Title: | Graphical models for biclustering and information retrieval in gene expression data |
Author(s): | Caldas, José |
Date: | 2012 |
Language: | en |
Pages: | 158 |
Department: | Tietojenkäsittelytieteen laitos Department of Information and Computer Science |
ISBN: | 978-952-60-4559-7 (electronic) 978-952-60-4558-0 (printed) |
Series: | Aalto University publication series DOCTORAL DISSERTATIONS, 33/2012 |
ISSN: | 1799-4942 (electronic) 1799-4934 (printed) 1799-4934 (ISSN-L) |
Supervising professor(s): | Kaski, Samuel, D.Sc. (Tech.) |
Thesis advisor(s): | Lahti, Leo, D.Sc. (Tech.) |
Subject: | Biotechnology |
Keywords: | probabilistic modelling, Bayesian network, biclustering, information retrieval, transcriptomics |
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Abstract:The cell coordinates its biological response to the environment partly via the selective synthesis of thousands of unique RNA and protein molecules. Understanding the molecular biology of the cell is thus essential to the advancement of areas such as health care, agriculture, and energy production, but requires the ability to simultaneously acquire information about thousands of molecules in a sample. Recent high-throughput measurement technologies address this concern. While being useful, they generate a high volume of data and bring in methodological challenges, effectively shifting the bottleneck in molecular biology research from data acquisition to data analysis. In particular, an important challenge is the genome-wide analysis of how RNA is transcribed under different conditions, organisms, and tissues, a process known as gene expression.
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Parts:[Publication 1]: José Caldas and Samuel Kaski. Bayesian biclustering with the plaid model. In Proceedings of the 2008 IEEE International Workshop on Machine Learning for Signal Processing XVIII, José Príncipe, Deniz Erdogmus, and Tulay Adali (editors), pages 291-296, IEEE, Piscataway, N.J., October 2008.[Publication 2]: José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, and Samuel Kaski. Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics, 25(12):i145-i153 (ISMB/ECCB 2009 Conference Proceedings), June 2009.[Publication 3]: José Caldas and Samuel Kaski. Hierarchical generative biclustering for microRNA expression analysis. Journal of Computational Biology, 18(3):251-261 (RECOMB 2010 Special Issue), March 2011.[Publication 4]: José Caldas and Samuel Kaski. A mixture-of-experts approach to biclustering. Submitted to a journal, 10 pages, 2011.[Publication 5]: José Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew G. Nicholson, Sakari Knuutila, Alvis Brazma, and Samuel Kaski. Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. Bioinformatics, 28(2):246-253, January 2012. |
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