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Items: 1 to 50 of 53

1.

Automated generation of bacterial resource allocation models.

Bulović A, Fischer S, Dinh M, Golib F, Liebermeister W, Poirier C, Tournier L, Klipp E, Fromion V, Goelzer A.

Metab Eng. 2019 Sep;55:12-22. doi: 10.1016/j.ymben.2019.06.001. Epub 2019 Jun 9.

PMID:
31189086
2.

Parameter balancing: consistent parameter sets for kinetic metabolic models.

Lubitz T, Liebermeister W.

Bioinformatics. 2019 Oct 1;35(19):3857-3858. doi: 10.1093/bioinformatics/btz129.

3.

Metabolite-Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks.

Noda-Garcia L, Liebermeister W, Tawfik DS.

Annu Rev Biochem. 2018 Jun 20;87:187-216. doi: 10.1146/annurev-biochem-062917-012023. Review.

PMID:
29925259
4.

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield.

Wortel MT, Noor E, Ferris M, Bruggeman FJ, Liebermeister W.

PLoS Comput Biol. 2018 Feb 16;14(2):e1006010. doi: 10.1371/journal.pcbi.1006010. eCollection 2018 Feb.

5.

Notions of similarity for systems biology models.

Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D.

Brief Bioinform. 2017 Sep 1;18(5):902. doi: 10.1093/bib/bbw146. No abstract available.

6.

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization.

Noor E, Flamholz A, Bar-Even A, Davidi D, Milo R, Liebermeister W.

PLoS Comput Biol. 2016 Nov 3;12(11):e1005167. doi: 10.1371/journal.pcbi.1005167. eCollection 2016 Nov.

7.

Notions of similarity for systems biology models.

Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D.

Brief Bioinform. 2018 Jan 1;19(1):77-88. doi: 10.1093/bib/bbw090. Erratum in: Brief Bioinform. 2017 Jan 17;:.

8.

Toward Community Standards and Software for Whole-Cell Modeling.

Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10.

9.

SBtab: a flexible table format for data exchange in systems biology.

Lubitz T, Hahn J, Bergmann FT, Noor E, Klipp E, Liebermeister W.

Bioinformatics. 2016 Aug 15;32(16):2559-61. doi: 10.1093/bioinformatics/btw179. Epub 2016 Apr 8.

10.

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements.

Davidi D, Noor E, Liebermeister W, Bar-Even A, Flamholz A, Tummler K, Barenholz U, Goldenfeld M, Shlomi T, Milo R.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3401-6. doi: 10.1073/pnas.1514240113. Epub 2016 Mar 7.

11.

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.

Smith LP, Hucka M, Hoops S, Finney A, Ginkel M, Myers CJ, Moraru I, Liebermeister W.

J Integr Bioinform. 2015 Sep 4;12(2):268. doi: 10.2390/biecoll-jib-2015-268.

12.

Visual account of protein investment in cellular functions.

Liebermeister W, Noor E, Flamholz A, Davidi D, Bernhardt J, Milo R.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8488-93. doi: 10.1073/pnas.1314810111. Epub 2014 Jun 2.

13.

Pathway thermodynamics highlights kinetic obstacles in central metabolism.

Noor E, Bar-Even A, Flamholz A, Reznik E, Liebermeister W, Milo R.

PLoS Comput Biol. 2014 Feb 20;10(2):e1003483. doi: 10.1371/journal.pcbi.1003483. eCollection 2014 Feb.

14.

Systematic construction of kinetic models from genome-scale metabolic networks.

Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W.

PLoS One. 2013 Nov 14;8(11):e79195. doi: 10.1371/journal.pone.0079195. eCollection 2013.

15.

Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load.

Tepper N, Noor E, Amador-Noguez D, Haraldsdóttir HS, Milo R, Rabinowitz J, Liebermeister W, Shlomi T.

PLoS One. 2013 Sep 26;8(9):e75370. doi: 10.1371/journal.pone.0075370. eCollection 2013.

16.

A note on the kinetics of enzyme action: a decomposition that highlights thermodynamic effects.

Noor E, Flamholz A, Liebermeister W, Bar-Even A, Milo R.

FEBS Lett. 2013 Sep 2;587(17):2772-7. doi: 10.1016/j.febslet.2013.07.028. Epub 2013 Jul 23. Review.

17.

Glycolytic strategy as a tradeoff between energy yield and protein cost.

Flamholz A, Noor E, Bar-Even A, Liebermeister W, Milo R.

Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):10039-44. doi: 10.1073/pnas.1215283110. Epub 2013 Apr 29.

18.

Spanning high-dimensional expression space using ribosome-binding site combinatorics.

Zelcbuch L, Antonovsky N, Bar-Even A, Levin-Karp A, Barenholz U, Dayagi M, Liebermeister W, Flamholz A, Noor E, Amram S, Brandis A, Bareia T, Yofe I, Jubran H, Milo R.

Nucleic Acids Res. 2013 May;41(9):e98. doi: 10.1093/nar/gkt151. Epub 2013 Mar 6.

19.

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P.

Science. 2012 Mar 2;335(6072):1103-6. doi: 10.1126/science.1206848.

20.

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.

Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U.

Science. 2012 Mar 2;335(6072):1099-103. doi: 10.1126/science.1206871.

21.

Propagating semantic information in biochemical network models.

Schulz M, Klipp E, Liebermeister W.

BMC Bioinformatics. 2012 Jan 30;13:18. doi: 10.1186/1471-2105-13-18.

22.

Sustainable model building the role of standards and biological semantics.

Krause F, Schulz M, Swainston N, Liebermeister W.

Methods Enzymol. 2011;500:371-95. doi: 10.1016/B978-0-12-385118-5.00019-0.

PMID:
21943907
23.

Retrieval, alignment, and clustering of computational models based on semantic annotations.

Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W.

Mol Syst Biol. 2011 Jul 19;7:512. doi: 10.1038/msb.2011.41.

24.

The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters.

Bar-Even A, Noor E, Savir Y, Liebermeister W, Davidi D, Tawfik DS, Milo R.

Biochemistry. 2011 May 31;50(21):4402-10. doi: 10.1021/bi2002289. Epub 2011 May 4.

PMID:
21506553
25.

Parameter balancing in kinetic models of cell metabolism.

Lubitz T, Schulz M, Klipp E, Liebermeister W.

J Phys Chem B. 2010 Dec 16;114(49):16298-303. doi: 10.1021/jp108764b. Epub 2010 Nov 1.

26.

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.

Yizhak K, Benyamini T, Liebermeister W, Ruppin E, Shlomi T.

Bioinformatics. 2010 Jun 15;26(12):i255-60. doi: 10.1093/bioinformatics/btq183.

27.

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.

Liebermeister W, Uhlendorf J, Klipp E.

Bioinformatics. 2010 Jun 15;26(12):1528-34. doi: 10.1093/bioinformatics/btq141. Epub 2010 Apr 12.

PMID:
20385728
28.

A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae.

Zi Z, Liebermeister W, Klipp E.

PLoS One. 2010 Mar 4;5(3):e9522. doi: 10.1371/journal.pone.0009522.

29.

Annotation and merging of SBML models with semanticSBML.

Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W.

Bioinformatics. 2010 Feb 1;26(3):421-2. doi: 10.1093/bioinformatics/btp642. Epub 2009 Nov 17.

PMID:
19933161
30.

Nested uncertainties in biochemical models.

Schaber J, Liebermeister W, Klipp E.

IET Syst Biol. 2009 Jan;3(1):1-9. doi: 10.1049/iet-syb:20070042.

PMID:
19154080
31.

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB.

Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492.

32.

Automatically generated model of a metabolic network.

Borger S, Liebermeister W, Uhlendorf J, Klipp E.

Genome Inform. 2007;18:215-24.

PMID:
18546489
33.

Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis.

Bruck J, Liebermeister W, Klipp E.

Genome Inform. 2008;20:1-14.

PMID:
19425118
34.

Integration of enzyme kinetic data from various sources.

Borger S, Uhlendorf J, Helbig A, Liebermeister W.

In Silico Biol. 2007;7(2 Suppl):S73-9. Review.

PMID:
17822393
35.

Structural analysis of expressed metabolic subnetworks.

Ebenhöh O, Liebermeister W.

Genome Inform. 2006;17(1):163-72.

PMID:
17503366
36.

Prediction of enzyme kinetic parameters based on statistical learning.

Borger S, Liebermeister W, Klipp E.

Genome Inform. 2006;17(1):80-7.

PMID:
17503358
37.

SBMLmerge, a system for combining biochemical network models.

Schulz M, Uhlendorf J, Klipp E, Liebermeister W.

Genome Inform. 2006;17(1):62-71. Review.

PMID:
17503356
38.

Systems biology standards--the community speaks.

Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J.

Nat Biotechnol. 2007 Apr;25(4):390-1. No abstract available.

PMID:
17420739
39.
40.

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.

Liebermeister W, Klipp E.

Theor Biol Med Model. 2006 Dec 15;3:41.

41.

Mathematical modeling of intracellular signaling pathways.

Klipp E, Liebermeister W.

BMC Neurosci. 2006 Oct 30;7 Suppl 1:S10. Review.

42.

Biochemical networks with uncertain parameters.

Liebermeister W, Klipp E.

Syst Biol (Stevenage). 2005 Sep;152(3):97-107.

PMID:
16986274
43.

A comprehensive library of fluorescent transcriptional reporters for Escherichia coli.

Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U.

Nat Methods. 2006 Aug;3(8):623-8.

PMID:
16862137
44.

Predicting physiological concentrations of metabolites from their molecular structure.

Liebermeister W.

J Comput Biol. 2005 Dec;12(10):1307-15.

PMID:
16379536
45.

Biochemical network models simplified by balanced truncation.

Liebermeister W, Baur U, Klipp E.

FEBS J. 2005 Aug;272(16):4034-43.

46.

Response to temporal parameter fluctuations in biochemical networks.

Liebermeister W.

J Theor Biol. 2005 Jun 7;234(3):423-38.

PMID:
15784276
47.

Inferring dynamic properties of biochemical reaction networks from structural knowledge.

Klipp E, Liebermeister W, Wierling C.

Genome Inform. 2004;15(1):125-37.

PMID:
15712116
48.

A theory of optimal differential gene expression.

Liebermeister W, Klipp E, Schuster S, Heinrich R.

Biosystems. 2004 Aug-Oct;76(1-3):261-78.

PMID:
15351149
49.

Does mapping reveal correlation between gene expression and protein-protein interaction?

Mrowka R, Liebermeister W, Holste D.

Nat Genet. 2003 Jan;33(1):15-6; author reply 16-7. No abstract available.

PMID:
12509776
50.

Linear modes of gene expression determined by independent component analysis.

Liebermeister W.

Bioinformatics. 2002 Jan;18(1):51-60.

PMID:
11836211

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