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Department: Any ÅAU / Department of Information Technologies UTU / Department of Information Technology UTU / Department of Mathematics and Statistics UTU / Turku School of Economics, Institute of Information Systems Sciences

Research Unit: Any Algorithmics and Computational Intelligence Group (ACI) Biomathematics Research Unit (BIOMATH) Communication Systems (ComSys) Computational Biomodeling Laboratory (Combio Lab) Data Mining and Knowledge Management Laboratory Distributed Systems Laboratory (DS Lab) Embedded Computer and Electronic Systems (ECES) Embedded Systems Laboratory (ESLAB) FUNDIM, Fundamentals of Computing and Discrete Mathematics Institute for Advanced Management Systems Research (IAMSR) Learning and Reasoning Lab Software Construction Laboratorium Software Development Laboratory (SwDev) Software Engineering Laboratory (SE Lab) Turku BioNLP Group Turku Optimization Group (TOpGroup) UTU Information Systems Science (ISS)

Publication type: Any Monographs Edited books Edited special issues of journals Edited proceedings Articles in journals Articles in proceedings Chapters in edited books Ph.D. thesis Lic. thesis Technical reports

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Articles in journals (67):

• Tuomas Nurmi, Stefan A.H. Geritz, Kalle Parvinen, Mats Gyllenberg, Evolution of Specialization in Resource Utilization in Structured Metapopulations. Journal of Biological Dynamics 2, 297–322, 2008.
• Arho Virkki, Olli Polo, Tarja Saaresranta, Anne Laapotti-Salo, Mats Gyllenberg, Tero Aittokallio, Overnight Features of Transcutaneous Carbon Dioxide Measurement as Predictors of Metabolic Status. Artificial Intelligence in Medicine 42(1), 55–65 , 2008.
• Arho Virkki, Olli Polo, Mats Gyllenberg, Tero Aittokallio, Can Carotid Body Perfusion Act as a Respiratory Controller?. Journal of Theoretical Biology 249(4), 737–748, 2007.
• Tero Aittokallio, Mats Gyllenberg, Olli Polo, Jenni Toivonen, Arho Virkki, Model-Based Analysis of Mechanisms Responsible for Sleep-Induced Carbon Dioxide Differences. Bulletin of Mathematical Biology 68(2), 315–341, 2006.
• Tero Aittokallio, Mats Gyllenberg, Olli Polo, Arho Virkki, Parameter Estimation of a Respiratory Control Model from Noninvasive Carbon Dioxide Measurements During Sleep. Mathematical Medicine and Biology , 2006.
• Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson, A Priori Contact Preferences in Molecular Recognition. Journal of Bioinformatics and Computational Biology 3(4), 861–890, 2005.
• Mats Gyllenberg, Yi Wang, Dynamics of the Periodic Type-K Competitive Kolmogorov Systems. J. Differential Equations 205, 50-76, 2004.
• Mats Gyllenberg, Yi Wang, Jifa Jiang, Asymptotic Spatial Homogeneity in Periodic Quasimonotone Reaction-Diffusion Systems with a First Integral. Nonlinear Analysis 59, 235-244, 2004.
• Mats Gyllenberg, Ping Yan, Jifa Jiang, The Qualitative Behavior of a Second Order System with Zero Diagonal Coefficient. Journal of Mathematical Analysis and Applications 291, 322–340, 2004.
• Tero Aittokallio, Mats Gyllenberg, Tarja Saaresranta, Olli Polo, Prediction of Inspiratory Flow Shapes During Sleep With a Mathematical Model of Upper Airway Forces. Sleep 26(7), 857–863, 2003.
• Mats Gyllenberg, Timo Koski, Peter Dawyndt, Tatu Lund, Fabiano Thompson, Brian Austin, Jean Swings, New Methods for the Analysis of Binarized BIOLOG GN Data of Vibrio Species: Minimization of Stochastic Complexity and Cumulative Classification. Systematic and Applied Microbiology 25, 403–415, 2003.
• Kalle Parvinen, Ulf Dieckmann, Mats Gyllenberg, J.A.J. Metz, Evolution of Dispersal in Metapopulations with Local Density Dependence and Demographic Stochasticity. Journal of Evolutionary Biology 16(1), 143–153, 2003.
• Tero Aittokallio, Mats Gyllenberg, Olli Polo, Adjustment of the Human Respiratory System to Increased Upper Airway Resistance During Sleep. Bulletin of Mathematical Biology 64(1), 3–28, 2002.
• Stefan A.H. Geritz, Mats Gyllenberg, Frans J.A. Jacobs, Kalle Parvinen, Invasion Dynamics and Attractor Inheritance. Journal of Mathematical Biology 44, 548–560, 2002.
• Mats Gyllenberg, Timo Koski, Bayesian predictiveness, exchangeablity and sufficientness in bacterial taxonomy. Mathematical Biosciences 177-178, 161–184, 2002.
• Mats Gyllenberg, Kalle Parvinen, Ulf Dieckmann, Evolutionary Suicide and Evolution of Dispersal in Structured Metapopulations. Journal of Mathematical Biology 45(2), 79–105, 2002.
• Mats Gyllenberg, Diana Preoteasa, Kari Saikkonen, Vertically Transmitted Symbionts in Structured Host Metapopulations. Bulletin of Mathematical Biology 64(5), 959–978, 2002.
• Mats Gyllenberg, Ping Yan, The Generalized Lienard Systems. Discrete and Continuous Dynamical Systems - Series A 8, 1043-1057, 2002.
• Thorsten Müller, Neli Noykova, Mats Gyllenberg, Jens Timmer, Parameter identification in microbial population dynamics models of anaerobic wastewater treatment. Mathematical Biosciences , 2002.
• Neli Noykova, Thorsten Müller, Mats Gyllenberg, Jens Timmer, Quantitative analyses of anaerobic waste water treatment processes: identifiability and parameter estimation. . Biotechnology and Bioengineering , 2002.
• Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson, A Dissimilarity Matrix between Protein Atom Classes based on Gaussian Mixtures. Bioinformatics 18, 1257–1263, 2002.
• Tero Aittokallio, Mats Gyllenberg, Olli Nevalainen, Olli Polo, Testing for periodicity in signals: an application to detect partial upper airway obstruction during sleep. Journal of Theoretical Medicine 3(4), 231–245, 2001.
• Tero Aittokallio, Mats Gyllenberg, Olli Polo, A model of a snorer's upper airway. Mathematical Biosciences 170(1), 79–90, 2001.
• Odo Diekmann, Mats Gyllenberg, H. Huang, M. Kirkilionis, J.A.J. Metz, On the formulation and analysis of general deterministic structured population models. Journal of Mathematical biology 43, 157–189, 2001.
• H.G. Gyllenberg, Mats Gyllenberg, Timo Koski, Sense in microbial taxonomy: Minimization of stochastic complexity as an objective taxonomic tool. Research Signpost 5, 211-221, 2001.
• Mats Gyllenberg, Timo Koski, Probabilistic Models for Bacterial Taxonomy. International Statistical Review 69, 249–276, 2001.
• Mats Gyllenberg, Kalle Parvinen, Necessary and Sufficient Conditions for Evolutionary Suicide. Bulletin of Mathematical Biology 63, 981–993, 2001.
• J.A.J. Metz, Mats Gyllenberg, How should we define fitness in structured metapopulation models? Including an application to the calculation of evolutionarily stable dispersal strategies. Proc. R. Soc. London B. 268, 499-508, 2001.
• Ville-Veikko Rantanen, Konstantin A. Denessiouk, Mats Gyllenberg, Timo Koski, Mark S. Johnson, A Fragment Library based on Gaussian Mixtures Predicting Favorable Molecular Interactions. Journal of Molecular Biology 313(1), 197–214, 2001.
• Tero Aittokallio, Mats Gyllenberg, Jaakko Järvi, Olli Nevalainen, Detection of high-frequency respiratory movements during sleep. Computer Methods and Programs in Biomedicine 61(3), 171-185, 2000.
• O. Diekmann, Mats Gyllenberg, H.R. Thieme, Lack of Uniqueness in Transport Equations with a Nonlocal Nonlinearity. Mathematical Models and Methods in Applied Sciences 10(4), 581–592, 2000.
• Pasi Fränti, Helge Gyllenberg, Mats Gyllenberg, Juha Kivijärvi, Timo Koski, Tatu Lund, Olli Nevalainen, Minimizing stochastic complexity using local search and GLA with applications to classification of bacteria. BioSystems 57(1), 37 – 48, 2000.
• Mats Gyllenberg, Dimitriv S. Silvestrov, Nonlinearly Pertubed Regenerative Processes and Pseudo-Stationary Phenomena for Stochastic Systems. Stochastic Processes and Their Applications 86(1), 1–27, 2000.
• Mats Gyllenberg, Timo Koski, Tatu Lund, Olli Nevalainen, Clustering by adaptive local search with multiple search operators. Pattern Analysis and Applications 3(4), 348 – 357, 2000.
• Mats Gyllenberg, K Sigmund, The Fibonacci chimney. The Mathematical Intelligencer , 2000.
• Mats Gyllenberg, Dimitriv S. Silvestrov, Cramér-Lundberg Approximation for Nonlinearly Pertubed Risk Processes. Insurance: Mathematics and Economics 26(1), 75-90, 2000.
• Nelly Noykova, Mats Gyllenberg, Sensitivity analysis and parameter estimation in a model of anaerobic waste water treatment processes with substrate inhibition. Bioprocess Engineering , 2000.
• S. Agur, J. Cushing, O. Diekmann, Mats Gyllenberg, H. Heesterbeek, P. Jagers, M. Kimmel, T. Kostova, F. Milner, Deterministic Models with Applications in Population Dynamics and Other Fields of Biology. Special issue of Mathematical Biosciences 157(1), i-viii,1-372, 1999.
• Tero Aittokallio, Mats Gyllenberg, Jarmo Hietarinta, Tom Kuusela, Tuomas Multamäki, Improving the False Nearest Neighbors Method with Graphical Analysis. Physical Review E 60(1), 416–421, 1999.
• Helge G. Gyllenberg, Mats Gyllenberg, Timo Koski, Tatu Lund, Heikki Mannila, Chris Meek, Singling out ill-fit items in a classification. Application to the taxonomy of <I>Enterobacteriaceae</I>. Archives of Control Sciences, Special Issue on Estimation and Control in Medicine and Biology 9, 97 - 105, 1999.
• Helge G. Gyllenberg, Mats Gyllenberg, Timo Koski, Tatu Lund, Jiri Schindler, An Assessment of Cumulative Classification. Quantitative Microbiology 1, 7-28, 1999.
• Helge G. Gyllenberg, Mats Gyllenberg, Timo Koski, Tatu Lund, Jiri Schindler, I Enterobacteriaceae taxonomy approached by minimization of stochastic complexity. Quantitative Microbiology 1, 157-170, 1999.
• Mats Gyllenberg, Jarmo Hemminki, Toomas Tammaru, Allee Effects Can Both Conserve and Create Spatial Heterogeneity in Population Densities. Theoretical Population Biology 56, 231–242, 1999.
• Mats Gyllenberg, Timo Koski, Tatu Lund, Helge G. Gyllenberg, Bayesian Predictive Identification and Cumulative Classification of Bacteria. Bulletin of Mathematical Biology 61(1), 85 – 111, 1999.
• Mats Gyllenberg, A.V. Osipov, Predelnye cikly v dvumernoj zadache Maya. Differentialnye Uravneniya 35(5), 733-737, 1999.
• Mats Gyllenberg, A.V. Osipov, Tipy dinamicheskogo povedniya v modeli Hanski-Hentonena. Differentialnye Uravneniya 35(7), 882-888, 1999.
• Mats Gyllenberg, Dimitriv S. Silvestrov, Cramér-Lundberg and diffusion approximations for nonlinearly pertubed risk processes including numerical computation of ruin probabilities. Theor. Stoch. Proc. 5(21), 6-21, 1999.
• O. Diekmann, Mats Gyllenberg, J.A.J. Metz, H.R. Thieme, On the formulation and analysis of general deterministic structured population models. I. Linear theory. J. Math. Biol. 36, 349-388, 1998.
• Helge G. Gyllenberg, Mats Gyllenberg, Timo Koski, Tatu Lund, Stochastic Complexity as a Taxonomic Tool. Computer Methods and Programs in Biomedicine 56(1), 11 – 22, 1998.
• Mats Gyllenberg, Timo Koski, Tatu Lund, Applications of machine learning to microbial taxonomy (in Finnish). (23), 1998.