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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 (102):

• Mika Murtojärvi, Olli Nevalainen, Ville Leppänen, Performance Tuning and Sparse Traversal Technique for a Cell-Based Fetch Length Algorithm on a GPU. Concurrency and Computation: Practice and Experience 27(17), 5114–5133, 2015.
• Olli Salli, Olli Nevalainen, Ville Leppänen, Event-Driven Asynchronous Method Calls with the D-Bus Message System. Software-Practice and Experience 45(1), 53–74, 2015.
• Frans Vainio, Tapio Pahikkala, Mika Johnsson, Olli S. Nevalainen, Timo Knuutila, Estimating the production time of a PCB assembly job without solving the optimised machine control. International Journal of Computer Integrated Manufacturing 27 (2014)(4/2014), 1 –13, 2014.
• Heta Mattila, Pertti Valli, Tapio Pahikkala, Jukka Teuhola, Olli S. Nevalainen, Esa Tyystjärvi, Comparison of Chlorophyll Fluorescence Curves and Texture Analysis for Automatic Plant Identification. Precision Agriculture 14(6), 621–636, 2013.
• Kai Kallio, Mika Johnsson, Olli S. Nevalainen, Estimating the Operation Time of Flexible Surface Mount Placement Machines. Production Engineering, Research and Development , 1–10, 2012.
• Maaria Tringham, Johanna Kurko, Laura Tanner, Johannes Tuikkala, Olli S. Nevalainen, Harri Niinikoski, Kirsti Näntö-Salonen, Marja Hietala, Olli Simell, Juha Mykkänen, Exploring the Transcriptomic Variation Caused by the Finnish Founder Mutation of Lysinuric Intolerance (LPI). Molecular genetics and metabolism (IF3.539) 105, 408-415, 2012.
• Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S. Nevalainen, Tero Aittokallio, A Multilevel Layout Algorithm for Visualizing Physical and Genetic Interaction Networks, with Emphasis on Their Modular Organization. Biodata Mining 5(2), , 2012.
• Mika Murtojärvi, Tapio Suominen, Esa Uusipaikka, Olli S. Nevalainen, Optimising an Observational Water Monitoring Network for Archipelago Sea, South West Finland. Computers & Geosciences 37(7), 844-854, 2011.
• Csaba Ráduly-Baka, Timo Knuutila, Mika Johnsson, OlliS. Nevalainen, Organizing the Operation of Radial Machine Sequencers for Multiple PCB Types. Computers & Industrial Engineering 61, 1003–1010, 2011.
• Aiying Rong, Attila Toth, Olli S. Nevalainen, Timo Knuutila, Risto Lahdelma, Modeling the machine configuration and line-balancing problem of a PCB assembly line with modular placement machines. International Journal of Advanced Manufacturing Technology 54, 349–360, 2011.
• Heidi Vähämaa, Ville R. Koskinen, Waltteri Hosia, Robert Moulder, Olli S. Nevalainen, Riitta Lahesmaa, Tero Aittokallio, Jussi Salmi, PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use. International Journal of Proteomics Vol. 2011 , 9, 2011.
• Marius C. Codrea, Marja Hakala-Yatkin, Anna Kårlund-Marttila, Ladislav Nedbal, Tero Aittokallio, Olli S. Nevalainen, Esa Tyystjärvi, Mahalanobis Distance Screening of Arabidopsis Mutans with Chlorophyll Fluorescence. Photosynthesis Research 105, 273–283, 2010.
• Stefan Emet, Timo Knuutila, Esa Alhoniemi, Michael Maier, Mika Johnsson, Olli S. Nevalainen, Workload Balancing in Printed Circuit Board Assembly. International Journal of Advanced Manufacturing Technology , 2010.
• Niina Lietzén, Lari Natri, Olli Nevalainen, Jussi Salmi, Tuula Nyman, Compid – A New Software Tool to Integrate and Compare MS/MS Based Protein Identification Results from Mascot and Paragon. Journal of Proteome Research , 2010.
• Mirva Piippo, Niina Lietzen, Olli S. Nevalainen, Jussi Salmi, Tuula A. Nyman, 233. Pripper: Prediction of Caspase Cleavage Sites from Whole Proteomes. BMC Bioinformatics DOI: 10.1186/1471-2105-11-320, 1–7, 2010.
• Csaba Raduly-Baka, Timo Knuutila, Mika Johnsson, Olli S. Nevalainen, Construction of Component Tapes for Radial Placement Machines. Computers & Operations Research Vol. 37, , 1488-1499, 2010.
• Attila Toth, Timo Knuutila, Olli S. Nevalainen, Reconfiguring Flexible Machine Modules of a PCB Assembly Line. Production Engineering Research and Development DOI 10.1007/s11740-009-0200-2(4), 85-94, 2010.
• Frans Vainio, Michael Maier, Timo Knuutila, Esa Alhoniemi, Mika Johnsson, Olli S Nevalainen, Estimating Printed Circuit Board Assembly Times Using Neural Networks. International journal of production research 48(8), 2201–2218, 2010.
• Mika Keränen, Eva-Mari Aro, Olli Nevalainen, Esa Tyystjärvi, Toxic and Non-Toxic Nodularia Strains Can Be Distinguished From Each Other and From Eukaryotic Algae with Chlorophyll Fluorescence Fingerprinting. Harmful Algae 8, 817–822, 2009.
• Harri Merisaari, Riitta Parkkola, Mika Teräs, Liisa Lehtonen, Leena Haataja, Helena Lapinleimu, Olli S Nevalainen, Gaussian Mixture Model-Based Segmentation of MR Images Taken from Premature Infant Brains. Journal of Neuroscience Methods 182(1), 110–122, 2009.
• Mika Antero Murtojärvi, Ville Leppänen, Olli S. Nevalainen, Determining Directional Distances Between Points and Shorelines Using Sweep Line Techniques. International Journal of Geographical Information Science 23(3), 2009.
• Csaba Raduly-Baka, Timo Knuutila, Mika Johnsson, Olli S. Nevalainen, Construction of Component Tapes for Radial Placement Machines. Computers & Operations Research Electronic edition, 1-35, 2009.
• Jussi Salmi, Tuula A. Nyman, Olli S. Nevalainen, Tero Aittokallio, Filtering Strategies for Improving Protein Identification in High-Volume MS/MS Studies. Proteomics 9(4), 848–860, 2009.
• Tiberiu Seceleanu, Ville Leppänen, Olli Nevalainen, Improving the Performance of Bus Platforms by Means of Segmentation and Optimized Resource Allocation. EURASIP Journal on Embedded Systems , 14 pages, 2009.
• Attila Toth, Timo Knuutila, Olli S. Nevalainen, Reconfiguring Flexible Machine Modules of a PCB Assembly Line. Production Engineering DOI 10.1007/s11740-009-0200-2, 2009.
• Mika Hirvikorpi, Timo Knuutila, Timo Leipälä, Olli Nevalainen, Job Scheduling and Management of Wearing Tools with Stochastic Tool Lifetimes. International Journal of Flexible Manufacturing Systems , 2008.
• Csaba Raduly-Baka, Timo Knuutila, Mika Johnsson, Olli S. Nevalainen, Selecting the Nozzle Assortment for a Gantry-Type Placement Machine. OR Spectrum 30, 493–513, 2008.
• Jussi Salmi, Tuula A. Nyman, Olli S. Nevalainen, Tero Aittokallio, Filtering strategies for improving protein identification in high-throughput MS/MS studies. Proteomics , 2008.
• Kati Talvinen, Johannes Tuikkala, Olli Nevalainen, A Rantanen, Pirkko Hirsimäki, Jari Sundström, Pauliina Kronqvist, Proliferation Marker Securin Identifies Favourable Outcome in Invasive Ductal Breast Cancer. British Journal of Cancer 99, 335–340, 2008.
• Johannes Tuikkala, Laura L. Elo, Olli S. Nevalainen, T. Aittokallio, Missing Value Imputation Improves Clustering and Interpretation of Gene Expression Microarray Data.. BMC Bioinformatics 9(202), 2008.
• Tero Aittokallio, Jani S. Malminen, Tapio Pahikkala, Olli Polo, Olli S. Nevalainen, Inspiratory Flow Shape Clustering: An Automated Method to Monitor Upper Airway Performance During Sleep. Computer Methods and Programs in Biomedicine 85(1), 8–18, 2007.
• Timo Knuutila, Sami Pyöttiälä, Olli S. Nevalainen, Minimizing the Number of Pickups on a Multi-Head Placement Machine. Journal of the Operational Research Society 58(1), 115–121, 2007.
• Harri Merisaari, Mika Teräs, Jussi Hirvonen, Olli Nevalainen, Jarmo Hietala, Evaluation of Partial Volume Effect Correction Methods for Brain Positron Emission Tomography: Quantification and Reproducibility. Journal of Medical Physics 32(3), 108-117, 2007.
• Mika Murtojarvi, Jouni Järvinen, Mika Johnsson, Timo Leipälä, Olli S. Nevalainen, Determining the Proper Number and Price of Software Licenses. IEEE Transactions on Software Engineering 33(5), 305−315, 2007.
• Mika Murtojärvi, Tapio Suominen, Harri Tolvanen, Ville Leppänen, Olli Nevalainen, Quantifying Distances from Points to Polygons - Applications in Determining Fetch in Coastal Environments. Computers & Geosciences 33(7), 843-852, 2007.
• Heidi Vähämaa, Pekka Ojala, Tapio Pahikkala, Olli S. Nevalainen, Riitta Lahesmaa, Tero Aittokallio, Computer-Assisted Identification of Multi-Trace Electrophoretic Patterns in Differential Display Experiments. Electrophoresis 28(6), 879–893, 2007.
• Mika Hirvikorpi, Olli S. Nevalainen, Timo Knuutila, Job Ordering and Management of Wearing Tools . Engineering Optimization 38(2), 227–244, 2006.
• Mika Hirvikorpi, Kari Salonen, Timo Knuutila, Olli Nevalainen, General Two-Level Storage Management Problem: A Reconsideration of the KTNS-Rule. European Journal of Operational Research 171(1), 189–207, 2006.
• Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli S. Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio, Quality Classification of Tandem Mass Spectrometry Data. Bioinformatics 22(4), 400–406, 2006.
• Kari Salonen, Timo Knuutila, Mika Johnsson, Olli S. Nevalainen, Planning and Controlling the Component Assembly for Multimodel PCBs. WSEAS Transactions on Systems 5(4), 855-863, 2006.
• Kari Salonen, Csaba Raduly-Baka, Olli S. Nevalainen, A Note on the Tool Switching Problem of a Flexible Machine. Computers & Industrial Engineering 50(4), 458-465, 2006.
• Kari Salonen, Jouni Smed, Mika Johnsson, Olli S. Nevalainen, Grouping and Sequencing PCB Assembly Jobs with Minimum Feeder Setups . Robotics and Computer-Integrated Manufacturing 22(4), 297–305, 2006.
• Kati Talvinen, Johannes Tuikkala, Juha Grönroos, Heikki Huhtinen, Pauliina Kronqvist, Tero Aittokallio, Olli S. Nevalainen, Heikki Hiekkanen, Timo Nevalainen, Jari Sundström, Biochemical and Clinical Approaches in Evaluating the Prognosis of Colonic Cancer. Anticancer Research 26(6), 2006.
• Johannes Tuikkala, Laura Elo, Olli S. Nevalainen, Tero Aittokallio, Improving Missing Value Estimation in Microarray Data with Gene Ontology. Bioinformatics 22(5), 566–572, 2006.
• Tero Aittokallio, Jussi Salmi, Tuula A. Nyman, Olli S. Nevalainen, Geometrical Distortions in Two-Dimensional Gels: Applicable Correction Methods. Journal of Chromatography 815(1-2), 25-37, 2005.
• Marius C. Codrea, Olli S. Nevalainen, Note: An Algorithm for Contour-Based Region Filling. Computers & Graphics 29(3), 441-450, 2005.
• Mika Hirvikorpi, Timo Knuutila, Mika Johnsson, Olli Nevalainen, A General Approach to Grouping of PCB Assembly Jobs. International Journal of Computer Integrated Manufacturing 18(8), 710–720, 2005.
• Timo Knuutila, Mika Hirvikorpi, Mika Johnsson, Olli S. Nevalainen, Grouping of PCB Assembly Jobs in the Case of Flexible Feeder Units. Engineering Optimization 37(1), 29–48, 2005.
• Robert Moulder, Jan-Jonas Filen, Jussi Salmi, Mikko Katajamaa, Olli Nevalainen, Matej Oresic, Tero Aittokallio, Riitta Lahesmaa, Tuula Nyman, A Comparative Evaluation of Software for the Analysis of Liquid Chromatography-Tandem Mass Spectrometry Data from Isotope Coded Affinity Tag Experiments. Proteomics 5(11), 2748–2760, 2005.
• Tuomas Nikula, Anne West, Mikko Katajamaa, Tapio Lönnberg, Rolf Sara, Tero Aittokallio, Olli Nevalainen, Riitta Lahesmaa, A Human ImmunoChip cDNA Microarray Provides a Comprehensive Tool to Study Immune Responses. Journal of Immunological Methods 303(1-2), 122–134, 2005.