| Bibliography of self-organizing map (SOM) papers: 1998–2001 addendum M Oja, S Kaski, T Kohonen Neural computing surveys 3 (1), 1-156, 2003 | 446 | 2003 |
| Trustworthiness and metrics in visualizing similarity of gene expression S Kaski, J Nikkilä, M Oja, J Venna, P Törönen, E Castrén BMC bioinformatics 4, 1-13, 2003 | 219 | 2003 |
| Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates M Häkkinen, M Arvas, M Oja, N Aro, M Penttilä, M Saloheimo, TM Pakula Microbial cell factories 11, 1-26, 2012 | 190 | 2012 |
| Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species E Pitkänen, P Jouhten, J Hou, MF Syed, P Blomberg, J Kludas, M Oja, ... PLoS computational biology 10 (2), e1003465, 2014 | 110 | 2014 |
| Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties M Vitikainen, M Arvas, T Pakula, M Oja, M Penttilä, M Saloheimo BMC genomics 11, 1-16, 2010 | 104 | 2010 |
| A unified multitask architecture for predicting local protein properties Y Qi, M Oja, J Weston, WS Noble PloS one 7 (3), e32235, 2012 | 82 | 2012 |
| Ploidy influences the functional attributes of de novo lager yeast hybrids K Krogerus, M Arvas, M De Chiara, F Magalhães, L Mattinen, M Oja, ... Applied microbiology and biotechnology 100, 7203-7222, 2016 | 80 | 2016 |
| Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data F Benachenhou, P Jern, M Oja, G Sperber, V Blikstad, P Somervuo, ... PloS one 4 (4), e5179, 2009 | 55 | 2009 |
| Methods for estimating human endogenous retrovirus activities from EST databases M Oja, J Peltonen, J Blomberg, S Kaski BMC bioinformatics 8, 1-10, 2007 | 45 | 2007 |
| Characterization and mutagenesis of two novel iron–sulphur cluster pentonate dehydratases M Andberg, N Aro-Kärkkäinen, P Carlson, M Oja, S Bozonnet, M Toivari, ... Applied microbiology and biotechnology 100, 7549-7563, 2016 | 42 | 2016 |
| Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups M Oja, GO Sperber, J Blomberg, S Kaski International Journal of Neural Systems 15 (03), 163-179, 2005 | 41 | 2005 |
| Identification of novel isoprene synthases through genome mining and expression in Escherichia coli M Ilmén, M Oja, A Huuskonen, S Lee, L Ruohonen, S Jung Metabolic Engineering 31, 153-162, 2015 | 38 | 2015 |
| Exploratory clustering of gene expression profiles of mutated yeast strains M Oja, J Nikkilä, P Törönen, G Wong, E Castrén, S Kaski Computational and Statistical Approaches to Genomics, 61-74, 2006 | 28 | 2006 |
| Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures S Alff-Tuomala, L Salusjärvi, D Barth, M Oja, M Penttilä, JP Pitkänen, ... Applied microbiology and biotechnology 100 (2), 969-985, 2016 | 26 | 2016 |
| A novel aldose-aldose oxidoreductase for co-production of D-xylonate and xylitol from D-xylose with Saccharomyces cerevisiae MG Wiebe, Y Nygård, M Oja, M Andberg, L Ruohonen, A Koivula, ... Applied microbiology and biotechnology 99, 9439-9447, 2015 | 25 | 2015 |
| Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction S Castillo, D Barth, M Arvas, TM Pakula, E Pitkänen, P Blomberg, ... Biotechnology for biofuels 9, 1-20, 2016 | 22 | 2016 |
| Clustering of human endogenous retrovirus sequences with median self-organizing map M Oja, P Somervuo, S Kaski, T Kohonen Proc. WSOM 3, 2003 | 21 | 2003 |
| Comparison of intracellular and secretion-based strategies for production of human α-galactosidase A in the filamentous fungus Trichoderma reesei W Smith, J Jäntti, M Oja, M Saloheimo BMC biotechnology 14, 1-12, 2014 | 18 | 2014 |
| L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces … N Aro-Kärkkäinen, M Toivari, H Maaheimo, M Ylilauri, OT Pentikäinen, ... Applied microbiology and biotechnology 98, 9653-9665, 2014 | 15 | 2014 |
| Machine learning of protein interactions in fungal secretory pathways J Kludas, M Arvas, S Castillo, T Pakula, M Oja, C Brouard, J Jäntti, ... PloS one 11 (7), e0159302, 2016 | 12 | 2016 |