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K. Kjeldsen, J. Nielsen (2009)
In silico genome‐scale reconstruction and validation of the Corynebacterium glutamicum metabolic networkBiotechnology and Bioengineering, 102
G. Thomas, Jeremy Zucker, S. Macdonald, A. Sorokin, I. Goryanin, A. Douglas (2009)
A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicolaBMC Systems Biology, 3
A. Manichaikul, L. Ghamsari, E. Hom, Chenwei Lin, Ryan Murray, Roger Chang, Santhanam Balaji, Tong Hao, Yun Shen, Arvind Chavali, Ines Thiele, Ines Thiele, Xinping Yang, Changyu Fan, Elizabeth Mello, D. Hill, M. Vidal, K. Salehi-Ashtiani, J. Papin (2009)
Metabolic network analysis integrated with transcript verification for sequenced genomesNature Methods, 6
Patrik Jones (2008)
Improving fermentative biomass-derived H2-production by engineering microbial metabolismInternational Journal of Hydrogen Energy, 33
M. Butler (2005)
Animal cell cultures: recent achievements and perspectives in the production of biopharmaceuticalsApplied Microbiology and Biotechnology, 68
M. Andersen, M. Nielsen, J. Nielsen (2008)
Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus nigerMolecular Systems Biology, 4
K. Radrich, Yoshimasa Tsuruoka, P. Dobson, A. Gevorgyan, Neil Swainston, J. Schwartz (2009)
Reconstruction of an in silico metabolic model of Arabidopsis thaliana through database integrationNature Precedings
Gino Baart, B. Zomer, A. Haan, L. Pol, E. Beuvery, J. Tramper, D. Martens (2007)
Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxesGenome Biology, 8
C. Bro, Birgitte Regenberg, Jochen Förster, J. Nielsen (2006)
In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production.Metabolic engineering, 8 2
J. Puchalka, M. Oberhardt, Miguel Godinho, Agata Bielecka, D. Regenhardt, K. Timmis, J. Papin, V. Santos (2008)
Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in BiotechnologyPLoS Computational Biology, 4
Hongwu Ma, I. Goryanin (2008)
Human metabolic network reconstruction and its impact on drug discovery and development.Drug discovery today, 13 9-10
B. Teusink, Anne Wiersma, D. Molenaar, C. Francke, W. Vos, R. Siezen, E. Smid (2006)
Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model*Journal of Biological Chemistry, 281
David Deutscher, I. Meilijson, M. Kupiec, E. Ruppin (2006)
Multiple knockout analysis of genetic robustness in the yeast metabolic networkNature Genetics, 38
S. Moon, Soon Hong, T. Kim, Sang Lee (2008)
Metabolic engineering of Escherichia coli for the production of malic acidBiochemical Engineering Journal, 40
R. Mahadevan, J. Edwards, F. Doyle (2002)
Dynamic flux balance analysis of diauxic growth in Escherichia coli.Biophysical journal, 83 3
Adam Feist, B. Palsson (2008)
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coliNature Biotechnology, 26
J. Nielsen, M. Jewett (2008)
Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae.FEMS yeast research, 8 1
I. Nookaew, M. Jewett, A. Meechai, C. Thammarongtham, K. Laoteng, S. Cheevadhanarak, J. Nielsen, S. Bhumiratana (2008)
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolismBMC Systems Biology, 2
Qingzhao Wang, Xun Chen, Yudi Yang, Xue-Ming Zhao (2006)
Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate productionApplied Microbiology and Biotechnology, 73
T. Shlomi, Moran Cabili, E. Ruppin (2009)
Predicting metabolic biomarkers of human inborn errors of metabolismMolecular Systems Biology, 5
R. Mahadevan, D. Bond, J. Butler, A. Estéve-Núñez, M. Coppi, B. Palsson, C. Schilling, D. Lovley (2006)
Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based ModelingApplied and Environmental Microbiology, 72
I. Thiele, Thuy Vo, N. Price, B. Palsson (2005)
Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion MutantsJournal of Bacteriology, 187
R. Senger, E. Papoutsakis (2008)
Genome‐scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysisBiotechnology and Bioengineering, 101
Molecular Systems Biology 3; Article number 101; doi:10.1038/msb4100141 Citation: Molecular Systems Biology 3:101
K. Lee, J. Park, T. Kim, H. Kim, S. Lee (2007)
Systems metabolic engineering of Escherichia coli for L-threonine productionMolecular Systems Biology, 3
Molecular Systems Biology 3; Article number 92; doi:10.1038/msb4100131 Citation: Molecular Systems Biology 3:92
Chiraphan Khannapho, Hongjuan Zhao, B. Bonde, A. Kierzek, C. Avignone-Rossa, M. Bushell (2008)
Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production.Metabolic engineering, 10 5
T. Kim, H. Kim, J. Park, Hyohak Song, J. Kim, S. Lee (2007)
Genome-scale analysis of Mannheimia succiniciproducens metabolism.Biotechnology and bioengineering, 97 4
Orland Gonzalez, Susanne Gronau, M. Falb, F. Pfeiffer, E. Mendoza, R. Zimmer, D. Oesterhelt (2008)
Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism.Molecular bioSystems, 4 2
Karthik Raman, Kalidas Yeturu, Nagasuma Chandra (2008)
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysisBMC Systems Biology, 2
A. Burgard, Prit Pharkya, C. Maranas (2003)
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimizationBiotechnology and Bioengineering, 84
Ali Navid, E. Almaas (2009)
Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001.Molecular bioSystems, 5 4
Csaba Pál, Balázs Papp, M. Lercher, P. Csermely, S. Oliver, L. Hurst (2006)
Chance and necessity in the evolution of minimal metabolic networksNature, 440
J. Park, K. Lee, T. Kim, S. Lee (2007)
Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulationProceedings of the National Academy of Sciences, 104
(2004)
Nature
I. Thiele, N. Jamshidi, Ronan Fleming, B. Palsson (2009)
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional CharacterizationPLoS Computational Biology, 5
Arvind Chavali, Jeffrey Whittemore, James Eddy, Kyle Williams, J. Papin (2008)
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania majorMolecular Systems Biology, 4
P. Suthers, Madhukar Dasika, V. Kumar, Gennady Denisov, J. Glass, C. Maranas (2009)
A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189PLoS Computational Biology, 5
K. Patil, I. Rocha, Jochen Förster, J. Nielsen (2005)
Evolutionary programming as a platform for in silico metabolic engineeringBMC Bioinformatics, 6
Pan-Jun Kim, Dong-Yup Lee, T. Kim, K. Lee, Hawoong Jeong, S. Lee, Sunwon Park (2007)
Metabolite essentiality elucidates robustness of Escherichia coli metabolismProceedings of the National Academy of Sciences, 104
Natalie Duarte, S. Becker, N. Jamshidi, I. Thiele, Monica Mo, Thuy Vo, R. Srivas, B. Palsson (2007)
Global reconstruction of the human metabolic network based on genomic and bibliomic dataProceedings of the National Academy of Sciences, 104
Y. Zhu, Yanping Zhang, Yin Li (2009)
Understanding the industrial application potential of lactic acid bacteria through genomicsApplied Microbiology and Biotechnology, 83
Kashif Sheikh, Jochen Förster, L. Nielsen (2008)
Modeling Hybridoma Cell Metabolism Using a Generic Genome‐Scale Metabolic Model of Mus musculusBiotechnology Progress, 21
Irina Borodina, Jeroen Siebring, Jie Zhang, Colin Smith, G. Keulen, L. Dijkhuizen, J. Nielsen (2008)
Antibiotic Overproduction in Streptomyces coelicolor A3(2) Mediated by Phosphofructokinase Deletion*Journal of Biological Chemistry, 283
C. Colijn, C. Colijn, C. Colijn, A. Brandes, Jeremy Zucker, D. Lun, D. Lun, B. Weiner, M. Farhat, T. Cheng, D. Moody, Megan Murray, J. Galagan, J. Galagan (2009)
Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid ProductionPLoS Computational Biology, 5
T. Zozio, Caroline Allix, S. Gunal, Z. Sarıbaş, A. Alp, R. Durmaz, M. Fauville-Dufaux, Nalin Rastogi, C. Sola (2005)
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotationBMC Microbiology, 5
Víctor Lorenzo (2008)
Systems biology approaches to bioremediation.Current opinion in biotechnology, 19 6
H. David, İ. Özçelik, G. Hofmann, J. Nielsen (2008)
Analysis of Aspergillus nidulans metabolism at the genome-scaleBMC Genomics, 9
Jong Lee, Erwin Gianchandani, James Eddy, J. Papin (2008)
Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory NetworksPLoS Computational Biology, 4
M. Abuoun, P. F. Suthers, G. I. Jones, B. R. Carter (2009)
Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain.
S. Meijer, M. Nielsen, L. Olsson, J. Nielsen (2009)
Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus nigerJournal of Industrial Microbiology & Biotechnology, 36
Daniel Segré, Dennis Vitkup, George Church (2002)
Analysis of optimality in natural and perturbed metabolic networksProceedings of the National Academy of Sciences of the United States of America, 99
B. Teusink, Anne Wiersma, L. Jacobs, Richard Notebaart, E. Smid (2009)
Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico OptimisationPLoS Computational Biology, 5
P. Fu (2009)
Genome‐scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertionJournal of Chemical Technology & Biotechnology, 84
(2009)
Genome Biol
J. Nogales, B. O. Palsson, I. Thiele (2008)
A genome‐scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory., 2
J. Reed, Thuy Vo, C. Schilling, B. Palsson (2003)
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)Genome Biology, 4
C. Ghim, K. Goh, B. Kahng (2004)
Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli.Journal of theoretical biology, 237 4
Thuy Vo, W. Lee, B. Palsson (2007)
Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome.Molecular genetics and metabolism, 91 1
(2005)
Biotechnol. Bioeng
(2006)
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
Monica Mo, B. Palsson, Markus Herrgård (2009)
Connecting extracellular metabolomic measurements to intracellular flux states in yeastBMC Systems Biology, 3
Jun Sun, Bahareh Sayyar, J. Butler, Prit Pharkya, T. Fahland, Iman Famili, C. Schilling, D. Lovley, R. Mahadevan (2009)
Genome-scale constraint-based modeling of Geobacter metallireducensBMC Systems Biology, 3
T. Shlomi, M. Cabili, Markus Herrgård, B. Palsson, E. Ruppin (2008)
Network-based prediction of human tissue-specific metabolismNature Biotechnology, 26
Hongwu Ma, A. Sorokin, A. Mazein, A. Selkov, E. Selkov, O. Demin, I. Goryanin (2007)
The Edinburgh human metabolic network reconstruction and its functional analysisMolecular Systems Biology, 3
O. Reséndis-Antonio, J. Reed, S. Encarnación-Guevara, J. Collado-Vides, B. Palsson (2007)
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etliPLoS Computational Biology, 3
H. Kim, T. Kim, S. Lee (2008)
Metabolic flux analysis and metabolic engineering of microorganisms.Molecular bioSystems, 4 2
D. Segrè, A. DeLuna, G. Church, R. Kishony (2005)
Modular epistasis in yeast metabolismNature Genetics, 37
T. Shlomi, Y. Eisenberg, R. Sharan, E. Ruppin (2007)
A genome‐scale computational study of the interplay between transcriptional regulation and metabolism., 3
N. Price, J. Reed, B. Palsson (2004)
Genome-scale models of microbial cells: evaluating the consequences of constraintsNature Reviews Microbiology, 2
M. Covert, E. Knight, J. Reed, Markus Herrgård, B. Palsson (2004)
Integrating high-throughput and computational data elucidates bacterial networksNature, 429
Prit Pharkya, C. Maranas (2006)
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems.Metabolic engineering, 8 1
S. Stolyar, S. Van Dien, K. L. Hillesland, N. Pinel (2007)
Metabolic modeling of a mutualistic microbial community., 3
H. Alper, K. Miyaoku, G. Stephanopoulos (2005)
Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targetsNature Biotechnology, 23
C. Schilling, M. Covert, Iman Famili, G. Church, J. Edwards, B. Palsson (2002)
Genome-Scale Metabolic Model of Helicobacter pylori 26695Journal of Bacteriology, 184
D. Kell, Marie Brown, H. Davey, W. Dunn, Irena Spasic, S. Oliver (2005)
Metabolic footprinting and systems biology: the medium is the messageNature Reviews Microbiology, 3
Adam Feist, Christopher Henry, Jennifer Reed, Markus Krummenacker, A. Joyce, Peter Karp, L. Broadbelt, V. Hatzimanikatis, B. Palsson (2007)
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic informationMolecular Systems Biology, 3
J. Trawick, C. Schilling (2006)
Use of constraint-based modeling for the prediction and validation of antimicrobial targets.Biochemical pharmacology, 71 7
Mark Roberts, Elias August, Abdullah Hamadeh, P. Maini, P. McSharry, Judith Armitage, A. Papachristodoulou (2009)
A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroidesBMC Systems Biology, 3
Prit Pharkya, A. Burgard, C. Maranas (2003)
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnockBiotechnology and Bioengineering, 84
J. Edwards, B. Palsson (2000)
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.Proceedings of the National Academy of Sciences of the United States of America, 97 10
S. Fong, A. Burgard, C. Herring, E. Knight, F. Blattner, C. Maranas, B. Palsson (2005)
In silico design and adaptive evolution of Escherichia coli for production of lactic acid.Biotechnology and bioengineering, 91 5
Deok-Sun Lee, H. Burd, Jiangxia Liu, E. Almaas, O. Wiest, A. Barabási, Z. Oltvai, V. Kapatral (2009)
Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug TargetsJournal of Bacteriology, 191
D. Beste, T. Hooper, G. Stewart, B. Bonde, C. Avignone-Rossa, M. Bushell, P. Wheeler, Steffen Klamt, A. Kierzek, J. McFadden (2007)
GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolismGenome Biology, 8
J. Park, T. Kim, S. Lee (2009)
Constraints-based genome-scale metabolic simulation for systems metabolic engineering.Biotechnology advances, 27 6
M. AbuOun, P. Suthers, Gareth Jones, Ben Carter, M. Saunders, C. Maranas, M. Woodward, M. Anjum (2009)
Genome Scale Reconstruction of a Salmonella Metabolic ModelThe Journal of Biological Chemistry, 284
S. Selvarasu, Victor Wong, I. Karimi, Dong-Yup Lee (2009)
Elucidation of metabolism in hybridoma cells grown in fed‐batch culture by genome‐scale modelingBiotechnology and Bioengineering, 102
Erwin Gianchandani, J. Papin, N. Price, A. Joyce, B. Palsson (2006)
Matrix Formalism to Describe Functional States of Transcriptional Regulatory SystemsPLoS Computational Biology, 2
(2007)
Mol. Genet. Metab
Prit Pharkya, A. Burgard, C. Maranas (2004)
OptStrain: a computational framework for redesign of microbial production systems.Genome research, 14 11
A. P. Oliveira, J. Nielsen, J. Forster (2005)
Modeling Lactococcus lactis using a genome‐scale flux model., 5
Jared Hjersted, M. Henson (2009)
Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae.IET systems biology, 3 3
N. Jamshidi, B. Palsson (2007)
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targetsBMC Systems Biology, 1
Jochen Förster, Iman Famili, P. Fu, B. Palsson, J. Nielsen (2003)
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.Genome research, 13 2
Mouse Consortium (2002)
Initial sequencing and comparative analysis of the mouse genomeNature, 420
A. Raghunathan, J. Reed, Sook-Il Shin, B. Palsson, S. Daefler (2009)
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interactionBMC Systems Biology, 3
M. Covert, Nan Xiao, Tiffany Chen, Jonathan Karr (2008)
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coliBioinformatics, 24 18
S. Lee, Dong-Yup Lee, T. Kim, Byung Kim, Jinwon Lee, Sang Lee (2005)
Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout SimulationApplied and Environmental Microbiology, 71
J. Edwards, R. Ibarra, B. Palsson (2001)
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental dataNature Biotechnology, 19
H. Alper, Yong‐Su Jin, J. Moxley, G. Stephanopoulos (2005)
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli.Metabolic engineering, 7 3
M. Oberhardt, J. Puchalka, K. Fryer, Vítor Santos, J. Papin (2008)
Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1Journal of Bacteriology, 190
姚利晓, 蔡幼民, 林矫矫, 刘金明 (2005)
IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW,Thompson RW,et al//Proc Natl Acad Sci U S A, 32
Irina Borodina, Preben Krabben, J. Nielsen (2005)
Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism.Genome research, 15 6
A. Raghunathan, N. Price, Michael Galperin, K. Makarova, S. Purvine, Alex Picone, T. Cherny, T. Xie, T. Reilly, R. Munson, R. Tyler, B. Akerley, Arnold Smith, B. Palsson, E. Kolker (2004)
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.Omics : a journal of integrative biology, 8 1
M. Asadollahi, J. Maury, K. Patil, M. Schalk, Anthony Clark, J. Nielsen (2009)
Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering.Metabolic engineering, 11 6
C. Schilling, B. Palsson (2000)
Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.Journal of theoretical biology, 203 3
M. Andersen, L. Lehmann, J. Nielsen (2009)
Systemic analysis of the response of Aspergillus niger to ambient pHGenome Biology, 10
Iman Famili, Jochen Förster, J. Nielsen, B. Palsson (2003)
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic networkProceedings of the National Academy of Sciences of the United States of America, 100
T. Kim, H. Kim, Hyohak Song, S. Lee (2009)
In silico analysis of the effects of H2 and CO2 on the metabolism of a capnophilic bacterium Mannheimia succiniciproducens.Journal of biotechnology, 144 3
P. Suthers, Ali Zomorrodi, C. Maranas (2009)
Genome-scale gene/reaction essentiality and synthetic lethality analysisMolecular Systems Biology, 5
Dominic Lee, Juyong Park, Krin Kay, N. Christakis, Zoltn Oltvai, A. Barabási (2008)
The implications of human metabolic network topology for disease comorbidityProceedings of the National Academy of Sciences, 105
T. Kim, H. Kim, S. Lee (2010)
Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks.Metabolic engineering, 12 2
M. Pastink, B. Teusink, P. Hols, S. Visser, W. Vos, J. Hugenholtz (2009)
Genome-Scale Model of Streptococcus thermophilus LMG18311 for Metabolic Comparison of Lactic Acid BacteriaApplied and Environmental Microbiology, 75
(2005)
BMC Microbiology BioMed Central Research article Modeling Lactococcus lactis using a genome-scale flux model
Natalie Duarte, Markus Herrgård, B. Palsson (2004)
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.Genome research, 14 7
Yohei Shinfuku, Natee Sorpitiporn, M. Sono, C. Furusawa, T. Hirasawa, H. Shimizu (2009)
Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicumMicrobial Cell Factories, 8
(2007)
PLoS Comput. Biol
(2006)
Appl. Microbiol. Biotechnol
(2008)
Bioinformatics
M. Covert, C. Schilling, B. Palsson (2001)
Regulation of gene expression in flux balance models of metabolism.Journal of theoretical biology, 213 1
Varun Mazumdar, E. Snitkin, S. Amar, D. Segrè (2008)
Metabolic Network Model of a Human Oral PathogenJournal of Bacteriology, 191
Jong Lee, Erwin Gianchandani, James Eddy, J. Papin (2008)
Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory NetworksPLoS Computational Biology, 4
Y. Oh, B. Palsson, S. Park, C. Schilling, R. Mahadevan (2007)
Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data*Journal of Biological Chemistry, 282
C. Henry, Jenifer Zinner, Matthew Cohoon, Rick Stevens (2009)
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotationsGenome Biology, 10
J. Lee, H. Yun, Adam Feist, B. Palsson, S. Lee (2008)
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic networkApplied Microbiology and Biotechnology, 80
W. Vongsangnak, P. Olsen, Han-Kyoung Kim, Steen Krogsgaard, J. Nielsen (2008)
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzaeBMC Genomics, 9
G. Stephanopoulos (1994)
Metabolic engineering.Current opinion in biotechnology, 5 2
Gian Oddone, D. Mills, D. Block (2009)
A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression.Metabolic engineering, 11 6
M. Durot, P. Bourguignon, V. Schachter (2008)
Genome-scale models of bacterial metabolism: reconstruction and applicationsFems Microbiology Reviews, 33
Matthias Heinemann, A. Kümmel, Reto Ruinatscha, S. Panke (2005)
In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network.Biotechnology and bioengineering, 92 7
Kenneth Kauffman, P. Prakash, J. Edwards (2003)
Advances in flux balance analysis.Current opinion in biotechnology, 14 5
M. Durot, F. Fèvre, V. Berardinis, A. Kreimeyer, D. Vallenet, C. Combe, Serge Smidtas, M. Salanoubat, J. Weissenbach, Vincent Schächter (2008)
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality dataBMC Systems Biology, 2
Sung Lee, Howard Chou, Timothy Ham, T. Lee, J. Keasling (2008)
Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels.Current opinion in biotechnology, 19 6
S. Gerdes, M. Scholle, J. Campbell, G. Balázsi, E. Ravasz, M. Daugherty, A. Somera, N. Kyrpides, I. Anderson, M. Gelfand, A. Bhattacharya, V. Kapatral, M. D'Souza, M. Baev, Y. Grechkin, F. Mseeh, M. Fonstein, R. Overbeek, A. Barabási, Z. Oltvai, A. Osterman (2003)
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655Journal of Bacteriology, 185
Erwin Gianchandani, A. Joyce, B. Palsson, J. Papin (2009)
Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory SystemPLoS Computational Biology, 5
Markus Herrgård, Baek-Seok Lee, Vasiliy Portnoy, B. Palsson (2006)
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.Genome research, 16 5
Adam Feist, Markus Herrgård, I. Thiele, Jennie Reed, B. Palsson (2009)
Reconstruction of biochemical networks in microorganismsNature Reviews Microbiology, 7
Mounir Izallalen, R. Mahadevan, A. Burgard, Bradley Postier, Raymond Didonato, Jun Sun, C. Schilling, D. Lovley (2008)
Geobacter sulfurreducens strain engineered for increased rates of respiration.Metabolic engineering, 10 5
Markus Herrgård, Neil Swainston, P. Dobson, W. Dunn, K. Arğa, Mikko Arvas, N. Blüthgen, S. Borger, R. Costenoble, Matthias Heinemann, M. Hucka, N. Novère, P. Li, Wolfram Liebermeister, Monica Mo, A. Oliveira, Dina Petranovic, S. Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasié, D. Weichart, R. Brent, D. Broomhead, H. Westerhoff, Betül Kürdar, M. Penttilä, E. Klipp, B. Palsson, U. Sauer, S. Oliver, P. Mendes, J. Nielsen, D. Kell (2008)
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biologyNature Biotechnology, 26
Driven by advancements in high‐throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Here, we review comprehensively the uses of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. While the use of in silico models is still in its early stages for delivering to industry, significant initial successes have been achieved. For the cases presented here, genome‐scale models predict engineering strategies to enhance properties of interest in an organism or to inhibit harmful mechanisms of pathogens. Going forward, genome‐scale in silico models promise to extend their application and analysis scope to become a transformative tool in biotechnology.
Biotechnology Journal – Wiley
Published: Dec 1, 2009
Keywords: ; ; ;
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