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Saccharomyces cerevisiae metabolism in ecological context.

Jouhten P, Ponomarova O, Gonzalez R, Patil KR.

FEMS Yeast Res. 2016 Nov;16(7). pii: fow080.


Yeast metabolic chassis designs for diverse biotechnological products.

Jouhten P, Boruta T, Andrejev S, Pereira F, Rocha I, Patil KR.

Sci Rep. 2016 Jul 19;6:29694. doi: 10.1038/srep29694.


Hypoxia and GABA shunt activation in the pathogenesis of Alzheimer's disease.

Salminen A, Jouhten P, Sarajärvi T, Haapasalo A, Hiltunen M.

Neurochem Int. 2016 Jan;92:13-24. doi: 10.1016/j.neuint.2015.11.005. Review.


Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures.

Alff-Tuomala S, Salusjärvi L, Barth D, Oja M, Penttilä M, Pitkänen JP, Ruohonen L, Jouhten P.

Appl Microbiol Biotechnol. 2016 Jan;100(2):969-85. doi: 10.1007/s00253-015-7038-7.


Labelling analysis for ¹³C MFA using NMR spectroscopy.

Jouhten P, Maaheimo H.

Methods Mol Biol. 2014;1191:143-64. doi: 10.1007/978-1-4939-1170-7_9.


Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae.

Lindfors E, Jouhten P, Oja M, Rintala E, Orešič M, Penttilä M.

BMC Syst Biol. 2014 Feb 14;8:16. doi: 10.1186/1752-0509-8-16.


Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.

Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, Oja M, Holm L, Penttilä M, Rousu J, Arvas M.

PLoS Comput Biol. 2014 Feb 6;10(2):e1003465. doi: 10.1371/journal.pcbi.1003465.


Metabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures.

Jordà J, Jouhten P, Cámara E, Maaheimo H, Albiol J, Ferrer P.

Microb Cell Fact. 2012 May 8;11:57. doi: 10.1186/1475-2859-11-57.


Metabolic modelling in the development of cell factories by synthetic biology.

Jouhten P.

Comput Struct Biotechnol J. 2012 Nov 12;3:e201210009. doi: 10.5936/csbj.201210009. Review.


Correlation of gene expression and protein production rate - a system wide study.

Arvas M, Pakula T, Smit B, Rautio J, Koivistoinen H, Jouhten P, Lindfors E, Wiebe M, Penttilä M, Saloheimo M.

BMC Genomics. 2011 Dec 20;12:616. doi: 10.1186/1471-2164-12-616.


Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism.

Rintala E, Jouhten P, Toivari M, Wiebe MG, Maaheimo H, Penttilä M, Ruohonen L.

OMICS. 2011 Jul-Aug;15(7-8):461-76. doi: 10.1089/omi.2010.0082.


A multi-level study of recombinant Pichia pastoris in different oxygen conditions.

Baumann K, Carnicer M, Dragosits M, Graf AB, Stadlmann J, Jouhten P, Maaheimo H, Gasser B, Albiol J, Mattanovich D, Ferrer P.

BMC Syst Biol. 2010 Oct 22;4:141. doi: 10.1186/1752-0509-4-141.


Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.

Nandy SK, Jouhten P, Nielsen J.

BMC Syst Biol. 2010 May 25;4:68. doi: 10.1186/1752-0509-4-68.


13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose.

Jouhten P, Pitkänen E, Pakula T, Saloheimo M, Penttilä M, Maaheimo H.

BMC Syst Biol. 2009 Oct 29;3:104. doi: 10.1186/1752-0509-3-104.


Inferring branching pathways in genome-scale metabolic networks.

Pitkänen E, Jouhten P, Rousu J.

BMC Syst Biol. 2009 Oct 29;3:103. doi: 10.1186/1752-0509-3-103.


Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A.

Jouhten P, Rintala E, Huuskonen A, Tamminen A, Toivari M, Wiebe M, Ruohonen L, Penttilä M, Maaheimo H.

BMC Syst Biol. 2008 Jul 9;2:60. doi: 10.1186/1752-0509-2-60.


An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments.

Rantanen A, Rousu J, Jouhten P, Zamboni N, Maaheimo H, Ukkonen E.

BMC Bioinformatics. 2008 Jun 6;9:266. doi: 10.1186/1471-2105-9-266.


ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.

Pitkänen E, Akerlund A, Rantanen A, Jouhten P, Ukkonen E.

J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-102.


Central carbon metabolism of Saccharomyces cerevisiae in anaerobic, oxygen-limited and fully aerobic steady-state conditions and following a shift to anaerobic conditions.

Wiebe MG, Rintala E, Tamminen A, Simolin H, Salusjärvi L, Toivari M, Kokkonen JT, Kiuru J, Ketola RA, Jouhten P, Huuskonen A, Maaheimo H, Ruohonen L, Penttilä M.

FEMS Yeast Res. 2008 Feb;8(1):140-54.

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