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A protocol for generating a high-quality genome-scale metabolic reconstruction.
Thiele I, Palsson BØ. Thiele I, et al. Nat Protoc. 2010 Jan;5(1):93-121. doi: 10.1038/nprot.2009.203. Epub 2010 Jan 7. Nat Protoc. 2010. PMID: 20057383 Free PMC article.
Recon3D enables a three-dimensional view of gene variation in human metabolism.
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. Brunk E, et al. Among authors: thiele i. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. Nat Biotechnol. 2018. PMID: 29457794 Free PMC article.
A community-driven global reconstruction of human metabolism.
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. Thiele I, et al. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. Nat Biotechnol. 2013. PMID: 23455439 Free PMC article.
Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe.
Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJ, Thiele I. Heinken A, et al. Among authors: thiele i. J Bacteriol. 2014 Sep;196(18):3289-302. doi: 10.1128/JB.01780-14. Epub 2014 Jul 7. J Bacteriol. 2014. PMID: 25002542 Free PMC article.
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.
Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RM, Thiele I. Magnúsdóttir S, et al. Among authors: thiele i. Nat Biotechnol. 2017 Jan;35(1):81-89. doi: 10.1038/nbt.3703. Epub 2016 Nov 28. Nat Biotechnol. 2017. PMID: 27893703
Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks.
Nogales J, Gudmundsson S, Thiele I. Nogales J, et al. Among authors: thiele i. Bioengineered. 2013 May-Jun;4(3):158-63. doi: 10.4161/bioe.22792. Epub 2012 Nov 8. Bioengineered. 2013. PMID: 23138691 Free PMC article.
What is flux balance analysis?
Orth JD, Thiele I, Palsson BØ. Orth JD, et al. Among authors: thiele i. Nat Biotechnol. 2010 Mar;28(3):245-8. doi: 10.1038/nbt.1614. Nat Biotechnol. 2010. PMID: 20212490 Free PMC article.
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.
Thiele I, Jamshidi N, Fleming RM, Palsson BØ. Thiele I, et al. PLoS Comput Biol. 2009 Mar;5(3):e1000312. doi: 10.1371/journal.pcbi.1000312. Epub 2009 Mar 13. PLoS Comput Biol. 2009. PMID: 19282977 Free PMC article.
However, they do not explicitly account for the synthesis of macromolecules (i.e., proteins and RNA). Here, we present the first genome-scale, fine-grained reconstruction of Escherichia coli's transcriptional and translational machinery, which produces 423 functional gene …
However, they do not explicitly account for the synthesis of macromolecules (i.e., proteins and RNA). Here, we present the first geno …
Estimation of the number of extreme pathways for metabolic networks.
Yeung M, Thiele I, Palsson BO. Yeung M, et al. Among authors: thiele i. BMC Bioinformatics. 2007 Sep 27;8(1):363. doi: 10.1186/1471-2105-8-363. BMC Bioinformatics. 2007. PMID: 17897474 Free PMC article.
In particular, it was found that log [p] had an exponential relationship with log[ summation operatori=1Rd-id+ici] MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9p …
In particular, it was found that log [p] had an exponential relationship with log[ summation operatori=1Rd-id+ici] MathType@MTEF@5@5@+=feaaf …
Global reconstruction of the human metabolic network based on genomic and bibliomic data.
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ. Duarte NC, et al. Among authors: thiele i. Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1777-82. doi: 10.1073/pnas.0610772104. Epub 2007 Jan 31. Proc Natl Acad Sci U S A. 2007. PMID: 17267599 Free PMC article.
We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50 years of legacy data (i.e., bibliomic data). Herein we describe the reconstruction process and demonstrate how the resultin …
We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation …
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