Publications


Books

Klipp, E., Liebermeister, L., Wierling, C. & Kowald, A.
(2016)

Systems Biology. A Textbook. (second revised edition)


Wiley-Blackwell, Weinheim, 504 p., ISBN:


Systems Biology. A textbook

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

available as e-book (2011) ISBN: 978-3-527-64497-1


Systems Biology. A textbook


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

available as e-book (2006) ISBN: 978-3-527-60488-3

Systems Biology in Practice

Book chapters

Münzner, U., Lubitz, T., Edda Klipp, E., & Krantz, M.
(2017)
Toward Genome-Scale Models of Signal Transduction Networks.
In: Nielsen, J. & Hohmann, S.
Systems Biology.
Wiley-VCH, ISBN: 978-3-527-33558-9,
215-242.
Text/Abstract
doi: 10.1002/9783527696130.ch8
Groth, P., Reuter, G., & Thieme, S.
(2015)
Analysis of genomic data in a cloud computing environment.
In: Wang, B., Li, R., & Perrizo, W.
Big Data Analytics in Bioinformatics and Healthcare.
IGI Global, ISBN: 978-1-4666-6611-5,
186-214.
Text/Abstract
doi: 10.4018/978-1-4666-6611-5
Kowald, A. & Klipp, E.
(2014)
Mathematical models of mitochondrial aging and dynamics.
In: Osiewacz, H.
The Mitochonrion in Aging and Disease (Prog. Mol. Biol. Transl. Sci. 127),
Elsevier, ISBN: 978-0-12-394625-6,
63-92.
Text/Abstract
doi: 10.1016/B978-0-12-394625-6.00003-9, PMID: 25149214
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,
3-29.
Text/Abstract
doi: 10.1142/9789814317931_0001
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,
77-98.
Text/Abstract
doi: 10.5772/22126
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 (Meth. Mol. Biol. 759),
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, 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.)
Stress-Activated Protein Kinases (Topics Curr. Gen. 20)
Springer, ISBN: 978-3-540-75568-7,
205-24.
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.
Fundación CajaMurcia, 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, ISBN: 978-0-387-34527-7,
95-106.
Text/Abstract
doi: 10.1007/0-387-36747-0
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 (Topics Curr. Gen. 13),
Springer, ISBN: 978-3-540-22968-1,
277-302.
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, ISBN: 0-262-08326-3,
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, 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, 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 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? (Modern Trends in Biothermokinetics 3).
Insbruck University Press, ISBN: 3-901249-17-6,
99-102.

Journal articles

2017

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(2017)
(),
.
Text/Abstract
doi: , PMID:
Auconi, A., Giansanti, A. & Klipp, E.
(2017)
Causal influence in linear Langevin networks without feedback
Phys. Rev. E
95
(4-1),
042315.
Text/Abstract
doi: 10.1103/PhysRevE.95.042315, PMID: 28505709
Del Rio, G., Klipp, E. & Herrmann, A.
(2017)
Using confocal microscopy and computational modeling to investigate the cell-penetrating properties of antimicrobial peptides
Methods Mol. Biol.
1548
, 191-9.
Text/Abstract
doi: 10.1007/978-1-4939-6737-7_13, PMID: 28013505
Heiske, M., Letellier T,. & Klipp, E.
(2017)
Comprehensive Mathematical Model of Oxidative Phosphorylation Valid for Physiological up to Pathological Conditions
FEBS J.
24 June
, Epub ahead of print.
Text/Abstract
doi: 10.1111/febs.14151, PMID: 28646582
Linke, C., Chasapi, A., González-Novo, A., Al Sawad, I., Tognetti, S., Klipp, E., Loog, M., Krobitsch, S., Posas, F., Xenarios, I. & Barberis M
(2017)
A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle
NPJ Syst. Biol. Appl.
3
, 7.
Text/Abstract
doi: 10.1038/s41540-017-0008-1, PMID: PMC5460246
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.
(2017)
Interaction dynamics determine signaling and output pathway responses
Cell Rep.
19
(1),
136-49.
Text/Abstract
doi: 10.1016/j.celrep.2017.03.029, PMID: 28380353

2016

Barros de Andrade e Sousa, L.C., Kühn, C., Tyc, K.M. & Klipp, E
(2016)
Dosage and dose schedule screening of drug combinations in agent-based models reveals hidden synergies
Front. Physiol.
6
, 398.
Text/Abstract
doi: 10.3389/fphys.2015.00398, PMID: 26779031
Chen, W.H., van Noort, V., Lluch-Senar, M., Hennrich, M.L., Wodke, J.A., Yus, E., Alibés, A., Roma, G., Mende, D.R., Pesavento, C., Typas, A., Gavin, A.C., Serrano, L., & Bork, P.
(2016)
Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances
Nucleic Acids Res.
44
(3),
1192-202.
Text/Abstract
doi: 10.1093/nar/gkw004, PMID: 26773059
Cvijovic, M., Höfer, T., Acimovic, J., Alberghina, L., Almaas, E., Besozzi, D., Blomberg, A., Bretschneider, T., Cascante, M., Collin, O., de Atauri, P., Depner, C., Dickinson, R., Dobrzynski, M., Fleck, C., Garcia-Ojalvo, J., Gonze, D., Hahn, J., Hess, H.M., Hollmann, S., Krantz, M., Kummer, U., Lundh, T., Martial, G., Dos Santos, V.M., Mauer-Oberthür, A., Regierer, B., Skene, B., Stalidzans, E., Stelling, J., Teusink, B., Workman, C.T. & Hohmann, S.
(2016)
Strategies for structuring interdisciplinary education in Systems Biology: an European perspective
NPJ Syst. Biol. Appl.
26
(2),
16011.
Text/Abstract
doi: 10.1038/npjsba.2016.11, PMID: 28725471
Gerber, S., Fröhlich, M., Lichtenberg-Fraté, H., Shabala, S., Shabala, L. & Klipp, E.
(2016)
A thermodynamic model of monovalent cation homeostasis in the yeast Saccharomyces cerevisiae
PLoS Comput. Biol.
12
(1),
e1004703.
Text/Abstract
doi: 10.1371/journal.pcbi.1004703, PMID: 26815455
Goldenbogen, B., Giese, W., Hemmen, M., Uhlendorf, J., Herrmann, A. & Klipp, E.
(2016)
Dynamics of cell wall elasticity pattern shapes the cell during yeast mating morphogenesis
Open Biol.
6
(9),
160136.
Text/Abstract
doi: 10.1098/rsob.160136, PMID: 27605377
Losensky, L., Goldenbogen, B., Holland, G., Laue, M., Petran, A., Liebscher, J., Scheidt, H.A., Vogel, A., Huster, D., Klipp, E., & Arbuzova A.
(2016)
Micro- and nano-tubules built from loosely and tightly rolled up thin sheets
Phys. Chem. Chem. Phys.
18
(2),
1292-301.
Text/Abstract
doi: 10.1039/C5CP06084B, PMID: 26659839
Lubitz, T., Hahn, J., Bergmann, F.T., Noor, E., Klipp, E. & Liebermeister, W.
(2016)
SBtab: a flexible table format for data exchange in systems biology
Bioinform.
32
(16),
2559-61.
Text/Abstract
doi: 10.1093/bioinformatics/btw1, PMID: 27153616
Pauling, J. & Klipp, E.
(2016)
Computational lipidomics and lipid bioinformatics: filling in the blanks
J. Integr. Bioinform.
13
(1),
299.
Text/Abstract
doi: 10.2390/biecoll-jib-2016-299, PMID: 28187425
Schelker, M., Mair, C.M., Jolmes, F., Welke, R.W., Klipp, E., Herrmann, A., Flöttmann, M. & Sieben, C.
(2016)
Viral RNA degradation and diffusion act as a bottleneck for the influenza A virus infection efficiency
PLoS Comput. Biol.
12
(10),
e1005075.
Text/Abstract
doi: 10.1371/journal.pcbi.1005075, PMID: 27780209
Schützhold, V., Hahn, J., Tummler, K. & Klipp, E.
(2016)
Computational modeling of lipid metabolism in yeast
Front. Mol. Biosci.
3
, 57.
Text/Abstract
doi: 10.3389/fmolb.2016.00057, PMID: 27730126
Spiesser, T., Kühn, C., Krantz, M., & Klipp, E.
(2016)
The MYpop toolbox: putting yeast stress responses in cellular context on single cell and population scales
Biotechnol. J.
11
(9)
, 1158-68.
Text/Abstract
doi: 10.1002/biot.201500344, PMID: 26952199
Talemi, S.R., Tiger, C.F., Andersson, M., Babazadeh, R., Welkenhuysen, N., Klipp, E., Hohmann, S. & Schaber, J.
(2016)
Systems level analysis of the yeast osmo-stat
Sci. Rep.
6
, 30950.
Text/Abstract
doi: 10.1038/srep30950, PMID: 27515486
Tyc, K.M., Herwald, S.E., Hogan, J.A., Pierce, J.V., Klipp, E. & Kumamoto, C.A.
(2016)
The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression
BMC Syst. Biol.
10
(1),
20.
Text/Abstract
doi: 10.1186/s12918-016-0268-1, PMID: 26927448
Waltemath, D., Karr, J.R., Bergmann, F.T., Chelliah, V., Hucka, M., Krantz, M., Liebermeister, W., Mendes, P., Myers, C.J., Pir, P., Alaybeyoglu, B., Aranganathan, N.K., Baghalian, K., Bittig, A.T., Pinto Burke, P.E., Cantarelli, M., Chew, Y.H., Costa, R.S., Cursons, J., Czauderna, T., Goldberg, A.P., Gómez, H.F., Hahn, J., Hameri, T., Hernande Gardiol, D.F., Kazakiewicz, D., Kiselev, I., Knight-Schrijver, V., Knüpfer, C., König, M., Lee, D., Lloret-Villas, A., Mandrik, N., Medley, J.K., Moreau, B., Naderi-Meshkin, H., Palaniappan, S.K., Priego-Espinosa, D., Scharm, M., Sharma, M., Smallbone, K., Stanford, N.J., Song, J.-H., Theile, T., Tokic, M., Tomar, N., Touré, V., Uhlendorf, J., Varusai, T.M., Watanabe, L.H., Wendland, F., Wolfien, M., Yurkovich, J.T., Zhu, Y., Zardilis, A., Zhukova, A., & Schreiber, F.
(2016)
Toward community standards and software for whole-cell modeling
IEEE Trans. Biomed. Eng.
63
(10),
2007-14.
Text/Abstract
doi: 10.1109/TBME.2016.2560762, PMID: 27305665

2015

Cheng, X., Dimou, E., Alborzinia, H., Wenke, F., Goehring, A., Reuter, S., Mah, N., Fuchs, H.R., Andrade-Navarro, M.A., Adjaye, J., Gul, S., Harms, C., Utikal, J., Klipp, E., Mrowka, R., & Wölfl. S.
(2015)
Identification of 2-[4-[(4-methoxyphenyl)methoxy]-phenyl]acetonitrile and derivatives as potent Oct3/4 inducers
J. Med. Chem.
58
(12)
4976-83
Text/Abstract
doi: 10.15252/msb.20145558, PMID: 25898186
Giese, W., Eigel, M, Westerheide, S, Engwer, C, & Klipp E.
(2015)
Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models
Phys. Biol.
12
(6),
066014.
Text/Abstract
doi: 10.1088/1478-3975/12/6/066014, PMID: 26599916
Lluch-Senar, M., Delgado, J., Chen, W.H., Lloréns-Rico, V., O′Reilly, F.J., Wodke, J.A., Unal, E.B., Yus, E., Martínez, S., Nichols, R.J., Ferrar, T., Vivancos, A., Schmeisky, A., Stülke, J., van Noort, V., Gavin, A.C., Bork, P., & Serrano, L.0.
(2015)
Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium
Mol. Syst. Biol.
21
(11),
780.
Text/Abstract
doi: 10.15252/msb.20145558 PMID: 25609650
Lubitz,, T., Welkenhuysen, N., Shashkova, S., Bendrioua, L., Hohmann, S., Klipp, E. & Krantz, M.
(2015)
Network reconstruction and validation of the Snf1/AMPK pathway in baker’s yeast based on a comprehensive literature review
npj Syst. Biol. Applic.
1
, 15007.
Text/Abstract
doi: 10.1038/npjsba.2015.7
Mori, T., Flöttmann, M., Krantz, M., Akutsu, T., & Klipp, E.
(2015)
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks
BMC Syst. Biol.
9
, 45.
Text/Abstract
doi: 10.1186/s12918-015-0193-8, PMID: 26259567
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.
(2015)
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
Bioinform.
31
(21)
, 3558-60.
Text/Abstract
doi: 10.1093/bioinformatics/btv405, PMID: 26142188
Spiesschaert, B., Goldenbogen, B., Taferner, S., Schade, M., Mahmoud, M., Klipp, E., Osterrieder, N., & Azab, W.
(2015)
Role of gB and pUS3 in EHV-1 transfer between PBMC and endothelial cells: a dynamic in vitro model
J. Virol.
89
(23)
, 11899-908.
Text/Abstract
doi: 10.1128/JVI.01809-15, PMID: 26378176
Spiesser, T.W., Kühn, C., Krantz, M., & Klipp, E.
(2015)
Bud-Localization of CLB2 mRNA can constitute a growth rate dependent daughter sizer
PLoS Comput. Biol.
11
(4),
e1004223.
Text/Abstract
doi: 10.1371/journal.pcbi.1004223, PMID: 25910075
Tummler,K., Kühn,C., & Klipp,E.
(2015)
Dynamic metabolic models in context: biomass backtracking
Integr. Biol.
7
(8),
940-51.
Text/Abstract
doi: 10.1039/c5IB00050e, PMID: 26189715
Wodke, J.A., Alibés, A., Cozzuto, L., Hermoso, A., Yus, E., Lluch-Senar, M., Serrano, L., & Roma G.
(2015)
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae
Nucleic Acids Res.
43
(D1)
, D618-23
Text/Abstract
doi: 10.1093/nar/gku1105, PMID: 25378328

2014

Ariño, J., Aydar, E., Drulhe, S., Ganser, D., Jorrín, J., Kahm, M., Krause, F., Petrezslyová, S., Yenush, L., Zimmermannová, O., van Heusden, G.P.H., Kschischo, M., Ludwig, J., Palmer, C., Ramos, J., & Sychrová, H.
(2014)
Systems biology of monovalent cation homeostasis in yeast: the translucent contribution
Adv. Microbial Physiol.
64
, 1–63.
Text/Abstract
doi: 10.1016/B978-0-12-800143-1.00001-4.PMID: 24797924
Bock, M., Scharp, T., Talnikar, C., & Klipp E.
(2014)
BooleSim: An interactive Boolean Network Simulator
Bioinform.
30
(1),
131-2.
Text/Abstract
doi: 10.1093/bioinformatics/btt568, PMID: 24078712
Cvijovic, M., Almquist, J., Hagmar, J., Hohmann, S., Kaltenbach, H.M., Klipp, E., Krantz, M., Mendes, P., Nelander, S., Nielsen, J., Pagnani, A., Przulj, N., Raue, A., Stelling, J., Stoma, S., Tobin, F., Wodke, J.A., Zecchina, R., & Jirstrand, M.
(2014)
Bridging the gaps in systems biology
Mol. Genet. Genomics
289
(5)
, 727-34.
Text/Abstract
doi: 10.1007/s00438-014-0843-3, PMID: 24728588
de Hijas-Liste, G.M., Klipp, E., Balsa-Canto, E., & Banga, J.R.
(2014)
Global dynamic optimization approach to predict activation in metabolic pathways
BMC Systems Biology
8
,
1.
Text/Abstract
doi: 10.1186/1752-0509-8-1, PMID: 24393148
Diener, C., Schreiber, G., Giese, W., del Rio, G., Schröder, A., & Klipp, E.
(2014)
Yeast mating and image-based quantification of spatial pattern formation
PLoS Comput. Biol.
10
(6),
e1003690.
Text/Abstract
doi: 10.1371/journal.pcbi.1003690, PMID: 24967739
Flöttmann, M., Uhlendorf, J., Scharp, T., Klipp E., & Spiesser T.W.
(2014)
SensA: web-based sensitivity analysis of SBML models
Bioinform.
30
(19)
, 2830-1.
Text/Abstract
doi: 10.1093/bioinformatics/btu378, PMID: 24903418
García-Salcedo, R., Lubitz, T., Beltran, G., Elbing, K., Tian, Y., Frey, S., Wolkenhauer, O., Krantz, M., Klipp, E. & Hohmann, S.
(2014)
Glucose derepression by yeast AMP-activated protein kinase SNF1 is controlled via at least two independent steps
FEBS J.
281
(7)
, 1901-07.
Text/Abstract
doi: 10.1111/febs.12753, PMID: 24529170
Guillaud, F., Dröse, S., Kowald, A., Brandt U., & Klipp, E.
(2014)
Superoxide production by cytochrome bc1 complex: A mathematical model
Biochim Biophys Acta
1837
(10)
, 1643-52.
Text/Abstract
doi: 10.1016/j.bbabio.2014.05.358, PMID: 24911293
Hilsch, M., Goldenbogen, B., Sieben, C., Höfer, C.T., Rabe, J.P., Klipp, E., Herrmann, A., & Chiantia, S.
(2014)
Influenza A matrix protein M1 multimerizes upon binding to lipid membranes
Biophys. J.
107
(4),
912-23.
Text/Abstract
doi: 10.1016/j.bpj.2014.06.042, PMID: 25140426
Hosiner, D., Gerber, S., Lichtenberg-Fraté, H., Glaser, W., Schüller, C., & Klipp, E.
(2014)
Impact of Acute Metal Stress in Saccharomyces cerevisiae
PLoS One
9
(1),
e83330.
Text/Abstract
doi: 10.1371/journal.pone.0083330, PMID: 24416162
Kummer, S., Flöttmann, M., Schwanhäusser, B., Sieben, C., Veit, M., Selbach, M., Klipp, E., & Herrmann, A.
(2014)
Alteration of Protein Levels during Influenza Virus H1N1 Infection in Host Cells: A Proteomic Survey of Host and Virus Reveals Differential Dynamics
PLoS One
9
(4),
e94257.
Text/Abstract
doi: 10.1371/journal.pone.0094257, PMID: 24718678
Rodriguez Plaza, J.G., Morales-Nava, R., Diener, C., Schreiber, G., Gonzalez, Z.D., Lara Ortiz, M.T., Ortega Blake, I., Pantoja, O., Volkmer, R., Klipp, E., Herrmann, A., & Del Rio G.
(2014)
Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin.
J. Biol. Chem.
289
(21)
, 14448-57.
05 April 2014.
Text/Abstract
doi: 10.1074/jbc.M113.515023, PMID: 24706763
Tummler, K., Lubitz, T., Schelker, M., & Klipp, E.
(2014)
New types of experimental data shape the use of enzyme kinetics for dynamic network modeling
FEBS J.
281
(2)
, 549-71.
Text/Abstract
doi: 10.1111/febs.12525, PMID: 24034816
Tyc, K.M., Kühn, C., Wilson, D. & Klipp, E.
(2014)
Assessing the advantage of morphological changes in Candida albicans: a game theoretical study
Front. Microbiol.
5
, 41.
Text/Abstract
doi: 10.3389/fmicb.2014.00041, PMID: 24567730
Uschner, F. & Klipp, E.
(2014)
Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system
Syst Synth Biol.
8
(4),
297-306.
Text/Abstract
doi: 10.1007/s11693-014-9146-6, PMID: 26396653
Vaga, S., Bernardo-Faura, M., Cokelaer, T., Maiolica, A., Barnes, C.A., Gillet, L.C., Hegemann, B., van Drogen, F., Sharifian, H., Klipp, E., Peter, M., Saez-Rodriguez, J., & Aebersold, R.
(2014)
Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast
Mol. Syst. Biol.
10
(12),
767.
Text/Abstract
doi: 10.15252/msb.20145112, PMID: 25492886

2013

Flöttmann, M., Krause, F., Klipp, E., & Krantz, M.
(2013)
Reaction-contingency based bipartite Boolean modelling
BMC Syst Biol.
7
(1),
58.
Text/Abstract
doi: 10.1186/1752-0509-7-58, PMID: 23835289
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
Linke, C., Klipp, E., Lehrach, H., Barberis, M., & Krobitsch, S.
(2013)
Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions
Front Physiol.
4
, 173.
Text/Abstract
doi: 10.3389/fphys.2013.00173, PMID: 23874301
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.
9
(8)
, 1993-2004.
Text/Abstract
doi: 10.1039/C3MB00005B, PMID: 23636168
Stanford, N.J., Lubitz, T., Smallbone, K., Klipp, E., Mendes, P., & Liebermeister, W.
(2013)
Systematic construction of kinetic models from genome-scale metabolic networks
PLoS One
8
(11),
e79195.
Text/Abstract
doi: 10.1371/journal.pone.0079195, PMID: 24324546
Supady, A,. Klipp, E., & Barberis, M.
(2013)
A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae
J. Biotechnol.
168
(2)
, 174-84.
Text/Abstract
doi: 10.1016/j.jbiotec.2013.06.022, PMID: 23850861
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
Barberis, M., Linke, C., Androver, M.À., González-Novo, A., Lehrach, H., Krobitsch, S., Posas, F., & Klipp, E.
(2012)
Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins
Biotechnol. Adv.
30
, 108-130.
Text/Abstract
doi: 10.1016/j.biotechadv.2011.09.004, PMID: 21963604
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 Res.
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
doi: 10.1186/1471-2164-13-554, PMID: 23066959
Handorf, T & Klipp, E
(2012)
Modeling mechanistic biological networks: an advanced Boolean approach.
Bioinform.
28
(4),
557-63
Text/Abstract
doi: 10.1093/bioinformatics/btr697, PMID: 22199382
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
doi: 10.3389/fphys.2012.00287, 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
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
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 Bioinform.
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
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
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
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
doi: 10.18632/aging.100268, 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, PMID: 21320423
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
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.
Bioinform.
26
(3),
421-2.
Text/Abstract
doi: 10.1093/bioinformatics/btp642, PMID: 19933161
Liebermeister, W., Uhlendorf, J. & Klipp, E.
(2010)
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.
Bioinform.
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
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, PMID: 19837130
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
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.
Bioinform.
26
(12),
i255-60.
Text/Abstract
doi: 10.1093/bioinformatics/btq183, PMID: 20529914
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, PMID: 19828076
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, PMID: 19763335
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, PMID: 19300528
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, PMID: 19941864
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, PMID: 19536204
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, PMID: 19698179
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, PMID: 19154080
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, PMID: 19840374
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, PMID: 19306105
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, PMID: 19965476

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
dou: 10.1142/9781848163003_0012, PMID: 19425129
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
PMID: 19425118
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
PMID: 19425152
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, PMID: 19020097
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
PMID: 19425122
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
doi: 10.1016/j.jtbi.2007.09.027, PMID: 17981303
Handorf, T., Christian, N., Ebenhöh O. & 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, PMID: 18086477
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, PMID: 18846089
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
PMID: 19425124
Schaber, J. & Klipp, E.
(2008)
Short-term volume and turgor regulation in yeast.
Essays Biochem.
45
, 147-60.
Text/Abstract
doi: 10.1042/BSE0450147, PMID: 18793130
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, PMID: 18706080

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
PMID: 18546477
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
doi: 10.1371/journal.pcbi.0030064, PMID: 17432928
Borger, S., Liebermeister, W., Uhlendorf, J. & Klipp, E.
(2007)
Automatically generated model of a metabolic network.
Genome Inform.
18
, 215-24.
Text/Abstract
PMID: 18546489
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, PMID: 17483511
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
doi: 10.1038/nbt0407-390, PMID: 17420739
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
PMID: 18546476
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, PMID: 18154684
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
doi: 10.1016/j.febslet.2007.08.047, PMID: 17825822
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
doi: 10.1371/jounal.phone.0000936, PMID: 17895977
Zi, Z. & Klipp, E.
(2007)
Steady state analysis of signal response in receptor trafficking networks.
Genome Inform.
18
, 100-8.
Text/Abstract
PMID: 18546478

2006

Borger, S., Liebermeister, W. & Klipp, E.
(2006)
Prediction of enzyme kinetic parameters based on statistical learning.
Genome Inform.
17
(1),
80-7.
Text/Abstract
PMID: 17503358
Bruck, J., Ebenhöh, O. & Heinrich, R.
(2006)
Patterns of interactions of reaction pairs in metabolic networks.
Genome Inform.
17
(1),
208-18.
Text/Abstract
PMID: 17503370
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
PMID: 16986316
Ebenhöh, O. & Liebermeister, W.
(2006)
Structural analysis of expressed metabolic subnetworks.
Genome Inform.
17
(1),
163-72.
Text/Abstract
PMID: 17503366
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
PMID: 17503366
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, PMID: 17118154
Kowald, A., Lehrach, H. & Klipp, E.
(2006)
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, PMID: 16085106
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, PMID: 17173669
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, PMID: 17173670
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, PMID: 16515725
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, PMID: 16884493
Schulz, M., Uhlendorf, J., Klipp, E. & Liebermeister, W.
(2006)
SBMLmerge, a system for combining biochemical network models.
Genome Inform.
17
(1),
62-71.
Text/Abstract
PMID: 17503356
Zi, Z. & Klipp, E.
(2006)
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
Bioinform.
22
(21),
2704-5.
Text/Abstract
doi: 10.1093/bioinformatics/btl443, PMID: 16926221

2005

Ebenhöh, O., Handorf, T. & Heinrich, R.
(2005)
A cross species comparison of metabolic network functions.
Genome Inform.
16
(1),
203-13.
Text/Abstract
PMID: 16362923
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, PMID: 16155745
Klipp, E. & Hohmann, S.
(2005)
Simulation von Lebensprozessen.
BIOForum
28
(10),
60-1.
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, PMID: 16025103
Le Novère, 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, PMID: 16333295
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, PMID: 16098187
Liebermeister, W. & Klipp, E.
(2005)
Biochemical networks with uncertain parameters.
IEE Proc. Syst. Biol.
152
(3),
97-107.
Text/Abstract
PMID: 16986274

2004

Ebenhöh, O., Handorf, T. & Heinrich R.
(2004)
Structural analysis of expanding metabolic networks.
Genome Inform.
15
(1),
35-45.
Text/Abstract
PMID: 15712108
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, PMID: 15268772
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
PMID: 15712116
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, PMID: 15300679
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
doi: 10.1016/j.biosystems.2004.05.022, PMID: 15351149

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, PMID: 12241036
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, PMID: 12423338
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, PMID: 10658833
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),
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, PMID: 9030739
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, PMID: 8944155
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
doi: 10.1006/jtbi.1994.1234, 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, PMID: 1943142
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
PMID: 2082929

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.
Text/Abstract
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.