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TranscriptomicsExpression analysis of protein production in the filamentous fungus Trichoderma reesei (Hypocrea jecorina)
Comparison of T. reesei grown on lactose fed chemostat cultivations in different growth rates and cell densities The analysis is further described in paper Correlation of gene expression and protein production rate - a system wide study. Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivi...
ORGANISM(S): Hypocrea jecorina 
2011-12-22 | E-GEOD-30458 | biostudies-arrayexpress
TranscriptomicsArrayCGH of Trichoderma reesei strains QM9123, QM9414, NG14 and RutC-30
Trichoderma reesei is the main industrial producer of cellulases and hemicellulases used to depolymerize biomass in many biotechnical applications. Many production strains in use have been generated by classical mutagenesis. In this study we characterized genomic alterations in hyperproducing mutant...
ORGANISM(S): Hypocrea jecorina 
2010-11-26 | E-GEOD-19606 | biostudies-arrayexpress
TranscriptomicsExpression analysis of L-rhamnose catabolism in the yeast Scheffersomyces stipitis
In Scheffersomyces stipitis and related fungal species the genes for L-rhamnose catabolism RHA1, LRA2, LRA3 and LRA4 but not LADH are clustered. We find that located next to the cluster is a transcription factor, TRC1, which is conserved among related species.Our transcriptome analysis shows that al...
ORGANISM(S): Scheffersomyces stipitis CBS 6054 
2011-11-23 | E-GEOD-28557 | biostudies-arrayexpress
TranscriptomicsDetecting novel genes with sparse arrays
Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods a...
ORGANISM(S): Hypocrea jecorina 
2010-08-12 | E-GEOD-12960 | biostudies-arrayexpress
ModelsCastillo2016 - Whole-genome metabolic model of U.reesii using CoReCo
This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapl...
2016-12-02 | MODEL1604280050 | BioModels
ModelsCastillo2016 - Whole-genome metabolic model of S.cerevisiae using CoReCo
This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapl...
2016-12-02 | MODEL1604280034 | BioModels
ModelsCastillo2016 - Whole-genome metabolic model of B.dendrobatidis using CoReCo
This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapl...
2016-12-02 | MODEL1604280048 | BioModels
ModelsCastillo2016 - Whole-genome metabolic model of E.cuniculi using CoReCo
This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapl...
2016-12-02 | MODEL1604280035 | BioModels
ModelsCastillo2016 - Whole-genome metabolic model of P.chrysogenum using CoReCo
This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapl...
2016-12-02 | MODEL1604280001 | BioModels
ModelsCastillo2016 - Whole-genome metabolic model of P.graminis using CoReCo
This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. and Arvas, M. (2014). Comparative Genome-Scale Reconstruction of Gapl...
2016-12-02 | MODEL1604280051 | BioModels
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