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Items: 1 to 50 of 151


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 Jun 9;55:12-22. doi: 10.1016/j.ymben.2019.06.001. [Epub ahead of print]


Signaling pathways in context.

Uschner F, Klipp E.

Curr Opin Biotechnol. 2019 Apr 8;58:155-160. doi: 10.1016/j.copbio.2019.03.011. [Epub ahead of print] Review.


A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae.

Münzner U, Klipp E, Krantz M.

Nat Commun. 2019 Mar 21;10(1):1308. doi: 10.1038/s41467-019-08903-w.


A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle.

Teufel L, Tummler K, Flöttmann M, Herrmann A, Barkai N, Klipp E.

Sci Rep. 2019 Mar 4;9(1):3343. doi: 10.1038/s41598-019-39850-7.


An Antimicrobial Peptide Induces FIG1-Dependent Cell Death During Cell Cycle Arrest in Yeast.

Arellano VJ, Martinell García P, Rodríguez Plaza JG, Lara Ortiz MT, Schreiber G, Volkmer R, Klipp E, Rio GD.

Front Microbiol. 2018 Jun 14;9:1240. doi: 10.3389/fmicb.2018.01240. eCollection 2018.


Alterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations.

Fritsche-Guenther R, Zasada C, Mastrobuoni G, Royla N, Rainer R, Roßner F, Pietzke M, Klipp E, Sers C, Kempa S.

Sci Rep. 2018 Jun 15;8(1):9204. doi: 10.1038/s41598-018-27394-1.


Transcriptional timing and noise of yeast cell cycle regulators-a single cell and single molecule approach.

Amoussouvi A, Teufel L, Reis M, Seeger M, Schlichting JK, Schreiber G, Herrmann A, Klipp E.

NPJ Syst Biol Appl. 2018 May 21;4:17. doi: 10.1038/s41540-018-0053-4. eCollection 2018.


Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.

Blazquez-Navarro A, Schachtner T, Stervbo U, Sefrin A, Stein M, Westhoff TH, Reinke P, Klipp E, Babel N, Neumann AU, Or-Guil M.

PLoS Comput Biol. 2018 May 10;14(5):e1005998. doi: 10.1371/journal.pcbi.1005998. eCollection 2018 May.


Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction.

Giese W, Milicic G, Schröder A, Klipp E.

PLoS Comput Biol. 2018 Apr 9;14(4):e1006075. doi: 10.1371/journal.pcbi.1006075. eCollection 2018 Apr.


General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks.

Reis M, Kromer JA, Klipp E.

J Math Biol. 2018 Aug;77(2):377-419. doi: 10.1007/s00285-018-1205-2. Epub 2018 Jan 20.


Estimation of immune cell content in tumour tissue using single-cell RNA-seq data.

Schelker M, Feau S, Du J, Ranu N, Klipp E, MacBeath G, Schoeberl B, Raue A.

Nat Commun. 2017 Dec 11;8(1):2032. doi: 10.1038/s41467-017-02289-3.


Monitoring cytochrome P450 activity in living hepatocytes by chromogenic substrates in response to drug treatment or during cell maturation.

Theobald J, Cheng X, Ghanem A, Gaitantzi H, Song G, Klipp E, Wodke J, Becker H, Mrowka R, Breitkopf-Heinlein K, Dooley S, Wölfl S.

Arch Toxicol. 2018 Mar;92(3):1133-1149. doi: 10.1007/s00204-017-2128-1. Epub 2017 Dec 5.


A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle.

Linke C, Chasapi A, González-Novo A, Al Sawad I, Tognetti S, Klipp E, Loog M, Krobitsch S, Posas F, Xenarios I, Barberis M.

NPJ Syst Biol Appl. 2017 Mar 6;3:7. doi: 10.1038/s41540-017-0008-1. eCollection 2017.


Comprehensive mathematical model of oxidative phosphorylation valid for physiological and pathological conditions.

Heiske M, Letellier T, Klipp E.

FEBS J. 2017 Sep;284(17):2802-2828. doi: 10.1111/febs.14151. Epub 2017 Jul 25.


Causal influence in linear Langevin networks without feedback.

Auconi A, Giansanti A, Klipp E.

Phys Rev E. 2017 Apr;95(4-1):042315. doi: 10.1103/PhysRevE.95.042315. Epub 2017 Apr 18.


Interaction Dynamics Determine Signaling and Output Pathway Responses.

Stojanovski K, Ferrar T, Benisty H, Uschner F, Delgado J, Jimenez J, Solé C, de Nadal E, Klipp E, Posas F, Serrano L, Kiel C.

Cell Rep. 2017 Apr 4;19(1):136-149. doi: 10.1016/j.celrep.2017.03.029.


Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

Pauling J, Klipp E.

J Integr Bioinform. 2016 Dec 22;13(1):299. doi: 10.2390/biecoll-jib-2016-299.


Using Confocal Microscopy and Computational Modeling to Investigate the Cell-Penetrating Properties of Antimicrobial Peptides.

Del Rio G, Klipp E, Herrmann A.

Methods Mol Biol. 2017;1548:191-199. doi: 10.1007/978-1-4939-6737-7_13.


Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency.

Schelker M, Mair CM, Jolmes F, Welke RW, Klipp E, Herrmann A, Flöttmann M, Sieben C.

PLoS Comput Biol. 2016 Oct 25;12(10):e1005075. doi: 10.1371/journal.pcbi.1005075. eCollection 2016 Oct.


Computational Modeling of Lipid Metabolism in Yeast.

Schützhold V, Hahn J, Tummler K, Klipp E.

Front Mol Biosci. 2016 Sep 27;3:57. eCollection 2016.


Dynamics of cell wall elasticity pattern shapes the cell during yeast mating morphogenesis.

Goldenbogen B, Giese W, Hemmen M, Uhlendorf J, Herrmann A, Klipp E.

Open Biol. 2016 Sep;6(9). pii: 160136. doi: 10.1098/rsob.160136.


Systems Level Analysis of the Yeast Osmo-Stat.

Talemi SR, Tiger CF, Andersson M, Babazadeh R, Welkenhuysen N, Klipp E, Hohmann S, Schaber J.

Sci Rep. 2016 Aug 12;6:30950. doi: 10.1038/srep30950.


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.


The MYpop toolbox: Putting yeast stress responses in cellular context on single cell and population scales.

Spiesser T, Kühn C, Krantz M, Klipp E.

Biotechnol J. 2016 Sep;11(9):1158-68. doi: 10.1002/biot.201500344. Epub 2016 Apr 29.


The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression.

Tyc KM, Herwald SE, Hogan JA, Pierce JV, Klipp E, Kumamoto CA.

BMC Syst Biol. 2016 Mar 1;10:20. doi: 10.1186/s12918-016-0268-1.


A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae.

Gerber S, Fröhlich M, Lichtenberg-Fraté H, Shabala S, Shabala L, Klipp E.

PLoS Comput Biol. 2016 Jan 27;12(1):e1004703. doi: 10.1371/journal.pcbi.1004703. eCollection 2016 Jan.


Dosage and Dose Schedule Screening of Drug Combinations in Agent-Based Models Reveals Hidden Synergies.

Barros de Andrade E Sousa LC, Kühn C, Tyc KM, Klipp E.

Front Physiol. 2016 Jan 6;6:398. doi: 10.3389/fphys.2015.00398. eCollection 2015.


Micro- and nano-tubules built from loosely and tightly rolled up thin sheets.

Losensky L, Goldenbogen B, Holland G, Laue M, Petran A, Liebscher J, Scheidt HA, Vogel A, Huster D, Klipp E, Arbuzova A.

Phys Chem Chem Phys. 2016 Jan 14;18(2):1292-301. doi: 10.1039/c5cp06084b.


Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models.

Giese W, Eigel M, Westerheide S, Engwer C, Klipp E.

Phys Biol. 2015 Nov 24;12(6):066014. doi: 10.1088/1478-3975/12/6/066014.


Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review.

Lubitz T, Welkenhuysen N, Shashkova S, Bendrioua L, Hohmann S, Klipp E, Krantz M.

NPJ Syst Biol Appl. 2015 Oct 22;1:15007. doi: 10.1038/npjsba.2015.7. eCollection 2015.


Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system.

Uschner F, Klipp E.

Syst Synth Biol. 2014 Dec;8(4):297-306. doi: 10.1007/s11693-014-9146-6. Epub 2014 Apr 19.


Role of gB and pUS3 in Equine Herpesvirus 1 Transfer between Peripheral Blood Mononuclear Cells and Endothelial Cells: a Dynamic In Vitro Model.

Spiesschaert B, Goldenbogen B, Taferner S, Schade M, Mahmoud M, Klipp E, Osterrieder N, Azab W.

J Virol. 2015 Dec;89(23):11899-908. doi: 10.1128/JVI.01809-15. Epub 2015 Sep 16.


Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks.

Mori T, Flöttmann M, Krantz M, Akutsu T, Klipp E.

BMC Syst Biol. 2015 Aug 11;9:45. doi: 10.1186/s12918-015-0193-8.


Dynamic metabolic models in context: biomass backtracking.

Tummler K, Kühn C, Klipp E.

Integr Biol (Camb). 2015 Aug;7(8):940-51. doi: 10.1039/c5ib00050e.


Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.

Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, Vanlier J, Tönsing C, Adlung L, Engesser R, Mader W, Heinemann T, Hasenauer J, Schilling M, Höfer T, Klipp E, Theis F, Klingmüller U, Schöberl B, Timmer J.

Bioinformatics. 2015 Nov 1;31(21):3558-60. doi: 10.1093/bioinformatics/btv405. Epub 2015 Jul 3.


Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer.

Spiesser TW, Kühn C, Krantz M, Klipp E.

PLoS Comput Biol. 2015 Apr 24;11(4):e1004223. doi: 10.1371/journal.pcbi.1004223. eCollection 2015 Apr.


Identification of 2-[4-[(4-Methoxyphenyl)methoxy]-phenyl]acetonitrile and Derivatives as Potent Oct3/4 Inducers.

Cheng X, Dimou E, Alborzinia H, Wenke F, Göhring A, Reuter S, Mah N, Fuchs H, Andrade-Navarro MA, Adjaye J, Gul S, Harms C, Utikal J, Klipp E, Mrowka R, Wölfl S.

J Med Chem. 2015 Jun 25;58(12):4976-83. doi: 10.1021/acs.jmedchem.5b00144. Epub 2015 May 7.


Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.

Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R.

Mol Syst Biol. 2014 Dec 9;10:767. doi: 10.15252/msb.20145112.


Mathematical models of mitochondrial aging and dynamics.

Kowald A, Klipp E.

Prog Mol Biol Transl Sci. 2014;127:63-92. doi: 10.1016/B978-0-12-394625-6.00003-9. Review.


Influenza A matrix protein M1 multimerizes upon binding to lipid membranes.

Hilsch M, Goldenbogen B, Sieben C, Höfer CT, Rabe JP, Klipp E, Herrmann A, Chiantia S.

Biophys J. 2014 Aug 19;107(4):912-23. doi: 10.1016/j.bpj.2014.06.042.


Yeast mating and image-based quantification of spatial pattern formation.

Diener C, Schreiber G, Giese W, del Rio G, Schröder A, Klipp E.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003690. doi: 10.1371/journal.pcbi.1003690. eCollection 2014 Jun.


Superoxide production by cytochrome bc1 complex: a mathematical model.

Guillaud F, Dröse S, Kowald A, Brandt U, Klipp E.

Biochim Biophys Acta. 2014 Oct;1837(10):1643-52. doi: 10.1016/j.bbabio.2014.05.358. Epub 2014 Jun 7.


SensA: web-based sensitivity analysis of SBML models.

Floettmann M, Uhlendorf J, Scharp T, Klipp E, Spiesser TW.

Bioinformatics. 2014 Oct;30(19):2830-1. doi: 10.1093/bioinformatics/btu378. Epub 2014 Jun 5.


Bridging the gaps in systems biology.

Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M.

Mol Genet Genomics. 2014 Oct;289(5):727-34. doi: 10.1007/s00438-014-0843-3. Epub 2014 Apr 13. Review.


Alteration of protein levels during influenza virus H1N1 infection in host cells: a proteomic survey of host and virus reveals differential dynamics.

Kummer S, Flöttmann M, Schwanhäusser B, Sieben C, Veit M, Selbach M, Klipp E, Herrmann A.

PLoS One. 2014 Apr 9;9(4):e94257. doi: 10.1371/journal.pone.0094257. eCollection 2014.


Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin.

Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G.

J Biol Chem. 2014 May 23;289(21):14448-57. doi: 10.1074/jbc.M113.515023. Epub 2014 Apr 5.


Assessing the advantage of morphological changes in Candida albicans: a game theoretical study.

Tyc KM, Kühn C, Wilson D, Klipp E.

Front Microbiol. 2014 Feb 6;5:41. doi: 10.3389/fmicb.2014.00041. eCollection 2014.


Glucose de-repression by yeast AMP-activated protein kinase SNF1 is controlled via at least two independent steps.

García-Salcedo R, Lubitz T, Beltran G, Elbing K, Tian Y, Frey S, Wolkenhauer O, Krantz M, Klipp E, Hohmann S.

FEBS J. 2014 Apr;281(7):1901-17. doi: 10.1111/febs.12753. Epub 2014 Mar 4.


Impact of acute metal stress in Saccharomyces cerevisiae.

Hosiner D, Gerber S, Lichtenberg-Fraté H, Glaser W, Schüller C, Klipp E.

PLoS One. 2014 Jan 9;9(1):e83330. doi: 10.1371/journal.pone.0083330. eCollection 2014.


Global dynamic optimization approach to predict activation in metabolic pathways.

de Hijas-Liste GM, Klipp E, Balsa-Canto E, Banga JR.

BMC Syst Biol. 2014 Jan 6;8:1. doi: 10.1186/1752-0509-8-1.

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