2012

Tuomela S, Salo V, Tripathi SK, Chen Z, Laurila K, Äijö T, Gupta B, Oikari L, Stockinger B, Lähdesmäki H and Lahesmaa R,
Identification of early gene expression changes during human Th17 cell differentiation,
Blood, In press.
[abstract, pdf, suppl.] [pdf]

Lehmusvaara S, Erkkilä T,  Urbanucci A, Waltering K, Seppälä J, Tuominen V, Isola J, Kujala P, Lähdesmäki H, Kaipia A, Tammela TLJ and Visakorpi T,
Chemical castration and antiandrogens induce differential gene expression in prostate cancer,
The Journal of Pathology, in press.
[abstract, html, pdf, suppl.] [pdf]

Jalava SE, Urbanucci A, Latonen LM, Waltering KK, Sahu B, Jänne OA, Seppälä J, Lähdesmäki H, Tammela TLJ and Visakorpi T,
Androgen-regulated miR-32 targets BTG2 and is overexpressed in castration-resistant prostate cancer,
Oncogene, in press.
[abstract, html, pdf, suppl.] [pdf]

Urbanucci A, Sahu B, Seppälä J, Larjo A, Latonen LM, Waltering KK, Tammela TLJ, Vessella RL, Lähdesmäki H, Jänne OA and Visakorpi T,
Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer,
Oncogene, Vol. 31, No. 17, pp. 2153-2163, 2012.
[abstract, html, pdf, suppl.] [pdf]

Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo J-P, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A and Lahesmaa R,
RNA binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation,
Stem Cells, Vol. 30, No. 3, pp. 452-460, 2012.
[abstract, pdf] [pdf]

2011

Annala, M., Laurila, K., Lähdesmäki, H., and Nykter, M.,
A linear model for transcription factor binding affinity prediction in protein binding microarrays,
PLoS ONE, 6(5): e20059, 2011.
[html, pdf] [pdf]
[software]

Porkka, K. P., Ogg, E.-L., Saramäki, O. R., Vessella, R. L., Pukkila, H., Lähdesmäki, H., van Weerden, W. M., Wolf, M., Kallioniemi, O. P., Jenster, G. and Visakorpi, T.,
The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers,
Genes, Chromosomes and Cancer, Vol. 50, No. 7, pp. 499-509, 2011.
[abstract, html, pdf] [pdf]

2010

Erkkilä, T., Lehmusvaara, S., Ruusuvuori, P., Visakorpi, T., Shmulevich, I. and Lähdesmäki, H.,
Probabilistic analysis of gene expression measurements from heterogeneous tissues,
Bioinformatics, Vol. 26, No. 20, pp. 2571-2577, 2010.
[abstract, html, pdf, supplementary material] [pdf, supplementary material]
[software, web tool]

Elo, L. L., Järvenpää, H., Tuomela, S., Raghav, S., Ahlfors, H., Laurila, K., Gupta, B., Lund, R. J., Tahvanainen, J., Hawkins, D., Oresic, M., Lähdesmäki, H., Rasool, O., Rao, K. V., Aittokallio, T. and Lahesmaa, R.,
Genome-wide Profiling of Interleukin-4 and STAT6 Transcription Factor Regulation of Human Th2 Cell Programming,
Immunity, Vol. 32, No. 6, pp. 727-862, 2010.
[abstract, html, pdf, supplementary material] [pdf]

Aho, T., Almusa, H., Matilainen, J., Larjo, A., Ruusuvuori, P., Aho, K.-L., Wilhelm, T., Lähdesmäki, H., Beyer, A., Harju, M., Chowdhury, S., Leinonen, K, Roos, C. and Yli-Harja, O.,
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network,
PLoS ONE, 5(5):e10662, 2010.
[html, pdf] [pdf]

Dai, X. and Lähdesmäki, H.,
Novel data fusion method and exploration of multiple information sources for transcription factor target gene prediction,
EURASIP Journal on Advances in Signal Processing, Special issue on Genomic Signal Processing, Vol. 2010, Article ID 235795, 2010.
[abstract, html, pdf] [pdf]

2009

Laurila, K. and Lähdesmäki, H.,
A protein-protein interaction guided method for competitive transcription factor binding improves target predictions,
Nucleic Acids Research, Vol. 37, No. 22, e146, 2009.
[abstract, html, pdf, supplementary material: pdf]
[software]

Äijö, T. and Lähdesmäki, H.,
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics,
Bioinformatics, Vol. 25, No. 22, pp. 2937-2944, 2009.
[abstract, pdf] [pdf, supplementary material: pdf]
[software]

Laurila, K. and Lähdesmäki, H.,
Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding,
In Silico Biology, Vol. 9, 0018, 2009.
[abstract, html] [pdf-preprint]

Dai, X., Erkkilä, T., Yli-Harja, O. and Lähdesmäki, H.,
A joint mixture model for clustering genes from Gaussian and beta distributed data,
BMC Bioinformatics 10:165, 2009.
[abstract, html, pdf] [pdf]

Dai, X., Lähdesmäki, H. and Yli-Harja, O.,
A stratified beta-Gaussian mixture model for clustering genes with multiple data sources,
International Journal on Advances in Life Sciences, Vol. 1, No. 1, pp. 14-25, 2009.
[pdf]

Nykter, M., Lähdesmäki, H., Rust, A. G., Thorsson, V. and Shmulevich, I.,
A data integration framework for prediction of transcription factor targets: a BCL6 case study,
Annals of the New York Academy of Sciences, Vol. 1158, pp. 205-214, 2009.
[abstract, html, pdf] [pdf]

2008

Lähdesmäki, H., Rust, A. G. and Shmulevich, I.,
Probabilistic inference of transcription factor binding from multiple data sources,
PLoS ONE, Vol. 3, No. 3, e1820, 2008.
[pdf, html] [pdf]
[web tool, software]

Lähdesmäki, H. and Shmulevich, I.,
Learning the structure of dynamic Bayesian networks from time series and steady state measurements,
Machine Learning, Vol. 71, No. 2-3, pp. 185-217, 2008.
[abstract, pdf] [pdf]
[software]

Liu, W., Lähdesmäki, H., Dougherty, E. R. and Shmulevich, I.,
Inference of Boolean networks using sensitivity regularization,
EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541, 12 pages, 2008.
[abstract, pdf] [pdf]

2007

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, html, pdf] [pdf, supplementary material and software]

2006

Lähdesmäki, H., Hautaniemi, S., Shmulevich, I. and Yli-Harja, O.,
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks,
Signal Processing , Vol. 86, No. 4, pp. 814-834, April 2006.
[pdf] [html, pdf]

2005

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] [pdf, supplementary material and software]
(*equally contributing authors)

Lähdesmäki, H., Shmulevich, I., Dunmire, V., Yli-Harja O. and Zhang, W.,
In silico microdissection of microarray data from heterogeneous cell populations,
BMC Bioinformatics, 6:54, 2005.
[abstract, html, pdf] [pdf]

2004

Lähdesmäki, H., Hao, X., Sun, B., Hu, L., Yli-Harja, O., Shmulevich, I. and Zhang, W.,
Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis,
International Journal of Oncology, Vol. 24, No. 6, pp. 1589-1596, June 2004.
[pdf] 

Hao, X., Sun, B., Hu, L., Lähdesmäki, H., Dunmire, V., Feng, Y., Zhang, S.-W., Wang, H., Wu, C., Wang, H., Fuller, G. N., Symmans, W. F., Shmulevich, I. and Zhang, W.,
Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis,
Cancer, Vol. 100, No. 6, pp. 1110-1122, 2004.
[pdf] [abstract, html, pdf]

Shmulevich, I. Lähdesmäki, H. and Egiazarian, K.
Spectral methods for testing membership in certain Post classes and the class of forcing functions,
IEEE Signal Processing Letters, Vol. 11, No. 2, pp. 289-292, 2004.
[pdf] [abstract, pdf]

2003

Shmulevich, I., Lähdesmäki, H., Dougherty, E. R., Astola, J. and Zhang, W.,
The role of certain Post classes in Boolean network models of genetic networks,
Proceedings of the National Academy of Sciences of the USA, Vol. 100, No. 19, pp. 10734-10739, 2003.
[pdf] [abstract, html, pdf]

Lähdesmäki, H., Shmulevich, I. and Yli-Harja, O.,
On learning gene regulatory networks under the Boolean network model,
Machine Learning, Vol. 52, No. 1-2, pp. 147-167, June - August 2003.
[pdf] [abstract, pdf]

Lähdesmäki, H., Huttunen, H., Aho, T., Linne, M.-L., Niemi, J., Kesseli, J., Pearson, R. and Yli-Harja, O.,
Estimation and inversion of the effects of cell population asynchrony in gene expression time-series,
Signal Processing, Vol. 83, No. 4, pp. 835-858, April 2003.
[pdf] [abstract, html, pdf]

Larjo A, Shmulevich I and Lähdesmäki H,
Structure learning for Bayesian networks as models of biological networks,
In H. Mamitsuka, C. DeLisi and M. Kanehisa (Eds.), Data Mining for Systems Biology, Methods in Molecular Biology, Springer, to appear.

Lähdesmäki H, Shmulevich I, Yli-Harja O. and Astola J,
Inference of genetic regulatory networks via Best-Fit extensions,
In W. Zhang and I. Shmulevich (Eds.), Computational And Statistical Approaches To Genomics (2nd Ed.), Boston: Kluwer Academic Publishers, pp. 259-278, 2006.

Refereed Conference Papers:

2010

Erkkilä, T., Thorsson, V., Lähdesmäki, H. and Shmulevich, I.,
Inferring genetic regulatory interactions from time-collapsed Boolean summary variables,
In Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010.
[pdf]

2009

Laurila, K. and Lähdesmäki, H.,
A probabilistic model for competitive binding of transcription factors,
In Sixth International Workshop on Computational Systems Biology, WCSB 2009, Århus, Denmark, June 10-12, 2009.
[pdf]

Dai, X. and Lähdesmäki, H.,
A unified probabilistic framework for clustering genes from gene expression and protein-protein interaction data,
In Sixth International Workshop on Computational Systems Biology, WCSB 2009, Århus, Denmark, June 10-12, 2009.
[pdf]

2008

Dai, X., Lähdesmäki, H. and Yli-Harja, O.,
sBGMM: a stratified Beta-Gaussian mixture model for clustering genes with multiple data sources,
In International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies, BIOTECHNO 2008, June 29 - July 5, 2008 - Bucharest, Romania.
[pdf]

Laurila, K. and Lähdesmäki, H.,
Effects of disease-related mutations on transcription factor binding,
In Fifth International Workshop on Computational Systems Biology (WCSB08), Leipzig, Germany, June 11-13, 2008.
[pdf]

Larjo, A., Lähdesmäki, H., Facciotti, M., Baliga, N., Yli-Harja, O. and Shmulevich, I.,
Active learning of Bayesian network structure in a realistic setting,
In Fifth International Workshop on Computational Systems Biology (WCSB08), Leipzig, Germany, June 11-13, 2008.
[pdf]

Nikkilä, J., Erkkilä, T. and Lähdesmäki, H.,
Decomposing gene expression into regulatory and differential parts with Bayesian data fusion,
In Fifth International Workshop on Computational Systems Biology (WCSB08), Leipzig, Germany, June 11-13, 2008.
[pdf]

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,
In Fifth International Workshop on Computational Systems Biology (WCSB08), Leipzig, Germany, June 11-13, 2008.
[pdf]

Dai, X., Lähdesmaki, H. and Yli-Harja, O.,
BGMM: a Beta-Gaussian mixture model for clustering genes with multiple data sources,
In Fifth International Workshop on Computational Systems Biology (WCSB08), Leipzig, Germany, June 11-13, 2008.
[pdf]

2007

Lähdesmäki, H. and Shmulevich, I.,
Probabilistic framework for transcription factor binding prediction,
In Fifth IEEE International Workshop on Genomic Signal Processing and Statistics (Gensips'07), Tuusula, FINLAND, June 10-12, 2007.
[pdf]

Ahdesmäki, M., Lähdesmäki, H. and Yli-Harja O.,
Robust Fisher's test for periodicity detection in noisy biological time series,
In Fifth IEEE International Workshop on Genomic Signal Processing and Statistics (Gensips'07), Tuusula, FINLAND, June 10-12, 2007.
[pdf]

2005

Lähdesmäki, H., Yli-Harja, O., Zhang, W. and Shmulevich, I.,
Intrinsic dimensionality in gene expression analysis,
In IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) 2005, Hyatt Regent Hotel, Newport, Rhode Island, May 22 - 24, 2005.
[pdf]

2003

Pearson, R. K., Lähdesmäki, H., Huttunen, H. and Yli-Harja, O.,
Detecting periodicity in nonideal datasets,
In SIAM International Conference on Data Mining (2003), Cathedral Hill Hotel, San Francisco, CA, May 1-3, 2003.
[pdf]

2001

Lähdesmäki, H., Shmulevich, I., Pezzati, L. and Tozzi, A.,
Optimization of edge detectors for topographic maps of cave inscriptions,
In 12th Scandinavian Conference on Image Analysis (SCIA 2001), Bergen, Norway, June 11-14, 2001, pp. 280-287.
[pdf]

Proceedings:

Manninen, T., Wiuf, C., Lähdesmäki, H., Grzegorczyk, M., Rahnenführer, J., Ahdesmäki, M., Linne, M.-L., and Yli-Harja O. (Eds.)
Proceedings of the Sixth TICSP Workshop on Computational Systems Biology,
Århus, Denmark, June 10-12, 2009.
[TOC: pdf] [Proceedings: pdf]

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.
[TOC: pdf] [Proceedings: pdf]

Aho, T., Lähdesmäki, H. and Yli-Harja, O. (Eds.)
Proceedings of the 2nd TICSP Workshop on Computational Systems Biology,
Helsinki - St. Petersburg, June 14-16, 2004.
[TOC: pdf]

Technical Reports:

Lähdesmäki, H. and Shmulevich I.,
Learning the structure of dynamic Bayesian networks from time series and steady state measurements,
Technical Report 1-2007, Tampere University of Technology, Institute of Signal Processing, 2007.
[I recommend to read our slightly updated journal publication instead.]

Lähdesmäki, H., Aho, T., Huttunen, H., Linne, M.-L., Niemi, J., Kesseli, J., Pearson, R., Yli-Harja, O.,
Using signal processing tools to improve the quality of microarray time-series measurements,
Technical Report 2-2002, Tampere University of Technology, 2002.
[pdf I recommend to read our slightly updated journal publication instead.]

Theses:

Lähdesmäki, H.,
Computational Methods for Systems Biology: Analysis of High-Throughput Measurements and Modeling of Genetic Regulatory Networks,
Ph.D. Thesis, Tampere University of Technology, October 2005.
[Table of Contents: pdf][*pdf]
*The doctoral thesis consists of an introduction (94 pages) and nine (9) original publications that are included as an appendix. Please note that the original publications are not included into the pdf-file. Most of the original publications can be found from this web page.

Lähdesmäki, H.,
Enhancement and Segmentation of Topographic Maps of Petroglyphs,
M.Sc. Thesis, Tampere University of Technology, August 2001.
[abstract: pdf] [pdf]

Presentations and Abstracts: (not updated)

2010:

Laurila, K., Vahedi, G., Kanno, Y., Lahesmaa, R., O'Shea, J.,  and Lähdesmäki, H.,
Cross-species comparison of STAT6 transcription factor regulation in mice and human,
In The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges, New York, NY, USA, November 16-20, 2010.
[abstract: pdf] [poster: pdf]

Larjo, A. and Lähdesmäki, H.,
Efficient learning of signaling network model structures using Bayesian networks,
In The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges, New York, NY, USA, November 16-20, 2010.
[abstract: pdf] [poster: pdf]

Annala, M., Laurila, K., Nykter, M., and Lähdesmäki, H.,
A linear model for transcription factor binding affinity prediction in PBM microarrays,
In The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges, New York, NY, USA, November 16-20, 2010. (invited presentation)
[abstract: pdf] [presentation: pdf]

Äijö, T., Lönnberg, T., Edelman, S., Tuomela, S., Järvenpää, H., Lahesmaa, R., and Lähdesmäki, H.,
Comparing multiple time-course differentiation profiles of human T helper cells using a Bayesian approach,
In The 7th Annual RECOMB Satellite on Regulatory Genomics, the 6th Annual RECOMB Satellite on Systems Biology, and the 5th Annual DREAM reverse engineering challenges, New York, NY, USA, November 16-20, 2010.
[abstract: pdf] [poster: pdf]

Äijö, T., Yli-Harja, O. and Lähdesmäki, H.,
Learning gene regulatory networks with delayed ODEs and continuous-time expression representation,
In Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, June 16-18, 2010.
[abstract: pdf] [presentation: pdf]

Urbanucci, A., Sahu, B., Seppälä, J., Kukkola, S., Waltering, K., Lähdesmäki, H., Jänne, O. and Visakorpi, T.,
The effect of AR expression level on the chromatin binding of the receptor,
In AACR 101st Annual Meeting 2010, Washington, DC, USA, April 17-21, 2010.
[abstract: pdf] [poster: pdf]

Lehmusvaara, S., Erkkilä, T., Lähdesmäki, H., Kujala, P., Tammela, T.L.J. and Visakorpi, T.,
Effects of endocrine therapy on mRNAand microRNA expression profiles in prostate cancer,
In AACR 101st Annual Meeting 2010, Washington, DC, USA, April 17-21, 2010.
[abstract: pdf] [poster: pdf]

2009

Laurila, K., Pukkila, H., Yli-Harja, O. and Lähdesmäki, H.,
Protein-protein interactions improve multiple transcription factor binding site prediction,
In The Joint RECOMB Satellite on Regulatory Genomics, Systems Biology, and DREAM reverse engineering challenges, MIT/Broad Institute/CSAIL, Boston, MA, USA, December 2 - 6, 2009.
[abstract: pdf] [poster: pdf]

Äijö, T. and Lähdesmäki, T.,
Learning gene regulatory networks with delayed ODEs and continuous-time expression representation
In The Joint RECOMB Satellite on Regulatory Genomics, Systems Biology, and DREAM reverse engineering challenges, MIT/Broad Institute/CSAIL, Boston, MA, USA, December 2 - 6, 2009.
[abstract: pdf] [poster: pdf]

Erkkilä, T., Ruusuvuori, P., Lehmusvaara, S., Visakorpi, T., Shmulevich, I. and Lähdesmäki, H.,
Incorporating spatial information of heterogeneous cell populations into Bayesian mRNA- and miRNA-expression analysis,
In The Joint RECOMB Satellite on Regulatory Genomics, Systems Biology, and DREAM reverse engineering challenges, MIT/Broad Institute/CSAIL, Boston, MA, USA, December 2 - 6, 2009.
[abstract: pdf] [poster: pdf]

Aho, T., Almusa, H., Matilainen, J., Larjo, A., Ruusuvuori, P., Aho, K.-L., Wilhelm, T., Lähdesmäki, H., Beyer, A., Harju, M., Chowdhury, S., Leinonen, K., Roos, C. and Yli-Harja, O.,
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network,
In The Joint RECOMB Satellite on Regulatory Genomics, Systems Biology, and DREAM reverse engineering challenges, MIT/Broad Institute/CSAIL, Boston, MA, USA, December 2 - 6, 2009.
[abstract: pdf] [poster: pdf]

Laurila, K. and Lähdesmäki, H.,
A probabilistic model for competitive binding of transcription factors,
In 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden, June 27 - July 3, 2009.
[abstract: pdf] [poster: pdf]

Äijö, T. and Lähdesmäki, H.,
Learning the structure of a gene regulatory network from gene expression measurements using non-parametric molecular kinetics,
In 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB), Stockholm, Sweden, June 27 - July 3, 2009.
[abstract: pdf] [poster: pdf]

Laurila, K. and Lähdesmäki, H.,
Computational analysis of disease-related mutation effects on transcription factor binding,
In The Seventh Asia-Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009.
[abstract: pdf] [poster: pdf]

Dai, X., Erkkilä, T., Yli-Harja, O. and Lähdesmäki, H.,
A joint mixture model for clustering genes from Gaussian and beta distributed data,
In The Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, January 13-16, 2009.
[abstract: pdf] [poster: pdf]

2008

Dai, X. and Lähdesmäki, H.
Inferring transcription factor targets from multiple heterogeneous data sources,
In The 5th Annual RECOMB Satellite on Regulatory Genomics, the 4th Annual RECOMB Satellite on Systems Biology, and the 3rd Annual DREAM reverse engineering challenges, Boston/MIT/Broad, MA, USA, October 29 - November 2, 2008.
[abstract: pdf] [poster: pdf]

Lähdesmäki, H.,
Computational modeling of transcriptional regulation using multiple heterogeneous data sources,
In Murikka Minisymposium 2008: Cell signalling and its transcriptional readout, Tampere, Finland, August 16, 2008. (invited)
[pdf]

Laurila, K. and Lähdesmäki, H.,
Effects of disease-related mutations on transcription factor binding,
In 16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008.
[abstract: pdf] [poster: pdf]

Lähdesmäki, H., Rust, A. G. and Shmulevich, I.,
Probabilistic data fusion for transcription factor binding prediction,
In The Institute for Systems Biology's Seventh Annual International Symposium: Systems Biology & Engineering, Seattle, WA, USA, April 20-21, 2008.
[poster: pdf]

2007

Lähdesmäki, H., Rust, A. G. and Shmulevich, I.,
Probabilistic transcription factor binding prediction: joint inference from multiple data sources,
In 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, AUSTRIA, July 21-25, 2007.
[abstract: pdf] [poster: pdf]

Lähdesmäki, H., Rust, A. G. and Shmulevich, I.,
Probabilistic inference of transcription factor binding from multiple data sources,
In The Institute for Systems Biology's Sixth Annual International Symposium: Systems Biology and the Environment, Seattle, WA, USA, April 22-23, 2007. (invited)
[poster: pdf]

Lähdesmäki, H., Larjo, A., Yli-Harja, O. and Shmulevich, I.,
Inferring dynamic signalling networks from steady state measurements,
In Eleventh Annual International Conference on Research in Computational Molecular Biology, Oakland, CA, USA, April 21-25, 2007.
[2-page abstract: pdf] [poster: pdf]

2006

Harri Lähdesmäki, Nathan Price, Seungchan Kim, Cristian Mircean, Tohru Kobayashi, Greg Fuller, Jeff Trent, Ioan Tabus, Edward R. Dougherty, Wei Zhang and Ilya Shmulevich
Disease classification issues in cancer genomics
The Institute for Systems Biology's Fifth Annual International Symposium: Systems Biology and Medicine, Seattle, WA, USA, April 23-24, 2006. (invited)
[poster: pdf]

2005

Lähdesmäki, H.,
Spectral methods for testing membership in certain Post classes and the class of forcing functions,
In 3rd TICSP Workshop on Computational Systems Biology (WCSB 2005), Tampere, Finland, June 13-14, 2005. (invited)
[pdf]

Ahdesmäki, M., Lähdesmäki, H., Pearson, R., Huttunen, H. and Yli-Harja, O.,
Robust detection of periodically behaving biological time series,
In 3rd TICSP Workshop on Computational Systems Biology (WCSB 2005), Tampere, Finland, June 13-14, 2005.
[2-page abstract: pdf] [poster: pdf]

2004

Lähdesmäki, H., Shmulevich, I., Dunmire, V., Yli-Harja, O. and Zhang, W.,
In silico microdissection of microarray data from heterogeneous cell populations,
In 12th International Conference on Intelligent Systems for Molecular Biology (ISMB) / 3rd European Conference on Computational Biology (ECCB), Glasgow, UK, July 31-August 4, 2004, and In 2nd TICSP Workshop on Computational Systems Biology, Helsinki - St. Petersburg, June 14-16, 2004. (invited)
[abstract: pdf] [poster: pdf]

2003

Lähdesmäki, H.,
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks,
In Workshop on Discrete Models for Genetic Regulatory Networks, Texas A&M University, College Station, TX, USA, November 5-6, 2003. (invited)
[pdf]

Lähdesmäki, H., Yli-Harja, O., Shmulevich, I. and Zhang, W.,
Distinguishing key biological pathways by knowledge-based multidimensional scaling analysis: application to discriminate between primary breast cancers and their lymph node metastases,
In Bioinformatics 2003, Helsinki, Finland, May 22-24, 2003, and In TICSP Workshop on Computational Systems Biology, Tampere, Finland, June 16-17, 2003.
[abstract: pdf] [poster: pdf]

Aho, T., Saarinen, A., Niemi, J., Nicorici, D., Kesseli, J., Rämö, P., Lähdesmäki, H., Medina, J. L., Nykter, M., Linne, M.-L. and Yli-Harja, O.,
Simulation and modeling tools for genetic regulatory networks,
In Bioinformatics 2003, Helsinki, Finland, May 22-24, 2003, and In TICSP Workshop on Computational Systems Biology, Tampere, Finland, June 16-17, 2003.
[poster: pdf]

Lähdesmäki, H., Hao, X., Sun, B., Hu, L., Yli-Harja, O., Fuller, G. N., Shmulevich, I. and Zhang, W.,
Distinguishing primary breast cancers and their lymph node metastases by knowledge-based multidimensional scaling analysis,
In Oncogenomics 2003, Phoenix, Arizona, USA, January 29-February 2, 2003.
[abstract: pdf] [poster: pdf]

2002

Pearson, R., Lähdesmäki, H., Huttunen, H. and Yli-Harja, O.,
Analysis of microarray time-series based on binary correlation and a first order model of the involved cellular processes,
In 2002 SIAM 50th Anniversary and Annual Meeting, Philadelphia, PA, USA, July 8-12, 2002.
[abstract: pdf]

Aho, T., Lähdesmäki, H., Huttunen, H., Linne, M.-L., Niemi, J. and Yli-Harja, O.,
Modelling of distortion of microarray time-series experiments caused by loss of cell synchrony,
In Bioinformatics 2002, Bergen, Norway, April 4-7, 2002.
[abstract: pdf]