNA Genes in Drosophila SpeciesMasafumi Nozawa, Sayaka Miura, Masatoshi Nei · 2010 · Genome Biology and Evolution
- Deregulation of S-adenosylmethionine biosynthesis and regeneration improves methylation in the E. coli de novo vanillin biosynthesis pathwayAditya M. Kunjapur, Jason C. Hyun, Kristala L. J. Prather · 2016 · Microbial Cell Factories
- Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenumKaspar Valgepea, Quang K. Loi, James B. Y. H. Behrendorff, Renato de Souza Pinto Lemgruber, Manuel R. Plan, Mark P. Hodson, Michael Köpke, Lars Keld Nielsen, Esteban Marcellin · 2017 · Metabolic Engineering
- Synthetic Microbial Ecology: Engineering Habitats for Modular ConsortiaSami Ben Said, Dani Or · 2017 · Frontiers in Microbiology
- Systematic overexpression study to find target enzymes enhancing production of terpenes in Synechocystis PCC 6803, using isoprene as a model compoundElias Englund, Kiyan Shabestary, Elton Paul Hudson, Pia Lindberg · 2018 · Metabolic Engineering
- A multi-tissue genome-scale metabolic modeling framework for the analysis of whole plant systemsCristiana Gomes de Oliveira Dal’Molin, Lake‐Ee Quek, Pedro A. Saa, Lars Keld Nielsen · 2015 · Frontiers in Plant Science
- Dynamic control of endogenous metabolism with combinatorial logic circuitsFelix Moser, Amin Espah Borujeni, Amar Ghodasara, Ewen Cameron, Yongjin Park, Christopher A. Voigt · 2018 · Molecular Systems Biology
- Synergistic substrate cofeeding stimulates reductive metabolismJunyoung O. Park, Nian Liu, Kara M. Holinski, David Frederic Emerson, Kangjian Qiao, Benjamin M. Woolston, Jingyang Xu, Zbigniew Lazar, M. Ahsanul Islam, Charles Vidoudez et al. · 2019 · Nature Metabolism
- Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable ProductsIsabel Bator, Andreas Wittgens, Frank Rosenau, Till Tiso, Lars M. Blank · 2020 · Frontiers in Bioengineering and Biotechnology
- A systems biology approach to studying the role of microbes in human healthThiele, Ines, Heinken, Almut, Fleming, Ronan MT · 2013 · Current Opinion in Biotechnology
- Genome‐scale metabolic modeling of a clostridial co‐culture for consolidated bioprocessingFahimeh Salimi, Kai H. Zhuang, Radhakrishnan Mahadevan · 2010 · Biotechnology Journal
- Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol productionJosefine Anfelt, Danuta Kaczmarzyk, Kiyan Shabestary, Björn Renberg, Johan Rockberg, Jens Nielsen, Mathias Uhlén, Elton Paul Hudson · 2015 · Microbial Cell Factories
- MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networksMathias Ganter, Thomas Bernard, Sébastien Moretti, Jörg Stelling, Marco Pagni · 2013 · Bioinformatics
- Metabolic engineering strategies to bio-adipic acid productionNicholas S. Kruyer, Pamela Peralta‐Yahya · 2017 · Current Opinion in Biotechnology
- Nutrient limitation determines the fitness of cheaters in bacterial siderophore cooperationD. Joseph Sexton, Martín Schuster · 2017 · Nature Communications