Merja Oja
Position: Postdoc
Noble lab
University of Washington
Office: Foege Building, S220
Tel: +1 206 616 5021
Fax: +1 206 685 7301
Address: Genome Sciences, Box 355065
1705 NE Pacific St.
Seattle, WA 98195-5065
Email:
Merja Oja

Curriculum vitae

My CV in pdf-format can be found from here.

Publications

  1. Merja Oja. In Silico Expression Profiles of Human Endogenous Retroviruses In Jagath C. Rajapakse, Bertil Schmidt, and Gwenn Volkert, editors, Proceedings of Workshop on Pattern Recognition in Bioinformatics PRIB 2007, Lecture Notes in Bioinformatics, pages 253-263, 2007. (abstract, pdf)

  2. Merja Oja, Jaakko Peltonen, Jonas Blomberg and Samuel Kaski. Methods for estimating human endogenous retrovirus activities from EST databases. BMC Bioinformatics, 8(Suppl 2):S11, 2007.

  3. Merja Oja, Jaakko Peltonen, and Samuel Kaski. Estimation of human endogenous retrovirus activities from expressed sequence databases. In Juho Rousu, Samuel Kaski, and Esko Ukkonen, editors, Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006), workshop proceedings, pages 50-54, Helsinki University Printing House, 2006. (abstract, gzipped postscript)

  4. Merja Oja, Göran O. Sperper, Jonas Blomberg and Samuel Kaski. Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups. International Journal of Neural Systems Vol. 15, No. 3 (2005) 163-179. (abstract, postprint pdf, publisher's page, Supplemental information)

  5. Merja Oja, Göran Sperber, Jonas Blomberg, and Samuel Kaski. Grouping and Visualizing Human Endogenous Retroviruses by Bootstrapping Median Self-organizing Maps. In Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. San Diego, California, USA, 7-8 October, pages 95-101. 2004. (preprint abstract, preprint pdf, publisher's page)

  6. Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna, Petri Törönen, and Eero Castrén. Trustworthiness and metrics in visualizing similarity of gene expression. BMC Bioinformatics, 4:48, 2003.

  7. Merja Oja, Panu Somervuo, Samuel Kaski, and Teuvo Kohonen Clustering of human endogenous retrovirus sequences with median self-organizing map In Workshop on Self-Organizing Maps, 11-14 September 2003. Hibikino, Japan. Proceedings on CD. (abstract,postscript, gzipped postscript)

  8. Merja Oja, Samuel Kaski, and Teuvo Kohonen, Bibliography of Self-Organizing Map (SOM) Papers: 1998-2001 Addendum, Neural Computing Surveys, Volume 3, pages 1-156, 2003. (pdf)

  9. Merja Oja, Janne Nikkilä, Petri Törönen, Eero Castrén, and Samuel Kaski. Learning metrics for visualizing gene functional similarities. In Pekka Ala-Siuru and Samuel Kaski, editors, STeP 2002 - Intelligence, The Art of Natural and Artificial. The 10th Finnish Artificial Intelligence Conference, Oulu, Finland 15-17 Dec. 2002, pages 31-40, 2002. (abstract, postscript, gzipped postscript)

  10. Merja Oja, Janne Nikkilä, Petri Törönen, Garry Wong, Eero Castrén, and Samuel Kaski. Exploratory clustering of gene expression profiles of mutated yeast strains. In Wei Zhang and Ilya Shmulevich, editors, Computational And Statistical Approaches To Genomics, pages 65-78. Kluwer Acadmic Publishers, 2002. (abstract, postscript, gzipped postscript)

Conference posters

  1. Merja Oja and William Stafford Noble. A two level machine learning approach to the prediction of beta sheet structures. Poster in Intelligent Systems for Molecular Biology 2008 (ISMB). Toronto, Canada, July 19-23, 2008.

  2. Merja Oja, Jaakko Peltonen, Jonas Blomberg and Samuel Kaski. Estimating human endogenous retrovirus activities in various tissues with a hidden Markov mixture model. Poster in Intelligent Systems for Molecular Biology & European Conference on Computational Biology 2007 (ISMB/ECCB). Vienna, Austria, July 21-25, 2007. (abstract)

  3. Merja Oja, Jaakko Peltonen, and Samuel Kaski. A hidden Markov model mixture for estimating human endogenous retrovirus activities from expressed sequence databases. Poster in European Conference on Computational Biology 2006 (ECCB). Eilat, Israel, January 21-24, 2007. (abstract)

  4. Merja Oja, Jonas Blomberg, and Samuel Kaski. Class discovery and visualization for human endogenous retroviruses by bootstrapping Median Self-organizing Maps In Bioinformatics 2004, Linköping, Sweden, June 3-6, 2004. A poster. (abstract, postscript (A4 size), gzipped postscript (A4 size))

  5. Merja Oja, Petri Törönen, Janne Nikkilä, Eero Castrén, and Samuel Kaski. Learning metrics for SOM-based clustering and visualization of yeast gene expression data. In Bioinformatics 2002, Bergen, Norway, April 4-7, 2002. A poster. (abstract, postscript (A4 size), gzipped postscript (A4 size))

Theses

  1. Merja Oja. PhD Thesis: Methods for exploring genomic data sets: Application to human endogenous retroviruses. Dissertations in Computer and Information Science, report D23, 2007. PhD Thesis, Helsinki University of Technology, Finland. (abstract and the overview in pdf-format)

  2. Merja Oja. Master's Thesis: Gene expression data mining using self-organizing maps and learning metrics (in Finnish), Helsinki University of Technology, Department of Engineering Physics and Mathematics, April 2002.