Pekka Marttinen

Postdoctoral Researcher, Assistant Professor, Academy Research Fellow

Research outputs

  1. 2019
  2. Accepted/In press

    Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium.

    Arredondo-Alonso, S., Top, J., McNally, A., Puranen, S., Pesonen, M., Pensar, J., Marttinen, P., Braat, J., Rogers, M., van Schaik, W. & 4 others, Kaski, S., Willems, R. J. L., Corander, J. & Schürch, A., 23 Dec 2019, (Accepted/In press) In : MBIO.

    Research output: Contribution to journalArticle

  3. Published
  4. Published

    Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

    AstraZeneca-Sanger Drug Combination DREAM Consortium, Kaski, S. & Marttinen, P., 17 Jun 2019, In : Nature Communications. 10, 1, p. 1-17 17 p., 2674.

    Research output: Contribution to journalArticle

  5. Published

    Efficient acquisition rules for model-based approximate Bayesian computation

    Järvenpää, M., Gutmann, M. U., Pleska, A., Vehtari, A. & Marttinen, P., Jun 2019, In : Bayesian Analysis. 14, 2, p. 595-622 28 p.

    Research output: Contribution to journalArticle

  6. Published

    International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

    Global Pneumococcal Sequencing, May 2019, In : Ebiomedicine. 43, p. 338-346 9 p.

    Research output: Contribution to journalArticle

  7. Published

    A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

    Järvenpää, M., Sater, M. R. A., Lagoudas, G. K., Blainey, P. C., Miller, L. G., McKinnell, J. A., Huang, S. S., Grad, Y. H. & Marttinen, P., 1 Apr 2019, In : PLoS computational biology. 15, 4, p. 1-25 e1006534.

    Research output: Contribution to journalArticle

  8. E-pub ahead of print

    Predicting utilization of healthcare services from individual disease trajectories using RNNs with multi-headed attention

    Kumar, Y., Salo, H., Nieminen, T., Vepsäläinen, K., Kulathinal, S. & Marttinen, P., 2019, Machine Learning for Health (ML4H) at NeurIPS 2019. (Conference on Neural Information Processing Systems).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  9. 2018
  10. Published
  11. Published

    A Bayesian model of acquisition and clearance of bacterial colonization

    Järvenpää, M., Sater, M., Lagoudas, G., Blainey, P. C., Miller, L., McKinnell, J., Huang, S., Grad, Y. & Marttinen, P., Dec 2018

    Research output: Other contributionScientificpeer-review

  12. Published

    ELFI: Engine for likelihood-free inference

    Lintusaari, J., Vuollekoski, H., Kangasrääsiö, A., Skytén, K., Järvenpää, M., Marttinen, P., Gutmann, M. U., Vehtari, A., Corander, J. & Kaski, S., 1 Aug 2018, In : Journal of Machine Learning Research. 19, p. 1-7 7 p.

    Research output: Contribution to journalArticle

  13. Published

    Bacmeta: Simulator for genomic evolution in bacterial metapopulations

    Sipola, A., Marttinen, P. & Corander, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. 2308-2310 3 p.

    Research output: Contribution to journalArticle

  14. Published
  15. 2017
  16. Published

    Efficient acquisition rules for model-based approximate Bayesian computation

    Järvenpää, M., Gutmann, M., Pleska, A., Vehtari, A. & Marttinen, P., Dec 2017

    Research output: Other contributionScientificpeer-review

  17. Published
  18. Published

    Speciation trajectories in recombining bacterial species

    Marttinen, P. & Hanage, W. P., 3 Jul 2017, In : PLoS computational biology. 13, 7, p. 1-15 15 p., e1005640.

    Research output: Contribution to journalArticle

  19. Published

    Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

    David, S., Sánchez-Busó, L., Harris, S. R., Marttinen, P., Rusniok, C., Buchrieser, C., Harrison, T. G. & Parkhill, J., 1 Jun 2017, In : PLoS Genetics. 13, 6, p. 1-21 e1006855.

    Research output: Contribution to journalArticle

  20. Published

    Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations

    Mostowy, R., Croucher, N. J., Andam, C. P., Corander, J., Hanage, W. P. & Marttinen, P., 1 May 2017, In : MOLECULAR BIOLOGY AND EVOLUTION. 34, 5, p. 1167-1182 16 p.

    Research output: Contribution to journalArticle

  21. Published

    Interactive Elicitation of Knowledge on Feature Relevance Improves Predictions in Small Data Sets

    Micallef, L., Sundin, I., Marttinen, P., Ammad-Ud-Din, M., Peltola, T., Soare, M., Jacucci, G. & Kaski, S., 7 Mar 2017, IUI 2017 - Proceedings of the 22nd International Conference on Intelligent User Interfaces. p. 547-552 6 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  22. Published

    Cluster analysis to estimate the risk of preeclampsia in the high-risk Prediction and Prevention of Preeclampsia and Intrauterine Growth Restriction (PREDO) study

    Villa, P. M., Marttinen, P., Gillberg, J., Inkeri Lokki, A., Majander, K., Ordén, M. R., Taipale, P., Pesonen, A., Räikkönen, K., Hämäläinen, E. & 2 others, Kajantie, E. & Laivuori, H., 1 Mar 2017, In : PloS one. 12, 3, p. 1-14 e0174399.

    Research output: Contribution to journalArticle

  23. Published

    Bacmeta: simulation for genomic evolution in bacterial metapopulations

    Sipola, A., Marttinen, P. & Corander, J., 2017, In : bioRxiv.

    Research output: Contribution to journalArticle

  24. Published

    biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements

    Pirinen, M., Benner, C., Marttinen, P., Järvelin, M-R., Rivas, M. A. & Ripatti, S., 2017, In : Bioinformatics. 33, 15, p. 2405-2407 3 p.

    Research output: Contribution to journalArticle

  25. 2016
  26. Published

    Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

    Harms, K., Lunnan, A., Hülter, N., Mourier, T., Vinner, L., Andam, C. P., Marttinen, P., Fridholm, H., Hansen, A. J., Hanage, W. P. & 3 others, Nielsen, K. M., Willerslev, E. & Johnsen, P. J., 27 Dec 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 52, p. 15066-15071 6 p.

    Research output: Contribution to journalArticle

  27. Published

    Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

    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. & 4 others, Honkela, A., Parkhill, J., Bentley, S. D. & Corander, J., 16 Sep 2016, In : Nature Communications. 7, 8 p., 12797.

    Research output: Contribution to journalArticle

  28. Published

    Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

    Sieberts, S. K., Zhu, F., García-García, J., Stahl, E., Pratap, A., Pandey, G., Pappas, D., Aguilar, D., Anton, B., Bonet, J. & 83 others, Eksi, R., Fornés, O., Guney, E., Li, H., Marín, M. A., Panwar, B., Planas-Iglesias, J., Poglayen, D., Cui, J., Falcao, A. O., Suver, C., Hoff, B., Balagurusamy, V. S. K., Dillenberger, D., Neto, E. C., 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. A., Kramer, E. R., Marttinen, P., Mezlini, A. M., 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. E., 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. P., Gerlag, D., Huizinga, T. W. J., Kurreeman, F., Allaart, C. F., Louis Bridges, S., Criswell, L., Moreland, L., Klareskog, L., Saevarsdottir, S., Padyukov, L., Gregersen, P. K., Friend, S., Plenge, R., Stolovitzky, G., Oliva, B., Guan, Y. & Mangravite, L. M., 23 Aug 2016, In : Nature Communications. 7, p. 1-9 12460.

    Research output: Contribution to journalArticle

  29. Published

    metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis

    Cichonska, A., Rousu, J., Marttinen, P., Kangas, A. J., Soininen, P., Lehtimaki, T., Raitakari, O., Jarvelin, M-R., Salomaa, V., Ala-Korpela, M. & 2 others, Ripatti, S. & Pirinen, M., 1 Jul 2016, In : Bioinformatics. 32, 13, p. 1981-1989 9 p.

    Research output: Contribution to journalArticle

  30. Published

    Multiple output regression with latent noise

    Gillberg, L., Marttinen, P., Pirinen, M., Kangas, A. J., Soininen, P., Ali, M., Havulinna, A. S., Järvelin, M. R., Ala-Korpela, M. & Kaski, S., 1 Jun 2016, In : Journal of Machine Learning Research. 17, p. 1-35 35 p.

    Research output: Contribution to journalArticle

  31. Published

    The impact of host metapopulation structure on the population genetics of colonizing bacteria

    Numminen, E., Gutmann, M., Shubin, M., Marttinen, P., Méric, G., van Schaik, W., Coque, T. M., Baquero, F., Willems, R. J. L., Sheppard, S. K. & 3 others, Feil, E. J., Hanage, W. P. & Corander, J., 7 May 2016, In : Journal of Theoretical Biology. 396, p. 53-62 10 p.

    Research output: Contribution to journalArticle

  32. Published
  33. 2015
  34. Published

    Recombination produces coherent bacterial species clusters in both core and accessory genomes

    Marttinen, P., Croucher, N. J., Gutmann, M. U., Corander, J. & Hanage, W. P., 2015, In : Microbial Genomics. 1

    Research output: Contribution to journalArticle

  35. 2014
  36. Published

    Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression

    Marttinen, P., Pirinen, M., Sarin, A-P., Gillberg, J., Kettunen, J., Surakka, I., Kangas, A. J., Soininen, P., "O'Reilly", P., Kaakinen, M. & 8 others, Kähönen, M., Lehtimäki, T., Ala-Korpela, M., Raitakari, O. T., Salomaa, V., Järvelin, M-R., Ripatti, S. & Kaski, S., 2014, In : Bioinformatics. 30, 14, p. 2026-2034

    Research output: Contribution to journalArticle

  37. Published

    Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

    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. & 3 others, Turner, P., Bentley, S. D. & Parkhill, J., 2014, In : PLoS Genetics. 10, 8, p. 1-11 e1004547.

    Research output: Contribution to journalArticle

  38. Published

    Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

    Sheppard, S. K., Cheng, L., Méric, G., Haan, C., Llarena, A-K., Marttinen, P., Vidal, A., Ridley, A., Clifton-Hadley, F. & Connor, T. R., 2014, In : MOLECULAR ECOLOGY. 23, 10, p. 2442-2451

    Research output: Contribution to journalArticle

  39. Published

    Dense genomic sampling identifies highways of pneumococcal recombination

    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. & 8 others, Salter, S. J., Harris, D., Nosten, F., Goldblatt, D., Corander, J., Parkhill, J., Turner, P. & Bentley, S. D., 2014, In : NATURE GENETICS. 46, 3, p. 305-309

    Research output: Contribution to journalArticle

  40. Published

    Plant Sterol Feeding Induces Tumor Formation and Alters Sterol Metabolism in the Intestine of Apc(Min) Mice

    Marttinen, M., Pajari, A-M., Paivarinta, E., Storvik, M., Marttinen, P., Nurmi, T., Niku, M., Piironen, V. & Mutanen, M., 2014, In : NUTRITION AND CANCER: AN INTERNATIONAL JOURNAL. 66, 2, p. 259-269

    Research output: Contribution to journalArticle

  41. Published

    Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

    Kashtan, N., Roggensack, S. E., Rodrigue, S., Thompson, J. W., Biller, S. J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R. R. & Stocker, R., 2014, In : Science. 344, 6182, p. 416-420

    Research output: Contribution to journalArticle

  42. 2013
  43. Published

    Genome-wide association studies with high-dimensional phenotypes

    Marttinen, P., Gillberg, L., Havulinna, A., Corander, J. & Kaski, S., 2013, In : STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY. 12, 4, p. 413-431

    Research output: Contribution to journalArticle

  44. 2012
  45. Published

    Bayesian Variable Selection in Searching for Additive and Dominant Effects in Genome-Wide Data

    Peltola, T., Marttinen, P., Jula, A., Salomaa, V., Perola, M. & Vehtari, A., 2012, In : PloS one. 7, 1, p. 1-11 e29115.

    Research output: Contribution to journalArticle

  46. Published
  47. Published

    Phylogeographic variation in recombination rates within a global clone of Methicillin-Resistant Staphylococcus aureus (MRSA)

    Castillo-Ramirez, S., Corander, J., Marttinen, P., Aldeljawi, M., Hanage, W. P., Westh, H., Boye, K., Gulay, Z., Bentley, S. D., Parkhill, J. & 2 others, Holden, M. T. & Feil, E. J., 2012, In : GENOME BIOLOGY. 13, 12, p. pp. R126

    Research output: Contribution to journalArticle

  48. Published

    Serum and CSF soluble CD26 and CD30 concentrations in healthy pediatric surgical outpatients

    Delezuch, W., Marttinen, P., Kokki, H., Heikkinen, M., Vanamo, K., Pulkki, K. & Matinlauri, I., 2012, In : TISSUE ANTIGENS. 80, 4, p. 368-375

    Research output: Contribution to journalArticle

  49. 2011
  50. Published

    Detection of recombination events in bacterial genomes from large population samples

    Marttinen, P., Hanage, W. P., Croucher, N. J., Connor, T. R., Harris, S. R., Bentley, S. D. & Corander, J., 2011, In : Nucleic Acids Research. 40, 1, p. e6

    Research output: Contribution to journalArticle

  51. 2010
  52. Published

    Efficient Bayesian approach for multilocus association mapping including gene-gene interactions

    Marttinen, P. & Corander, J., 2010, In : BMC Bioinformatics. 11, p. 443

    Research output: Contribution to journalArticle

  53. Published

    Reconstructing Population Histories from Single-Nucleotide Polymorphism Data

    Sirén, J., Marttinen, P. & Corander, J., 2010, In : MOLECULAR BIOLOGY AND EVOLUTION. 28, 1, p. 673-683

    Research output: Contribution to journalArticle

ID: 87245