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Kirjasto - Tampereen teknillinen yliopisto

Browsing by Author "Yli-Harja, Olli"

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  • Aho, Kaisa-Leena; Kerkelä, Erja; Yli-Harja, Olli; Roos, Christophe (2010)
    We present how we used a workflow system to create a computational pipeline for storing, preprocessing and statistically analyzing gene expression microarray data together with public annotation information. The pipeline ...
  • S. Ribeiro, Andre; Smolander, Olli-Pekka; Rajala, Tiina; Häkkinen, Antti; Yli-Harja, Olli (2009)
    We present a delayed stochastic model of transcription at the single nucleotide level. The model accounts for the promoter open complex formation and includes alternative pathways to elongation, namely pausing, arrest, ...
  • Rajala, Tiina; Häkkinen, Antti; Healy, Shannon; Yli-Harja, Olli; S. Ribeiro, Andre (2010)
    Stochasticity in gene expression affects many cellular processes and is a source of phenotypic diversity between genetically identical individuals. Events in elongation, particularly RNA polymerase pausing, are a source ...
  • Mäki-Marttunen, Tuomo; Acimovic, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena (2011)
    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and ...
  • Chowdhury, Sharif; Lloyd-Price, Jason; Smolander, Olli-Pekka; Baici, Wayne C. V.; Hughes, Timothy R.; Yli-Harja, Olli; Chua, Gordon; S. Ribeiro, Andre (2010)
    Background A gene network's capacity to process information, so as to bind past events to future actions, depends on its structure and logic. From previous and new microarray measurements in Saccharomyces cerevisiae ...
  • Farhan, Muhammad; Yli-Harja, Olli; Niemistö, Antti (2012-11-22)
    A novel nonparametric concavity point analysis-based method for splitting clumps of convex objects in binary images is presented. The method is based on finding concavity point-pairs by using a variable-size rectangular ...
  • Mäki-Marttunen, Tuomo; Kesseli, Juha; Kauffman, Stuart; Yli-Harja, Olli; Nykter, Matti (2011)
    We study the complexity of network dynamics in a couple of very different model classes: The traditional random Boolean networks (RBN) and Frisch-Hasslacher-Pomeau lattice gas automata (FHP). For this we formulate the FHP ...