| A
sorted
list of publications. |
| Refereed international scientific journals: |
|
| Richard D. Kennedy, Max Bylesjo, Peter Kerr, Timothy Davison, Julie M. Black, Elaine W. Kay, Robert J. Holt, Vitali Proutski, Miika Ahdesmaki et al. Development and Independent Validation of a Prognostic Assay for Stage II Colon Cancer
Using Formalin-Fixed Paraffin-Embedded Tissue. Journal of Clinical Oncology, JCO.2011.35.4498. [abstract, pdf] |
|
| Ahdesmäki,M., and Strimmer,K. Feature selection in omics prediction problems using cat
scores and false non-discovery rate control. Annals of Applied Statistics 4:1, 2010, pp. 503-519. [abstract, preprint
pdf] |
|
| Ahdesmäki,M.,
Lähdesmäki,H.,
Gracey,A., Shmulevich,I. and Yli-Harja,O. Robust regression for periodicity
detection
in non-uniformly sampled time-course gene expression data. BMC Bioinformatics, 8:233, 2007.
[abstract, pdf] |
|
| Niemistö,A*., Nykter,M*., Aho,T., Jalovaara,H., Marjanen,K., Ahdesmäki,M., Ruusuvuori,P., Tiainen,M., Linne,M-L. and Yli-Harja,O. Computational methods for estimation of cell cycle distributions of yeast cells. EURASIP Journal on Bioinformatics and Systems Biology, 2007. [abstract, pdf] *Equally contributing authors | |
|
Nykter,M., Aho,T.,
Ahdesmäki,M.,
Ruusuvuori,P., Lehmussola,A. and Yli-Harja,O. Simulation of microarray data
with
realistic characteristics, BMC
Bioinformatics, 7:349,
2006. [abstract,
pdf] |
|
| Ahdesmäki,M.*, Lähdesmäki,H.*, Pearson,R., Huttunen,H. and Yli-Harja,O. Robust detection of periodic time series measured from biological systems, BMC Bioinformatics, 6:117, 2005. [abstract, html, pdf] *Equally contributing authors. | |
| Articles in refereed international scientific conference proceedings: |
|
| Ahdesmäki,M. and Strimmer,K. Comparison of the Gaussian Process Classification Approach with
Classical Penalised Classification Methods in High Dimensional Omics Data WCSB 2009, June
10-12, 2009.
Aarhus, Denmark. [preprint] |
|
| Erkkilä,T., Nykter,M.,
Lähdesmäki,H., Ahdesmäki,M. and Yli-Harja,O. Testing for Differential Expression in Simulated and Real cDNA
Microarray Data Using Frequentist and Bayesian Methods WCSB 2008, June
11-13, 2008.
Leipzig, Germany. [proceedings] |
|
| Ahdesmäki,M.,
Thusberg,J.,
Huttunen,H., Vihinen,M. and Yli-Harja,O. Detection of pathogenic mutation
prone
locations from sequences using solvent accessibility measurements. IEEE GENSIPS'07, June
10-12, 2007.
Tuusula, Finland. [pdf] |
|
| Ahdesmäki,M., Lähdesmäki,H. and Yli-Harja,O. Robust Fisher's test for periodicity detection in noisy biological time series. IEEE GENSIPS'07, June 10-12, 2007. Tuusula, Finland. [pdf] | |
| Niemistö,A.,
Nykter,M., Aho,T.,
Jalovaara,H.,
Marjanen,K., Ahdesmäki,M., ,
Ruusuvuori,P., Tiainen,M., Linne.M-L. & Yli-Harja,O. Distribution estimation of
synchronized budding yeast population, In: Aleksey, M.
et al. (eds.). Proceedings of
the Winter International Symposium on Information and Communication
Technologies, WISICT 2004, Cancun, Mexico, 5-8 January 2004, pp. 243-248, 2004. [abstract] |
|
| Theses: |
|
| Ahdesmäki,M. Robust Signal Processing Methods for Genomic Time Series and Protein Accessibility Data. PhD/D. Tech. thesis, Tampere University of Technology, December 2007 (thesis defense November 28 2007). [abstract, pdf] | |
| Ahdesmäki,M. Periodicity detection in
microarray data.
M.Sc. thesis, Tampere University of Technology, April 2005. |
|
| Other scientific publications: |
|
| Ahdesmäki,M., Strimmer,K., Radde,N., Rahnenführer,J., Klemm,K., Lähdesmäki,H. and Yli-Harja,O. (Eds.) Proceedings of the Fifth TICSP Workshop on Computational Systems Biology, Leipzig, Germany, June 11-13, 2008. | |
| Ahdesmäki,M., Lähdesmäki,H., Pearson,R., Huttunen,H. & Yli-Harja,O., Robust detection of periodically behaving biological time series, In: Manninen, T. et al. (eds.). Proceedings of The 3rd TICSP Workshop on Computational Systems Biology, WCSB 2005, Tampere, Finland, 13-14 June 2005, pp. 39-40, 2005. | |
| Ahdesmäki,M., Data dependent cdna-microarray simulator, In: Aho, T., Lähdesmäki, H. & Yli-Harja, O. (eds.). Proceedings of the 2nd TICSP Workshop on Computational Systems Biology, WCSB 2004, Silja Opera, Helsinki-St.Petersburg, 14-16 June 2004, pp. 25-26, 2004. | |
|
Nykter,M., Aho,T., Ahdesmäki,M.
&
Yli-Harja,O., Cell DNA
content
estimation by flow cytometry time series data, In: Yli-Harja, O., Shmulevich, I.
& Aho,
T. (eds.). Proceedings of the TICSP Workshop in Computational Systems
Biology,
WCSB 2003, Tampere, Finland, 16-17 June 2003, pp. 26, 2003. |