2012
J Nykyri, O Niemi, P Koskinen, J Nokso-Koivisto, M Pasanen, M Broberg, I ... Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193 PLoS Pathogens 8 (11), e1003013 1 2012

JP Koskinen, P Laine, O Niemi, J Nykyri, H Harjunpää, P Auvinen, L Paulin, M ... Genome Sequence of Pectobacterium sp. Strain SCC3193 Journal of bacteriology 194 (21), 6004-6004 2012

JP Koskinen, L Holm SANS: high-throughput retrieval of protein sequences allowing 50% mismatches Bioinformatics 28 (18), i438-i443 1 2012

J Kantelinen, M Kansikas, S Candelin, H Hampel, B Smith, L Holm, R Kariola ... Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients Human Mutation 2012

I Plyusnin, L Holm Comprehensive comparison of graph based multiple protein sequence alignment strategies BMC bioinformatics 13 (1), 64 3 2012

A Katz, AN Freiberg, V Backström, L Holm, A Vaheri, R Flick, A Plyusnin Mutational analysis of positively charged amino acid residues of Uukuniemi phlebovirus nucleocapsid protein Virus Research

Tollenaere, CMJ, Susi, H, Nokso-Koivisto, JP, Koskinen, P, Tack, AJM, Auvinen, P, Paulin, L, Frilander, M, Lehtonen, RJ, Laine, A-L 2012, 'SNP Design from 454 Sequencing of Podosphaera plantaginis Transcriptome Reveals a Genetically Diverse Pathogen Metapopulation with High Levels of Mixed-Genotype Infection' PLoS One, vol 7, no. 12, pp. e52492.

2011
Astikainen K, Holm L, Pitkänen E, Szedmak S, Rousu J (2011) Structured output prediction of novel enzyme function with reaction kernels. Biomedical Engineering Systems and Technologies: Communications in Computer and Information Science, 127. Springer Verlag
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Matthieu Louis. A theoretical model for the regulation of Sex-lethal gene, Ph.D. thesis, University of Cambridge.
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