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• Metabolic modelling in the development of cell factories by synthetic biology

  Jouhten, P., 2012, In: Computational and Structural Biotechnology Journal. 3, 4, 9 p., e201210009.

  Research output: Contribution to journal › Review Article › peer-review

  Open Access
  16 Citations (Scopus)

• Synthetic biology and biocolours

  Toivari, M., Hilditch, S., Szilvay, G., Arias Barrantes, M., Molnar, I. & Penttilä, M., 2023, BioColours: Sustainable stories from nature, lab and industry. Niinimäki, K. & Lohmann, J. (eds.). Aalto ARTS Books, p. 77-98 21 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter or book article › Professional

  Open Access

• Modular Synthetic Biology Toolkit for Filamentous Fungi

  Mózsik, L., Pohl, C., Meyer, V., Bovenberg, R. A. L., Nygård, Y. & Driessen, A. J. M. (Corresponding Author), 19 Nov 2021, In: ACS Synthetic Biology. 10, 11, p. 2850-2861 12 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  38 Citations (Scopus)

• Plant biotechnology beyond genome era in the dawn of synthetic biology

  Oksman-Caldentey, K.-M., 2018, The 3rd Conference of the International Society for Plant Molecular Farming: June 11-13, 2018: Book of abstracts. VTT Technical Research Centre of Finland, p. 41 1 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference abstract in proceedings › Scientific

• Doing synthetic biology with photosynthetic microorganisms

  Vavitsas, K., Kugler, A., Satta, A., Hatzinikolaou, D. G., Lindblad, P., Fewer, D. P., Lindberg, P., Toivari, M. & Stensjö, K. (Corresponding Author), Oct 2021, In: Physiologia Plantarum. 173, 2, p. 624-638 15 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  22 Citations (Scopus)

• Editorial: 4th Applied Synthetic Biology in Europe

  François, J. M. (Corresponding Author), Jäntti, J. & Daboussi, F., 6 May 2020, In: Frontiers in Bioengineering and Biotechnology. 8, 431.

  Research output: Contribution to journal › Article › Scientific

  Open Access

  File
  43 Downloads (Pure)

• Synthetic biology as an enabler of sustainable bioeconomy: A roadmap for Finland

  Penttilä, M., 2017, Espoo: VTT Technical Research Centre of Finland. 36 p.

  Research output: Book/Report › Report

  Open Access

• SynBiopython: An open-source software library for Synthetic Biology

  Yeoh, J. W., Swainston, N. (Corresponding Author), Vegh, P., Zulkower, V., Carbonell, P., Holowko, M. B., Peddinti, G. & Poh, C. L. (Corresponding Author), 2021, In: Synthetic Biology. 6, 1, ysab001.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  10 Citations (Scopus)

• Standards for plant synthetic biology: A common syntax for exchange of DNA parts

  Patron, N. J. (Corresponding Author), Orzaez, D. ,., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., Raitskin, O., Leveau, A., Farré, G., Rogers, C., Smith, A., Hibberd, J., Webb, A. A. R., Locke, J., Schornack, S., Ajioka, J., Baulcombe, D. C., Zipfel, C., Kamoun, S. & Jones, J. D. G. & 30 others, Kuhn, H., Robatzek, S., Van Esse, H. P., Sanders, D., Oldroyd, G., Martin, C., Field, R., O'Connor, S., Fox, S., Wulff, B., Miller, B., Breakspear, A., Radhakrishnan, G., Delaux, P.-M., Loqué, D., Granell, A., Tissier, A., Shih, P., Brutnell, T. P., Quick, W. P., Rischer, H., Fraser, P. D., Aharoni, A., Raines, C., South, P. F., Ané, J.-M., Hamberger, B. R., Langdale, J., Stougaard, J. & Bouwmeester, H., 2015, In: New Phytologist. 208, 1, p. 13-19

  Research output: Contribution to journal › Article › Scientific › peer-review
  199 Citations (Scopus)

• Synthetic Toolkit for Complex Genetic Circuit Engineering in Saccharomyces cerevisiae

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

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  42 Citations (Scopus)

• Control of D-lactic acid content in P(LA-3HB) copolymer in the yeast Saccharomyces cerevisiae using a synthetic gene expression system

  Ylinen, A., Salusjärvi, L., Toivari, M. & Penttilä, M., Jun 2022, In: Metabolic Engineering Communications. 14, e00199.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  5 Citations (Scopus)

  58 Downloads (Pure)

• Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

  Canelas, A. B., Harrison, N., Fazio, A., Zhang, J., Pitkänen, J. P., Van Den Brink, J., Bakker, B. M., Bogner, L., Bouwman, J., Castrillo, J. I., Cankorur, A., Chumnanpuen, P., Daran-Lapujade, P., Dikicioglu, D., Van Eunen, K., Ewald, J. C., Heijnen, J. J., Kirdar, B., Mattila, I. & Mensonides, F. I. C. & 15 others, Niebel, A., Penttilä, M., Pronk, J. T., Reuss, M., Salusjärvi, L., Sauer, U., Sherman, D., Siemann-Herzberg, M., Westerhoff, H., De Winde, J., Petranovic, D., Oliver, S. G., Workman, C. T., Zamboni, N. & Nielsen, J. (Corresponding Author), 1 Dec 2010, In: Nature Communications. 1, 9, 145.

  Research output: Contribution to journal › Article › Scientific › peer-review
  91 Citations (Scopus)

• A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

  Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Büthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E. & Smallbone, K. & 14 others, Spasić, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttilä, M., Klipp, E., Palsson, B., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J. & Kell, D. B. (Corresponding Author), 1 Oct 2008, In: Nature Biotechnology. 26, 10, p. 1155-1160

  Research output: Contribution to journal › Article › Scientific › peer-review
  479 Citations (Scopus)

• Filamentous fungi as emerging cell factories for the production of aromatic compounds

  Umashankar, P. & Nygård, Y., 14 Nov 2024, In: Fungal Biology and Biotechnology. 11, 19, 19.

  Research output: Contribution to journal › Review Article › peer-review

  Open Access

• Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica

  Vartiainen, E., Blomberg, P., Ilmén, M., Andberg, M., Toivari, M. (Corresponding Author) & Penttilä, M., 17 Dec 2019, In: Fungal Biology and Biotechnology. 6, 27.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  18 Citations (Scopus)

• Inducible Synthetic Growth Regulation Using the ClpXP Proteasome Enhances cis,cis-Muconic Acid and Glycolic Acid Yields in Saccharomyces cerevisiae

  Kakko, N., Rantasalo, A., Koponen, T., Vidgren, V., Kannisto, M., Maiorova, N., Nygren, H., Mojzita, D., Penttilä, M. & Jouhten, P. (Corresponding Author), 21 Apr 2023, In: ACS Synthetic Biology. 12, 4, p. 1021-1033

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  1 Citation (Scopus)

• Pushing the limits of automatic computational protein design: Design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold

  Glykys, D. J., Szilvay, G. R., Tortosa, P., Suárez Diez, M., Jaramillo, A. & Banta, S. (Corresponding Author), Jun 2011, In: Systems and Synthetic Biology. 5, 1, p. 45-58 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
  8 Citations (Scopus)

• The synthetic potential of fungal feruloyl esterases: A correlation with current classification systems and predicted structural properties

  Antonopoulou, I., Dilokpimol, A., Iancu, L., Mäkelä, M. R., Varriale, S., Cerullo, G., Hüttner, S., Uthoff, S., Jütten, P., Piechot, A., Steinbüchel, A., Olsson, L., Faraco, V., Hildén, K. S., de Vries, R. P., Rova, U. & Christakopoulos, P., 7 Jun 2018, In: Catalysts. 8, 6, 242.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  15 Citations (Scopus)

• Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi

  Mózsik, L., Iacovelli, R., Bovenberg, R. A. L. & Driessen, A. J. M. (Corresponding Author), 15 Jul 2022, In: Frontiers in Bioengineering and Biotechnology. 10, 901037

  Research output: Contribution to journal › Review Article › peer-review

  Open Access
  22 Citations (Scopus)

• CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum

  Pohl, C., Kiel, J. A. K. W., Driessen, A. J. M., Bovenberg, R. A. L. & Nygård, Y. (Corresponding Author), 15 Jul 2016, In: ACS Synthetic Biology. 5, 7, p. 754-764 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  269 Citations (Scopus)

• Multimodal Microorganism Development: Integrating Top-Down Biological Engineering with Bottom-Up Rational Design

  Dahabieh, M. S., Thevelein, J. M. & Gibson, B. (Corresponding Author), Mar 2020, In: Trends in Biotechnology. 38, 3, p. 241-253 13 p.

  Research output: Contribution to journal › Review Article › peer-review
  14 Citations (Scopus)

• Metabolic anchor reactions for robust biorefining

  Jouhten, P., Huerta-Cepas, J., Bork, P. & Patil, K. R. (Corresponding Author), 1 Mar 2017, In: Metabolic Engineering. 40, p. 1-4 4 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  11 Citations (Scopus)

• Yeast metabolic chassis designs for diverse biotechnological products

  Jouhten, P., Boruta, T., Andrejev, S., Pereira, F., Rocha, I. & Patil, K. R., 19 Jul 2016, In: Scientific Reports. 6, 29694.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  25 Citations (Scopus)

• A polycistronic system for multiplexed and precalibrated expression of multigene pathways in fungi

  Yue, Q., Meng, J., Qiu, Y., Yin, M., Zhang, L., Zhou, W., An, Z., Liu, Z., Yuan, Q., Sun, W., Li, C., Zhao, H., Molnár, I. (Corresponding Author), Xu, Y. (Corresponding Author) & Shi, S. (Corresponding Author), 17 Jul 2023, In: Nature Communications. 14, 1, p. 4267 10 p., 4267.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  12 Citations (Scopus)

• Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates

  Cámara, E., Olsson, L., Zrimec, J., Zelezniak, A., Geijer, C. & Nygård, Y. (Corresponding Author), 1 Jul 2022, In: Biotechnology Advances. 57, 107947.

  Research output: Contribution to journal › Review Article › peer-review

  Open Access
  35 Citations (Scopus)

• Protein folding and conformational stress in microbial cells producing recombinant proteins: A host comparative overview

  Gasser, B., Saloheimo, M., Rinas, U., Dragosits, M., Rodriguez-Carmona, E., Baumann, K., Giuliani, M., Parrilli, E., Branduardi, P., Lang, C., Porro, D., Ferrer, P., Tutino, M., Mattanovich, D. (Corresponding Author) & Villaverde, A., 2008, In: Microbial Cell Factories. 7, 11, 11.

  Research output: Contribution to journal › Review Article › peer-review

  Open Access
  275 Citations (Scopus)

• Following nature's roadmap: folding factors from plasma cells led to improvements in antibody secretion in S. cerevisiae

  Koskela, E., de Ruijter, J. & Frey, A., Aug 2017, In: Biotechnology Journal. 12, 8, 1600631.

  Research output: Contribution to journal › Article › Scientific › peer-review
  11 Citations (Scopus)

• Bioprocess performance analysis of novel methanol-independent promoters for recombinant protein production with Pichia pastoris

  Garrigós-Martínez, J., Vuoristo, K., Nieto-Taype, M. A., Tähtiharju, J., Uusitalo, J., Tukiainen, P., Schmid, C., Tolstorukov, I., Madden, K., Penttilä, M., Montesinos-Seguí, J. L., Valero, F., Glieder, A. (Corresponding Author) & Garcia-Ortega, X., Dec 2021, In: Microbial Cell Factories. 20, 1, 12 p., 74.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  23 Citations (Scopus)

  166 Downloads (Pure)

• Process engineering for bioflavour production with metabolically active yeasts: A mini-review

  Carlquist, M., Gibson, B., Karagul Yuceer, Y., Paraskevopolou, A., Sandell, M., Angelov, A. I., Gotcheva, V., Angelov, A. D., Etschmann, M., de Billerbeck, G. M. & Liden, G. (Corresponding Author), 2015, In: Yeast. 32, 1, p. 123-143

  Research output: Contribution to journal › Review Article › peer-review
  62 Citations (Scopus)

• Plasmid Copy Number Engineering Accelerates Fungal Polyketide Discovery upon Unnatural Polyketide Biosynthesis

  Li, Y., Lin, P., Lu, X., Yan, H., Wei, H., Liu, C., Liu, X., Yang, Y., Molnár, I. (Corresponding Author) & Bai, Z. (Corresponding Author), 18 Jul 2023, In: ACS Synthetic Biology. 12, 8, p. 2226-2235 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
  3 Citations (Scopus)

• Microbially induced corrosion of copper in simulated anoxic groundwater

  Carpén, L., Rajala, P. & Bomberg, M., 2016, Eurocorr 2016 proceedings. 11 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific

  Open Access
  1 Citation (Scopus)

• Pure protein bilayers and vesicles from native fungal hydrophobins

  Hähl, H., Vargas, J., Griffo, A., Laaksonen, P., Szilvay, G., Lienemann, M., Jacobs, K. (Corresponding Author), Seemann, R. & Fleury, J.-B., 1 Jan 2017, In: Advanced Materials. 29, 1, 1602888.

  Research output: Contribution to journal › Article › Scientific › peer-review
  25 Citations (Scopus)

• Towards valorization of pectin-rich agro-industrial residues: Engineering of Saccharomyces cerevisiae for co-fermentation of D-galacturonic acid and glycerol

  Perpelea, A., Wijaya, A. W., Martins, L. C., Rippert, D., Klein, M., Angelov, A., Peltonen, K., Teleki, A., Liebl, W., Richard, P., Thevelein, J. M., Takors, R., Sá-Correia, I. & Nevoigt, E. (Corresponding Author), Jan 2022, In: Metabolic Engineering. 69, p. 1-14 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  11 Citations (Scopus)

  73 Downloads (Pure)

• Re‐Engineering Fungal Nonribosomal Peptide Synthetases by Module Dissection and Duplicated Thiolation Domains

  Yin, M., Xie, L., Chen, K., Zhang, L., Yue, Q., Wang, C., Zeng, J., Hao, X., Gu, X., Molnár, I. (Corresponding Author) & Xu, Y., 12 Aug 2024, In: Angewandte Chemie: International Edition. 63, 33, e202406360.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  4 Downloads (Pure)

• Strain design optimization using reinforcement learning

  Sabzevari, M. (Corresponding Author), Szedmak, S., Penttilä, M., Jouhten, P. & Rousu, J., Jun 2022, In: PLoS Computational Biology. 18, 6, e1010177.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  14 Citations (Scopus)

• Yeast oligo-mediated genome engineering (YOGE)

  Dicarlo, J. E., Conley, A. J., Penttilä, M., Jäntti, J., Wang, H. H. & Church, G. M. (Corresponding Author), 20 Dec 2013, In: ACS Synthetic Biology. 2, 12, p. 741-749

  Research output: Contribution to journal › Article › Scientific › peer-review
  131 Citations (Scopus)

• Identification of the decumbenone biosynthetic gene cluster in penicillium decumbens and the importance for production of calbistrin

  Grijseels, S., Pohl, C., Nielsen, J. C., Wasil, Z., Nygård, Y., Nielsen, J., Frisvad, J. C., Nielsen, K. F., Workman, M., Larsen, T. O., Driessen, A. J. M. & Frandsen, R. J. N. (Corresponding Author), 2018, In: Fungal Biology and Biotechnology. 5, 1, p. 1-17 17 p., 18.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  21 Citations (Scopus)

• A disposable, roll-to-roll hot-embossed inertial microfluidic device for size-based sorting of microbeads and cells

  Wang, X., Liedert, C., Liedert, R. & Paputsky, I. (Corresponding Author), 2016, In: Lab on a Chip. 16, 10, p. 1821-1830

  Research output: Contribution to journal › Article › Scientific › peer-review
  53 Citations (Scopus)

• Catch and Release: Engineered Allosterically Regulated β-Roll Peptides Enable On/Off Biomolecular Recognition

  Bulutoglu, B., Dooley, K., Szilvay, G., Blenner, M. & Banta, S. (Corresponding Author), 15 Sept 2017, In: ACS Synthetic Biology. 6, 9, p. 1732-1741 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
  13 Citations (Scopus)

• Production and sensory analysis of grape flavoured beer by co-fermentation of an industrial and a genetically modified laboratory yeast strain

  de Ruijter, J. C. (Corresponding Author), Aisala, H., Jokinen, I., Krogerus, K., Rischer, H. & Toivari, M., Aug 2023, In: European Food Research and Technology. 249, 8, p. 1991–2000 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  4 Citations (Scopus)

  61 Downloads (Pure)

• Development of an Haa1-Based Biosensor for Acetic Acid Sensing in Saccharomyces cerevisiae

  Blick, E., Mormino, M., Siewers, V. & Nygård, Y., 2024, Synthetic Promoters: Methods and Protocols. Marchisio, M. A. (ed.). New York: Humana Press, p. 221-238 (Methods in Molecular Biology, Vol. 2844).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter or book article › Scientific › peer-review

• Gene expression engineering in fungi

  Mojzita, D., Rantasalo, A. & Jäntti, J. (Corresponding Author), Oct 2019, In: Current Opinion in Biotechnology. 59, p. 141-149

  Research output: Contribution to journal › Review Article › peer-review

  Open Access
  13 Citations (Scopus)

• Protein-Based Biological Materials: Molecular Design and Artificial Production

  Miserez, A., Yu, J. & Mohammadi, P., 8 Mar 2023, In: Chemical Reviews. 123, 5, p. 2049-2111 63 p.

  Research output: Contribution to journal › Review Article › peer-review

  Open Access

  File
  75 Citations (Scopus)

  197 Downloads (Pure)

• MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometrybased molecular profile data

  Pluskal, T. (Corresponding Author), Castillo, S., Villar-Briones, A. & Oresic, M., 2010, In: BMC Bioinformatics. 11, 395, 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  2922 Citations (Scopus)

• A unified multitask architecture for predicting local protein properties

  Qi, Y., Oja, M., Weston, J. & Noble, W. S. (Corresponding Author), 2012, In: PLoS ONE. 7, 3, 11 p., e32235.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  45 Citations (Scopus)

• A Universal Gene Expression System for Novel Yeast Species

  Mojzita, D. (Corresponding author), Rantasalo, A. & Ilmén, M., 2022, Yeast Metabolic Engineerin. Mapelli, V. & Bettiga, M. (eds.). Humana Press, p. 221-242 22 p. (Methods in Molecular Biology, Vol. 2513).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter or book article › Scientific › peer-review
  1 Citation (Scopus)

• Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion

  Konstantinidis, D., Pereira, F., Geissen, E. M., Grkovska, K., Kafkia, E., Jouhten, P., Kim, Y., Devendran, S., Zimmermann, M. & Patil, K. R. (Corresponding Author), 9 Aug 2021, In: Molecular Systems Biology. 17, 8, 20 p., e10189.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  23 Citations (Scopus)

  79 Downloads (Pure)

• Identification of peak V in brainstem auditory evoked potentials with neural networks

  Habraken, J. B. A., van Gils, M. J. & Cluitmans, P. J. M., 1 Jan 1993, In: Computers in Biology and Medicine. 23, 5, p. 369-380

  Research output: Contribution to journal › Article › Scientific › peer-review
  18 Citations (Scopus)

• The seco-iridoid pathway from Catharanthus roseus

  Miettinen, K., Dong, L., Navrot, N., Schneider, T., Burlat, V., Pollier, J., Woittiez, L., van der Krol, S., Lugan, R., Ilc, T., Verpoorte, R., Oksman-Caldentey, K.-M., Martinoia, E., Bouwmeester, H., Goossens, A., Memelink, J. (Corresponding Author) & Werck-Reichhart, D. (Corresponding Author), 2014, In: Nature Communications. 5, p. 3606-3616

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
  396 Citations (Scopus)

• Polyhydroxyalkanoate production in yeast Saccharomyces cerevisiae

  Ylinen, A., 2 Sept 2022, Aalto University. 74 p.

  Research output: Thesis › Dissertation › Collection of Articles

  Open Access