Publications


Books

Klipp, E., Liebermeister, L., Wierling, C., Kowald, A., Lehrach, H. & Herwig, R.
(2009)

Systems Biology. A Textbook.


Wiley-Blackwell, Weinheim, 569 p., ISBN:
978-3-527-31874-2


Systems Biology. A textbook

View the video tutorials
accompanying this book

Klipp, E., Herwig, R., Kowald, A.,Wierling, C. & Lehrach,H.
(2005)

Systems Biology in Practice: Concepts, Implementation and Application.


Wiley-VCH, Weinheim, 465 p., ISBN:
3-527-31078-9

Systems Biology in Practice

Book chapters

Floettmann, M., Scharp, T., & Klipp E.
(2012)
Computational Modeling of Biochemical Processes and Cell Differentiation.
In: Stachowiak, M.K. & Tzankakis, E.S.
Stem Cells. From Mechanisms to Technologies.
World Scientific, ISBN: 978-981-4317-70-2.
Text/Abstract
Kahlem, P., DiCara, A., Durot, M., Hancock, J.M., Klipp, E., Schächter, V., Segal, E., Xenarios, I., Birney, E. & Mendoza, L.
(2011)
Strengths and weaknesses of selected modeling methods used in systems biology.
In: Yang, N.-S. (Ed.)
Systems and Computational Biology - Bioinformatics and Computational Modeling.
InTech Open Access Publischer, ISBN: 978-953-307-875-5.
Text/Abstract
Klipp E.
(2011)
Computational yeast systems biology: a case study for the MAP kinase cascade.
In: Castrillo, J.I. & Oliver, S.G.
Yeast Systems Biology. Methods ans Protocols. Methods in Molecular Biology 759 (Part 3),
Humana Press, ISBN: 978-1-61779-172-7,
323-43.
Text/Abstract
doi: 10.1007/978-1-61779-173-4_19, PMID: 21863496
Schulz, M. & Klipp, E.
(2010)
Introduction to systems biology.
In: Tretter, F., Gebicke-Haerter, P., Mendoza, E.R. & Winterer, G. (eds.)
Systems Biology in Psychiatric Research. From High-Throughput Data to Mathematical Modeling.
Wiley-VCH, Weinheim, ISBN: 978-3-527-32503-0,
81-96.
Text/Abstract
Klipp, E. & Schaber, J.
(2008)
Modeling the dynamics of stress activated protein kinases (SAPK) in cellular stress response.
In: Posas, F. & Nebreda, A.R. (eds.)
SAPK - Stress-Activated Protein Kinases.
Book Series: Topics in Current Genetics 20,
Springer, Berlin, ISBN: 978-3-540-75568-7,
205-24.
Text/Abstract
Text/Abstract
doi:10.1007/4735_2007_0241
Klipp, E. & Schaber, J.
(2006)
Modelling of signal transduction in yeast - Sensitivity and model analysis.
In: Cánovas, M., Iborra, J.L. & Manjón, A. (eds.)
Understanding and Exploiting Systems Biology in Bioprocesses and Biomedicine.
Fundacion CajaMurcia, Murcia (Spain), ISBN: 84-611-1135-4,
15-30.
Text/Abstract
Schuster, S., Klipp, E. & Marhl, M.
(2006)
The predictive power of molecular network modelling - case studies of predictions with subsequent experimental verification.
In: Eisenhaber, F. (Ed.)
Discovering Biomolecular Mechanisms with Computational Biology.
Landes Bioscience, Georgetown and Springer, New York, ISBN: 978-0-387-34527-7,
95-106.
Text/Abstract
Text/Abstract
Nordlander, B., Klipp, E., Kofahl, B. & Hohmann, S.
(2005)
Modelling signalling pathways - a yeast approach.
In: Alberghina, L. & Westerhoff, H.V. (eds.)
Systems Biology. Definitions and Perspectives.
Book Series: Topics in Current Genetics 13,
Springer, Berlin, ISBN: 978-3-540-22968-X,
277-302.
Text/Abstract
Text/Abstract
doi:10.1007/b95175
Lachmann, M., Blackstone, N.W., Haig, D., Kowald, A., Michod, R.E., Szathmary, E., Werren, J.H. & Wolpert, L.
(2003)
Cooperation and conflict in the evolution of genomes, cells, and multicellular organisms.
In: Hammerstein, P. (Ed.)
Genetic and Cultural Evolution of Cooperation.
MIT Press, Cambridge (USA), ISBN: 0-262-08326-4,
327-56.
Text/Abstract
Klipp, E.
(1998)
Relations between flux control coefficients and enzyme concentrations in states of minimized total amount of enzyme.
In: Larsson, C., Pahlman, I.L. & Gustafsson, L. (eds.)
Biothermokinetics in the Post Genomic Era.
University, Chalmers Reproservice, Göteborg, ISBN: 91-630-7048-0,
27-9.
Klipp, E.
(1996)
Maximization of enzyme activity under consideration of various constraints.
In: Ghista, D.N. (Ed.)
Biomedical and Life Physics.
Vieweg, Braunschweig, ISBN: 3-528-06877-9,
71-84.
Klipp, E. & Heinrich, R.
(1996)
Kinetic optimization of multienzyme systems.
In: Westerhoff, H.V., Snoep, J.L., Sluse, F.E., Wijker, J.E. & Kholodenko, B.N. (eds.)
Biothermokinetics of the Living Cell.
Biothermokinetic Press, Amsterdam, ISBN: 90-803184-1-8,
210-13.
Heinrich, R., Klipp, E., Stephani, A. & Wilhelm, T.
(1994)
Evolutionary optimization of enzyme on the basis of kinetic and thermodynamic principles.
In: Gnaiger, E., Gellerich, F.N. & Wyss, M. (eds.)
What is Controlling Life? 50 Years after Erwin Schroedinger's What is Life?
Insbruck University Press, ISBN: 3-901249-17-6,
99-102.

Journal articles

2013
Krause, F., Schulz, M., Ripkens, B., Flöttmann, M., Krantz, M., Klipp, E., & Handorf, T.
(2013)
biographer: web based editing and rendering of SBGN compliant biochemical networks
Bioinform.
29
(11),
1467-8.
Text/Abstract
doi: 10.1093/bioinformatics/btt159, PMID: 23574737
Kühn, C., & Gennemark, P.
(2013)
Modeling yeast osmoadaptation at different levels of resolution.
J. Bioinform. Comput. Biol.
11
(2),
1330001.
Text/Abstract
doi: 10.1142/S0219720013300013, PMID: 23600818
Petelenz-Kurdziel. E., Kuehn., C., Nordlander, B., Klein, D., Hong, K., Jacobson, T., Dahl, P., Schaber, J., Nielsen, J., Hohmann, S., & Klipp, E.
(2013)
Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress
PLoS Comput. Biol.
9
(6),
e1003084.
Text/Abstract
doi: 10.1371/journal.pcbi.1003084, PMID: 23762021
Rother, M., Münzner, U., Thieme, S., & Krantz, M.
(2013)
Information content and scalability in signal transduction network reconstruction formats.
Mol. Biosyst.
2013.
Text/Abstract
doi: 10.1039/C3MB00005B, PMID: 23636168
Wodke, J.A.H., Puchalka, J., Lluch-Senar, M., Marcos, J., Yus, E., Godinho, M., Gutiérrez-Gallego, R., Martins dos Santos, V.A.P., Serrano, L., Klipp, E., & Maier, T.
(2013)
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling
Mol. Syst. Biol.
9
653.
Text/Abstract
doi:10.1038/msb.2013.6, PMID: 23549481

2012
Barberis, M.
(2012)
Molecular systems biology of Sic1 in yeast cell cycle regulation through multiscale modeling
Adv. Exp. Med. Biol.
736
, 135-67.
Text/Abstract
doi: 10.1007/978-1-4419-7210-1_7, PMID: 22161326
Barberis, M.
(2012)
Sic1 as a timer of Clb cyclin waves in the yeast cell cycle - design principle of not just an inhibitor.
FEBS J.
279
(18),
, 3386-410.
Text/Abstract
doi: 10.1111/j.1742-4658.2012.08542.x, PMID: 22356687
Buescher, J.M., Liebermeister, W., Jules, M., Uhr, M., Muntel, J., Botella, E., Hessling, B., Kleijn, R.J., Le Chat, L., Lecointe, F., Mäder, U., Nicolas, P., Piersma, S., Rügheimer, F., Becher, D., Bessieres, P., Bidnenko, E., Denham, E.L., Dervyn, E., Devine, K.M., Doherty, G., Drulhe, S., Felicori, L., Fogg, M.J., Goelzer, A., Hansen, A., Harwood, C.R., 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, J.M., Veiga, P., Walsh, S., Wilkinson, A.J., Stelling, J., Aymerich, S., & Sauer, U.
(2012)
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.
Science
335
(6072),
1099-103.
Text/Abstract
doi: 10.1126/science.1206871, PMID: 22383848
Flöttmann, M., Scharp, T. & Klipp, E.
(2012)
A stochastic model of epigenetic dynamics in somatic cell reprogramming
Front. Comput. Physiol. Med.
3
, 216.
Text/Abstract
doi: 10.3389/fphys.2012.00216, PMID: 22754535
Fuellen, G., Dengiel, J., Hoeflich, A., Hoeijemakers, J., Kestler, H.A., Kowald, A., Priebe, S., Rebholz-Schuhmann, D., Schmeck, B., Schmitz, U., Stolzing, A., Sühnel, J., Wuttke, D., & Vera, J.
(2012)
Systems Biology and Bioinformatics in Aging Research: A Workshop Report.
Rejuvenation Research
15
(6),
631-41.
Text/Abstract
doi:10.1089/rej.2012.1360, PMID: 22950424
Geijer, C., Pirkov, I., Vongsangnak, W., Ericsson, A., Nielsen, J., Krantz, M., & Hohmann, S.
(2012)
Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response.
BMC Genomics
13
(1),
, 554.
Text/Abstract
PMID: 23066959
Hoffman-Sommer, M., Supady, A., & Klipp, E.
(2012)
Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates.
Front Physiol.
3
, 287.
Text/Abstract
PMID: 22934039
Kirkwood, T.B. & Kowald, A.
(2012)
The free-radical theory of ageing--older, wiser and still alive: modelling positional effects of the primary targets of ROS reveals new support.
Bioessays
34
(8),
692-700.
Text/Abstract
Text/Abstract
doi: 10.1002/bies.201200014, PMID: 22641614
Kowald, A., Hamann, A., Zintel, S., Ullrich, S., Klipp, E., & Osiewacz, H.D.
(2012)
A systems biological analysis links ROS metabolism to mitochondrial protein quality control.
Mech. Ageing Dev.
133
(5),
331-7.
Text/Abstract
doi: 10.1016/j.mad.2012.03.008, PMID: 22449407
Kühn, C. & Klipp E.
(2012)
Zooming in on yeast osmoadaptation.
Adv. Exp. Med. Biol.
736
, 293-310.
Text/Abstract
doi: 10.1007/978-1-4419-7210-1_17, PMID: 22161336
Leach, M.D., Klipp, E., Cowen, L.E. & Brown, A.J.
(2012)
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs.
Nat. Rev. Microbiol.
10
(10),
693-704.
Text/Abstract
Text/Abstract
doi: 10.1038/nrmicro2875, PMID: 22976491
Leach, M.D., Tyc, K.M., Brown, A.J., & Klipp, E.
(2012)
Modelling the Regulation of Thermal Adaptation in Candida albicans, a Major Fungal Pathogen of Humans.
PLoS One
7
(3),
e32467.
Text/Abstract
doi: 10.1371/journal.pone.0032467, PMID: 22448221
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, E.L., Fogg, M.J., Fromion, V., Goelzer, A., Hansen, A., Härtig, E., Harwood, C.R., Homuth, G., Jarmer, H., Jules, M., Klipp, E., Le Chat, L., Lecointe, F., Lewis, P., Liebermeister, W., March, A., Mars, R.A., Nannapaneni, P., Noone, D., Pohl, S., Rinn, B., Rügheimer, F., Sappa, P.K., Samson, F., Schaffer, M., Schwikowski, B., Steil, L., Stülke, J., Wiegert, T., Devine, K.M., Wilkinson, A.J., van Dijl, J.M., Hecker, M., Völker, U., Bessičres, P., & Noirot, P.
(2012)
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science
335
(6072),
1103-6.
Text/Abstract
doi: 10.1126/science.1206848, PMID: 22383849
Rubelt, F., Sievert, V., Knaust, F., Diener, C., Lim, T.S., Skriner, K., Klipp, E., Reinhardt, R., Lehrach, H. & Konthur, Z.
(2012)
Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires.
PLoS One
7
(11),
e49774.
Text/Abstract
doi: 10.1371/journal.pone.0049774, PMID: 23226220
Schaber J, Baltanas R, Bush A, Klipp E & Colman-Lerner A.
(2012)
Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast.
Mol. Syst. Biol.
13
(8),
622.
Text/Abstract
doi: 10.1038/msb.2012.53, PMID: 23149687
Schulz, M., Klipp, E., & Liebermeister, W.
(2012)
Propagating semantic information in biochemical network models.
BMC Bioinformatics
13
(1),
18.
Text/Abstract
doi: 10.1186/1471-2105-13-18, PMID: 22289386
Spiesser, T.W., Müller, C., Schreiber, G., Krantz, M., & Klipp, E.
(2012)
Size homeostasis can be intrinsic to growing cell populations and explained without size sensing or signalling.
FEBS J.
279
(22),
4213-30.
Text/Abstract
Text/Abstract
doi: 10.1111/febs.12014, PMID: 23013467
Tiger, C.-F., Krause, F., Cedersund, G., Palmér, R., Klipp. E., Hohmann, S., Kitano, H. & Krantz, M.
(2012)
A framework for mapping, visualisation and automatic model creation of signal transduction networks.
Molecular Systems Biology
8
, 578.
Text/Abstract
doi: 10.1038/msb.2012.12, PMID: 22531118


2011
Adrover, M.A., Zi, Z., Duch, A., Schaber, J., González-Novo, A., Jimenez, J., Nadal-Ribelles, M., Clotet, J., Klipp, E., & Posas, F.
(2011)
Time-dependent quantitative multicomponent control of the G1-S network by the stress-activated protein kinase Hog1 upon osmostress.
Sci. Signal.
4
(192),
ra63.
Text/Abstract
Text/Abstract
doi: 10.1126/scisignal.2002204, PMID: 21954289
Barberis, M., Beck, C., Amoussouvi, A., Schreiber, G., Diener, C., Herrmann, A. & Klipp, E.
(2011)
A low number of SIC1 mRNA molecules ensures a low noise level in cell cycle progression of budding yeast.
Mol. Biosyst.
7
(10)
, 2804-12.
Text/Abstract
doi: 10.1039/C1MB05073G, PMID: 21717009
Barberis M, Linke C, Adrover MA, González-Novo A, Lehrach H, Krobitsch S, Posas F, & Klipp E.
(2011)
Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins.
Biotechnol. Adv.
, Epub ahead of print.
Text/Abstract
doi: 10.1016/j.biotechadv.2011.09.004, PMID: 21963604
Handorf, T & Klipp, E
(2011)
Modeling mechanistic biological networks: an advanced Boolean approach.
Bioinformatics
December 22,
Text/Abstract
Text/Abstract
doi: 10.1093/bioinformatics/btr697, PMID: 22199382
Kowald, A.
(2011)
The glyoxalase system as an example of a cellular maintenance pathway with relevance to aging.
Aging (Albany NY)
3
(1),
17-8.
Text/Abstract
Text/Abstract
PMID: 21266742
Kowald, A. & Kirkwood, T.B.
(2011)
Evolution of the mitochondrial fusion-fission cycle and its role in aging.
Proc. Natl. Acad. Sci. USA.
108
(25),
10237-42.
Text/Abstract
doi: 10.1073/pnas.1101604108, PMID: 21646529
Kowald, A. & Schmeier, S.
(2011)
Text mining for systems modeling.
Methods Mol. Biol.
696
(1),
305-18.
Text/Abstract
doi: 10.1007/978-1-60761-987-1_19, PMID: 21063956
Kowald, A. & Wierling C.
(2011)
Standards, tools, and databases for the analysis of yeast 'omics data.
Methods Mol. Biol.
759
, 345-65.
Text/Abstract
doi: 10.1007/978-1-61779-173-4_20, PMID: 21863497
Mah, N., Wang, Y., Liao, M.-C., Prigione, A., Jozefczuk, J., Lichtner, B., Wolfrum, K., Haltmeier, M., Flöttmann, M., Schaefer M., Hahn, A., Mrowka, R., Klipp, E., Andrade-Navarro, M.A., & Adjaye, J.
(2011)
Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory.
PLoS ONE
6
(8),
e24351.
Text/Abstract
doi: 10.1371/journal.pone.0024351, PMID: 21909390
Schaber, J. & Klipp, E.
(2011)
Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks.
Curr. Opin. Biotechnol.
22
(1),
109-16.
Text/Abstract
doi: 10.1016/j.copbio.2010.09.014, PMID: 20970318
Schaber, J., Flöttmann, M., Li, J., Tiger, C.F., Hohmann, S. & Klipp E.
(2011)
Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway.
PLoS One
6
(3),
e14791.
Text/Abstract
doi: 10.1371/journal.pone.0014791, PMID: 21483474
Schreiber G, Barberis M, Scolari S, Klaus C, Herrmann A, & Klipp E.
(2011)
Unraveling interactions of cell cycle-regulating proteins Sic1 and B-type cyclins in living yeast cells: a FLIM-FRET approach.
FASEB J.
26
(2)
, 546-54.
Text/Abstract
doi: 10.1096/fj.11-192518, PMID: 22002907
Schulz , M., Krause, F., Le Novère, N., Klipp, E. & Liebermeister, W.
(2011)
Retrieval, alignment, and clustering of computational models based on semantic annotations.
Mol. Syst. Biol.
7
, 512.
Text/Abstract
doi: 10.1038/msb.2011.41, PMID: 21772260
Schütze, J., Mair, T., Hauser, M.J., Falcke, M. & Wolf, J.
(2011)
Metabolic synchronization by traveling waves in yeast cell layers.
Biophys. J.
100
(4),
809-13.
Text/Abstract
doi: 10.1016/j.bpj.2010.12.3704
Stoma, S., Fröhlich, M., Gerber, S. & Klipp, E.
(2011)
STSE: Spatio-temporal simulation environment dedicated to biology.
BMC Bioinform.
12
, 126.
Text/Abstract
doi: 10.1186/1471-2105-12-126, PMID: 21527030
Tyc, K. & Klipp E.
(2011)
Modeling dissemination of pathogenic fungi within a host: a cartoon for the interactions of two complex systems.
J. Comput. Sci. Syst. Biol.
S1
001.
Text/Abstract
doi: 10.4172/jcsb.S1-001
Waltemath, D., Adams, R., Beard, D.A., Bergmann, F.T., Bhalla, U.S., Britten, R., Chelliah, V., Cooling, M.T., Cooper, J., Crampin, E.J., Garny, A., Hoops, S., Hucka, M., Hunter, P., Klipp, E., Laibe, C., Miller, A.K., Moraru, I., Nickerson, D., Nielsen, P., Nikolski, M., Sahle, S., Sauro, H.M., Schmidt, H., Snoep, J.L., Tolle, D., Wolkenhauer, O. & Le Novčre, N.
(2011)
Minimum information about a simulation experiment (MIASE).
PLoS Comput. Biol.
7
(4),
e1001122.
Text/Abstract
doi: 10.1371/journal.pcbi.1001122, PMID: 21552546
Waltermann C, & Klipp E.
(2011)
Information theory based approaches to cellular signaling.
Biochim. Biophys. Acta.
1810
(10),
924-32.
Text/Abstract
Text/Abstract
doi: 10.1016/j.bbagen.2011.07.009, PMID: 21798319
Zi, Z., Feng, Z., Chapnick, D.A., Dahl, M., Deng, D., Klipp, E., Moustakas, A. & Liu, X.
(2011)
Quantitative analysis of transient and sustained transforming growth factor-ß signaling dynamics.
Mol. Syst. Biol.
7
, 492.
Text/Abstract
doi: 10.1038/msb.2011.22, PMID: 21613981

2010
Barberis, M., Linke, C., Adrover, M.A., Lehrach, H., Posas, F., Krobitsch, S. & Klipp, E.
(2010)
Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins in yeast.
FEBS J.
277
(Suppl. s1),
174.
Text/Abstract
doi: 10.1111/j.1742-4658.2010.07680.x
Barberis, M., Spiesser, T.W. & Klipp, E.
(2010)
Replication origins and timing of temporal replication in budding yeast: how to solve the conundrum?
Curr Genomics
11
(3),
199-211.
Text/Abstract
doi: 10.2174/138920210791110942, PMID: 21037857
Klipp, E., Wade, R.C. & Kummer, U.
(2010)
Biochemical network-based drug-target prediction.
Curr. Opin. Biotechnol.
21
(4),
511-6.
Text/Abstract
doi: 10.1016/j.copbio.2010.05.004, PMID: 20554441
Krause, F., Uhlendorf, J., Lubitz, T., Schulz, M., Klipp, E. & Liebermeister, W.
(2010)
Annotation and merging of SBML models with semanticSBML.
Bioinformatics
26
(3),
421-2.
Text/Abstract
doi: 10.1093/bioinformatics/btp642
Liebermeister, W., Uhlendorf, J. & Klipp, E.
(2010)
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.
Bioinformatics
26
(12),
1528-34.
Text/Abstract
doi: 10.1093/bioinformatics/btq141, PMID: 20385728
Lubitz, T., Schulz, M., Klipp, E. & Liebermeister, W.
(2010)
Parameter balancing in kinetic models of cell metabolism.
J. Phys. Chem. B
114
(49),
16298-303.
Text/Abstract
Text/Abstract
doi: 10.1021/jp108764b, PMID: 21038890
Podo F, Buydens LM, Degani H, Hilhorst R, Klipp E, Gribbestad IS, Van Huffel S, van Laarhoven HW, Luts J, Monleon D, Postma GJ, Schneiderhan-Marra N, Santoro F, Wouters H, Russnes HG, Sørlie T, Tagliabue E, & Břrresen-Dale AL (FEMME Consortium)
(2010)
Triple-negative breast cancer: present challenges and new perspectives.
Mol. Oncol.
4
(3),
209-29.
Text/Abstract
doi: 10.1016/j.molonc.2010.04.006, PMID: 20537966
Schaber, J., Adrover, M.A., Eriksson, E., Pelet, S., Petelenz-Kurdziel, E., Klein, D., Posas, F., Goksör, M., Peter, M., Hohmann, S. & Klipp, E.
(2010)
Biophysical properties of Saccharomyces cerevisiae and their relationship with HOG pathway activation.
Eur. Biophys. J.
39
(11),
1547-56.
Text/Abstract
doi: 10.1007/s00249-010-0612-0, PMID: 20563574
Schütze, J. & Wolf, J.
(2010)
Spatio-temporal dynamics of glycolysis in cell layers. A mathematical model.
Biosystems
99
(2),
104-8.
Text/Abstract
doi: 10.1016/j.biosystems.2009.10.002
Spiesser, T.W., Diener, C., Barberis, M. & Klipp, E.
(2010)
What influences DNA replication rate in budding yeast?
PLoS One
5
(4),
e10203.
Text/Abstract
doi: 10.1371/journal.pone.0010203, PMID: 20436919
Stoma, S. & Klipp , E.
(2010)
Spatio-temporal simulation environment. A microscopy image based modelization framework.
Microscopy and Microanalysis
16
(Suppl. S2),
734-5.
Text/Abstract
doi: 10.1017/S1431927610060083
Waltermann, C. & Klipp, E.
(2010)
Signal integration in budding yeast.
Biochem. Soc. Trans.
38
(5),
1257-64.
Text/Abstract
Supplementary Data
doi: 10.1042/BST0381257, PMID: 20863295
Yizhak, K., Benjamini, T., Liebermeister, W., Ruppin, E. & Shlomi, T.
(2010)
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.
Bioinformatics
26
(12),
i255-60.
Text/Abstract
doi: 10.1093/bioinformatics/btq183
Zi, Z., Liebermeister, W. & Klipp, E.
(2010)
A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae.
PLoS One
5
(3),
e9522.
Text/Abstract
doi: 10.1371/journal.pone.0009522, PMID: 20209100

2009
Alfieri, R., Barberis, M., Chiaradonna, F., Gaglio, D., Milanesi, L., Vanoni, M., Klipp, E. & Alberghina, L.
(2009)
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation.
BMC Bioinform.
10
(Suppl. 12),
S16.
Text/Abstract
doi: 10.1186/1471-2105-10-S12-S16
Christian, N., May, P., Kempa, S., Handorf, T. & Ebenhöh, O.
(2009)
An integrative approach towards completing genome-scale metabolic networks.
Mol. BioSyst.
5
, 1889-1903.
Text/Abstract
doi: 10.1039/b915913b
Ebenhöh, O & Handorf, T.
(2009)
Functional classification of genome-scale metabolic networks.
EURASIP J. Bioinform. Syst. Biol.
2009
, Article ID 570456.
Text/Abstract
doi: 10.1155/2009/570456
Gerber, S., Hasenbrink, G., Hendriksen, W., van Heusden, P., Ludwig, J., Klipp, E. & Lichtenberg-Fraté, H.
(2009)
Graphical analysis and experimental evaluation of Saccharomyces cerevisiae P_TRK1/2 and P_BMH1/2 promoter region.
Genome Inform.
22
, 11-20.
Text/Abstract
PMID: 20238415
Klipp, E.
(2009)
Timing matters.
FEBS Lett.
583
(24),
4013-8.
Text/Abstract
doi: 10.1016/j.febslet.2009.11.065
Krantz, M., Ahmadpour, D., Ottosson, L.G., Warringer, J., Waltermann, C., Nordlander, B., Klipp, E., Blomberg, A., Hohmann, S. & Kitano, H.
(2009)
Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway.
Mol. Syst. Biol.
5
, 281.
Text/Abstract
doi: 10.1038/msb.2009.36
Kühn, C., Prasad, K.V.S., Klipp, E. & Gennemark, P.
(2009)
Formal representation of the high osmolarity glycerol pathway in yeast.
Genome Inform.
22
, 69-83.
Text/Abstract
PMID: 20238420
Kühn, C., Wierling, C., Kühn, A., Klipp, E., Panopoulou, G., Lehrach, H. & Poustka, A.J.
(2009)
Monte Carlo analysis of an ODE model of the sea urchin endomesoderm network.
BMC Syst. Biol.
3
, 83.
Text/Abstract
doi: 10.1186/1752-0509-3-83
Schaber, J., Liebermeister, W. & Klipp, E.
(2009)
Nested uncertainties in biochemical models.
IET Syst. Biol.
3
(1),
1-9.
Text/Abstract
doi: 10.1049/iet-syb:20070042
Schulz, M., Bakker, B.M. & Klipp, E.
(2009)
TIde: a software for the systematic scanning of drug targets in kinetic network models.
BMC Bioinform.
10
, 344.
Text/Abstract
doi: 10.1186/1471-2105-10-344
Spiesser, T.W., Klipp, E. & Barberis, M.
(2009)
A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae.
Mol. Genet. Genomics
282
(1),
25-35.
Text/Abstract
doi: 10.1007/s00438-009-0443-9
Yus, E., Maier, T., Michalodimitrakis, K., van Noor, V., Yamada, T., Chen, W.H., Wodke, J.A.H., Güell, M., Martínez, S., Bourgeois, R., Kühner, S., Raineri, E., Letunic, I., Kalinina, O.V., Rode, M., Herrmann, R., Gutiérrez-Gallego, R., Russell, R.B., Gavin, A.C., Bork, P. & Serrano, L.
(2009)
Impact of genome reduction on bacterial metabolism and its regulation.
Science
326
(5957),
1263-8.
Text/Abstract
doi: 10.1126/science.1177263

2008
Barberis, M. & Klipp, E.
(2008)
Sic1 can regulate the fundamental events in the budding yeast cell cycle.
FEBS J.
275
(Suppl. s1),
441.
Text/Abstract
doi: 10.1111/j.1742-4658.2008.06447.x
Basler G., Nikoloski, Z., Ebenhöh, O. & Handorf, T.
(2008)
Biosynthetic potentials from species-specific metabolic networks.
Genome Inform.
20
, 135-48.
Text/Abstract
Bruck, J., Liebermeister, W. & Klipp, E.
(2008)
Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis.
Genome Inform.
20
, 1-14.
Text/Abstract
Cvijovic, M., Soueidan, H., Sherman, D.J., Klipp, E. & Nikolski, M.
(2008)
Exploratory simulation of cell ageing using hierarchical models.
Genome Inform.
21
, 114-25.
Text/Abstract
Erjavec, N., Cvijovic, M., Klipp, E. & Nyström, T.
(2008)
Selective benefits of damage partitioning in unicellular systems and its effects on aging.
Proc. Natl. Acad. Sci.
105
(48),
18764-9.
Text/Abstract
doi: 10.1073/pnas.0804550105
Flöttmann, M., Schaber, J., Hoops, S., Klipp, E. & Mendes, P.
(2008)
ModelMage: a tool for automatic model generation, selection, and management.
Genome Inform.
20
, 52-63.
Text/Abstract
Gerber, S., Aßmus, H., Bakker, B. & Klipp, E.
(2008)
Drug-efficacy depends on the inhibitor type and the target position in a metabolic network - A systematic study.
J. Theor. Biol.
252
(3),
442-55.
Text/Abstract
Text/Abstract
doi: 10.1016/j.jtbi.2007.09.027, PMID: 17981303
Handorf T., Ebenhöh O., Christian N. & Kahn D.
(2008)
An environmental perspective on metabolism.
J. Theor. Biol.
252
(3),
530-7.
Text/Abstract
doi: 10.1016/j.jtbi.2007.10.036
Herrgard, M.J., Swainston, N., Dobson, P., Dunn, W.B., Arga, K.Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M.L., Oliveira, A.P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasie, I., Weichart, D., Brent, R., Broomhead, D.S., Westerhoff, H.V., Kürdar, B., Penttilä, M., Klipp, E., Palsson, B.O., Sauer, U., Oliver, S.G., Mendes, P., Nielsen, J. & Kell, D.B.
(2008)
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Nature Biotechnol.
26
(10),
1155-60.
Text/Abstract
doi: 10.1038/nbt1492
Kühn, C., Petelenz, E., Nordlander, B., Schaber, J., Hohmann, S. & Klipp, E.
(2008)
Exploring the impact of osmoadaptation on glycolysis using time-varying response coefficients.
Genome Inform.
20
, 77-90.
Text/Abstract
Schaber, J. & Klipp, E.
(2008)
Short-term volume and turgor regulation in yeast.
Essays Biochem.
45
, 147-60.
Text/Abstract
Zi, Z., Zheng, Y., Rundell, A.E. & Klipp, E.
(2008)
SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.
BMC Bioinform.
9
, 342.
Text/Abstract
doi: 10.1186/1471-2105-9-342

2007
Barberis, M. & Klipp, E.
(2007)
Insights into the network controlling the G1/S transition in budding yeast.
Genome Inform.
18
, 85-99.
Text/Abstract
Barberis, M., Klipp, E., Vanoni, M. & Alberghina, L.
(2007)
Modeling of the G(1)/S transition in yeast cell cycle.
FEBS J.
274
(Suppl. s1),
248.
Text/Abstract
doi: 10.1111/j.0014-2956.2007.05861_5.x
Barberis, M., Klipp, E., Vanoni, M. & Alberghina, A.
(2007)
Cell size at S phase initiation: an emergent property of the G1/S network.
PLoS Comput. Biol.
3
(4),
e64.
Text/Abstract
Text/Abstract
doi: 10.1371/journal.pcbi.0030064
Borger, S., Liebermeister, W., Uhlendorf, J. & Klipp, E.
(2007)
Automatically generated model of a metabolic network.
Genome Inform.
18
, 215-24.
Text/Abstract
Handorf, T. & Ebenhöh, O.
(2007)
MetaPath Online: a web server implementation of the network expansion algorithm.
Nucleic Acids Res.
35
(Suppl. 2),
W613-8.
Text/Abstract
doi: 10.1093/nar/gkm287
Klipp, E.
(2007)
Modeling dynamic processes in yeast. Review.
Yeast
24
(11),
943-59.
Text/Abstract
doi: 10.1002/yea.1544, PMID: 17868189
Klipp, E.
(2007)
Modeling of yeast cell stress response.
FEBS J.
274
(Suppl. s1),
53.
Text/Abstract
doi: 10.1111/j.0014-2956.2007.05866_4.x
Klipp, E., Liebermeister, W., Helbig, A., Kowald, A. & Schaber, J.
(2007)
Systems Biology standards - the community speaks.
Nature Biotechnol.
25
(4),
390-1.
Text/Abstract
Supplement 1
Supplement 2
doi: 10.1038/nbt0407-390
Kühn, C., Kühn, A., Poustka, A. & Klipp, E.
(2007)
Modeling development. Spikes of the sea urchin.
Genome Inform.
18
, 75-84.
Text/Abstract
Supplement 1
Supplement 2
Ralser, M., Wamelink, M.M., Kowald, A., Gerisch,B., Heeren, G., Struys, E.A., Klipp, E., Jakobs, C., Breitenbach, M., Lehrach, H. & Krobitsch, S.
(2007)
Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress.
J. Biol.
6
(4),
10.
Text/Abstract
doi: 10.1186/jbiol61
Zi, Z. & Klipp, E.
(2007)
Cellular signaling is potentially regulated by cell density in receptor trafficking networks.
FEBS Lett.
581
(24),
4589-95.
Text/Abstract
Text/Abstract
doi: 10.1016/j.febslet.2007.08.047
Zi, Z. & Klipp, E.
(2007)
Constraint-based modeling and kinetic analysis of the Smad dependent TGF-β signaling pathway.
PLoS One
2
(9),
e936.
Text/Abstract
Text/Abstract
Text/Abstract
doi: 10.1371/jounal.phone.0000936
Zi, Z. & Klipp, E.
(2007)
Steady state analysis of signal response in receptor trafficking networks.
Genome Inform.
18
, 100-8.
Text/Abstract

2006
Borger, S., Liebermeister, W. & Klipp, E.
(2006)
Prediction of enzyme kinetic parameters based on statistical learning.
Genome Inform.
17
(1),
80-7.
Bruck, J., Ebenhöh, O. & Heinrich, R.
(2006)
Patterns of interactions of reaction pairs in metabolic networks.
Genome Inform.
17
(1),
208-18.
Ebenhöh, O., Handorf, T. & Kahn, D.
(2006)
Evolutionary changes of metabolic networks and their biosynthetic capacities.
IEE Proc. Syst. Biol.
153
(5),
354-8.
Text/Abstract
Ebenhöh, O. & Liebermeister, W.
(2006)
Structural analysis of expressed metabolic subnetworks.
Genome Inform.
17
(1),
163-72.
Handorf, T., Ebenhöh, O., Kahn, D. & Heinrich, R.
(2006)
Hierarchy of metabolic compounds based on their synthetic capacity.
IEE Proc. Syst. Biol.
153
(5),
359-63.
Text/Abstract
Klipp, E. & Liebermeister, W.
(2006)
Mathematical modeling of intracellular signaling pathways.
BMC Neurosci.
7
(Suppl 1),
S10.
Text/Abstract
doi: 10.1186/1471-2202-7-S1-S10
Liebermeister, W. & Klipp, E.
(2006)
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints.
Theor. Biol. Med. Model.
3
, 41.
Text/Abstract
doi: 10.1186/1742-4682-3-41
Liebermeister, W. & Klipp, E.
(2006)
Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data.
Theor. Biol. Med. Model.
3
, 42.
Text/Abstract
doi: 10.1186/1742-4682-3-42
Salazar, C., Schütze, J. & Ebenhöh, O.
(2006)
Bioinformatics meets systems biology.
Genome Biol.
7
, 303.
Text/Abstract
doi: 10.1186/gb-2006-7-1-303
Schaber, J., Kofahl, B., Kowald, A. & Klipp, E.
(2006)
A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast.
FEBS J.
273
(15),
3520-33.
Text/Abstract
doi: 10.1111/j.1742-4658.2006.05359.x
Schulz, M., Uhlendorf, J., Klipp, E. & Liebermeister, W.
(2006)
SBMLmerge, a system for combining biochemical network models.
Genome Inform.
17
(1),
62-71.
Zi, Z. & Klipp, E.
(2006)
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
Bioinformatics
22
(21),
2704-5.
Text/Abstract
doi: 10.1093/bioinformatics/btl443

2005
Ebenhöh, O., Handorf, T. & Heinrich, R.
(2005)
A cross species comparison of metabolic network functions.
Genome Inform.
16
(1),
203-13.
Text/Abstract
Handorf, T., Ebenhöh, O. & Heinrich, R.
(2005)
Expanding metabolic networks: scopes of compounds, robustness, and evolution.
J. Mol. Evol.
61
(4),
498-512.
Text/Abstract
doi: 10.1007/s00239-005-0027-1
Klipp, E. & Hohmann, S.
(2005)
Simulation von Lebensprozessen.
BIOForum
28
(10),
60-1.
Text/Abstract
Klipp, E., Nordlander, B., Krüger, R., Gennemark, P. & Hohmann, S.
(2005)
Integrative model of the response of yeast to osmotic shock.
Nature Biotechnol.
23
(8),
975-82.
Text/Abstract
doi: 10.1038/nbt1114
Kowald, A., Lehrach, H. & Klipp, E.
(2005)
Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase.
J. Theor. Biol.
238
(4),
828-40.
Text/Abstract
doi: 10.1016/j.jtbi.2005.06.034
Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D. & Wanner, B.L.
(2005)
Minimum information requested in the annotation of biochemical models (MIRIAM).
Nature Biotechnol.
23
(12),
1509-15.
Text/Abstract
doi: 10.1038/nbt1156
Liebermeister, W., Baur, U. & Klipp, E.
(2005)
Biochemical network models simplified by balanced truncation.
FEBS J.
272
(16),
4034-43.
Text/Abstract
doi: 10.1111/j.1742-4658.2005.04780.x
Liebermeister, W. & Klipp, E.
(2005)
Biochemical networks with uncertain parameters.
IEE Proc. Syst. Biol.
152
(3),
97-107.
Text/Abstract

2004
Ebenhöh, O., Handorf, T. & Heinrich R.
(2004)
Structural analysis of expanding metabolic networks.
Genome Inform.
15
(1),
35-45.
Text/Abstract
Hakenberg, J., Schmeier, S., Kowald, A., Klipp, E. & Leser, U.
(2004)
Finding kinetic parameters using text mining.
OMICS J. Integrat. Biol.
8
(2),
131-52.
Text/Abstract
doi: 10.1089/1536231041388366
Klipp, E., Liebermeister, W. & Wierling, C.
(2004)
Inferring dynamic properties of biochemical reaction networks from structural knowledge.
Genome Inform.
15
(1),
125-37.
Text/Abstract
Klipp, E., Nordlander, B., Kofahl, B. & Hohmann, S.
(2004)
Shutting the MAP off - and on again?
Curr. Genomics
5
(8),
637-47.
Text/Abstract
Kofahl, B. & Klipp, E.
(2004)
Modeling the dynamics of the yeast pheromone pathway.
Yeast
21
(10),
831-50.
Text/Abstract
doi: 10.1002/yea.1122
Kowald, A. & Klipp, E.
(2004)
Alternative pathways might mediate toxicity of high concentrations of superoxide dismutase.
Ann. New York Acad. Sci.
1019
, 370-4.
Text/Abstract
doi: 10.1196/annals.1297.065, PMID: 15247047
Liebermeister, W., Klipp, E., Schuster, S. & Heinrich, R.
(2004)
A theory of optimal differential gene expression.
Biosystems
76
(1/3),
261-78.
Text/Abstract
Text/Abstract
doi: 10.1016/j.biosystems.2004.05.022

2003 and before
Bakker, B.M., Assmus, H.E., Bruggeman, F., Haanstra, J.R., Klipp, E. & Westerhoff, H.
(2002)
Network-based selectivity of antiparasitic inhibitors.
Mol. Biol. Rep.
29
(1/2),
1-5.
Text/Abstract
doi: 10.1023/A:1020397513646
Klipp, E., Heinrich, R. & Holzhütter, H.G.
(2002)
Prediction of temporal gene expression. Metabolic optimisation by re-distribution of enzyme activities.
Eur. J. Biochem.
269
(22),
5406-13.
Text/Abstract
doi: 10.1046/j.1432-1033.2002.03223.x
Klipp, E. & Heinrich, R.
(1999)
Competition for enzymes in metabolic pathways: implications for optimal distributions of enzyme concentrations and for the distribution of flux control.
BioSystems
54
(1/2),
1-14.
Text/Abstract
doi: 10.1016/S0303-2647(99)00059-3
Heinrich, R., Montero, F., Klipp, E., Waddell, T.G. & Meléndez-Hevia, E.
(1997)
Kinetic and thermodynamic constraints for the structural design of glycolysis.
Nonlinear Anal.
30
(3),
1793-1804.
Text/Abstract
Text/Abstract
doi: 10.1016/S0362-546X(97)00274-5
Heinrich, R., Montero, F., Klipp, E., Waddell, T.G. & Meléndez-Hevia, E.
(1997)
Theoretical approaches to the evolutionary optimization of glycolysis. Thermodynamic and kinetic constraints.
Eur. J. Biochem.
243
(1/2),
191-201.
Text/Abstract
doi: 10.1111/j.1432-1033.1997.0191a.x
Heinrich, R. & Klipp, E.
(1996)
Control analysis of unbranched enzymatic chains in states of maximal activity.
J. Theor. Biol.
182
(3),
243-52.
Text/Abstract
doi: 10.1006/jtbi.1996.0161
Klipp, E.
(1995)
Evolutionary optimization of enzyme kinetic parameters.
J. Biol. Syst.
3
(2),
363-76.
Text/Abstract
doi: 10.1142/S0218339095000344
Klipp, E. & Heinrich, R.
(1994)
Evolutionary optimization of enzyme kinetic parameters; effect of constraints.
J. Theor. Biol.
171
(3),
309-23.
Text/Abstract
PMID: 7869733
Wilhelm, T., Hoffmann-Klipp, E. & Heinrich, R.
(1994)
An evolutionary approach to enzyme kinetics: optimization of ordered mechanisms.
Bull. Math. Biol.
56
(1),
65-106.
Text/Abstract
doi: 10.1016/S0092-8240(05)80206-X
Heinrich, R. & Hoffmann, E.
(1991)
Kinetic parameters of enzymatic reactions in states of maximal activity; an evolutionary approach.
J. Theor. Biol.
151
(2),
249-83.
Text/Abstract
doi: 10.1016/S0022-5193(05)80363-7
Heinrich, R., Hoffmann, E. & Holzhütter, H.G.
(1990)
Calculation of kinetic parameters of a reversible enzymatic reaction in states of maximal activity.
Biomed. Biochim. Acta
49
(8/9),
891-902.
Text/Abstract

Proceedings

Stoma, S.
(2010)
Towards modeling of spatial dynamic systems based on microscopy images.
Proceedings of 6th Workshop on Computation of Biochemical Pathways and Genetic Networks.
Heidelberg (Germany), September 16-17, 2010.
Borger, S., Liebermeister, W. & Klipp, E.
(2005)
Distribution of a bifurcation parameter in a genetic network with uncertain parameters.
In: Kummer, Pahle, U.J., Surovtsova, I. & Zobeley, J. (eds.)
4th Workshop on Computation of Biochemical Pathways and Genetic Networks.
Heidelberg (Germany), September 12-13, 2005. Logos, Berlin, ISBN: 978-3-8325-1018-3,
95-101.
Klipp, E. & Liebermeister, W.
(2003)
Predicting dynamic properties of metabolic networks from structural knowledge.
Proceedings of the 4th International Conference on Systems Biology (ICSB2003).
St. Louis (USA), November 6-9, 2003.
Schmeier, S., Hakenberg, J., Kowald, A., Klipp, E. & Leser, U.
(2003)
Text mining for systems biology using statistical learning methods.
Proceedings der Workshop-Woche “Lehren – Lernen – Wissen – Adaptivität (LLWA 2003)“.
Karlsruhe (Germany), October 2003.
Klipp, E.
(2003)
Mathematical modeling of signal transduction in yeast.
Yeast
20
(Suppl. 1),
268.
Klipp, E. & Krüger, R.
(2002)
Kinetic modelling of signalling pathways for stress-induced changes of gene expression in yeast.
Proceedings of the 3rd International Conference on Systems Biology (ICSB2002).
Stockholm (Sweden), December, 2002.
Liebermeister, W., Schuster, S., Heinrich, R. & Klipp, E.
(2002)
Relating gene expression to function by an optimality postulate.
Proceedings of the European Conference on Cell Biology (ECCB) 2002.
Saarbrücken (Germany), October, 6-9, 2002.
Klipp, E.
(2001)
Reprogramming the metabolic system.
Trends in Nonlinear Analysis. Theory, Modelling and Computation.
Heidelberg (Germany), October 8 - 12, 2000,
126-8.
Klipp, E., Holzhütter, H.-G. & Heinrich, R.
(2000)
Reprogramming the metabolic system by altering gene expression.
In: Hofmeyr, J.-H.S., Rohwer, J.M. & Snoep, J.L., (eds.)
Animating the Cellular Map. Proceedings of the 9th Int. Meeting on BioThermoKinetics.
Stellenbosch (South Africa), April, 3-7, 2000.
165-70.