Metabolic network modelling (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Metabolic network modelling" in English language version.

refsWebsite

Global rank English rank

63nih.gov

4^th place

42doi.org

2^nd place

10harvard.edu

18^th place

17^th place

6semanticscholar.org

11^th place

8^th place

2arxiv.org

69^th place

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1wikidot.com

4,776^th place

4,391^st place

arxiv.org

Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, et al. (January 2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology". Briefings in Bioinformatics. 11 (1): 40–79. arXiv:1510.03964. doi:10.1093/bib/bbp043. PMC 2810111. PMID 19955237.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, et al. (December 2013). "SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools". BMC Systems Biology. 7 (1): 135. arXiv:1309.1910. Bibcode:2013arXiv1309.1910C. doi:10.1186/1752-0509-7-135. PMC 3892043. PMID 24321545.

doi.org

Francke C, Siezen RJ, Teusink B (November 2005). "Reconstructing the metabolic network of a bacterium from its genome". Trends in Microbiology. 13 (11): 550–558. doi:10.1016/j.tim.2005.09.001. PMID 16169729.
Thiele I, Palsson BØ (January 2010). "A protocol for generating a high-quality genome-scale metabolic reconstruction". Nature Protocols. 5 (1): 93–121. doi:10.1038/nprot.2009.203. PMC 3125167. PMID 20057383.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. (July 1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science. 269 (5223): 496–512. Bibcode:1995Sci...269..496F. doi:10.1126/science.7542800. PMID 7542800. S2CID 10423613.
The C. elegans Sequencing Consortium (December 1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". Science. 282 (5396): 2012–2018. Bibcode:1998Sci...282.2012.. doi:10.1126/science.282.5396.2012. PMID 9851916. S2CID 16873716.
Edwards JS, Palsson BO (May 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): 5528–5533. Bibcode:2000PNAS...97.5528E. doi:10.1073/pnas.97.10.5528. PMC 25862. PMID 10805808.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J (February 2003). "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network". Genome Research. 13 (2): 244–253. doi:10.1101/gr.234503. PMC 420374. PMID 12566402.
Sheikh K, Förster J, Nielsen LK (January 2005). "Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus". Biotechnology Progress. 21 (1): 112–121. doi:10.1021/bp0498138. PMID 15903248. S2CID 38627979.
Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD (June 2004). "Computational prediction of human metabolic pathways from the complete human genome". Genome Biology. 6 (1): R2. doi:10.1186/gb-2004-6-1-r2. PMC 549063. PMID 15642094.
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, et al. (February 2007). "Global reconstruction of the human metabolic network based on genomic and bibliomic data". Proceedings of the National Academy of Sciences of the United States of America. 104 (6): 1777–1782. Bibcode:2007PNAS..104.1777D. doi:10.1073/pnas.0610772104. PMC 1794290. PMID 17267599.
Jamshidi N, Palsson BØ (June 2007). "Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets". BMC Systems Biology. 1: 26. doi:10.1186/1752-0509-1-26. PMC 1925256. PMID 17555602.
Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R (September 2007). "Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data". The Journal of Biological Chemistry. 282 (39): 28791–28799. doi:10.1074/jbc.M703759200. PMID 17573341.
Fu P (October 2008). "Genome-scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertion". Journal of Chemical Technology and Biotechnology. 84 (4): 473–483. doi:10.1002/jctb.2065.
Raghunathan A, Reed J, Shin S, Palsson B, Daefler S (April 2009). "Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction". BMC Systems Biology. 3: 38. doi:10.1186/1752-0509-3-38. PMC 2678070. PMID 19356237.
de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (February 2010). "AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis". Plant Physiology. 152 (2): 579–589. doi:10.1104/pp.109.148817. PMC 2815881. PMID 20044452.
Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z (January 2020). "BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree". Nucleic Acids Research. 48 (D1): D402 – D406. doi:10.1093/nar/gkz1054. PMC 7145653. PMID 31696234.
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, et al. (January 2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology". Briefings in Bioinformatics. 11 (1): 40–79. arXiv:1510.03964. doi:10.1093/bib/bbp043. PMC 2810111. PMID 19955237.
Wrzodek C, Büchel F, Ruff M, Dräger A, Zell A (February 2013). "Precise generation of systems biology models from KEGG pathways". BMC Systems Biology. 7 (1): 15. doi:10.1186/1752-0509-7-15. PMC 3623889. PMID 23433509.
Wrzodek C, Dräger A, Zell A (August 2011). "KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats". Bioinformatics. 27 (16): 2314–2315. doi:10.1093/bioinformatics/btr377. PMC 3150042. PMID 21700675.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, et al. (December 2013). "SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools". BMC Systems Biology. 7 (1): 135. arXiv:1309.1910. Bibcode:2013arXiv1309.1910C. doi:10.1186/1752-0509-7-135. PMC 3892043. PMID 24321545.
Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (September 2010). "High-throughput generation, optimization and analysis of genome-scale metabolic models". Nature Biotechnology. 28 (9): 977–982. doi:10.1038/nbt.1672. PMID 20802497. S2CID 6641097.
Chindelevitch L, Stanley S, Hung D, Regev A, Berger B (January 2012). "MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis". Genome Biology. 13 (1): r6. doi:10.1186/gb-2012-13-1-r6. PMC 3488975. PMID 22292986.
Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, et al. (February 2014). "Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species". PLOS Computational Biology. 10 (2): e1003465. Bibcode:2014PLSCB..10E3465P. doi:10.1371/journal.pcbi.1003465. PMC 3916221. PMID 24516375.
Castillo S, Barth D, Arvas M, Pakula TM, Pitkänen E, Blomberg P, et al. (November 2016). "Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction". Biotechnology for Biofuels. 9: 252. doi:10.1186/s13068-016-0665-0. PMC 5117618. PMID 27895706.
Ivanova N, Lykidis A (2009). "Metabolic Reconstruction". (3rd ed.). pp. 607–621. doi:10.1016/B978-012373944-5.00010-9. ISBN 9780123739445. {{cite book}}: |journal= ignored (help); Missing or empty |title= (help)
Linster CL, Van Schaftingen E, Hanson AD (February 2013). "Metabolite damage and its repair or pre-emption". Nature Chemical Biology. 9 (2): 72–80. doi:10.1038/nchembio.1141. PMID 23334546.
Hanson AD, Henry CS, Fiehn O, de Crécy-Lagard V (April 2016). "Metabolite Damage and Metabolite Damage Control in Plants". Annual Review of Plant Biology. 67: 131–152. doi:10.1146/annurev-arplant-043015-111648. PMID 26667673.
Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO (August 2004). "Comparison of network-based pathway analysis methods". Trends in Biotechnology. 22 (8): 400–405. doi:10.1016/j.tibtech.2004.06.010. PMID 15283984.
Lewis NE, Nagarajan H, Palsson BO (February 2012). "Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods". Nature Reviews. Microbiology. 10 (4): 291–305. doi:10.1038/nrmicro2737. PMC 3536058. PMID 22367118.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO (November 2003). "Network-based analysis of metabolic regulation in the human red blood cell". Journal of Theoretical Biology. 225 (2): 185–194. Bibcode:2003JThBi.225..185P. doi:10.1016/s0022-5193(03)00237-6. PMID 14575652.
Papin JA, Price ND, Palsson BØ (December 2002). "Extreme pathway lengths and reaction participation in genome-scale metabolic networks". Genome Research. 12 (12): 1889–1900. doi:10.1101/gr.327702. PMC 187577. PMID 12466293.
Schuster S, Fell DA, Dandekar T (March 2000). "A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks". Nature Biotechnology. 18 (3): 326–332. doi:10.1038/73786. PMID 10700151. S2CID 7742485.
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (November 2002). "Metabolic network structure determines key aspects of functionality and regulation". Nature. 420 (6912): 190–193. Bibcode:2002Natur.420..190S. doi:10.1038/nature01166. PMID 12432396. S2CID 4301741.
Ullah E, Aeron S, Hassoun S (2015). "gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13 (1): 122–134. doi:10.1109/TCBB.2015.2430344. PMID 26886737.
Larhlimi A, Bockmayr A (2009). "A new constraint-based description of the steady-state flux cone of metabolic networks". Discrete Applied Mathematics. 157 (10): 2257–2266. doi:10.1016/j.dam.2008.06.039.
Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, et al. (January 2009). "Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies". BMC Systems Biology. 3 (5): 5. doi:10.1186/1752-0509-3-5. PMC 2661887. PMID 19144170.
Dräger A, Hassis N, Supper J, Schröder A, Zell A (April 2008). "SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks". BMC Systems Biology. 2 (1): 39. doi:10.1186/1752-0509-2-39. PMC 2412839. PMID 18447902.
Wunderlich Z, Mirny LA (September 2006). "Using the topology of metabolic networks to predict viability of mutant strains". Biophysical Journal. 91 (6): 2304–2311. Bibcode:2006BpJ....91.2304W. doi:10.1529/biophysj.105.080572. PMC 1557581. PMID 16782788.
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, et al. (January 2010). "The genetic landscape of a cell". Science. 327 (5964): 425–431. Bibcode:2010Sci...327..425C. doi:10.1126/science.1180823. PMC 5600254. PMID 20093466.
Fong SS, Marciniak JY, Palsson BØ (November 2003). "Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model". Journal of Bacteriology. 185 (21): 6400–6408. doi:10.1128/JB.185.21.6400-6408.2003. PMC 219384. PMID 14563875.
Ivanova A, Lykidis A (2009). "Metabolic Reconstruction". Encyclopedia of Microbiology. pp. 607–621. doi:10.1016/B978-012373944-5.00010-9. ISBN 9780123739445. {{cite book}}: |journal= ignored (help)
Whitmore LS, Nguyen B, Pinar A, George A, Hudson CM (September 2019). "RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms". BMC Bioinformatics. 20 (1): 461. doi:10.1186/s12859-019-3025-9. PMC 6734243. PMID 31500573.
Enuh BM, Nural Yaman B, Tarzi C, Aytar Çelik P, Mutlu MB, Angione C (October 2022). "Whole-genome sequencing and genome-scale metabolic modeling of Chromohalobacter canadensis 85B to explore its salt tolerance and biotechnological use". MicrobiologyOpen. 11 (5): e1328. doi:10.1002/mbo3.1328. PMC 9597258. PMID 36314754.

harvard.edu

ui.adsabs.harvard.edu

Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. (July 1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science. 269 (5223): 496–512. Bibcode:1995Sci...269..496F. doi:10.1126/science.7542800. PMID 7542800. S2CID 10423613.
The C. elegans Sequencing Consortium (December 1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". Science. 282 (5396): 2012–2018. Bibcode:1998Sci...282.2012.. doi:10.1126/science.282.5396.2012. PMID 9851916. S2CID 16873716.
Edwards JS, Palsson BO (May 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): 5528–5533. Bibcode:2000PNAS...97.5528E. doi:10.1073/pnas.97.10.5528. PMC 25862. PMID 10805808.
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, et al. (February 2007). "Global reconstruction of the human metabolic network based on genomic and bibliomic data". Proceedings of the National Academy of Sciences of the United States of America. 104 (6): 1777–1782. Bibcode:2007PNAS..104.1777D. doi:10.1073/pnas.0610772104. PMC 1794290. PMID 17267599.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, et al. (December 2013). "SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools". BMC Systems Biology. 7 (1): 135. arXiv:1309.1910. Bibcode:2013arXiv1309.1910C. doi:10.1186/1752-0509-7-135. PMC 3892043. PMID 24321545.
Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, et al. (February 2014). "Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species". PLOS Computational Biology. 10 (2): e1003465. Bibcode:2014PLSCB..10E3465P. doi:10.1371/journal.pcbi.1003465. PMC 3916221. PMID 24516375.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO (November 2003). "Network-based analysis of metabolic regulation in the human red blood cell". Journal of Theoretical Biology. 225 (2): 185–194. Bibcode:2003JThBi.225..185P. doi:10.1016/s0022-5193(03)00237-6. PMID 14575652.
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (November 2002). "Metabolic network structure determines key aspects of functionality and regulation". Nature. 420 (6912): 190–193. Bibcode:2002Natur.420..190S. doi:10.1038/nature01166. PMID 12432396. S2CID 4301741.
Wunderlich Z, Mirny LA (September 2006). "Using the topology of metabolic networks to predict viability of mutant strains". Biophysical Journal. 91 (6): 2304–2311. Bibcode:2006BpJ....91.2304W. doi:10.1529/biophysj.105.080572. PMC 1557581. PMID 16782788.
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, et al. (January 2010). "The genetic landscape of a cell". Science. 327 (5964): 425–431. Bibcode:2010Sci...327..425C. doi:10.1126/science.1180823. PMC 5600254. PMID 20093466.

nih.gov

pubmed.ncbi.nlm.nih.gov

Francke C, Siezen RJ, Teusink B (November 2005). "Reconstructing the metabolic network of a bacterium from its genome". Trends in Microbiology. 13 (11): 550–558. doi:10.1016/j.tim.2005.09.001. PMID 16169729.
Thiele I, Palsson BØ (January 2010). "A protocol for generating a high-quality genome-scale metabolic reconstruction". Nature Protocols. 5 (1): 93–121. doi:10.1038/nprot.2009.203. PMC 3125167. PMID 20057383.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, et al. (July 1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science. 269 (5223): 496–512. Bibcode:1995Sci...269..496F. doi:10.1126/science.7542800. PMID 7542800. S2CID 10423613.
The C. elegans Sequencing Consortium (December 1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology". Science. 282 (5396): 2012–2018. Bibcode:1998Sci...282.2012.. doi:10.1126/science.282.5396.2012. PMID 9851916. S2CID 16873716.
Edwards JS, Palsson BO (May 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): 5528–5533. Bibcode:2000PNAS...97.5528E. doi:10.1073/pnas.97.10.5528. PMC 25862. PMID 10805808.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J (February 2003). "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network". Genome Research. 13 (2): 244–253. doi:10.1101/gr.234503. PMC 420374. PMID 12566402.
Sheikh K, Förster J, Nielsen LK (January 2005). "Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus". Biotechnology Progress. 21 (1): 112–121. doi:10.1021/bp0498138. PMID 15903248. S2CID 38627979.
Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD (June 2004). "Computational prediction of human metabolic pathways from the complete human genome". Genome Biology. 6 (1): R2. doi:10.1186/gb-2004-6-1-r2. PMC 549063. PMID 15642094.
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, et al. (February 2007). "Global reconstruction of the human metabolic network based on genomic and bibliomic data". Proceedings of the National Academy of Sciences of the United States of America. 104 (6): 1777–1782. Bibcode:2007PNAS..104.1777D. doi:10.1073/pnas.0610772104. PMC 1794290. PMID 17267599.
Jamshidi N, Palsson BØ (June 2007). "Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets". BMC Systems Biology. 1: 26. doi:10.1186/1752-0509-1-26. PMC 1925256. PMID 17555602.
Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R (September 2007). "Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data". The Journal of Biological Chemistry. 282 (39): 28791–28799. doi:10.1074/jbc.M703759200. PMID 17573341.
Raghunathan A, Reed J, Shin S, Palsson B, Daefler S (April 2009). "Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction". BMC Systems Biology. 3: 38. doi:10.1186/1752-0509-3-38. PMC 2678070. PMID 19356237.
de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (February 2010). "AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis". Plant Physiology. 152 (2): 579–589. doi:10.1104/pp.109.148817. PMC 2815881. PMID 20044452.
Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z (January 2020). "BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree". Nucleic Acids Research. 48 (D1): D402 – D406. doi:10.1093/nar/gkz1054. PMC 7145653. PMID 31696234.
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, et al. (January 2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology". Briefings in Bioinformatics. 11 (1): 40–79. arXiv:1510.03964. doi:10.1093/bib/bbp043. PMC 2810111. PMID 19955237.
Wrzodek C, Büchel F, Ruff M, Dräger A, Zell A (February 2013). "Precise generation of systems biology models from KEGG pathways". BMC Systems Biology. 7 (1): 15. doi:10.1186/1752-0509-7-15. PMC 3623889. PMID 23433509.
Wrzodek C, Dräger A, Zell A (August 2011). "KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats". Bioinformatics. 27 (16): 2314–2315. doi:10.1093/bioinformatics/btr377. PMC 3150042. PMID 21700675.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, et al. (December 2013). "SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools". BMC Systems Biology. 7 (1): 135. arXiv:1309.1910. Bibcode:2013arXiv1309.1910C. doi:10.1186/1752-0509-7-135. PMC 3892043. PMID 24321545.
Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL (September 2010). "High-throughput generation, optimization and analysis of genome-scale metabolic models". Nature Biotechnology. 28 (9): 977–982. doi:10.1038/nbt.1672. PMID 20802497. S2CID 6641097.
Chindelevitch L, Stanley S, Hung D, Regev A, Berger B (January 2012). "MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis". Genome Biology. 13 (1): r6. doi:10.1186/gb-2012-13-1-r6. PMC 3488975. PMID 22292986.
Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, et al. (February 2014). "Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species". PLOS Computational Biology. 10 (2): e1003465. Bibcode:2014PLSCB..10E3465P. doi:10.1371/journal.pcbi.1003465. PMC 3916221. PMID 24516375.
Castillo S, Barth D, Arvas M, Pakula TM, Pitkänen E, Blomberg P, et al. (November 2016). "Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction". Biotechnology for Biofuels. 9: 252. doi:10.1186/s13068-016-0665-0. PMC 5117618. PMID 27895706.
Linster CL, Van Schaftingen E, Hanson AD (February 2013). "Metabolite damage and its repair or pre-emption". Nature Chemical Biology. 9 (2): 72–80. doi:10.1038/nchembio.1141. PMID 23334546.
Hanson AD, Henry CS, Fiehn O, de Crécy-Lagard V (April 2016). "Metabolite Damage and Metabolite Damage Control in Plants". Annual Review of Plant Biology. 67: 131–152. doi:10.1146/annurev-arplant-043015-111648. PMID 26667673.
Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO (August 2004). "Comparison of network-based pathway analysis methods". Trends in Biotechnology. 22 (8): 400–405. doi:10.1016/j.tibtech.2004.06.010. PMID 15283984.
Lewis NE, Nagarajan H, Palsson BO (February 2012). "Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods". Nature Reviews. Microbiology. 10 (4): 291–305. doi:10.1038/nrmicro2737. PMC 3536058. PMID 22367118.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO (November 2003). "Network-based analysis of metabolic regulation in the human red blood cell". Journal of Theoretical Biology. 225 (2): 185–194. Bibcode:2003JThBi.225..185P. doi:10.1016/s0022-5193(03)00237-6. PMID 14575652.
Papin JA, Price ND, Palsson BØ (December 2002). "Extreme pathway lengths and reaction participation in genome-scale metabolic networks". Genome Research. 12 (12): 1889–1900. doi:10.1101/gr.327702. PMC 187577. PMID 12466293.
Schuster S, Fell DA, Dandekar T (March 2000). "A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks". Nature Biotechnology. 18 (3): 326–332. doi:10.1038/73786. PMID 10700151. S2CID 7742485.
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (November 2002). "Metabolic network structure determines key aspects of functionality and regulation". Nature. 420 (6912): 190–193. Bibcode:2002Natur.420..190S. doi:10.1038/nature01166. PMID 12432396. S2CID 4301741.
Ullah E, Aeron S, Hassoun S (2015). "gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13 (1): 122–134. doi:10.1109/TCBB.2015.2430344. PMID 26886737.
Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, et al. (January 2009). "Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies". BMC Systems Biology. 3 (5): 5. doi:10.1186/1752-0509-3-5. PMC 2661887. PMID 19144170.
Dräger A, Hassis N, Supper J, Schröder A, Zell A (April 2008). "SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks". BMC Systems Biology. 2 (1): 39. doi:10.1186/1752-0509-2-39. PMC 2412839. PMID 18447902.
Wunderlich Z, Mirny LA (September 2006). "Using the topology of metabolic networks to predict viability of mutant strains". Biophysical Journal. 91 (6): 2304–2311. Bibcode:2006BpJ....91.2304W. doi:10.1529/biophysj.105.080572. PMC 1557581. PMID 16782788.
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, et al. (January 2010). "The genetic landscape of a cell". Science. 327 (5964): 425–431. Bibcode:2010Sci...327..425C. doi:10.1126/science.1180823. PMC 5600254. PMID 20093466.
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wikidot.com

cobramethods.wikidot.com

CoBRA Methods - Constraint-based analysis