Publications

Skwark, M. J. Croucher, N. J., Puranen, S., Chewapreecha, C., Pesonen, M., Xu, Y. Y.,  Turner, P. Harris, S. R., Beres, S. B., Musser, J. M., Parkhill, J., Bentley, S. D., Aurell, E. and Corander, J. (2017). Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis, PLoS Genetics. 13, 2, 24

Vanhatalo, J., Hosack, G. R., and Sweatman, H. (2017). Spatio-temporal modelling of crown-of-thorns starfish outbreaks on the Great Barrier Reef to inform control strategies. Journal of Applied Ecology, 54:188-197.

Gutmann, M. U. and Corander, J. (2016). Bayesian Optimization for Likelihood-Free Inference of Simulator-Based Statistical Models, Journal of Machine Learning Research, 17(125):1−47.

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

Benner C., Spencer C. C. A., Havulinna A. S., Salomaa V., Ripatti S., Pirinen M. (2016). FINEMAP: Efficient variable selection using summary data from genome-wide association studies. Bioinformatics, 32 (10): 1493-1501

Sankar, A., Malone, B. M., Bayliss, S. C., Pascoe, B., Méric, G., Hitchings, M. D., Sheppard, S. K., Feil, E. J., Corander, J. I. & Honkela, A. J. (2016). Bayesian identification of bacterial strains from sequencing data, Microbial Genomics, 2, 8, 9 p.

Rivas M. A., Pirinen M, Conrad D. F., Lek M., et al. (2015). Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348: 666-669.

Honkela, A., Peltonen, J., Topa, H., Charapitsa, I., Matarese, F., Grote, K., Stunnenberg, H. G., Reid, G., Lawrence, N. D. & Rattray, M. (2015). Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays. Proceedings of the National Academy of Sciences of the United States of America, 112(42): 13115-13120.

Vanhatalo, J., Riihimäki, J., Hartikainen, J., Jylänki, P. Tolvanen, V. and Aki Vehtari (2013). GPstuff: Bayesian Modeling with Gaussian Processes. Journal of Machine Learning Research, 14:1175-1179.

Glaus, P., Honkela, A. & Rattray, M. (2012). Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics, 28(13), 1721-1728.

 

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