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UNICELLSYS Publications

University of Gothenburg

Stefan Hohmann

Furukawa K, Randhawa A, Kaur H, Mondal AK, Hohmann S
Fungal fludioxonil sensitivity is diminished by a constitutively active form of the group III histidine kinase
FEBS Lett. 2012 Jul 30;586(16):2417-22
http://www.ncbi.nlm.nih.gov/pubmed/22687241

Geijer C, Ahmadpour D, Palmgren M, Filipsson C, Klein DM, Tamás MJ, Hohmann S, Lindkvist-Petersson K.
Yeast aquaglyceroporins use the transmembrane core to restrict glycerol transport.
J Biol Chem. 2012 Jul 6;287(28):23562-70
http://www.ncbi.nlm.nih.gov/pubmed/22593571

Tiger CF, Krause F, Cedersund G, Palmér R, Klipp E, Hohmann S, Kitano H, Krantz M.
A framework for mapping, visualisation and automatic model creation of signal-transduction networks.
Mol Syst Biol. 2012 Apr 24;8:578.
http://www.ncbi.nlm.nih.gov/pubmed/22531118

Furukawa K, Furukawa T, Hohmann S.
Efficient Construction of Homozygous Diploid Strains Identifies Genes Required for the Hyper-Filamentous Phenotype in Saccharomyces cerevisiae.
PLoS One. 2011;6
http://www.ncbi.nlm.nih.gov/pubmed/22039512

Babazadeh R, Moghadas Jafari S, Zackrisson M, Blomberg A, Hohmann S, Warringer J, Krantz M.
The Ashbya gossypiiEF-1α promoter of the ubiquitously used MX cassettes is toxic to Saccharomyces cerevisiae.
FEBS Lett. 2011 Oct 22
http://www.ncbi.nlm.nih.gov/pubmed/22033143

Krantz, M., Ahmadpour, D., Ottosson, L.-G., Warringer, J., Nordlander,
B., Blomberg, A., Hohmann, S., Kitano, H.
Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway.
Mol Syst Biol. 2009;5:281.
http://www.ncbi.nlm.nih.gov/pubmed/19536204

Furukawa K., Sidoux-Walter F. Hohmann S.
Expression of the yeast aquaporin Aqy2 affects cell surface properties under the control of osmoregulatory and morphogenic signalling pathways
Molecular Microbiology (2009) 74(5), 1272–1286
http://www.ncbi.nlm.nih.gov/pubmed/19889095

Anders Blomberg

Blomberg, A.
Measuring growth rate in high-throughput growth phenotyping.
Curr Opin Biotechnol. 2011 Feb;22(1):94-102.
http://www.ncbi.nlm.nih.gov/pubmed/21095113

Ottosson, L.-G., Logg, K., Ibstedt, S., Sunnerhagen, P., Käll, M.,
Blomberg, A., and Warringer, J. 
Sulfate assimilation mediates tellurite accumulation and toxicity in yeast
Eukaryot Cell. 2010 Oct;9(10):1635-47.
http://www.ncbi.nlm.nih.gov/pubmed/20675578

Liti, L., Carter, D., Moses, Warringer, J, A., Parts., L., James,
S.A., Robert, P.D., Roberts, I.N., Burt, A., Koufopanou, V., Tsai,
I.J., Bergman, B., Bensasson, D., O’Kelly, M.J.T., von Oudenaarden,
A., Barton, D.B.H., Bailes, E.,Nguyen, A.N., Jones, M., Qual, M.A.,
Goodhead, I., Sims, S., Smith, F., Blomberg, A., Durbin, R., and
Louis, E.J. 
Population genomics of domestic and wild yeasts
Nature 458:337, 2009
http://www.ncbi.nlm.nih.gov/pubmed/19212322

Gombault A, Warringer J, Caesar R, Godin F, Vallée B, Doudeau M,
Chautard H, Blomberg A, Bénédetti H. (2009)
A phenotypic study of TFS1 mutants differentially altered in the inhibition of Ira2p or CPY.
FEMS Yeast Res. 2009 Sep;9(6):867-74
http://www.ncbi.nlm.nih.gov/pubmed/19552705

Logg, K., Bodvard, K., Blomberg, A., and Käll, M. (2009)
Investigations on light induced stress in fluorescence microscopy
using nuclear localization of the transcription factor Msn2p as
reporter
FEMS Yeast Research, 9:875
http://www.ncbi.nlm.nih.gov/pubmed/19566686

Per Sunnerhagen

Garre E, Romero-Santacreu L, De Clercq N, Blasco-Angulo N, Sunnerhagen P, Alepuz P.
Yeast mRNA cap-binding protein Cbc1/Sto1 is necessary for the rapid reprogramming of translation after hyperosmotic shock.
Mol Biol Cell. 2012 Jan;23(1):137-50
http://www.ncbi.nlm.nih.gov/pubmed/22072789

J. Warringer, M. Hult, S. Regot, F. Posas & P. Sunnerhagen
The HOG pathway dictates the short-term translational response after hyperosmotic shock
Mol Biol Cell. 2010 Sep;21(17):3080-92.
http://www.ncbi.nlm.nih.gov/pubmed/20587780

Mattias Goksör

Petelenz-Kurdziel E, Eriksson E, Smedh M, Beck C, Hohmann S, Goksör M.
Quantification of cell volume changes upon hyperosmotic stress in Saccharomyces cerevisiae.
Integr Biol (Camb). 2011 Oct 31;3(11):1120-6
http://www.ncbi.nlm.nih.gov/pubmed/22012314

Thomas Nyström

Orlandi I, Bettiga M, Alberghina L, Nyström T, Vai M.
Sir2-dependent asymmetric segregation of damaged proteins in ubp10 null mutants is independent of genomic silencing.
Biochim Biophys Acta. 2010 May;1803(5):630-8.
http://www.ncbi.nlm.nih.gov/pubmed/20211662

Fraunhofer-Chalmers

Mats Jirstrand

Sunnaker M, Cedersund G, Jirstrand M.
A Method for Zooming of Nonlinear Models of Biochemical Systems.
BMC Syst Biol. 2011 Sep 7;5(1):140
http://www.ncbi.nlm.nih.gov/pubmed/21899762

Berglund M, Sunnåker M, Adiels M, Jirstrand M, Wennberg B.
Investigations of a compartmental model for leucine kinetics using non-linear mixed effects models with ordinary and stochastic differential equations.
Math Med Biol. 2011 Sep 30.
http://www.ncbi.nlm.nih.gov/pubmed/21965323

Jansson A, Jirstrand M.
Biochemical modeling with SBGN
Drug Discov Today. 2010 May;15(9-10):365-70
http://www.ncbi.nlm.nih.gov/pubmed/20211756

 

ETH Zürich

Uwe Sauer

Buescher JM, Moco S, Sauer U, Zamboni N.
Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites.
Anal Chem. 2010 Jun 1;82(11):4403-12.PMID: 20433152
http://www.ncbi.nlm.nih.gov/pubmed/20433152

Büscher JM, Czernik D, Ewald JC, Sauer U, Zamboni N.
Cross-platform comparison of methods for quantitative metabolomics of primary metabolism.
Anal Chem. 2009 Mar 15;81(6):2135-43.PMID: 19236023
http://www.ncbi.nlm.nih.gov/pubmed/19236023

Rudi Aebersold

Costenoble R, Picotti P, Reiter L, Stallmach R, Heinemann M, Sauer U, Aebersold R.
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics.
Mol Syst Biol. 2011 Feb 1;7:464.
http://www.ncbi.nlm.nih.gov/pubmed/21283140

Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R.
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes.
Nat Methods 7, 43-46 (2010).
http://www.ncbi.nlm.nih.gov/pubmed/19966807

Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B. & Aebersold, R.
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics.
Cell 138, 795-806 (2009).
http://www.ncbi.nlm.nih.gov/pubmed/19664813

Jörg Stelling

Kaltenbach H-M,  Constantinescu S,  Feigelman J and  Stelling J
Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems
Algorithms in Bioinformatics
Lecture Notes in Computer Science, 2011, Volume 6833/2011, 139-150,
http://www.springerlink.com/content/6340t21142016148/

Kaltenbach HM, Stelling J.
Modular analysis of biological networks.
Adv Exp Med Biol. 2012;736:3-17.
http://www.ncbi.nlm.nih.gov/pubmed/22161320

Gonnet P, Dimopoulos S, Widmer L, Stelling J.
A Specialized ODE Integrator for Efficient Computation of Parameter Sensitivities.
BMC Syst Biol. 2012 May 20;6(1):46
http://www.ncbi.nlm.nih.gov/pubmed/22607742

Kaltenbach HM, Dimopoulos S, Stelling J.
Systems analysis of cellular networks under uncertainty.
FEBS Lett. 2009 Dec 17;583(24):3923-30.
http://www.ncbi.nlm.nih.gov/pubmed/19879267

Uhr, M., Kaltenbach, H.-M., Conradi, C. and Stelling, J.
Analysis of Degenerate Chemical Reaction Networks
Proceedings of Positive Systems: Theory and Applications, Volume 389/2009, 163-171
http://www.springerlink.com/content/k74380g83423654x

Matthias Peter

Zechner C, Ruess J, Krenn P, Pelet S, Peter M, Lygeros J, Koeppl H.
Moment-based inference predicts bimodality in transient gene expression.
Proc Natl Acad Sci U S A. 2012 May 22;109(21):8340-5. Epub 2012 May 7.
http://www.ncbi.nlm.nih.gov/pubmed/22566653

Lee SS, Horvath P, Pelet S, Hegemann B, Lee LP, Peter M.
Quantitative and dynamic assay of single cell chemotaxis.
Integr Biol (Camb). 2012 Apr;4(4):381-90
http://www.ncbi.nlm.nih.gov/pubmed/22230969

Pelet S, Peter M.
Dynamic processes at stress promoters regulate the bimodal expression of HOG response genes.
Commun Integr Biol. 2011 Nov 1;4(6):699-702.
http://www.ncbi.nlm.nih.gov/pubmed/22446531

Pelet, S., Rudolf, F., Nadal-Ribelles, M., de Nadal, E., Posas, F. and Peter, M., ,
Transient activation of the HOG MAPK pathway regulates bimodal gene expression
Science. 2011 May 6;332(6030):732-5.
http://www.ncbi.nlm.nih.gov/pubmed/21551064

Pelet, S. and Peter, M.
Fluorescent-based quantitative measurements of signal transduction in single cells
Design and Analysis of Biomolecular Circuits
2011, pp 369-393
http://link.springer.com/chapter/10.1007/978-1-4419-6766-4_17?null

Kijanska M, Dohnal I, Reiter W, Kaspar S, Stoffel I, Ammerer G, Kraft C, Peter M.
Activation of Atg1 kinase in autophagy by regulated phosphorylation.
Autophagy 6:8, 1168-1178; November 16, 2010;
http://www.ncbi.nlm.nih.gov/pubmed/20953146

Dechant R, Binda M, Lee SS, Pelet S, Winderickx J, Peter M.
Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V-ATPase.
EMBO J. 2010 Aug 4;29(15):2515-26.
http://www.ncbi.nlm.nih.gov/pubmed/20581803

 

UPF Barcelona

Francesc Posas

Adrover MÀ, Zi Z, Duch A, Schaber J, González-Novo A, Jimenez J, Nadal-Ribelles M, Clotet J, Klipp E, Posas F.
Time-Dependent Quantitative Multicomponent Control of the G1-S Network by the Stress-Activated Protein Kinase Hog1 upon Osmostress
Sci Signal. 2011 Sep 27;4(192)
http://www.ncbi.nlm.nih.gov/pubmed/21954289

Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, Hohmann S, de Nadal E, Posas F, Solé R.
Distributed biological computation with multicellular engineered networks.
Nature. 2011 Jan 13;469(7329):207-11
http://www.ncbi.nlm.nih.gov/pubmed/21150900

de Nadal E, Posas F.
Multilayered control of gene expression by stress-activated protein kinases.
EMBO J. 2010 Jan 6;29(1):4-13. Review.
http://www.ncbi.nlm.nih.gov/pubmed/19942851

Yaakov G, Duch A, García-Rubio M, Clotet J, Jimenez J, Aguilera A, Posas F.
The stress-activated protein kinase Hog1 mediates S phase delay in response to
osmostress.
Mol Biol Cell. 2009 Aug;20(15):3572-82.
http://www.ncbi.nlm.nih.gov/pubmed/19477922

Eulalia de Nadal

Sole, C., Nadal-Ribelles, M., Kraft, C., Peter, M., Posas, F., and de Nadal, E.
Control of Ubp3 ubiquitin protease activity by the Hog1 SAPK modulates transcription upon osmostress.
EMBO J. 2011 Jul 8;30(16):3274-84
http://www.ncbi.nlm.nih.gov/pubmed/21743437

Ruiz-Roig C, Viéitez C, Posas F, de Nadal E.
The Rpd3L HDAC complex is essential for the heat stress response in yeast.
Mol Microbiol. 2010 May;76(4):1049-62.
http://www.ncbi.nlm.nih.gov/pubmed/20398213

 

CRG Barcelona

Luis Serrano

Güell M, Yus E, Lluch-Senar M, Serrano L.
Bacterial transcriptomics: what is beyond the RNA horiz-ome?
Nat Rev Microbiol. 2011 Aug 12;9(9):658-69
http://www.ncbi.nlm.nih.gov/pubmed/21836626

Maier T, Schmidt A, Güell M, Kühner S, Gavin AC, Aebersold R, Serrano L.
Quantification of mRNA and protein and integration with protein turnover in a bacterium.
Mol Syst Biol. 2011 Jul 19;7:511
http://www.ncbi.nlm.nih.gov/pubmed/21772259

Brooks MA, Gewartowski K, Mitsiki E, Létoquart J, Pache RA, Billier Y, Bertero M, Corréa M, Czarnocki-Cieciura M, Dadlez M, Henriot V, Lazar N, Delbos L, Lebert D, Piwowarski J, Rochaix P, Böttcher B, Serrano L, Séraphin B, van Tilbeurgh H, Aloy P, Perrakis A, Dziembowski A.
Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations.
Structure. 2010 Sep 8;18(9):1075-82.
http://www.ncbi.nlm.nih.gov/pubmed/20826334

Fernandez-Ballester G, Beltrao P, Gonzalez JM, Song YH, Wilmanns M, Valencia A, Serrano L.
Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions.
J Mol Biol. 2009 May 15;388(4):902-16.
http://www.ncbi.nlm.nih.gov/pubmed/19324052

 

VU Amsterdam

Hans Westerhoff

Adamczyk M, van Eunen K, Bakker BM, Westerhoff HV.
Enzyme kinetics for systems biology when, why and how.
Methods Enzymol. 2011;500:233-57.
http://www.ncbi.nlm.nih.gov/pubmed/21943901

van Eunen K, Rossell S, Bouwman J, Westerhoff HV, Bakker BM
Quantitative analysis of flux regulation through hierarchical regulation analysis.
Methods Enzymol. 2011;500:571-95.
http://www.ncbi.nlm.nih.gov/pubmed/21943915

Kolodkin A, Boogerd FC, Plant N, Bruggeman FJ, Goncharuk V, Lunshof J, Moreno-Sanchez R, Yilmaz N, Bakker BM, Snoep JL, Balling R, Westerhoff HV.
Emergence of the silicon human and network targeting drugs.
Eur J Pharm Sci. 2011 Jun 16
http://www.ncbi.nlm.nih.gov/pubmed/21704158

Kolodkin AN, Bruggeman FJ, Plant N, Moné MJ, Bakker BM, Campbell MJ, van Leeuwen JP, Carlberg C, Snoep JL, Westerhoff HV.
Design principles of nuclear receptor signaling: how complex networking improves signal transduction.
Mol Syst Biol. 2010 Dec 21;6:446.
http://www.ncbi.nlm.nih.gov/pubmed/21179018

van Eunen K, Dool P, Canelas AB, Kiewiet J, Bouwman J, van Gulik WM, Westerhoff HV, Bakker BM.
Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history.
IET Syst Biol. 2010 Mar;4(2):157-68.
http://www.ncbi.nlm.nih.gov/pubmed/20232995

van Eunen K, Bouwman J, Daran-Lapujade P, Postmus J, Canelas AB, Mensonides FI, Orij R, Tuzun I, van den Brink J, Smits GJ, van Gulik WM, Brul S, Heijnen JJ, de Winde JH, de Mattos MJ, Kettner C, Nielsen J, Westerhoff HV, Bakker BM.
Measuring enzyme activities under standardized in vivo-like conditions for systems biology.
FEBS J. 2010 Feb;277(3):749-60
http://www.ncbi.nlm.nih.gov/pubmed/20067525

van Eunen K, Bouwman J, Lindenbergh A, Westerhoff HV, Bakker BM.
Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast.
FEBS J. 2009 Oct;276(19):5521-36
http://www.ncbi.nlm.nih.gov/pubmed/19691496

Jacky Snoep

Conradie R, Bruggeman FJ, Ciliberto A, Csikász-Nagy A, Novák B, Westerhoff HV, Snoep JL.
Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex.
FEBS J. 2010 Jan;277(2):357-6
http://www.ncbi.nlm.nih.gov/pubmed/20015233

 

University of Manchester

Pedro Mendes

Dada JO, Mendes P.
Multi-scale modelling and simulation in systems biology.
Integr Biol (Camb). 2011 Feb;3(2):86-96
http://www.ncbi.nlm.nih.gov/pubmed/21212881

Dobson PD, Smallbone K, Jameson D, Simeonidis D, Lanthaler K, Pir P, Lu C, Swainston N, Dunn WB, Fisher P, Hull D, Brown D, Oshota O, Stanford NJ, Kell DB, King RD, Oliver SG, Stevens RD & Mendes, P
Further developments towards a genome-scale metabolic model of yeast.
BMC Syst Biol. 2010 Oct 28;4(1):145
http://www.ncbi.nlm.nih.gov/pubmed/21029416

 

Aberystwyth University

Ross King

King RD, Clare A, Liakata M, Lu C, Oliver SG, Soldatova, L
On the formalisation and re-use of scientific research
J R Soc Interface. 2011 Apr 13
http://www.ncbi.nlm.nih.gov/pubmed/21490004

Chuan Lu and Ross D. King,
An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems,
Bioinformatics, August 2009, Vol. 25, No. 16, pp.2020-2027
http://www.ncbi.nlm.nih.gov/pubmed/19535531

King RD, Rowland J, Oliver SG, Young M, Aubrey W, Byrne E, Liakata M, Markham M, Pir P, Soldatova LN, Sparkes A, Whelan KE, Clare A
The automation of science
Science 324, 85-89, 2009
http://www.ncbi.nlm.nih.gov/pubmed/19342587

 

University of Milano-Bicocca

Lilia Alberghina

Salazar C, Brümmer A, Alberghina L, Höfer T.
Timing control in regulatory networks by multisite protein modifications.
Trends in Cell Biology, Volume 20, Issue 11, November 2010, Pages 634-641
http://www.ncbi.nlm.nih.gov/pubmed/20869247

Tripodi F, Cirulli C, Reghellin V, Marin O, Brambilla L, Schiappelli MP, Porro D, Vanoni M, Alberghina L, Coccetti P.
CK2 activity is modulated by growth rate in Saccharomyces cerevisiae.
Biochem Biophys Res Commun. 2010 Jul 16;398(1):44-50.
http://www.ncbi.nlm.nih.gov/pubmed/20599749

Pessina S, Tsiarentsyeva V, Busnelli S, Vanoni M, Alberghina L, Coccetti P.
Snf1/AMPK promotes S-phase entrance by controlling CLB5 transcription in budding yeast.
Cell Cycle. 2010 Jun 22;9(11)
http://www.ncbi.nlm.nih.gov/pubmed/20505334

Palumbo P, Mavelli G, Farina L, Alberghina L.
Networks and circuits in cell regulation.
Biochem Biophys Res Commun. 2010 Jun 11;396(4):881-6
http://www.ncbi.nlm.nih.gov/pubmed/20457126

Alberghina L, Coccetti P, Orlandi I.
Mathematical modelling of DNA replication reveals a trade-off between coherence of origin activation and robustness against rereplication.
PLoS Comput Biol. 2010 May 13;6(5)
http://www.ncbi.nlm.nih.gov/pubmed/20485558

Brümmer A, Salazar C, Zinzalla V, Alberghina L, Höfer T.
Systems biology of the cell cycle of Saccharomyces cerevisiae: From network mining to system-level properties.
Biotechnol Adv. 2009 Nov-Dec;27(6):960-78
http://www.ncbi.nlm.nih.gov/pubmed/19465107

Alfieri R, Barberis M, Chiaradonna F, Gaglio D, Milanesi L, Vanoni M, Klipp E, Alberghina L.
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation.
BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S16.
http://www.ncbi.nlm.nih.gov/pubmed/19828076

Brocca S, Samalíková M, Uversky VN, Lotti M, Vanoni M, Alberghina L, Grandori R.
Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1.
Proteins. 2009 Aug 15;76(3):731-46.
http://www.ncbi.nlm.nih.gov/pubmed/19280601

Marco Vanoni

Sacco E, Hasan MM, Alberghina L, Vanoni M.
Comparative analysis of the molecular mechanisms controlling the initiation of chromosomal DNA replication in yeast and in mammalian cells.
Biotechnol Adv. 2011 Sep 22
http://www.ncbi.nlm.nih.gov/pubmed/21963686

Busti S, Gotti L, Balestrieri C, Querin L, Drovandi G, Felici G, Mavelli G, Bertolazzi P, Alberghina L, Vanoni M.
Overexpression of Far1, a cyclin-dependent kinase inhibitor, induces a large transcriptional reprogramming in which RNA synthesis senses Far1 in a Sfp1-mediated way.
Biotechnol Adv. 2011 Sep 21
http://www.ncbi.nlm.nih.gov/pubmed/21964263

Alberghina L, Mavelli G, Drovandi G, Palumbo P, Pessina S, Tripodi F, Coccetti P, Vanoni M.
Cell growth and cell cycle in Saccharomyces cerevisiae: Basic regulatory design and protein-protein interaction network.
Biotechnol Adv. 2011 Jul 22
http://www.ncbi.nlm.nih.gov/pubmed/21821114

Busti S., Coccetti P., Alberghina L., Vanoni M
Glucose Signaling-Mediated Coordination of Cell Growth and Cell Cycle in Saccharomyces Cerevisiae
Sensors 2010, 10 6195-6240
http://www.mdpi.com/1424-8220/10/6/6195/

Alberghina L, Höfer T, Vanoni M.
Molecular networks and system-level properties. - review
J Biotechnol. 2009 Nov;144(3):224-33.
http://www.ncbi.nlm.nih.gov/pubmed/19616593

Enzo Martegani

Belotti F, Tisi R, Paiardi C, Rigamonti M, Groppi S, Martegani E.
Localization of Ras signaling complex in budding yeast.
Biochim Biophys Acta. 2012 Jul;1823(7):1208-16
http://www.ncbi.nlm.nih.gov/pubmed/22575457

Belotti F, Tisi R, Paiardi C, Groppi S, Martegani E.
PKA-dependent regulation of Cdc25 RasGEF localization in budding yeast.
FEBS Lett. 2011 Oct 25
http://www.ncbi.nlm.nih.gov/pubmed/22036786

Pescini D, Cazzaniga P, Besozzi D, Mauri G, Amigoni L, Colombo S, Martegani E.
Simulation of the Ras/cAMP/PKA pathway in budding yeast highlights the establishment of stable oscillatory states.
Biotechnol Adv. 2011 Jun 29.
http://www.ncbi.nlm.nih.gov/pubmed/21741466

Tisi R, Belotti F, Paiardi C, Brunetti F, Martegani E.
The budding yeast RasGEF Cdc25 reveals an unexpected nuclear localization.
Biochim Biophys Acta. 2008 Dec;1783(12):2363-74.
http://www.ncbi.nlm.nih.gov/pubmed/18930081

Leadsham JE, Miller K, Ayscough KR, Colombo S, Martegani E, Sudbery P, Gourlay CW.
Whi2p links nutritional sensing to actin-dependent Ras-cAMP-PKA regulation and apoptosis in yeast.
J Cell Sci. 2009 Mar 1;122(Pt 5):706-15.
http://www.ncbi.nlm.nih.gov/pubmed/19208759

 

University of Oxford

Bela Novák

He E, Kapuy O, Oliveira RA, Uhlmann F, Tyson JJ, Novák B.
System-level feedbacks make the anaphase switch irreversible.
Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):10016-21
http://www.ncbi.nlm.nih.gov/pubmed/21617094

Vinod PK, Freire P, Rattani A, Ciliberto A, Uhlmann F, Novak B.
Computational modelling of mitotic exit in budding yeast: the role of separase and Cdc14 endocycles.
J R Soc Interface. 2011 Feb 2.
http://www.ncbi.nlm.nih.gov/pubmed/21288956

Novák, B., Vinod, P.K. , Freire, P. & Kapuy, O. :
Systems-level feedbacks in cell cycle control.
Biochem. Soc. Trans. (2010) 38, 1242–1246;
http://www.ncbi.nlm.nih.gov/pubmed/20863292

Tyson, J.J. & Novák, B
Functional motifs in biochemical reaction networks.
Annu. Rev. Phys. Chem. 2010. 61:219–40
http://www.ncbi.nlm.nih.gov/pubmed/20055671

Barik, D., Baumann, W.T., Paul, M.R., Novák, B. &Tyson, J.J.
 A model of yeast cell-cycle regulation based on multisite phosphorylation.
Mol Syst Biol. 6: 405. 2010
http://www.ncbi.nlm.nih.gov/pubmed/20739927

Lopez-Avilés, S., Kapuy, O., Novák, B. & Uhlmann, F. 
Irreversibility of mitotic exit is the consequence of systems level feedback.
Nature. 2009 May 28;459(7246):592-5.
http://www.ncbi.nlm.nih.gov/pubmed/19387440

Kapuy, O,, He, E., López-Avilés, S., Uhlmann, F., Tyson, J.J. & Novák, B.  
System-level feedbacks control cell cycle progression.
FEBS Letters 583 (2009) 3992–3998
http://www.ncbi.nlm.nih.gov/pubmed/19703449

Kapuy, O., Barik, D., Sananes, M.R., Tyson, J.J. & Novák, B.
Bistability by multiple phosphorylation of regulatory proteins.
Progress in Biophysics and Molecular Biology 100 (2009) 47–56
http://www.ncbi.nlm.nih.gov/pubmed/19523976

 

Medical University of Vienna

Karl Kuchler

Landstetter N, Glaser W, Gregori C, Seipelt J, Kuchler K.
Functional genomics of drug-induced ion homeostasis identifies a novel regulatory crosstalk of iron and zinc regulons in yeast.
OMICS. 2010 Dec;14(6):651-63.
http://www.ncbi.nlm.nih.gov/pubmed/20695822

Gustav Ammerer

Reiter W, Anrather D, Dohnal I, Pichler P, Veis J, Grøtli M, Posas F, Ammerer G.
Validation of regulated protein phosphorylation events in yeast by quantitative mass spectrometry analysis of purified proteins.
Proteomics. 2012 Aug 14. 
http://www.ncbi.nlm.nih.gov/pubmed/22890988

University of Edinburgh

David Tollervey

Wiebke Wlotzka, Grzegorz Kudla, Sander Granneman and David Tollervey
The Nuclear RNA Polymerase II Surveillance System Adds Short OligoA Tails and Targets Polymerase III Transcripts
EMBO J. 2011 Jul 20;30(14):2982.
http://www.ncbi.nlm.nih.gov/pubmed/21772328

 

Chalmers University of Technology 

Jens Nielsen

Hong KK, Vongsangnak W, Vemuri GN, Nielsen J.
Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis.
Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12179-84.
http://www.ncbi.nlm.nih.gov/pubmed/21715660

Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, Ewald JC, Heijnen JJ, Kirdar B, Mattila I, Mensonides FI, Niebel A, Penttilä M, Pronk JT, Reuss M, Salusjärvi L, Sauer U, Sherman D, Siemann-Herzberg M, Westerhoff H, de Winde J, Petranovic D, Oliver SG, Workman CT, Zamboni N, Nielsen J.
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.
Nat Commun. 2010;1:145
http://www.ncbi.nlm.nih.gov/pubmed/21266995

Jie Zhang, Lisbeth Olsson and Jens Nielsen*
The b-subunits of the Snf1 kinase in Saccharomyces cerevisiae, Gal83 and Sip2, but not Sip1, are redundant in glucose derepression and regulation of sterol biosynthesis
Molecular Microbiology (2010) 77(2), 371–383
http://www.ncbi.nlm.nih.gov/pubmed/20545859

Jie Zhang, Goutham Vemuri and Jens Nielsen
Systems biology of energy homeostasis in yeast - review
Curr Opin Microbiol. 2010 Jun;13(3):382-8.
http://www.ncbi.nlm.nih.gov/pubmed/20439164

Renata Usaite, Michael C Jewett, Ana Paula Oliveira, John R Yates III, Lisbeth Olsson and Jens Nielsen
Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator
Molecular Systems Biology 5:319, 2009
http://www.ncbi.nlm.nih.gov/pubmed/19888214

Nandy SK, Jouhten P, Nielsen J.
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation
 BMC Systems Biology 2010, 4:68
http://www.ncbi.nlm.nih.gov/pubmed/20500839

 T. S. Christensen; A. P. Olivaira; J. Nielsen
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae.
BMC Systems Biol. 3:7, 2009
http://www.ncbi.nlm.nih.gov/pubmed/19144179

Nielsen, J.
Systems biology of lipid metabolism: From yeast to human  -review
FEBS Letters 583 (2009) 3905–3913
http://www.ncbi.nlm.nih.gov/pubmed/19854183

Petranovic, D & Nielsen, J.
Can yeast systems biology contribute to the understanding of human disease?  - review
Trends in Biotechnology Vol.26 No.11
http://www.ncbi.nlm.nih.gov/pubmed/18801589

 

University of Cambridge

Steve Oliver

Dikicioglu D, Dunn WB, Kell DB, Kirdar B, Oliver SG.
Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment.
Mol Biosyst. 2012 Jun;8(6):1760-74
http://www.ncbi.nlm.nih.gov/pubmed/22491778

Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG.
Evaluation and properties of the budding yeast phosphoproteome.
Mol Cell Proteomics. 2012 Jun;11(6):M111.009555
http://www.ncbi.nlm.nih.gov/pubmed/22286756

Pir P, Gutteridge A, Wu J, Rash B, Kell DB, Zhang N, Oliver SG.
The genetic control of growth rate: a systems biology study in yeast.
BMC Syst Biol. 2012 Jan 13;6:4
http://www.ncbi.nlm.nih.gov/pubmed/22244311

Castrillo JI, Oliver SG.
Yeast systems biology: the challenge of eukaryotic complexity.
Methods Mol Biol. 2011;759:3-28
http://www.ncbi.nlm.nih.gov/pubmed/21863478

Zhang N, Bilsland E.
Contributions of Saccharomyces cerevisiae to understanding mammalian gene function and therapy.
Methods Mol Biol. 2011;759:501-23
http://www.ncbi.nlm.nih.gov/pubmed/21863505

Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, Dunn WB, Winder CL, Lanthaler K, Pir P, Malys N, Kell DB, Oliver SG, Gaskell SJ, Beynon RJ.
Absolute Quantification of the Glycolytic Pathway in Yeast:: DEPLOYMENT OF A COMPLETE QconCAT APPROACH.
Mol Cell Proteomics. 2011 Dec;10(12)
http://www.ncbi.nlm.nih.gov/pubmed/21931151

Zakrzewska A, van Eikenhorst G, Burggraaff JE, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ.
Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness.
Mol Biol Cell. 2011 Nov;22(22):4435-46.
http://www.ncbi.nlm.nih.gov/pubmed/21965291

Quan Z, Oliver SG, Zhang N.
JmjN interacts with JmjC to ensure selective proteolysis of Gis1 by the proteasome.
Microbiology. 2011 Sep;157(Pt 9):2694-701
http://www.ncbi.nlm.nih.gov/pubmed/21680636

Dikicioglu D, Karabekmez E, Rash B, Pir P, Kirdar B, Oliver SG
How yeast re-programmes its transcriptional profile in response to different nutrient impulses.
BMC Syst Biol. 2011 Sep 25;5(1):148.
http://www.ncbi.nlm.nih.gov/pubmed/21943358

Bonzanni N, Zhang N, Oliver SG, Fisher J.
The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in Saccharomyces cerevisiae.
Bioinformatics. 2011 Jul 1;27(13):i283-7.
http://www.ncbi.nlm.nih.gov/pubmed/21685082

Castrillo JI, Oliver SG
Yeast Systems Biology: The challenge of eukaryotic complexity.
Methods Mol Biol. 2011;759:3-28.
http://www.ncbi.nlm.nih.gov/pubmed/21863478

Szappanos B, Kovács K, Szamecz B, Honti F, Costanzo M, Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, Andrews BJ, Boone C, Oliver SG, Pál C, Papp B.
An integrated approach to characterize genetic interaction networks in yeast metabolism.
Nat Genet. 2011 May 29;43(7):656-62
http://www.ncbi.nlm.nih.gov/pubmed/21623372

de Clare M, Pir P, Oliver SG
Haploinsufficiency and the sex chromosomes from yeasts to humans.
BMC Biol. 2011 Feb 28;9:15.
http://www.ncbi.nlm.nih.gov/pubmed/21356089

Zhang, N, Bisland E 
Contributions of Saccharomyces cerevisiae towards understanding mammalian gene function and therapy
Methods Mol Biol. 2011;759:501-23
http://www.ncbi.nlm.nih.gov/pubmed/21863505

Roberts IN, Oliver SG
The Yin and Yang of Yeast: Biodiversity research and systems biology as complementary forces driving innovation in biotechnology. Biotech
Biotechnol Lett. 2011 Mar;33(3):477-87
http://www.ncbi.nlm.nih.gov/pubmed/21125415

Barton MD, Delneri D, Oliver SG, Rattray M, Bergman CM (2010)
Evolutionary systems biology of amino acid biosynthetic cost in yeast.
PLoS One. 2010 Aug 17;5(8)
http://www.ncbi.nlm.nih.gov/pubmed/20808905

Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, Oliver SG
Nutrient control of eukaryote cell growth: a systems biology study in yeast
 BMC Biology. 8: 68 , 2010
http://www.ncbi.nlm.nih.gov/pubmed/20497545

Zhang N, Oliver SG (2010)
The transcription activity of Gis1 is modulated by proteasome-mediated limited proteolysis.
J Biol Chem. 2010 Feb 26;285(9):6465-76
http://www.ncbi.nlm.nih.gov/pubmed/20022953

Zhang N, Wu J, Oliver SG
Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast
Microbiology. 2009 May;155(Pt 5):1690-8.
http://www.ncbi.nlm.nih.gov/pubmed/19383711

 

Humboldt-Universität zu Berlin

Edda Klipp

Klipp E.
Computational yeast systems biology: a case study for the MAP kinase cascade.
Methods Mol Biol. 2011;759:323-43.
http://www.ncbi.nlm.nih.gov/pubmed/21863496

Schreiber G, Barberis M, Scolari S, Klaus C, Herrmann A, Klipp E.
Unraveling interactions of cell cycle-regulating proteins Sic1 and B-type cyclins in living yeast cells: a FLIM-FRET approach.
FASEB J. 2011 Oct 14
http://www.ncbi.nlm.nih.gov/pubmed/22002907

Barberis M, Linke C, Adrover MA, González-Novo A, Lehrach H, Krobitsch S, Posas F, Klipp E.
Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins.
Biotechnol Adv. 2011 Sep 18
http://www.ncbi.nlm.nih.gov/pubmed/21963604

Waltermann C, Klipp E.
Information theory based approaches to cellular signaling.
Biochim Biophys Acta. 2011 Jul 23.
http://www.ncbi.nlm.nih.gov/pubmed/21798319

Waltermann C, Klipp E.
Signal integration in budding yeast.
Biochem Soc Trans. 2010 Oct;38(5):1257-64.PMID: 20863295
http://www.ncbi.nlm.nih.gov/pubmed/20863295

Schaber J, Adrover MA, Eriksson E, Pelet S, Petelenz-Kurdziel E, Klein D, Posas F, Goksör M, Peter M, Hohmann S, Klipp E.
Biophysical properties of Saccharomyces cerevisiae and their relationship with HOG pathway activation.
Eur Biophys J. 2010 Oct;39(11):1547-56
http://www.ncbi.nlm.nih.gov/pubmed/20563574

Zi Z, Liebermeister W, Klipp E.
A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae.
PLoS One. 2010 Mar 4;5(3):e9522.
http://www.ncbi.nlm.nih.gov/pubmed/20209100

 

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