José Caldas

I'm a Phd student at the Statistical Machine Learning and Bioinformatics group. I'm working on applying machine learning techniques to biclustering and information retrieval problems in bioinformatics.

Publications

• 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.


• 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).


• 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).


• 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.

Contact information