Applications
Methodology
Sipola, A., Marttinen, P., and Corander, J. (2018). Bacmeta: simulator for genomic evolution in bacterial metapopulations. Bioinformatics, bty093. Available online
Järvenpää, M., Gutmann, M., Vehtari, A., and Marttinen, P. (2018). Gaussian process modeling in approximate Bayesian computation to estimate horizontal gene transfer in bacteria. Annals of Applied Statistics, Accepted for publication. Preprint
Marttinen, P. and Hanage, W.P. (2017). Speciation trajectories in recombining bacterial species. PLOS Computational Biology, 13(7):e1005640. Available online
David, S., Sanchez-Buso, L., Harris, S.R., Marttinen, P., Rusniok, C., Buchrieser, C., Harrison, T.G., and Parkhill, J. (2017). Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLOS Genetics, 13(6):e1006855. Available online
Pirinen, M., Benner, C., Marttinen, P., Järvelin, M.-R., Rivas, M.A., and Ripatti, S. (2017). biMM: Efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements. Bioinformatics, 33(15):2405-2407. Available online
Villa, P.M., Marttinen, P., Gillberg, L., Lokki, A.I., Majander, K., Taipale, P., Pesonen, A., Räikkönen, K., Hämäläinen, E., Kajantie, E., and Laivuori, H. (2017). Cluster Analysis to Estimate the Risk of Preeclampsia in the High-Risk Prediction and Prevention of Preeclampsia and Intrauterine Growth Restriction (PREDO) Study. PLoS ONE, 12(3): e0174399. Available online
Mostowy, R., Croucher, N.J., Andam, C.P., Corander, J., Hanage, W.P., and Marttinen, P. (2017). Efficient inference of recent and ancestral recombination within bacterial populations. Molecular Biology and Evolution, 34(5):1167-1182. Available online
Pre-printHarms, K., Lunnan, A., Hülter, N., Mourier, T., Vinner, L., Andam, C.P., Marttinen, P., Fridholm, H., Hansen, A.J., Hanage, W.P., Nielsen, K.M., Willerslev, E., and Johnsen, P.J. (2016). Substitutions of short heterologous DNA segments of intra- or extragenomic origins produce clustered genomic polymorphisms. Proceedings of the National Academy of Sciences of the United States of America, 113(52):15066-15071. doi:10.1073/pnas.1615819114. Available online
Lees, J.A., Vehkala, M., Välimäki, N., Harris, S.R., Chewapreecha, C., Croucher, N.J., Marttinen, P., Davies, M.R., Steer, A.C., Tong, S.Y.C., Honkela, A., Parkhill, J., Bentley, S.D., and Corander, J. (2016). Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nature Communications, 7:12797, doi:10.1038/ncomms12797. Available online
Gillberg, J., Marttinen, P., Pirinen, M., Kangas, A.-J., Soininen, P., Ali, M., Havulinna, A. S., Järvelin, M.-R., Ala-Korpela, M., and Kaski, S. (2016). Multiple output regression with latent noise. Journal of Machine Learning Research, 17:1-35. Available online
Sieberts, S., Zhu, F., García-García, J., Stahl, E., Pratap, A., Pandey, G., Pappas, D., Aguilar, D., Anton, B., Bonet, J., Eksi, R., Fornés, O., Guney, E., Li, H., Marín, M., Panwar, B., Planas-Iglesias, J., Poglayen, D., Cui, J., Falcao, A., Suver, C., Hoff, B., Balagurusamy, V., Dillenberger, D., Chaibub Neto, E., Norman, T., Aittokallio, T., Ammad-ud-din, M., Azencott, C.-A., Bellón, V., Boeva, V., Bunte, K., Chheda, H., Cheng, L., Corander, J., Dumontier, M., Goldenberg, A., Gopalacharyulu, P., Hajiloo, M., Hidru, D., Jaiswal, A., Kaski, S., Khalfaoui, B., Khan, S., Kramer, E., Marttinen, P., Mezlini, A., Molparia, B., Pirinen, M., Saarela, J., Samwald, M., Stoven, V., Tang, H., Tang, J., Torkamani, A., Vert, J.P., Wang, B., Wang, T., Wennerberg, K., Wineinger, N., Xiao, G., Xie, Y., Yeung, R., Zhan, X., Zhao, C., Greenberg, J., Kremer, J., Michaud, K., Barton, A., Coenen, M., Mariette, X., Miceli, C., Shadick, N., Weinblatt, M., de Vries, N, Tak, P., Gerlag, D., Huizinga, T.W.J., Kurreeman, F., Allaart, C., Bridges, S., Criswell, L., Moreland, L., Klareskog, L., Saevarsdottir, S., Padyukov, L., Gregersen, P., Friend, S., Plenge, R., Stolovitzky, G., Oliva, B., Guan, Y., and Mangravite, L. (2016). Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7:12460, doi:10.1038/ncomms12460 Available online
Numminen, E., Gutmann, M., Shubin, M., Marttinen, P., Meric, G.,van Schaik, W., Coque, T., Baquero, F., Willems, R., Sheppard, S., Feil, E., Hanage, W.P., and Corander, J. (2016). The impact of host metapopulation structure on the population genetics of colonizing bacteria. Journal of Theoretical Biology, 396: 53-62. Pre-print
Cichonska, A., Rousu, J., Marttinen, P., Kangas, A.J., Soininen, P., Lehtimäki, T., Raitakari, O.T., Järvelin, M.-R., Salomaa, V., Ala-Korpela, M., Ripatti, S. and Pirinen, M. (2016). metaCCA: Summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis. Bioinformatics, 32(13):1981-1989, doi: 10.1093/bioinformatics, Available online
Marttinen, P., Croucher, N.J., Gutmann, M.U., Corander, J. and Hanage, W.P. (2015). Recombination produces coherent bacterial species clusters in both core and accessory genomes. Microbial Genomics, 1, doi:10.1099/mgen.0.000038, Available online (Supplement)
Chewapreecha, C., Marttinen, P., Croucher, N.J.,Salter, S.J., Harris, S.R., Mather, A.E.,Hanage, W.P., Goldblatt, D., Nosten, F.H., Turner, C., Turner, P., Bentley, S.D. and Parkhill, J. (2014). Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genetics, 10(8):e1004547. doi:10.1371/journal.pgen.1004547
Sheppard, S.K., Cheng, L., Méric, G., de Haan, C.P.A., Llarena, A.-K., Marttinen, P., Vidal, A., Ridley, A., Clifton-Hadley, F., Connor, T.R., Strachan, N.J.C, Forbes, K., Colles, F.M., Jolley, K.A., Bentley, S.D., Maiden, M.C.J., Hänninen, M.-L., Parkhill, J., Hanage, W.P. and Corander, J. (2014). Cryptic ecology among host generalist Campylobacter jejuni in domestic animals. Molecular Ecology, 23(10):2442-51. doi: 10.1111/mec.12742
Kashtan, N., Roggensack, S.E., Rodrigue, S., Thompson, J.W., Biller, S.J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R.R., Stocker, R., Follows, M.J., Stepanauskas, R. and Chisholm, S.W. (2014). Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science, 344(6182): 416-420.
Marttinen, P., Pirinen, M., Sarin, A.P., Gillberg, J., Kettunen, J., Surakka, I., Kangas, A.J., Soininen, P., O’Reilly, P.F., Kaakinen, M., Kähönen, M., Lehtimäki, T., Ala-Korpela, M., Raitakari, O.T., Salomaa, V., Järvelin, M.-R., Ripatti, S. and Kaski, S. (2014). Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression. Bioinformatics, 30(14):2026-34. doi: 10.1093/bioinformatics/btu140
Chewapreecha, C., Harris, S.R., Croucher, N.J., Turner, C., Marttinen, P., Cheng, L., Pessia, A., Aanensen, D.M., Mather, A.E., Page, A.J., Salter, S.J., Harris, D., Nosten, F., Goldblatt, D., Corander, J., Parkhill, J., Turner, P. and Bentley, S.D. (2014). Dense genomic sampling identifies highways of pneumococcal recombination. Nature Genetics, 46: 305-309.
Marttinen, M., Pajari, A.-M., Päivärinta, E., Storvik, M., Marttinen, P., Nurmi, T., Niku, M., Piironen, V. and Mutanen, M. (2014). Plant sterol feeding induces tumor formation and alters sterol metabolism in the intestine of ApcMin mice. Nutrition and Cancer: An International Journal, 66(2). doi: 10.1080/01635581.2014.865244
Marttinen, P., Gillberg, J., Havulinna, A., Corander, J. and Kaski, S. (2013). Genome-wide association studies with high-dimensional phenotypes. Statistical Applications in Genetics and Molecular Biology, 12(4): 413-431.
Castillo-Ramírez, S., Corander, J., Marttinen, P., Aldeljawi, M., Hanage, W.P., Westh, H., Boye, K.,Gulay, Z., Bentley, S.D., Parkhill, J., Holden M.T. and Feil, E.J. (2012). Phylogeographic variation in recombination rates within a global clone of Methicillin-Resistant Staphylococcus aureus (MRSA). Genome Biology, 13(12):R126. doi:10.1186/gb-2012-13-12-r126
Peltola, T., Marttinen P., and Vehtari, A. (2012). Finite Adaptation and Multistep Moves in the Metropolis-Hastings Algorithm for Variable Selection in Genome-Wide Association Analysis. PLoS ONE, 7(11): e49445. doi:10.1371/journal.pone.0049445
Delezuch, W., Marttinen, P., Kokki, H., Heikkinen, M., Lintula, H., Vanamo, K., Pulkki, K. and Matinlauri, I. (2012). Serum and CSF soluble CD26 and CD30 concentrations in healthy pediatric surgical outpatients. Tissue antigens, doi: 10.1111/j.1399-0039.2012.01938.x.
Peltola, T., Marttinen, P., Jula, A., Salomaa, V., Perola, M. and Vehtari, A. (2012). Bayesian variable selection in searching for additive and dominant effects in genome-wide data. PLoS ONE, 7(1): e29115. doi:10.1371/journal.pone.0029115.
Marttinen, P., Hanage, W.P., Nicholas, J.C., Connor, T.C., Harris, S.R., Bentley, S.D. and Corander, J. (2012). Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Research, 40(1): e6. doi: 10.1093/nar/gkr928.
Sirén, J., Marttinen, P. and Corander, J. (2010). Reconstructing population histories from single-nucleotide polymorphism data. Molecular Biology and Evolution, 28(1):673-683.
Marttinen, P. and Corander, J. (2010). Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. BMC Bioinformatics, 11:443.
Törönen, P., Ojala, P.J., Marttinen, P. and Holm, L. (2009). Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinformatics, 10:307.
Marttinen, P., Myllykangas, S. and Corander, J. (2009). Bayesian clustering and feature selection for cancer tissue samples. BMC Bioinformatics, 10:90.
Marttinen, P. and Corander, J. (2009). Bayesian learning of graphical vector autoregressions with unequal lag-lengths. Machine Learning, 75:217-243.
Marttinen, P., Tang, J., De Baets, B., Dawyndt, P. and Corander, J. (2009). Bayesian clustering of fuzzy feature vectors using a quasi-likelihood approach. IEEE Transactions on Pattern Analysis and Machine Intelligence, 31:74-85.
Corander, J., Marttinen, P., Sirén, J. and Tang, J. (2008). Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics, 9:539.
Marttinen, P., Baldwin, A., Hanage, W.P., Dowson, C., Mahenthiralingam, E. and Corander, J. (2008). Bayesian modeling of recombination events in bacterial populations. BMC Bioinformatics, 9:421.
Marttinen, P., Corander, J., Törönen, P. and Holm, L. (2006). Bayesian search of functionally divergent protein subgroups and their function specific residues. Bioinformatics, 22:2466-2474.
Corander, J. and Marttinen, P. (2006). Bayesian identification of admixture events using multi-locus molecular markers. Molecular Ecology, 15:2833-2843.
Corander, J., Marttinen, P. and Mäntyniemi, S. (2006). Bayesian identification of stock mixtures from molecular marker data. Fishery Bulletin, 104:550-558.
Corander, J. and Marttinen, P. (2006). Bayesian model learning based on predictive entropy. Journal of Logic, Language and Information, 15:5-20.
Corander, J., Waldmann, P., Marttinen, P. and Sillanpää, M.J. (2004). BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics, 20:2363-2369.
Sundin, I.*, Peltola, T.*, Micallef, L., Afrabandpey, H., Soare, M., Majumder, M.M., Daee, P., He, C., Serim, B., Havulinna, A., Heckman, C., Jacucci, G., Marttinen, P., and Kaski, S. (2018). Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge. Proceedings of the 26th Conference on Intelligent Systems for Molecular Biology (ISMB 2018), Accepted for publication. (*equal contribution)
Micallef, L.*, Sundin, I.*, Marttinen, P.*, Ammad-ud-din. M., Peltola, T., Soare, M., Jacucci, G., and Kaski, S. (2017). Interactive Elicitation of Knowledge on Feature Relevance Improves Predictions in Small Data Sets. Proceedings of the 22nd International Conference on Intelligent User Interfaces (IUI '17), accepted for publication. (*equal contribution)
Marttinen, P. (2008). Discovering hidden structures in molecular data using a Bayesian partition model approach. Dissertation for the degree of Doctor of Philosophy, University of Helsinki, https://oa.doria.fi/handle/10024/42023
Marttinen, P. (2004). Populaatioiden geneettisen rakenteen bayesläinen estimointi (Bayesian estimation of the genetic structure of populations). Master's thesis, University of Helsinki.
I have authored/co-authored the following software:
Spring 2018: CS-E4820 Machine Learning: Advanced Probabilistic Methods
Fall 2017: CS-E5860 Computational Genomics
Spring 2017: CS-E5860 Computational Genomics
Spring 2017: CS-E4820 Machine Learning: Advanced Probabilistic Methods
Spring 2016: CS-E4820 Machine Learning: Advanced Probabilistic Methods
Spring 2015: Information Visualization
Spring 2015: T-61.5140 Machine Learning: Advanced Probabilistic Methods
Fall 2011: S-114.2601 Introduction to Bayesian Modeling
Fall 2010: S-114.2601 Introduction to Bayesian Modeling
Spring 2010: S-114.4610 Special Course in Bayesian Modeling (Bayesian Networks)