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Publications by the members of SMACK group |
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2010 Sirén J, Marttinen P and Corander J. (2010) Reconstructing population histories from single-nucleotide polymorphism data. Molecular Biology and Evolution, in press, doi: 10.1093/molbev/msq236. Marttinen P and Corander J. (2010) Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. BMC Bioinformatics, 11:443. de Haan CPA, Kivistö R, Hakkinen M, Corander J and Hänninen M-L. Multilocus sequence types of Finnish bovine Campylobacter jejuni isolates and their attribution to human infections. BMC Microbiology 2010, 10:200. Johansson A, Santtila P, Corander J, Alanko K, Jern P, von der Pahlen B and Sandnabba NK. Genetic effects on anger control and their interaction with alcohol intoxication: A self-report study. Biological Psychology, in press. Helen E Jenkins, R. Bruce Aylward, Alex Gasasira, Christl A Donnelly, Michael Mwanza, Jukka Corander, Sandra Garnier, Claire Chauvin, Emmanuel Abanida, Muhammad Ali Pate, Festus Adu, Marycelin Baba, Nicholas C Grassly (2010). Implications of a circulating vaccine-derived poliovirus (cVDPV) in Nigeria for polio eradication. New England Journal of Medicine, 362, 2360-2369. Moroni R, Blomstedt P, Wilhelm L, Reinikainen T, Sippola E, Corander J (2010). Statistical modelling of measurement errors in gas chromatographic analyses of blood alcohol content. Forensic Science International, 202, 71-74. Corander, J., Gyllenberg, M. and Koski, T. (2010). Learning genetic population structures using minimization of stochastic complexity. Entropy, 12, 1102-1124. doi:10.3390/e12051102. Mark A. Beaumont, Rasmus Nielsen, Christian Robert, Jody Hey, Oscar Gaggiotti, Lacey Knowles, Arnaud Estoup, Mahesh Panchal, Jukka Corander, Mike Hickerson, Scott A. Sisson, Nelson Fagundes, Lounès Chikhi, Peter Beerli, Renaud Vitalis, Jean-Marie Cornuet, John Huelsenbeck, Matthieu Foll, Ziheng Yang, Francois Rousset, David Balding, Laurent Excoffier. (2010). In defense of model-based inference in phylogeography. Molecular Ecology, 19, 436-446. 2009 Hanage WP, Fraser C, Tang J, Connor T, Corander J. (2009). Hyper-recombination, diversity and antibiotic resistance in the pneumococcus. Science, 324, 1454-1457. Tang J, Hanage WP, Fraser C, Corander J. (2009). Identifying currents in the gene pool for bacterial populations using an integrative approach. PLoS Computational Biology, 5(8): e1000455. Corander J, Ekdahl M, Koski T. (2009). Bayesian unsupervised learning of DNA regulatory binding regions. Advances in Artificial Intelligence. DOI:10.1155/2009/219743 Pitkäniemi J, Varvio S-L, Corander J, Lehti N, Partanen J, Tuomilehto-Wolf E, Tuomilehto J, Thomas A, Arjas E. (2009). Full likelihood analysis of genetic risk with variable age at onset disease - combining population-based registry data and demographic information. PLoS ONE, 4(8): e6836. Marttinen P Tang J, De Baets B, Dawyndt P, 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. Marttinen P, Corander J (2009). Bayesian learning of graphical vector autoregressions with unequal lag-lengths. Machine Learning, 75, 217-243. Corander, J., Gyllenberg, M. and Koski, T. (2009). Bayesian unsupervised classification framework based on stochastic partitions of data and a parallel search strategy. Advances in Data Analysis and Classification, 3, 3-24. Marttinen P, Myllykangas S, Corander J (2009). Bayesian clustering and feature selection for cancer tissue samples. BMC Bioinformatics 10:90. Krogius-Kurikka, L., Kassinen, A., Paulin, L., Corander, J., Mäkivuokko, H., Tuimala, J., and Palva, A. (2009). Sequence Analysis of Percent G+C Fraction Libraries of Human Faecal. Bacterial DNA Reveals a High Number of Actinobacteria. BMC Microbiology 9:68. 2008 Kohonen J, Talikota S, Corander J, Auvinen P, Arjas E (2008). A naive Bayes classifier for protein function prediction. In Silico Biology, 9, 0003. Corander, J., Sirén, J. and Arjas, E. (2008). Bayesian spatial modelling of genetic population structure. Computational Statistics, 23, 111-129. Orsini L, Corander J, Alasentie A, Hanski, I (2008) Genetic spatial structure in a butterfly metapopulation correlates better with past than present demographic structure. Molecular Ecology, 17, 2629-2642. Smýkal P, Hýbl M, Corander J, Jarkovský J, Flavell AJ, Griga M (2008) Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theoretical and Applied Genetics, 117, 413-424. Marttinen P, Baldwin A, Hanage WP, Dowson C, Mahenthiralingam E, Corander J (2008). Bayesian modeling of recombination events in bacterial populations. BMC Bioinformatics 9:421. Corander J, Marttinen P, Sirén J, Tang J (2008). Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics, 9:539. Corander, J., Ekdahl, M. and Koski, T. (2008). Parallell interacting MCMC for learning of topologies of graphical models. Data Mining and Knowledge Discovery, 17, 431-456. Sistonen, J.M., Sajantila, A.J., Lao, O., Corander, J., Barbujani, G. and Fuselli, S. (2007). CYP2D6 worldwide genetic variation shows high frequency of altered activity variants and no continental structure. Pharmacogenetics and Genomics, 17, 93-101. Corander, J., Gyllenberg, M. and Koski, T. (2007). Random Partition models and Exchangeability for Bayesian Identification of Population Structure. Bulletin of Mathematical Biology, 69, 797-815. Corander, J. and Tang, J. (2007). Bayesian analysis of population structure based on linked molecular information. Mathematical Biosciences, 205, 19-31. Mäki-Petäys, H., Corander, J., Aalto, J., Liukkonen, T., Helle, P. and Orell, M. (2007). No genetic evidence of sex-biased effective dispersal in a lekking bird, the capercaillie (tetrao urogallus). Journal of Evolutionary Biology, 20, 865-873. A Kassinen, L Krogius-Kurikka, H Mäkivuokko, L Paulin, T Rinttilä, J Corander, E Malinen, J Apajalahti and A Palva. (2007). The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology, 133, 24-33. Tang, J., Tao J., Urakawa, H. and Corander, J. (2007). T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data. Statistical Applications in Genetics and Molecular Biology, 6. 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, Marttinen, P. (2006). Bayesian identification of admixture events using multi-locus molecular markers. Molecular Ecology, 15, 2833-2843. Corander, J., Gyllenberg, M. and Koski, T. (2006). Bayesian model learning based on a parallel MCMC strategy. Statistics and Computing, 16, 355-362. Corander, J. and Villani, M. (2006). A Bayesian Approach to Modelling Graphical Vector Autoregressions, Journal of Time Series Analysis, 27, 141-156. Corander, J. and Marttinen, P. (2006). Bayesian model learning based on predictive entropy. Journal of Logic, Language and Information, 15, 5-20. Corander, J. (2006). Is There a Real Bayesian Revolution in Pattern Recognition for Bioinformatics?, Current Bioinformatics, 1, 161-165. Corander, J., Marttinen, P. and Mäntyniemi, S. (2006). Bayesian identification of stock mixtures from molecular marker data. Fishery Bulletin, 104, 550-558. Mäki-Petäys, H., Zakharov, A., Viljakainen, L, Corander, J. and Pamilo, P. (2005). Genetic changes associated to declining populations of formica ants in fragmented forest landscape. Molecular Ecology, 14, 733-742. Corander, J. and Villani, M. (2004). Bayesian assessment of dimensionality in multivariate reduced rank regression. Statistica Neerlandica, 58, 255-270. 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. Seppä, P., Gyllenstrand, N., Corander, J. and Pamilo P. (2004). Coexistence of the social types: Genetic population structure in the ant, formica exsecta. Evolution, 58, 2462-2471. Corander, J. (2003). Bayesian graphical model determination using decision theory. Journal of Multivariate Analysis. 85, 253-266. Corander, J. (2003). Labeled graphical models. Scandinavian Journal of Statistics. 30, 493-508. Corander, J. Waldmann, P. and Sillanpää, M.J. (2003). Bayesian analysis of genetic differentiation between populations. Genetics, 163, 367-374. Corander, J. and Sillanpää, M. J. (2002). A unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. Journal of Theoretical Biology, 218, 435-446. Sillanpää, M. J. and Corander, J. (2002). Model choice in gene mapping: What and why, Trends in Genetics, 18, 301-307. |