Patrik Koskinen


Description of research and teaching

I completed my M.Sc. in bioinformatics/computer sciences at the University of Turku in early 2008. I joined the prof. Liisa Holm's bioinformatics group in 2007 where I also made my master’s thesis. I graduated from the ILS doctoral school in 2014 as a PhD while I worked in both prof. Liisa Holm's and prof. Ilkka Hanski's research groups. I joined the MRG in 2010 and I worked with the Glanville fritillary butterfly genome and genetics until the end of 2012. Nowadays I work at the Saimaa Ringed Seal genome project, where my resposibilites are bioinformatics analysis and other postdoc tasks.

My research is related to genomic annotation in quite wide range. Before the Melitae Cinxia and Pusa Hispida Saimensis genomes I have worked in multiple bacterial genome projects. I have experience from all stages of genome projects. My special interest is in functional annotation, which was also the topic of my PhD thesis. 


During the PhD studies I have taught at the following courses: 

52929 Lab course in Bioinformatics 5cr.

52931 Practical Course in Protein Analysis 5cr.


Curriculum Vitae

Latest publications

  1. BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing

    Somervuo, P., Koskinen, P., Mei, P., Holm, L., Auvinen, P. & Paulin, L., 5 Jul 2018, In : BMC Bioinformatics. 19, 257, 6 p., 257.

    Research output: Contribution to journalArticleScientificpeer-review

  2. Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1

    Niemi, O., Laine, P., Koskinen, P., Pasanen, M., Pennanen, V., Harjunpaa, H., Nykyri, J., Holm, L., Paulin, L., Auvinen, P., Palva, E. T. & Pirhonen, M., 20 Dec 2017, In : Standards in Genomic Sciences. 12, 8 p., 87.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

    Salojärvi, J., Smolander, O-P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., Lamminmäki, A., Immanen, J., Lan, T., Tanskanen, J., Rastas, P., Amiryousefi, A., Jayaprakash, B., Kammonen, J. I., Hagqvist, R., Eswaran, G., Ahonen, V. H., Serra, J. A., Asiegbu, F. O., Barajas-Lopez, J. D. D. & 65 othersBlande, D., Blokhina, O., Blomster, T., Broholm, S., Brosche, M., Cui, F., Dardick, C., Ehonen, S. E., Elomaa, P., Escamez, S., Fagerstedt, K. V., Fujii, H., Gauthier, A., Gollan, P. J., Halimaa, P., Heino, P. I., Himanen, K., Hollender, C., Kangasjarvi, S., Kauppinen, L., Kelleher, C. T., Kontunen-Soppela, S., Koskinen, J. P., Kovalchuk, A., Karenlampi, S. O., Kärkönen, A. K., Lim, K-J., Leppälä, J., Macpherson, L., Mikola, J., Mouhu, K., Mähönen, A. P., Niinemets, U., Oksanen, E., Overmyer, K., Palva, E. T., Pazouki, L., Pennanen, V., Puhakainen, T., Poczai, P., Possen, B. J. H. M., Punkkinen, M., Rahikainen, M. M., Rousi, M., Ruonala, R., van der Schoot, C., Shapiguzov, A., Sierla, M., Sipilä, T. P., Sutela, S., Teeri, T. H., Tervahauta, A. I., Vaattovaara, A., Vahala, J., Vetchinnikova, L., Welling, A., Wrzaczek, M., Xu, E., Paulin, L. G., Schulman, A. H., Lascoux, M., Albert, V. A., Auvinen, P., Helariutta, Y. & Kangasjarvi, J., 8 May 2017, In : Nature Genetics. 49, 6, p. 904-912 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

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