José Caldas
I have recently graduated from my PhD studies at the Statistical Machine Learning and Bioinformatics group,
where I worked on applying machine learning techniques to biclustering and information retrieval problems in bioinformatics.
PhD Dissertation
Graphical Models for Biclustering and Information Retrieval in Gene Expression Data.
J. Caldas, Aalto University School of Science, 2012.
Publications
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Data-Driven Information Retrieval in Heterogeneous Collections of Transcriptomics Data Links SIM2s to Malignant Pleural Mesothelioma.
J. Caldas*, N. Gehlenborg*, E. Kettunen, A. Faisal, M. Rönty, A. G. Nicholson, S. Knuutila, A. Brazma, and S. Kaski.
Bioinformatics, 28(2):246-253, 2012.
*Joint first author.
Supplementary website.
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Hierarchical generative biclustering for microRNA expression analysis.
J. Caldas and S. Kaski. Journal of Computational Biology, 18(3):251-261, 2011.
Software,
earlier version of the paper (RECOMB 2010).
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Probabilistic retrieval and
visualization of biologically relevant microarray experiments.
J. Caldas, N. Gehlenborg, A Faisal, A. Brazma, and S. Kaski. Bioinformatics, 25(12):i145-i153 (ISMB/ECCB), 2009.
Software,
Poster (best poster award at the 5th ISCB Student Council Symposium).
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Bayesian biclustering with the plaid model.
J. Caldas and S. Kaski. In Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing (MLSP), 2008.