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2018
2 Citations (Scopus)

A High-Throughput Workflow for CRISPR/Cas9 Mediated Combinatorial Promoter Replacements and Phenotype Characterization in Yeast

Kuivanen, J., Holmström, S., Lehtinen, B., Penttilä, M. & Jäntti, J., 1 Sep 2018, In : Biotechnology Journal. 13, 9, 1700593.

Research output: Contribution to journalArticleScientificpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Workflow
Yeasts
Phenotype
Transketolase
7 Citations (Scopus)

A universal gene expression system for fungi

Rantasalo, A., Landowski, C. P., Kuivanen, J., Korppoo, A., Reuter, L., Koivistoinen, O., Valkonen, M., Penttilä, M., Jäntti, J. & Mojzita, D., 1 Jan 2018, In : Nucleic Acids Research. 46, 18, 15 p., e111.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Fungi
Transcription Factors
Synthetic Genes
Gene Expression
Gene Expression Regulation
2 Citations (Scopus)

Coacervation of resilin fusion proteins containing terminal functionalities

Fang, W., Nonappa, Vitikainen, M., Mohammadi, P., Koskela, S., Soikkeli, M., Westerholm-Parvinen, A., Landowski, C. P., Penttilä, M., Linder, M. B. & Laaksonen, P., 1 Nov 2018, In : Colloids and Surfaces B: Biointerfaces. 171, p. 590-596 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Fusion reactions
fusion
proteins
Proteins
Peptides
2 Citations (Scopus)

Enhanced triacylglycerol production with genetically modified Trichosporon oleaginosus

Koivuranta, K., Castillo, S., Jouhten, P., Ruohonen, L., Penttilä, M. & Wiebe, M. G., 21 Jun 2018, In : Frontiers in Microbiology. 9, JUN, 1337.

Research output: Contribution to journalArticleScientificpeer-review

Trichosporon
Pyruvic Acid
Triglycerides
Xylose
Oxidoreductases
9 Citations (Scopus)

Phase transitions as intermediate steps in the formation of molecularly engineered protein fibers

Mohammadi, P., Aranko, A. S., Lemetti, L., Cenev, Z., Zhou, Q., Virtanen, S., Landowski, C. P., Penttilä, M., Fischer, W. J., Wagermaier, W. & Linder, M. B., 2018, In : Communications biology. 1, 12 p., 86.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Phase transitions
Fibers
Phase separation
Silk
Proteins
7 Citations (Scopus)

Synthetic Toolkit for Complex Genetic Circuit Engineering in Saccharomyces cerevisiae

Rantasalo, A., Kuivanen, J., Penttilä, M., Jäntti, J. & Mojzita, D., 15 Jun 2018, In : ACS Synthetic Biology. 7, 6, p. 1573-1587 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Genetic Engineering
Gene expression
Yeast
Saccharomyces cerevisiae
Transcription factors
4 Citations (Scopus)

Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili

Lienemann, M., TerAvest, M. A., Pitkänen, J. P., Stuns, I., Penttilä, M., Ajo-Franklin, C. M. & Jäntti, J., 1 Nov 2018, In : Microbial Biotechnology. 11, 6, p. 1184-1194 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Immobilization
Escherichia coli
Biofilms
Mannose
Shewanella
2017
12 Citations (Scopus)

A design-build-test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Miskovic, L., Alff-Tuomala, S., Soh, K. C., Barth, D., Salusjärvi, L., Pitkänen, J-P., Ruohonen, L., Penttilä, M. & Hatzimanikatis, V., 2017, In : Biotechnology for Biofuels. 10, 1, 166.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Xylose
Glycolysis
Saccharomyces cerevisiae
kinetics
Kinetics
6 Citations (Scopus)

Elastic and pH responsive hybrid interfaces created with engineered resilin and nanocellulose

Fang, W., Paananen, A., Vitikainen, M., Koskela, S., Westerholm-Parvinen, A., Joensuu, J., Landowski, C., Penttilä, M., Linder, M. B. & Laaksonen, P., 12 Jun 2017, In : Biomacromolecules. 18, 6, p. 1866-1873 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Cellulose
Proteins
Fusion reactions
Hydrogel
Polypeptides
16 Citations (Scopus)

Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae

Salusjärvi, L., Toivari, M., Vehkomäki, M-L., Koivistoinen, O., Mojzita, D., Niemelä, K., Penttilä, M. & Ruohonen, L., 1 Nov 2017, In : Applied Microbiology and Biotechnology. 101, 22, p. 8151-8163 13 p.

Research output: Contribution to journalArticleScientificpeer-review

glycolic acid
Ethylene Glycol
Xylose
Saccharomyces cerevisiae
Acids
3 Citations (Scopus)

Single-Molecule Force Spectroscopy Study on Modular Resilin Fusion Protein

Griffo, A., Hähl, H., Grandthyll, S., Müller, F., Paananen, A., Ilmén, M., Szilvay, G., Landowski, C. P., Penttilä, M., Jacobs, K. & Laaksonen, P., 1 Jan 2017, In : ACS Omega. 2, 10, p. 6906-6915 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Fusion reactions
Spectroscopy
Proteins
Molecules
Cellulose
7 Citations (Scopus)

The Crystal Structure of a Bacterial l -Arabinonate Dehydratase Contains a [2Fe-2S] Cluster

Rahman, M., Andberg, M., Thangaraj, S., Parkkinen, T., Penttilä, M., Jänis, J., Koivula, A., Rouvinen, J. & Hakulinen, N., 21 Jul 2017, In : ACS Chemical Biology. 12, 7, p. 1919-1927 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Hydro-Lyases
Bacterial Structures
Dimers
Catalytic Domain
Crystal structure
2 Citations (Scopus)

Yeast as a tool to express sugar acid transporters with biotechnological interest

Ribas, D., Sá-Pessoa, J., Soares-Silva, I., Paiva, S., Nygård, Y., Ruohonen, L., Penttilä, M. & Casal, M., 1 Mar 2017, In : FEMS Yeast Research. 17, 2, fox005.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Sugar Acids
Yeasts
Membrane Transport Proteins
Carboxylic Acids
Saccharomyces cerevisiae
2016
14 Citations (Scopus)

Characterization and mutagenesis of two novel iron-sulphur cluster pentonate dehydratases

Andberg, M., Aro-Kärkkäinen, N., Carlson, P., Oja, M., Bozonnet, S., Toivari, M., Hakulinen, N., O'Donohue, M., Penttilä, M. & Koivula, A., 2016, In : Applied Microbiology and Biotechnology. 100, 17, p. 7549-7563

Research output: Contribution to journalArticleScientificpeer-review

Hydro-Lyases
Sulfur
Mutagenesis
Iron
Sugar Acids
2 Citations (Scopus)

Characterization of a unique Caulobacter crescentus aldose-aldose oxidoreductase having dual activities

Andberg, M., Maaheimo, H., Kumpula, E-P., Boer, H., Toivari, M., Penttilä, M. & Koivula, A., 2016, In : Applied Microbiology and Biotechnology. 100, 2, p. 673-685

Research output: Contribution to journalArticleScientificpeer-review

Caulobacter crescentus
Oxidoreductases
Arabinose
Monosaccharides
Xylose
9 Citations (Scopus)

Genome wide analysis of protein production load in Trichoderma reesei

Pakula, T., Nygrén, H., Barth, D., Heinonen, M., Castillo, S. D., Penttilä, M. E. & Arvas, M., 2016, In : Biotechnology for Biofuels. 9, 26 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Trichoderma
genome
Genes
Genome
Proteins
4 Citations (Scopus)

Machine learning of protein interactions in fungal secretory pathways

Kludas, J., Arvas, M., Castillo, S., Pakula, T., Oja, M., Brouard, C., Jäntti, J., Penttilä, M. & Rousu, J., 1 Jul 2016, In : PLoS ONE. 11, 7, e0159302.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
artificial intelligence
Secretory Pathway
Learning systems
seeds
Proteins
16 Citations (Scopus)

Production and applications of carbohydrate-derived sugar acids as generic biobased chemicals

Mehtiö, T., Toivari, M., Wiebe, M. G., Harlin, A., Penttilä, M. & Koivula, A., 2016, In : Critical Reviews in Biotechnology. 36, 5, p. 904-916

Research output: Contribution to journalArticleScientificpeer-review

Sugar Acids
Carbohydrates
Sequestering Agents
Uronic Acids
Hydrogels
14 Citations (Scopus)

Synthetic transcription amplifier system for orthogonal control of gene expression in saccharomyces cerevisiae

Rantasalo, A., Czeizler, E., Virtanen, R., Rousu, J., Lähdesmäki, H., Penttilä, M., Jäntti, J. & Mojzita, D., 2016, In : PLoS ONE. 11, 2, e0148320.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Transcription
Gene expression
Yeast
Saccharomyces cerevisiae
Transcription Factors
3 Citations (Scopus)

Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Castillo, S., Barth, D., Arvas, M., Pakula, T. M., Pitkänen, E., Blomberg, P., Seppänen-Laakso, T., Nygren, H., Sivasiddarthan, D., Penttilä, M. & Oja, M., 2016, In : Biotechnology for Biofuels. 9, 252, 20 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
19 Citations (Scopus)

Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures

Alff-Tuomala, S., Salusjärvi, L., Barth, D., Oja, M., Penttilä, M. E., Pitkänen, J. P., Ruohonen, L. & Jouhten, P., 2016, In : Applied Microbiology and Biotechnology. 100, 2, p. 969-985

Research output: Contribution to journalArticleScientificpeer-review

Xylose
Saccharomyces cerevisiae
Gene Expression
Glucose
xylose-glucose
2015
8 Citations (Scopus)

A novel aldose-aldose oxidoreductase for co-production of D-xylonate and xylitol from D-xylose with Saccharomyces cerevisiae

Wiebe, M. G., Nygård, Y., Oja, M., Andberg, M., Ruohonen, L., Koivula, A., Penttilä, M. & Toivari, M., 2015, In : Applied Microbiology and Biotechnology. 99, 22, p. 9439-9447

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Xylitol
Xylose
Saccharomyces cerevisiae
Caulobacter crescentus
Oxidoreductases
18 Citations (Scopus)

Capillary electrophoresis with laser-induced fluorescence detection for studying amino acid uptake by yeast during beer fermentation

Turkia, H., Sirén, H., Penttilä, M. & Pitkänen, J-P., 2015, In : Talanta. 131, p. 366-371

Research output: Contribution to journalArticleScientificpeer-review

Beer
Capillary electrophoresis
Capillary Electrophoresis
Yeast
Fermentation
23 Citations (Scopus)

Enabling low cost biopharmaceuticals: A systematic approach to delete proteases from a well-known protein production host trichoderma reesei

Landowski, C. P., Huuskonen, A., Wahl, R., Westerholm-Parvinen, A., Kanerva, A., Hänninen, A-L., Salovuori, N., Penttilä, M., Natunen, J., Ostermeier, C., Helk, B., Saarinen, J. & Saloheimo, M., 2015, In : PLoS ONE. 10, 8, e0134723.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
biopharmaceuticals
Trichoderma reesei
Trichoderma
Peptide Hydrolases
proteinases
18 Citations (Scopus)

Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production

Kuivanen, J., Richard, P. & Penttilä, M., 2015, In : Microbial Cell Factories. 14, 9 p., 2.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Metabolic engineering
Metabolic Engineering
Ascorbic acid
Ascorbic Acid
Acids
19 Citations (Scopus)

Overexpression of PAD1 and FDC1 results in significant cinnamic acid decarboxylase activity in Saccharomyces cerevisiae

Richard, P., Viljanen, K. & Penttilä, M., 2015, In : AMB Express. 5, 12, 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Styrene
Saccharomyces cerevisiae
ferulic acid
Phenylalanine Ammonia-Lyase
Coumaric Acids

Removing boundaries for therapeutic protein production in the filamentous fungus Trichoderma reesei: Reduction of the host protease load

Landowski, C., Huuskonen, A., Wahl, R., Westerholm-Parvinen, A., Sommer, B., Penttilä, M., Natunen, J., Ostermeier, C., Helk, B., Saarinen, J. & Saloheimo, M., 2015.

Research output: Contribution to conferenceConference AbstractScientific

biopharmaceuticals
Trichoderma reesei
proteinases
fungi
interferons
3 Citations (Scopus)

Structure and function of Caulobacter crescentus aldose-aldose oxidoreductase

Taberman, H., Andberg, M., Koivula, A., Hakulinen, N., Penttilä, M., Rouvinen, J. & Parkkinen, T., 2015, In : Biochemical Journal. 472, 3, p. 297-307

Research output: Contribution to journalArticleScientificpeer-review

37 Citations (Scopus)
Cellulose 1,4-beta-Cellobiosidase
Cellobiose
Oligosaccharides
Glucans
Cellulase
26 Citations (Scopus)
2014
2 Citations (Scopus)

Anaerobic carbon metabolism of saccharomyces cerevisiae

Jouhten, P. & Penttilä, M., 1 Apr 2014, Molecular Mechanisms in Yeast Carbon Metabolism. Springer, p. 57-82 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter or book articleProfessional

Anaerobiosis
Saccharomyces cerevisiae
Carbon
Oxygen
Eukaryota
9 Citations (Scopus)

Categorisation of sugar acid dehydratases in Aspergillus niger

Motter, F. A., Kuivanen, J., Keränen, H., Hilditch, S., Penttilä, M. & Richard, P., 1 Mar 2014, In : Fungal Genetics and Biology. 64, p. 67-72 6 p.

Research output: Contribution to journalArticleScientificpeer-review

galactonate dehydratase
Hydro-Lyases
Sugar Acids
Aspergillus niger
Proteins
34 Citations (Scopus)

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Pitkänen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttilä, M., Rousu, J. & Arvas, M., 1 Jan 2014, In : PLoS Computational Biology. 10, 2, e1003465.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Metabolic Network
Metabolic Networks and Pathways
Genome
genome
Genes
21 Citations (Scopus)

Engineering chimeric thermostable GH7 cellobiohydrolases in Saccharomyces cerevisiae

Voutilainen, S. P., Nurmi-Rantala, S., Penttilä, M. & Koivula, A., 1 Jan 2014, In : Applied Microbiology and Biotechnology. 98, 7, p. 2991-3001

Research output: Contribution to journalArticleScientificpeer-review

Cellulose 1,4-beta-Cellobiosidase
Saccharomyces cerevisiae
Hydrolysis
Enzymes
Cellulose
2 Citations (Scopus)

Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae

Lindfors, E., Jouhten, P., Oja, M., Rintala, E., Orešič, M. & Penttilä, M., 14 Feb 2014, In : BMC Systems Biology. 8, 1, 16.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Saccharomyces Cerevisiae
Transcription
Phenotype
Yeast
Saccharomyces cerevisiae
5 Citations (Scopus)

Intracellular pH responses in the industrially important fungus Trichoderma reesei

Valkonen, M., Penttilä, M. & Benčina, M., 1 Jan 2014, In : Fungal Genetics and Biology. 70, p. 86-93

Research output: Contribution to journalArticleScientificpeer-review

Trichoderma
Fungi
galactonate dehydratase
Lactose
Cytosol
4 Citations (Scopus)

Investigation of protein secretion and secretion stress in Ashbya gossypii

Aguiar, T. Q., Ribeiro, O., Arvas, M., Wiebe, M. G., Penttilä, M. & Domingues, L., 18 Dec 2014, In : BMC Genomics. 15, 1, 1137.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Unfolded Protein Response
Proteins
Dithiothreitol
Fungi
Secretory Pathway
6 Citations (Scopus)

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

Aro-Kärkkäinen, N., Toivari, M., Maaheimo, H., Ylilauri, M., Pentikäinen, O. T., Andberg, M., Oja, M., Penttilä, M., Wiebe, M. G., Ruohonen, L. & Koivula, A., 1 Jan 2014, In : Applied Microbiology and Biotechnology. 98, 23, p. 9653-9665 13 p.

Research output: Contribution to journalArticleScientificpeer-review

galactose dehydrogenase
Rhizobium leguminosarum
Arabinose
Saccharomyces cerevisiae
Yeasts
9 Citations (Scopus)

L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene

Koivuranta, K., Ilmen, M., Wiebe, M., Ruohonen, L., Suominen, P. & Penttilä, M., 2014, In : Microbial Cell Factories. 13, 107.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Gene encoding
Xylose
Candida
Lactic acid
L-Lactate Dehydrogenase
11 Citations (Scopus)

Molecular and functional characterization of an invertase secreted by Ashbya gossypii

Aguiar, T. Q., Dinis, C., Magalhães, F., Oliveira, C., Wiebe, M. G., Penttilä, M. & Domingues, L., 1 Jan 2014, In : Molecular Biotechnology. 56, 6, p. 524-534 11 p.

Research output: Contribution to journalArticleScientificpeer-review

beta-Fructofuranosidase
Genes
Sugar (sucrose)
Fungi
Yeast
88 Citations (Scopus)
Open Access
Trichoderma
Cellulase
Screening
Genes
gene
13 Citations (Scopus)

Single cell and in vivo analyses elucidate the effect of xylC lactonase during production of D-xylonate in Saccharomyces cerevisiae

Nygård, Y., Maaheimo, H., Mojzita, D., Toivari, M., Wiebe, M., Resnekov, O., Gustavo Pesce, C., Ruohonen, L. & Penttilä, M., 1 Jan 2014, In : Metabolic Engineering. 25, p. 238-247

Research output: Contribution to journalArticleScientificpeer-review

Xylose
Lactones
Yeast
Saccharomyces cerevisiae
Fluorescence
7 Citations (Scopus)

Structure and function of a decarboxylating Agrobacterium tumefaciens Keto-deoxy-D-galactarate dehydratase

Taberman, H., Andberg, M., Parkkinen, T., Jänis, J., Penttilä, M., Hakulinen, N., Koivula, A. & Rouvinen, J., 30 Dec 2014, In : Biochemistry. 53, 51, p. 8052-8060 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Hydro-Lyases
Agrobacterium tumefaciens
uronate dehydrogenase
Genes
Crystal structure
13 Citations (Scopus)

The diverse role of Pdr12 in resistance to weak organic acids

Nygård, Y., Mojzita, D., Toivari, M., Penttilä, M., Wiebe, M. G. & Ruohonen, L., 1 Jan 2014, In : Yeast. 31, 6, p. 219-232 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Organic acids
Acids
Acetic acid
Acetic Acid
Propionic acid
2 Citations (Scopus)

The industrial potential of bio-based glycolic acid and polyglycolic acid: Short survey

Gädda, T. M., Pirttimaa, M. M., Koivistoinen, O., Richard, P., Penttilä, M. & Harlin, A., 1 Jan 2014, In : Appita Journal. 67, 1, 1 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

Acids
Packaging
Fermentation
Carbon footprint
Consumer products
32 Citations (Scopus)

The role of CRE1 in nucleosome positioning within the cbh1 promoter and coding regions of Trichoderma reesei

Ries, L., Belshaw, N. J., Ilmén, M., Penttilä, M. E., Alapuranen, M. & Archer, D. B., 1 Jan 2014, In : Applied Microbiology and Biotechnology. 98, 2, p. 749-762 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Trichoderma
Nucleosomes
Genetic Promoter Regions
Cellulose 1,4-beta-Cellobiosidase
Cellulases
4 Citations (Scopus)

Transcriptome of Saccharomyces cerevisiae during production of D-xylonate

Mojzita, D., Oja, M., Rintala, E., Wiebe, M., Penttilä, M. & Ruohonen, L., 5 Sep 2014, In : BMC Genomics. 15, 1, 763.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
Transcriptome
Saccharomyces cerevisiae
Cell Wall
Acids
Yeasts
2013
12 Citations (Scopus)

Capillary electrophoresis for the monitoring of phenolic compounds in bioprocesses

Turkia, H., Sirén, H., Penttilä, M. & Pitkänen, J. P., 22 Feb 2013, In : Journal of Chromatography A. 1278, p. 175-180

Research output: Contribution to journalArticleScientificpeer-review

Capillary electrophoresis
Capillary Electrophoresis
Monitoring
Phenols
Microbiota