SYSFYS Project
Experimental and computational analysis of physiological regulation at transcriptome, proteome and metabolome level.SYSFYS is a four-year project (2004-2007) in the Systems Biology and Bioinformatics programme funded by the Academy of Finland.
Publications
- Esa Pitkänen, Paula Jouhten, Juho Rousu: Inferring branching pathways in genome-scale metabolic networks. BMC Systems Biology, 3:103, 2009.
- Paula Jouhten, Esa Pitkänen, Tiina Pakula, Markku Saloheimo, Merja Penttilä, Hannu Maaheimo: 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. BMC Systems Biology, 3:104, 2009
- Esa Pitkänen, Arto Åkerlund, Ari Rantanen, Paula Jouhten, Esko Ukkonen: ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. Journal of Integrative Bioinformatics, 5(2):102, 2008.
- Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen A computational method for reconstructing gapless metabolic networks. 2nd International Conference on Bioinformatics Research and Development (BIRD'08), Communications in Computer and Information Science, Vol. 13, Springer, 2008.
- Markus Heinonen, Ari Rantanen, Taneli Mielikäinen, Esa Pitkänen, Juha Kokkonen, Juho Rousu: Ab Initio Prediction of Molecular Fragments from Tandem Mass Spectroscopy Data. German Conference on Bioinformatics 2006 (GCB 2006). Lecture Notes in Informatics Vol. P-83 (2006), pp. 40-53.
- Pekko Parikka, Esa Pitkänen, Ari Rantanen, Arto Åkerlund, Esko Ukkonen: Pathway Assistant: a web portal for metabolic modelling. Network Tools and Applications in Biology (NETTAB'06), pp. 90 - 96, 2006.
- Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen: Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes (extended version of GCB2005 manuscript). Bioinformatics, 22(10), pp. 1198 - 1206, 2006.
- Ari Rantanen, Taneli Mielikäinen, Juho Rousu and Esko Ukkonen. Planning isotopomer measurements for estimation of metabolic fluxes. German Conference on Bioinformatics 2005, Lecture Notes in Informatics vol. P-71, pp. 177 - 191, 2005
- Esa Pitkänen, Ari Rantanen, Juho Rousu and Esko Ukkonen. Finding Feasible Pathways in Metabolic Networks. Advances in Informatics: 10th Panhellenic Conference on Informatics (PCI 2005), Lecture Notes in Computer Science 3746, pp. 123 - 133, 2005.
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Ari Rantanen,
Juho Rousu,
Esa Pitkänen,
Hannu Maaheimo and
Esko Ukkonen.
Flow analysis of metabolite fragments for flux estimation.
Computational Methods in Systems Biology, Edinburgh, Scotland, pp. 242 - 255, 2005.
Supplementary material: Metabolic network, dominator trees. - Juho Rousu, Ari Rantanen, Raimo A. Ketola and Juha T. Kokkonen. Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra. Spectroscopy 19(1), pp. 53 - 67, 2005.
Software
- PIDC (Positional Isotopomer Distribution Calculator) v2.00 beta (Software, User Guide)
- All releases in detail
Collaboration
- VTT Biotechnology
- VTT Processes
- Institute of Biotechnology, University of Helsinki
- Department of Computer Science, University of Helsinki
People
- Esko Ukkonen, Professor
- Juho Rousu, Professor
- Taneli Mielikäinen, Postdoctoral researcher
- Ari Rantanen, Postdoctoral researcher
- Esa Pitkänen, PhD student
- Paula Jouhten, PhD student
- Pekko Parikka, MSc student
- Arto Åkerlund, MSc student
- Markus Heinonen, MSc student
- Antti Tani, MSc student
Previous work
- ICOMIC, a three-year project funded by the Academy of Finland
Previous update: 29.10.2009 - Esa Pitkänen