Journal Articles

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2017

Gnugge R, Rudolf F (2017) Saccharomyces cerevisiae shuttle vectors. Yeast. http://doi.org/10.1002/yea.3228.

2016

Barillari C, Ottoz DS, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudolf F (2016) openBIS ELN-LIMS: an open-source database for academic laboratories. Bioinformatics 32: 638-640. http://doi.org/10.1093/bioinformatics/btv606.

Cvijovic M, Höfer T, Aćimović 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 HM, Hollmann S, Krantz M, Kummer U, Lundh T, Martial G, dos Santos VM, Mauer-Oberthür A, Regierer B, Skene B, Stalidzans E, Stelling J, Teusink B, Workman CT, Hohmann S (2016) Strategies for structuring interdisciplinary education in Systems Biology: an European perspective. npj Systems Biology and Applications 2: 16011. http://doi.org/10.1038/npjsba.2016.11.

Gnugge R, Dharmarajan L, Lang M, Stelling J (2016) An Orthogonal Permease-Inducer-Repressor Feedback Loop Shows Bistability. ACS Synth Biol. http://doi.org/10.1021/acssynbio.6b00013.

Gnugge R, Liphardt T, Rudolf F (2016) A shuttle vector series for precise genetic engineering of Saccharomyces cerevisiae. Yeast 33: 83-98. http://doi.org/10.1002/yea.3144.

Haandbæk N, Bürgel SC, Rudolf F, Heer F, Hierlemann A (2016) Characterization of Single Yeast Cell Phenotypes Using Microfluidic Impedance Cytometry and Optical Imaging. ACS Sensors 1: 1020-1027. http://doi.org/10.1021/acssensors.6b00286.

Lang M, Stelling J (2016) Modular Parameter Identification of Biomolecular Networks. SIAM Journal on Scientific Computing 38: B988-B1008. http://doi.org/10.1137/15m103306x.

Roberts TM, Rudolf F, Meyer A, Pellaux R, Whitehead E, Panke S, Held M (2016) Identification and Characterisation of a pH-stable GFP. Sci Rep 6: 28166. http://doi.org/10.1038/srep28166.

van Heck RG, Ganter M, Martins Dos Santos VA, Stelling J (2016) Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PLoS Comput Biol 12: e1005085. http://doi.org/10.1371/journal.pcbi.1005085.

Xie M, Ye H, Wang H, Charpin-El Hamri G, Lormeau C, Saxena P, Stelling J, Fussenegger M (2016) beta-cell-mimetic designer cells provide closed-loop glycemic control. Science 354: 1296-1301. http://doi.org/10.1126/science.aaf4006.  

2015

Zhu Z, Frey O, Haandbaek N, Franke F, Rudolf F, Hierlemann A (2015) Time-lapse electrical impedance spectroscopy for monitoring the cell cycle of single immobilized S. pombe cells. Scientific Reports 5, 17180. http://doi.org/10.1038/srep17180 

Schillings C, Sunnåker M, Stelling J, Schwab C (2015) Efficient Characterization of Parametric Uncertainty of Complex (Bio) chemical Networks. PLoS Comput Biol 11: e1004457. http://doi.org/10.1371/journal.pcbi.1004457.

Abel JH, Widmer LA, John PCS, Stelling J, Doyle FJ (2015) A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior. IEEE Life Sciences Letters 1: 3-6. http://doi.org/10.1109/lls.2015.2439498.

Chawla K, Bürgel SC, Schmidt GW, Rudolf F, Frey O, Hierlemann A (2015) Microfluidic Cell Culturing Platform Combining Long-term, High-resolution Imaging with Impedance Spectroscopy. Procedia Engineering 120: 154-157. http://doi.org/doi:10.1016/j.proeng.2015.08.592.

Prescott TP, Lang M, Papachristodoulou A (2015) Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering. PLoS Comput Biol 11: e1004235. http://doi.org/10.1371/journal.pcbi.1004235.

Oliveira AP, Dimopoulos S, Busetto AG, Christen S, Dechant R, Falter L, Haghir Chehreghani M, Jozefczuk S, Ludwig C, Rudroff F, Schulz JC, Gonzalez A, Soulard A, Stracka D, Aebersold R, Buhmann JM, Hall MN, Peter M, Sauer U, Stelling J (2015) Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome. Molecular Systems Biology 11: 802-802. http://doi.org/10.15252/msb.20145475.

Frey O, Rudolf F, Schmidt GW, Hierlemann A (2015) Versatile, Simple-to-Use Microfluidic Cell-Culturing Chip for Long-Term, High-Resolution, Time-Lapse Imaging. Analytical Chemistry. http://doi.org/10.1021/ac504611t.

Egli A, Humar A, Widmer LA, Lisboa LF, Santer DM, Mueller T, Stelling J, Baluch A, O'Shea D, Houghton M, Kumar D (2015) Effect of Immunosuppression on Th2 and B-cell Responses to Influenza Vaccination. J Infect Dis. http://doi.org/10.1093/infdis/jiv015.

2014

Auslander D, Auslander S, Charpin-El Hamri G, Sedlmayer F, Muller M, Frey O, Hierlemann A, Stelling J, Fussenegger M (2014) A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Mol Cell 55: 397-408. http://doi.org/10.1016/j.molcel.2014.06.007.

Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M (2014) Bridging the gaps in systems biology. Mol Genet Genomics 289: 727-734. http://doi.org/10.1007/s00438-014-0843-3.

Dimopoulos S, Mayer CE, Rudolf F, Stelling J (2014) Accurate cell segmentation in microscopy images using membrane patterns. Bioinformatics 30: 2644-2651. http://doi.org/10.1093/bioinformatics/btu302.

Ganter M, Kaltenbach HM, Stelling J (2014) Predicting network functions with nested patterns. Nat Commun 5: 3006. http://doi.org/10.1038/ncomms4006.

Lang M, Summers S, Stelling J (2014) Cutting the wires: modularization of cellular networks for experimental design. Biophys J 106: 321-331. http://doi.org/10.1016/j.bpj.2013.11.2960.

O'Shea D, Widmer LA, Stelling J, Egli A (2014) Changing face of vaccination in immunocompromised hosts. Curr Infect Dis Rep 16: 420. http://doi.org/10.1007/s11908-014-0420-2.

Otero Muras I, Yordanov P, Stelling J (2014) A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves. BMC Syst Biol 8: 114. http://doi.org/10.1186/s12918-014-0114-2.

Ottoz DS, Rudolf F, Stelling J (2014) Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae. Nucleic Acids Res 42: e130. http://doi.org/10.1093/nar/gku616.

Sunnaker M, Zamora-Sillero E, Lopez Garcia de Lomana A, Rudroff F, Sauer U, Stelling J, Wagner A (2014) Topological augmentation to infer hidden processes in biological systems. Bioinformatics 30: 221-227. http://doi.org/10.1093/bioinformatics/btt638.

2013

Busetto AG, Hauser A, Krummenacher G, Sunnaker M, Dimopoulos S, Ong CS, Stelling J, Buhmann JM (2013) Near-optimal experimental design for model selection in systems biology. Bioinformatics 29: 2625-2632. http://doi.org/10.1093/bioinformatics/btt436.

Chubukov V, Uhr M, Le Chat L, Kleijn RJ, Jules M, Link H, Aymerich S, Stelling J, Sauer U (2013) Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis. Mol Syst Biol 9: 709. http://doi.org/10.1038/msb.2013.66.

Ganter M, Bernard T, Moretti S, Stelling J, Pagni M (2013) MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. Bioinformatics 29: 815-816. http://doi.org/10.1093/bioinformatics/btt036.

Marchisio MA, Colaiacovo M, Whitehead E, Stelling J (2013) Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. BMC Syst Biol 7: 42. http://doi.org/10.1186/1752-0509-7-42.

Mayer C, Dimopoulos S, Rudolf F, Stelling J (2013) Using CellX to quantify intracellular events. Curr Protoc Mol Biol Chapter 14: Unit 14 22. http://doi.org/10.1002/0471142727.mb1422s101.

Sunnaker M, Busetto AG, Numminen E, Corander J, Foll M, Dessimoz C (2013) Approximate Bayesian computation. PLoS Comput Biol 9: e1002803. http://doi.org/10.1371/journal.pcbi.1002803.

Sunnaker M, Zamora-Sillero E, Dechant R, Ludwig C, Busetto AG, Wagner A, Stelling J (2013) Automatic generation of predictive dynamic models reveals nuclear phosphorylation as the key Msn2 control mechanism. Sci Signal 6: ra41. http://doi.org/10.1126/scisignal.2003621.

Widmer LA, Stelling J, Doyle FJ, 3rd (2013) Note: Parameter-independent bounding of the stochastic Michaelis-Menten steady-state intrinsic noise variance. J Chem Phys 139: 166102. http://doi.org/10.1063/1.4827496.

2012

Bacchus W, Lang M, El-Baba MD, Weber W, Stelling J, Fussenegger M (2012) Synthetic two-way communication between mammalian cells. Nat Biotechnol 30: 991-996. http://doi.org/10.1038/nbt.2351.

Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mader U, Nicolas P, Piersma S, Rugheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U (2012) Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 335: 1099-1103. http://doi.org/10.1126/science.1206871.

Gonnet P, Dimopoulos S, Widmer L, Stelling J (2012) A specialized ODE integrator for the efficient computation of parameter sensitivities. BMC Syst Biol 6: 46. http://doi.org/10.1186/1752-0509-6-46.

Jol SJ, Kummel A, Terzer M, Stelling J, Heinemann M (2012) System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes. PLoS Comput Biol 8: e1002415. http://doi.org/10.1371/journal.pcbi.1002415.

Kaltenbach HM, Stelling J (2012) Modular analysis of biological networks. Adv Exp Med Biol 736: 3-17. http://doi.org/10.1007/978-1-4419-7210-1_1.

Lang M, Rudolf F, Stelling J (2012) Use of YouScope to implement systematic microscopy protocols. Curr Protoc Mol Biol. pp. Unit 14 21 11-23. http://doi.org/10.1002/0471142727.mb1421s98.

Otero-Muras I, Banga JR, Alonso AA (2012) Characterizing multistationarity regimes in biochemical reaction networks. PLoS One 7: e39194. http://doi.org/10.1371/journal.pone.0039194.

Zhu Z, Frey O, Ottoz DS, Rudolf F, Hierlemann A (2012) Microfluidic single-cell cultivation chip with controllable immobilization and selective release of yeast cells. Lab Chip 12: 906-915. http://doi.org/10.1039/c2lc20911j.

2011

Lang M, Marquez-Lago TT, Stelling J, Waldherr S (2011) Autonomous synchronization of chemically coupled synthetic oscillators. Bull Math Biol 73: 2678-2706. http://doi.org/10.1007/s11538-011-9642-8.

Marchisio MA, Rudolf F (2011) Synthetic biosensing systems. Int J Biochem Cell Biol 43: 310-319. http://doi.org/10.1016/j.biocel.2010.11.012.

Marchisio MA, Stelling J (2011) Automatic design of digital synthetic gene circuits. PLoS Comput Biol 7: e1001083. http://doi.org/10.1371/journal.pcbi.1001083.

Mirsky HP, Taylor SR, Harvey RA, Stelling J, Doyle FJ (2011) Distribution-based sensitivity metric for highly variable biochemical systems. IET Syst Biol 5: 50. http://doi.org/10.1049/iet-syb.2009.0064.

Sunnaker M, Cedersund G, Jirstrand M (2011) A method for zooming of nonlinear models of biochemical systems. BMC Syst Biol 5: 140. http://doi.org/10.1186/1752-0509-5-140.

Zamora-Sillero E, Hafner M, Ibig A, Stelling J, Wagner A (2011) Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Syst Biol 5: 142. http://doi.org/10.1186/1752-0509-5-142.

2010

Kemmer C, Gitzinger M, Daoud-El Baba M, Djonov V, Stelling J, Fussenegger M (2010) Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat Biotechnol 28: 355-360. http://doi.org/10.1038/nbt.1617.

Marquez-Lago TT, Stelling J (2010) Counter-intuitive stochastic behavior of simple gene circuits with negative feedback. Biophys J 98: 1742-1750. http://doi.org/10.1016/j.bpj.2010.01.018.

Susaki EA, Stelling J, Ueda HR (2010) Challenges in synthetically designing mammalian circadian clocks. Current Opinion in Biotechnology 21: 556-565. http://doi.org/10.1016/j.copbio.2010.07.011.

Tigges M, Denervaud N, Greber D, Stelling J, Fussenegger M (2010) A synthetic low-frequency mammalian oscillator. Nucleic Acids Res 38: 2702-2711. http://doi.org/10.1093/nar/gkq121.

2009

Kaltenbach HM, Dimopoulos S, Stelling J (2009) Systems analysis of cellular networks under uncertainty. FEBS Letters 583: 3923-3930. http://doi.org/10.1016/j.febslet.2009.10.074.

Marchisio MA, Stelling J (2009) Computational design tools for synthetic biology. Curr Opin Biotechnol 20: 479-485. http://doi.org/10.1016/j.copbio.2009.08.007.

Muller D, Stelling J (2009) Precise regulation of gene expression dynamics favors complex promoter architectures. PLoS Comput Biol 5: e1000279. http://doi.org/10.1371/journal.pcbi.1000279.

Stelling J, Kholodenko BN (2009) Signaling cascades as cellular devices for spatial computations. J Math Biol 58: 35-55. http://doi.org/10.1007/s00285-008-0162-6.

Terzer M, Maynard ND, Covert MW, Stelling J (2009) Genome-scale metabolic networks. Wiley Interdisciplinary Reviews-Systems Biology and Medicine 1: 285-297. http://doi.org/10.1002/Wsbm.37.

Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M (2009) A tunable synthetic mammalian oscillator. Nature 457: 309-312. http://doi.org/10.1038/nature07616.

2008

Bagheri N, Lawson MJ, Stelling J, Doyle FJ, 3rd (2008) Modeling the Drosophila melanogaster circadian oscillator via phase optimization. J Biol Rhythms 23: 525-537. http://doi.org/10.1177/0748730408325041.

Bagheri N, Stelling J, Doyle FJ, 3rd (2008) Circadian phase resetting via single and multiple control targets. PLoS Comput Biol 4: e1000104. http://doi.org/10.1371/journal.pcbi.1000104.

Marchisio MA, Stelling J (2008) Computational design of synthetic gene circuits with composable parts. Bioinformatics 24: 1903-1910. http://doi.org/10.1093/bioinformatics/btn330.

Terzer M, Stelling J (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 24: 2229-2235. http://doi.org/10.1093/bioinformatics/btn401.

2007

Bagheri N, Stelling J, Doyle FJ (2007) Circadian phase entrainment via nonlinear model predictive control. International Journal of Robust and Nonlinear Control 17: 1555-1571. http://doi.org/10.1002/Rnc.1209.

Bagheri N, Stelling J, Doyle FJ, 3rd (2007) Quantitative performance metrics for robustness in circadian rhythms. Bioinformatics 23: 358-364. http://doi.org/10.1093/bioinformatics/btl627.

Conradi C, Flockerzi D, Raisch J, Stelling J (2007) Subnetwork analysis reveals dynamic features of complex (bio)chemical networks. Proc Natl Acad Sci U S A 104: 19175-19180. http://doi.org/10.1073/pnas.0705731104.

Kuepfer L, Peter M, Sauer U, Stelling J (2007) Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol 25: 1001-1006. http://doi.org/10.1038/nbt1330.

Stelling J (2007) Understandable complexity. Sci STKE 2007: pe9. http://doi.org/10.1126/stke.3762007pe9.

Terzer M, Jovanovic M, Choutko A, Nikolayeva O, Korn A, Brockhoff D, Zürcher F, Friedmann M, Schütz R, Zitzler E, Stelling J, Panke S (2007) Design of a biological half adder. IET Synth Biol 1: 53-58. http://doi.org/10.1049/iet-stb:20070013.

Weber W, Stelling J, Rimann M, Keller B, Daoud-El Baba M, Weber CC, Aubel D, Fussenegger M (2007) A synthetic time-delay circuit in mammalian cells and mice. Proc Natl Acad Sci U S A 104: 2643-2648. http://doi.org/10.1073/pnas.0606398104.

1998 - 2006

Anders A, Lilie H, Franke K, Kapp L, Stelling J, Gilles ED, Breunig KD (2006) The galactose switch in Kluyveromyces lactis depends on nuclear competition between Gal4 and Gal1 for Gal80 binding. J Biol Chem 281: 29337-29348. http://doi.org/10.1074/jbc.M604271200.

Doyle FJ, 3rd, Stelling J (2006) Systems interface biology. J R Soc Interface 3: 603-616. http://doi.org/10.1098/rsif.2006.0143.

Zak DE, Stelling J, Doyle FJ (2005) Sensitivity analysis of oscillatory (bio)chemical systems. Computers & Chemical Engineering 29: 663-673. http://doi.org/10.1016/j.compchemeng.2004.08.021.

Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO (2004) Comparison of network-based pathway analysis methods. Trends in Biotechnology 22: 400-405. http://doi.org/10.1016/j.tibtech.2004.06.010.

Stelling J (2004) Mathematical models in microbial systems biology. Curr Opin Microbiol 7: 513-518. http://doi.org/10.1016/j.mib.2004.08.004.

Stelling J, Gilles ED (2004) Mathematical modeling of complex regulatory networks. IEEE Trans Nanobioscience 3: 172-179. http://doi.org/10.1109/TNB.2004.833688.

Stelling J, Gilles ED, Doyle FJ, 3rd (2004) Robustness properties of circadian clock architectures. Proc Natl Acad Sci U S A 101: 13210-13215. http://doi.org/10.1073/pnas.0401463101.

Stelling J, Sauer U, Szallasi Z, Doyle FJ, 3rd, Doyle J (2004) Robustness of cellular functions. Cell 118: 675-685. http://doi.org/10.1016/j.cell.2004.09.008.

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin, II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531. http://doi.org/10.1093/bioinformatics/btg015.

Klamt S, Stelling J (2003) Two approaches for metabolic pathway analysis? Trends Biotechnol 21: 64-69. http://doi.org/10.1016/S0167-7799(02)00034-3.

Klamt S, Stelling J, Ginkel M, Gilles ED (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19: 261-269. http://doi.org/10.1093/bioinformatics/19.2.261

Klamt S, Stelling J (2002) Combinatorial complexity of pathway analysis in metabolic networks. Mol Biol Rep 29: 233-236. http://doi.org/10.1023/A:1020390132244.

Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193. http://doi.org/10.1038/nature01166.

Desbrosses G, Stelling J, Renaudin JP (1998) Dephosphorylation activates the purified plant plasma membrane H+-ATPase--possible function of phosphothreonine residues in a mechanism not involving the regulatory C-terminal domain of the enzyme. Eur J Biochem 251: 496-503. http://doi.org/10.1046/j.1432-1327.1998.2510496.x.

 
 
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24.04.2017
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