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Items: 14


Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis.

Tymoshenko S, Oppenheim RD, Agren R, Nielsen J, Soldati-Favre D, Hatzimanikatis V.

PLoS Comput Biol. 2015 May 22;11(5):e1004261. doi: 10.1371/journal.pcbi.1004261. eCollection 2015 May.


Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling.

Agren R, Mardinoglu A, Asplund A, Kampf C, Uhlen M, Nielsen J.

Mol Syst Biol. 2014 Mar 19;10:721. doi: 10.1002/msb.145122.


Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease.

Mardinoglu A, Agren R, Kampf C, Asplund A, Uhlen M, Nielsen J.

Nat Commun. 2014;5:3083. doi: 10.1038/ncomms4083.


Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production.

Agren R, Otero JM, Nielsen J.

J Ind Microbiol Biotechnol. 2013 Jul;40(7):735-47. doi: 10.1007/s10295-013-1269-3. Epub 2013 Apr 23.


The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.

Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J.

PLoS Comput Biol. 2013;9(3):e1002980. doi: 10.1371/journal.pcbi.1002980. Epub 2013 Mar 21.


Integration of clinical data with a genome-scale metabolic model of the human adipocyte.

Mardinoglu A, Agren R, Kampf C, Asplund A, Nookaew I, Jacobson P, Walley AJ, Froguel P, Carlsson LM, Uhlen M, Nielsen J.

Mol Syst Biol. 2013;9:649. doi: 10.1038/msb.2013.5.


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.

Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3.


Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT.

Agren R, Bordel S, Mardinoglu A, Pornputtapong N, Nookaew I, Nielsen J.

PLoS Comput Biol. 2012;8(5):e1002518. doi: 10.1371/journal.pcbi.1002518. Epub 2012 May 17.


Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials.

Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J.

BMC Syst Biol. 2012 Apr 4;6:24. doi: 10.1186/1752-0509-6-24.


MEMOSys: Bioinformatics platform for genome-scale metabolic models.

Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z.

BMC Syst Biol. 2011 Jan 31;5:20. doi: 10.1186/1752-0509-5-20.


Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes.

Bordel S, Agren R, Nielsen J.

PLoS Comput Biol. 2010 Jul 15;6(7):e1000859. doi: 10.1371/journal.pcbi.1000859.


BioMet Toolbox: genome-wide analysis of metabolism.

Cvijovic M, Olivares-Hernández R, Agren R, Dahr N, Vongsangnak W, Nookaew I, Patil KR, Nielsen J.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W144-9. doi: 10.1093/nar/gkq404. Epub 2010 May 18.


Use of genome-scale metabolic models for understanding microbial physiology.

Liu L, Agren R, Bordel S, Nielsen J.

FEBS Lett. 2010 Jun 18;584(12):2556-64. doi: 10.1016/j.febslet.2010.04.052. Epub 2010 Apr 24. Review.


Waiting for surgery; living a life on hold--a continuous struggle against a faceless system.

Sjöling RN, Agren RN, Olofsson N, Hellzén RN, Asplund RN.

Int J Nurs Stud. 2005 Jul;42(5):539-47.

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