Publications
Thesis
- Esa Pitkänen: Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks. PhD Thesis. University of Helsinki, Department of Computer Science, Series of Publications A, Report A-2010-4, 2010.
Peer-reviewed articles
- Esa Pitkänen, Mikko Arvas, Juho Rousu: Minimum mutation algorithm for gapless metabolic network evolution. Bioinformatics Models, Methods and Algorithms, 2011.
- Esa Pitkänen, Juho Rousu, Esko Ukkonen: Computational methods for metabolic reconstruction. Current Opinion in Biotechnology, 21(1):70-77, 2010.
- Katja Astikainen, Liisa Holm, Esa Pitkänen, Sandor Szedmak, Juho Rousu: Reaction kernels: structured output prediction approaches for novel enzyme function. 1st International Conference on Bioinformatics, Valencia, Spain, January 2010.
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Esa Pitkänen,
Paula Jouhten,
Juho Rousu:
Inferring branching pathways in genome-scale metabolic networks.
BMC Systems
Biology, 3:103, 2009.
→ ReTrace - 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
- Katja Astikainen, Liisa Holm, Esa Pitkänen, Sandor Szedmak, Juho Rousu: Towards structured output prediction of enzyme function. BMC Proceedings, 2(Suppl 4):S2, 2008.
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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.
→ ReMatch - 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.
- Katja Astikainen, Liisa Holm, Esa Pitkänen, Sandor Szedmak, Juho Rousu. Towards Structured Prediction of Enzyme Function. Machine Learning in Systems Biology (MLSB-2007), Evry, France, September 2007
- 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, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen. Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation (extended version of CMSB05 manuscript). Transactions on Computational Systems Biology VI, Lecture Notes in Bioinformatics 4220 (2006), pp. 198 - 220.
- 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, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen. A method for estimating metabolic fluxes from incomplete isotopomer information. Proceedings of international Workshop on Computational Methods in Systems Biology, Rovereto Italy, February 2003. Lecture Notes in Computer Science 2602 (2003), pp. 88-103.
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Last updated 01.04.2011 14:20