Deliverables Documents, reports (2) A new validated method for FACS-based screening of engineered proteins A new validated method for FACS-based screening of engineered proteins Public dissemination summary "The Dissemination and Communication Plan will be updated by Dissemination and Communication Manager (DTU) and ESR Board on a regular basis. All the conducted activities will be registered and will eventually comprise the final ""Public dissemination summary""." Other (1) Conference I, II, and III Three annual network conferences with the presence of all ESRs and the participation of all the beneficiaries and partner organizations. ESRs will have the opportunity to present their research objectives and results to the network, including ESR colleagues, and to receive feedback. Participants from outside of the network will be invited to each conference. Websites, patent fillings, videos etc. (3) Characterized Parts Library Characterization data on regulatory parts library incl. upload to online open-access data repository PAcMEN website Public website will be created in the very beginning of the project and will be maintained throughout the project duration. The website will announce the new discoveries and publications from PAcMEN ESRs, the upcoming presentations by PAcMEN ESRs at scientific and industry-relevant conferences and workshops, reports/pictures/videos from the dissemination events, press-releases in local and international media, and so on. Comprehensive ChIP-exo and CAGE database 2 Next-generation genome-scale model of S. cerevisiae with regulatory information Demonstrators, pilots, prototypes (2) TFA + Lipids Modeling of Yarrowia Kinetic models of native metabolism and production pathway in S. cerevisiae Temperature constraint GEM and GEM including protein synthesis Next-generation genome-scale model of S. cerevisiae with included protein synthesis Publications Peer reviewed articles (27) The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability Author(s): Christoph S Börlin, Jens Nielsen, Verena Siewers Published in: FEMS Microbiology Letters, Issue 367/13, 2020, ISSN 1574-6968 Publisher: Microbiology Letters DOI: 10.1093/femsle/fnaa107 Adaptive Laboratory Evolution and Reverse Engineering of Single-Vitamin Prototrophies in Saccharomyces cerevisiae Author(s): Thomas Perli, Dewi P. I. Moonen, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran Published in: Applied and Environmental Microbiology, 2020, ISSN 0099-2240 Publisher: American Society for Microbiology DOI: 10.1128/aem.00388-20 Regulatory control circuits for stabilizing long-term anabolic product formation in yeast Author(s): VasilD'Ambrosio, Eleonora Dorea, Roberto Di Blasi, Marcel van den Broek, Suresh Sudarsan, Jolanda ter Horst, Francesca Ambri, Morten O.A. Sommer, Peter Rugbjerg, Jay D.Keasling, Robert Mansb, Michael K.Jensen Published in: Metabolic Engineering, 2020, ISSN 1096-7176 Publisher: Academic Press DOI: 10.1016/j.ymben.2020.07.006 Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power Author(s): Jasmin Hafner, Homa MohammadiPeyhani, Anastasia Sveshnikova, Alan Scheidegger, Vassily Hatzimanikatis Published in: ACS Synthetic Biology, Issue 9/6, 2020, Page(s) 1479-1482, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.0c00052 Exploiting the Diversity of Saccharomycotina Yeasts To Engineer Biotin-Independent Growth of Saccharomyces cerevisiae Author(s): Anna K. Wronska, Meinske P. Haak, Ellen Geraats, Eva Bruins Slot, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran Published in: Applied and Environmental Microbiology, Issue 86/12, 2020, ISSN 0099-2240 Publisher: American Society for Microbiology DOI: 10.1128/aem.00270-20 The Transcriptome and Flux Profiling of Crabtree‐Negative Hydroxy Acid‐Producing Strains of Saccharomyces cerevisiae Reveals Changes in the Central Carbon Metabolism Author(s): Mathew M. Jessop‐Fabre, Jonathan Dahlin, Mathias B. Biron, Vratislav Stovicek, Birgitta E. Ebert, Lars M. Blank, Itay Budin, Jay D. Keasling, Irina Borodina Published in: Biotechnology Journal, Issue 14/9, 2019, Page(s) 1900013, ISSN 1860-6768 Publisher: Wiley - VCH Verlag GmbH & CO. KGaA DOI: 10.1002/biot.201900013 Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism Author(s): Jie Zhang, Søren D. Petersen, Tijana Radivojevic, Andrés Ramirez, Andrés Pérez-Manríquez, Eduardo Abeliuk, Benjamín J. Sánchez, Zak Costello, Yu Chen, Michael J. Fero, Hector Garcia Martin, Jens Nielsen, Jay D. Keasling, Michael K. Jensen Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-020-17910-1 Bayesian genome scale modelling identifies thermal determinants of yeast metabolism Author(s): Gang Li; Yating Hu; Hao Wang; Aleksej Zelezniak; Boyang Ji; Jan Zrimec; Jens Nielsen Published in: Crossref, Issue 2, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1101/2020.04.01.019620 Engineering microbial fatty acid metabolism for biofuels and biochemicals Author(s): Eko Roy Marella, Carina Holkenbrink, Verena Siewers, Irina Borodina Published in: Current Opinion in Biotechnology, Issue 50, 2018, Page(s) 39-46, ISSN 0958-1669 Publisher: Elsevier BV DOI: 10.1016/j.copbio.2017.10.002 pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis Author(s): Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis Published in: Bioinformatics, 2018, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/bty499 Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals Author(s): Farshad Darvishi, Mehdi Ariana, Eko Roy Marella, Irina Borodina Published in: Applied Microbiology and Biotechnology, Issue 102/14, 2018, Page(s) 5925-5938, ISSN 0175-7598 Publisher: Springer Verlag DOI: 10.1007/s00253-018-9099-x Modular 5′-UTR hexamers for context-independent tuning of protein expression in eukaryotes Author(s): Søren D Petersen, Jie Zhang, Jae S Lee, Tadas Jakočiūnas, Lise M Grav, Helene F Kildegaard, Jay D Keasling, Michael K Jensen Published in: Nucleic Acids Research, 2018, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gky734 Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid Author(s): Hannes Juergens, Javier A Varela, Arthur R Gorter de Vries, Thomas Perli, Veronica J M Gast, Nikola Y Gyurchev, Arun S Rajkumar, Robert Mans, Jack T Pronk, John P Morrissey, Jean-Marc G Daran Published in: FEMS Yeast Research, Issue 18/3, 2018, ISSN 1567-1364 Publisher: Oxford Academic DOI: 10.1093/femsyr/foy012 Lighting up yeast cell factories by transcription factor-based biosensors Author(s): Vasil D'Ambrosio, Michael K. Jensen Published in: FEMS Yeast Research, Issue 17/7, 2017, ISSN 1567-1364 Publisher: Oxford University Press DOI: 10.1093/femsyr/fox076 A single-host fermentation process for the production of flavor lactones from non-hydroxylated fatty acids Author(s): Eko Roy Marella, Jonathan Dahlin, Marie Inger Dam, Jolanda ter Horst, Hanne Bjerre Christensen, Suresh Sudarsan, Guokun Wang, Carina Holkenbrink, Irina Borodina Published in: Metabolic Engineering, 2019, ISSN 1096-7176 Publisher: Academic Press DOI: 10.1016/j.ymben.2019.08.009 Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica Author(s): Jonathan Dahlin, Carina Holkenbrink, Eko Roy Marella, Guokun Wang, Ulf Liebal, Christian Lieven, Dieter Weber, Douglas McCloskey, Birgitta E. Ebert, Markus J. Herrgård, Lars Mathias Blank, Irina Borodina Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021 Publisher: Frontiers Media DOI: 10.3389/fgene.2019.00747 Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions Author(s): Christoph S Börlin, Nevena Cvetesic, Petter Holland, David Bergenholm, Verena Siewers, Boris Lenhard, Jens Nielsen Published in: FEMS Yeast Research, Issue 19/2, 2018, ISSN 1567-1364 Publisher: Fems Yeast Research DOI: 10.1093/femsyr/foy128 A bioinformatic pipeline to analyze ChIP-exo datasets Author(s): Christoph S Börlin, David Bergenholm, Petter Holland, Jens Nielsen Published in: Biology Methods and Protocols, Issue 4/1, 2019, ISSN 2396-8923 Publisher: Biology Methods & Protocols DOI: 10.1093/biomethods/bpz011 A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism Author(s): Hongzhong Lu, Feiran Li, Benjamín J. Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, Petre Mihail Anton, Dimitra Lappa, Christian Lieven, Moritz Emanuel Beber, Nikolaus Sonnenschein, Eduard J. Kerkhoven, Jens Nielsen Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-019-11581-3 Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions Author(s): Petter Holland, David Bergenholm, Christoph S Börlin, Guodong Liu, Jens Nielsen Published in: Nucleic Acids Research, Issue 47/10, 2019, Page(s) 4986-5000, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkz253 The pan-genome of Saccharomyces cerevisiae Author(s): Gang Li, Boyang Ji, Jens Nielsen Published in: FEMS Yeast Research, Issue 19/7, 2019, ISSN 1567-1356 Publisher: Blackwell DOI: 10.1093/femsyr/foz064 Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima Author(s): Gang Li, Kersten S. Rabe, Jens Nielsen, Martin K. M. Engqvist Published in: ACS Synthetic Biology, Issue 8/6, 2019, Page(s) 1411-1420, ISSN 2161-5063 Publisher: American Chemical Society DOI: 10.1021/acssynbio.9b00099 Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites Author(s): Noushin Hadadi, Homa MohammadiPeyhani, Ljubisa Miskovic, Marianne Seijo, Vassily Hatzimanikatis Published in: Proceedings of the National Academy of Sciences, Issue 116/15, 2019, Page(s) 7298-7307, ISSN 0027-8424 Publisher: National Academy of Sciences DOI: 10.1073/pnas.1818877116 The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models Author(s): Pierre Salvy, Vassily Hatzimanikatis Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-019-13818-7 Display of functional nucleic acid polymerase on Escherichia coli surface and its application in directed polymerase evolution Author(s): Mu‐En Chung, Kati Goroncy, Alisa Kolesnikova, David Schönauer, Ulrich Schwaneberg Published in: Biotechnology and Bioengineering, 2020, ISSN 0006-3592 Publisher: Wiley - V C H Verlag GmbbH & Co. DOI: 10.1002/bit.27542 Vitamin requirements and biosynthesis in Saccharomyces cerevisiae Author(s): Thomas Perli, Anna K. Wronska, Raúl A. Ortiz‐Merino, Jack T. Pronk, Jean‐Marc Daran Published in: Yeast, 2020, ISSN 0749-503X Publisher: John Wiley & Sons Inc. DOI: 10.1002/yea.3461 Directed evolution of VanR biosensor specificity in yeast Author(s): Vasil D'Ambrosio, Subrata Pramanik, Kati Goroncy, Tadas Jakočiūnas, David Schönauer, Mehdi D. Davari, Ulrich Schwaneberg, Jay D. Keasling, Michael K. Jensen Published in: Biotechnology Notes, Issue 1, 2020, Page(s) 9-15, ISSN 2665-9069 Publisher: Biotechnology Notes DOI: 10.1016/j.biotno.2020.01.002 Book chapters (1) Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges Author(s): Yu Chen, Gang Li, Jens Nielsen Published in: Yeast Systems Biology - Methods and Protocols, Issue 2049, 2019, Page(s) 329-345, ISBN 978-1-4939-9735-0 Publisher: Springer New York DOI: 10.1007/978-1-4939-9736-7_19 Other (1) ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints Author(s): Salvy, Pierre; Hatzimanikatis, Vassily Published in: Issue 1, 2020 Publisher: TBA DOI: 10.1101/590992 Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available