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Items: 18


Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.

Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO.

Nat Biotechnol. 2013 Aug;31(8):759-65. doi: 10.1038/nbt.2624. Epub 2013 Jul 21.


A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.

Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I.

BMC Syst Biol. 2011 Oct 31;5:180. doi: 10.1186/1752-0509-5-180.


The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.

Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J.

Nat Biotechnol. 2011 Jul 31;29(8):735-41. doi: 10.1038/nbt.1932.


Genome-scale constraint-based modeling of Geobacter metallireducens.

Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.

BMC Syst Biol. 2009 Jan 28;3:15. doi: 10.1186/1752-0509-3-15.


Towards multidimensional genome annotation.

Reed JL, Famili I, Thiele I, Palsson BO.

Nat Rev Genet. 2006 Feb;7(2):130-41. Review.


k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.

Famili I, Mahadevan R, Palsson BO.

Biophys J. 2005 Mar;88(3):1616-25. Epub 2004 Dec 30.


Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space.

Wiback SJ, Famili I, Greenberg HJ, Palsson BØ.

J Theor Biol. 2004 Jun 21;228(4):437-47.


Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

Covert MW, Famili I, Palsson BO.

Biotechnol Bioeng. 2003 Dec 30;84(7):763-72. Review.


Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.

Famili I, Forster J, Nielsen J, Palsson BO.

Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13134-9. Epub 2003 Oct 24.


Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.

Förster J, Famili I, Palsson BO, Nielsen J.

OMICS. 2003 Summer;7(2):193-202.


Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.

Förster J, Famili I, Fu P, Palsson BØ, Nielsen J.

Genome Res. 2003 Feb;13(2):244-53.


Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices.

Price ND, Reed JL, Papin JA, Famili I, Palsson BO.

Biophys J. 2003 Feb;84(2 Pt 1):794-804.


Extreme pathways and Kirchhoff's second law.

Price ND, Famili I, Beard DA, Palsson BØ.

Biophys J. 2002 Nov;83(5):2879-82. No abstract available.


Genome-scale metabolic model of Helicobacter pylori 26695.

Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO.

J Bacteriol. 2002 Aug;184(16):4582-93.


Metabolic modeling of microbial strains in silico.

Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO.

Trends Biochem Sci. 2001 Mar;26(3):179-86. Review.


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