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Merja Oja · SciRah

Researcher profile · Semantic Scholar

Merja Oja

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Merja Oja — researcher profile on SciRah

h-index: 16
Works: 43
Citations: 1,452

Most-cited papers

Bibliography of Self-Organizing Map SOM) Papers: 1998-2001 Addendum
Merja Oja, Samuel Kaski, T. Kohonen
2003403 citations
Semantic Scholar
Trustworthiness and metrics in visualizing similarity of gene expression
Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna +2 more
2003BMC Bioinformatics182 citations Open access
Semantic Scholar
Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates
Mari Häkkinen, Mikko Arvas, Merja Oja, N. Aro +3 more
2012Microbial Cell Factories178 citations Open access
Semantic Scholar
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species
E. Pitkänen, P. Jouhten, Jian Hou, Muhammad Fahad Syed +7 more
2014PLoS Comput. Biol.113 citations Open access
Semantic Scholar
Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties
M. Vitikainen, Mikko Arvas, T. Pakula, Merja Oja +2 more
2010BMC Genomics91 citations Open access
Semantic Scholar
Ploidy influences the functional attributes of de novo lager yeast hybrids
K. Krogerus, Mikko Arvas, M. De Chiara, F. Magalhães +6 more
2016Applied Microbiology and Biotechnology78 citations Open access
Semantic Scholar
A Unified Multitask Architecture for Predicting Local Protein Properties
Yan-Jun Qi, Merja Oja, J. Weston, William Stafford Noble
2012PLoS ONE64 citations Open access
Semantic Scholar
Methods for estimating human endogenous retrovirus activities from EST databases
Merja Oja, Jaakko Peltonen, J. Blomberg, Samuel Kaski
2007BMC Bioinformatics40 citations Open access
Semantic Scholar
Evolutionary Conservation of Orthoretroviral Long Terminal Repeats (LTRs) and ab initio Detection of Single LTRs in Genomic Data
F. Benachenhou, P. Jern, Merja Oja, G. Sperber +4 more
2009PLoS ONE39 citations Open access
Semantic Scholar
Identification of novel isoprene synthases through genome mining and expression in Escherichia coli.
M. Ilmén, Merja Oja, Anne Huuskonen, Sang-Min Lee +2 more
2015Metabolic Engineering36 citations
Semantic Scholar
Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups
Merja Oja, G. Sperber, J. Blomberg, Samuel Kaski
2005International Journal of Neural Systems34 citations
Semantic Scholar
Characterization and mutagenesis of two novel iron–sulphur cluster pentonate dehydratases
M. Andberg, Niina Aro-Kärkkäinen, P. Carlson, Merja Oja +6 more
2016Applied Microbiology and Biotechnology28 citations
Semantic Scholar
Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures
Susanne Alff-Tuomala, Laura Salusjärvi, D. Barth, Merja Oja +4 more
2015Applied Microbiology and Biotechnology27 citations
Semantic Scholar
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction
Sandra Castillo, D. Barth, Mikko Arvas, T. Pakula +7 more
2016Biotechnology for Biofuels24 citations Open access
Semantic Scholar
A novel aldose-aldose oxidoreductase for co-production of D-xylonate and xylitol from D-xylose with Saccharomyces cerevisiae
M. Wiebe, Yvonne Nygård, Merja Oja, M. Andberg +4 more
2015Applied Microbiology and Biotechnology17 citations Open access
Semantic Scholar
l-Arabinose/d-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of l-arabinose to l-arabonate with Saccharomyces cerevisiae
Niina Aro-Kärkkäinen, Mervi Toivari, H. Maaheimo, Mikko Ylilauri +7 more
2014Applied Microbiology and Biotechnology17 citations
Semantic Scholar
Comparison of intracellular and secretion-based strategies for production of human α-galactosidase A in the filamentous fungus Trichoderma reesei
Wesley Smith, J. Jäntti, Merja Oja, M. Saloheimo
2014BMC Biotechnology15 citations Open access
Semantic Scholar
Exploratory Clustering of Gene Expression Profiles of Mutated Yeast Strains
Merja Oja, Janne Nikkilä, P. Törönen, Garry Wong +2 more
200315 citations
Semantic Scholar
Clustering of Human Endogenous Retrovirus Sequences with Median Self-Organizing Map
Merja Oja, P. Somervuo, Samuel Kaski, T. Kohonen
200315 citations
Semantic Scholar
Machine Learning of Protein Interactions in Fungal Secretory Pathways
J. Kludas, Mikko Arvas, Sandra Castillo, T. Pakula +5 more
2016PLoS ONE12 citations Open access
Semantic Scholar
Grouping and visualizing human endogenous retroviruses by bootstrapping median self-organizing maps
Merja Oja, G. Sperber, J. Blomberg, Samuel Kaski
20042004 Symposium on Computational Intelligence in Bioinformatics and Computational Biology7 citations Open access
Semantic Scholar
Transcriptome of Saccharomyces cerevisiae during production of D-xylonate
Dominik Mojzita, Merja Oja, E. Rintala, M. Wiebe +2 more
2014BMC Genomics6 citations Open access
Semantic Scholar
Learning Metrics for Visualizing Gene Functional Similarities
Merja Oja, Janne Nikkilä, P. Törönen, E. Castrén +1 more
20024 citations
Semantic Scholar
Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae
Erno Lindfors, P. Jouhten, Merja Oja, E. Rintala +2 more
2014BMC Systems Biology3 citations Open access
Semantic Scholar
In Silico Expression Profiles of Human Endogenous Retroviruses
Merja Oja
2007Pattern Recognition in Bioinformatics2 citations Open access
Semantic Scholar
Transcriptional and genomic profiling of industrial Trichoderma reesei strains
Susanna Mäkinen, M. Paloheimo, T. Pakula, Mikko Arvas +6 more
20111 citations
Semantic Scholar
Estimation of human endogenous retrovirus activities from expressed sequence databases
Merja Oja, Jaakko Peltonen, Samuel Kaski
20061 citations
Semantic Scholar
Identifying novel enzymes for metabolic engineering using homology based sequence searches
Merja Oja, S. Castillo, Gopal Peddinti
20170 citations Open access
Semantic Scholar
Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures
Susanne Alff-Tuomala, Laura Salusjärvi, D. Barth, Merja Oja +4 more
2015Applied Microbiology and Biotechnology0 citations
Semantic Scholar
Systems biology for studying the physiology of acid producing yeast
Merja Oja, P. Jouhten, E. Rintala, Mervi Toivari +3 more
2012Annual International Conference on Research in Computational Molecular Biology0 citations
Semantic Scholar
Transcriptome and proteome analysis of an antibody Fab fragment producing Trichoderma reesei strain and its parental strain at different cultivation temperatures
T. Pakula, Lise Bernard-Granger, Jaana H Toikkanen, Merja Oja +3 more
20100 citations
Semantic Scholar
Bioinformatics and Neuroinformatics
Samuel Kaski, Janne Nikkilä, Merja Oja, Jaakko Peltonen +8 more
20080 citations
Semantic Scholar
Methods for exploring genomic data sets : application to human endogenous retroviruses
Merja Oja
20070 citations
Semantic Scholar
Methods for estimating human endogenous retrovirus activities from EST databases
Merja Oja, Jaakko Peltonen, J. Blomberg, S. Kaski
20070 citations
Semantic Scholar
METHODS FOR EXPLORING GENOMIC DATA SETS : APPLICATION TO HUMAN ENDOGENOUS RETROVIRUSES
Merja Oja
20070 citations
Semantic Scholar
2 Yeast systems biology
Samuel Kaski, Janne Nikkilä, Merja Oja, L. Lahti +3 more
20060 citations
Semantic Scholar
SELF-ORGANIZING MAP-BASED DISCOVERY AND VISUALIZATION OF HUMAN ENDOGENOUS RETROVIRAL SEQUENCE GROUPS
Merja Oja
20050 citations
Semantic Scholar
Chapter 8 Self-organizing map
T. Kohonen, Samuel Kaski, P. Somervuo, K. Lagus +2 more
20040 citations
Semantic Scholar
Trustworthiness and metrics in visualizing similarity of gene expression
Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna +2 more
20030 citations
Semantic Scholar
Trustworthiness and metrics in visualizing similarity of gene expression
Samuel Kaski, Janne Nikkilä, Merja Oja, Jarkko Venna +2 more
20030 citations
Semantic Scholar
Chapter 1 EXPLORATORY CLUSTERING OF GENEEXPRESSION PROFILES OF MUTATEDYEAST STRAINS
Merja Oja, Janne Nikkil, Onen, GarryWong +1 more
20020 citations
Semantic Scholar
Learning Metrics for SOM-Based Clustering and Visualization of Yeast Gene Expression Data
Merja Oja, P. Törönen, Janne Nikkilä, E. Castrén +1 more
20020 citations
Semantic Scholar
9 . 1 Self-Organizing Maps : introduction
T. Kohonen, Merja Oja, Samuel Kaski, P. Somervuo
0 citations
Semantic Scholar

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