Predictive and Accelerated Metabolic Engineering Network (PAcMEN)
Marie Curie-Innovative Training Networks
Duration: 2016-2020
Coordinator: Technical University of Denmark
Lighting up yeast cell factories by transcription factor-based biosensors - Vasil D'ambrosio, Michael K. Jensen
Engineering microbial fatty acid metabolism for biofuels and biochemicals - Eko Roy Marella, Carina Holkenbrink, Varena Siewers, Irina Borodina
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis - Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
Modular 5′-UTR hexamers for context-independent tuning of protein expression in eukaryotes - Søren D Petersen, Jie Zhang, Jae S Lee, Tadas Jakočiūnas, Lise M Grav, Helene F Kildegaard, Jay D Keasling, Michael K Jensen
Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals - Farshad Darvishi, Mehdi Ariana, Eko Roy Marella, Irina Borodina
Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions - Christoph S Boerlin, Nevena Cvetesic, Petter Holland, David Bergenholm, Verena Siewers, Boris Lenhard, Jens Nielsen
Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid - 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, Jonh P Morrissey, Jean-Marc G Daran.
Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites - Noushin Hadadi, Homa Mohamadi Peyhani, Ljubisa Miskovic, Marianne Seijo, Vassily Hatzimanikatis
Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima - Gang Li, Kersten S. Rabe, Jens Nielsen and Martin K. M. Engqvist
ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints - Pierre Salvy, Vassily Hatzimanikatis
A bioinformatic pipeline to analyze ChIP-exo datasets - Christoph S Börlin, David Bergenholm, Petter Holland, Jens Nielsen
The pan-genome of Saccharomyces cerevisiae - Gang Li, Boyang Ji, Jens Nielsen
A single-host fermentation process for the production of flavor lactones from non-hydroxylated fatty acids - Eko RoyMarella, JonathanDahlin, Marie Inger Dam, Jolanda ter Horst, Hanne Bjerre Christensen, Suresh Sudarsan, Guokun Wang, Carina Holkenbrink, Irina Borodina
Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica - 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 and Irina Borodina
Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges - Yu Chen, Gang Li, Jens Nielsen
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism - 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
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models - Pierre Salvy & Vassily Hatzimanikatis
High-Resolution Scanning of Optimal Biosensor Reporter Promoters in Yeast - Francesca Ambri, Vasil D’Ambrosio, Roberto Di Blasi, Jerome Maury, Simo Abdessamad Baallal Jacobsen, Douglas McCloskey, Michael K. Jensen, Jay. D Keasling
Vitamin requirements and biosynthesis in Saccharomyces cerevisiae - Thomas Perli, Anna K. Wronska, Raul A. Ortiz-Merino, Jack T. Pronk, Jean-Marc Daran
Adaptive laboratory evolution and reverse engineering of single-vitamin prototrophies in Saccharomyces cerevisiae- Thomas Perli, Dewi P.I. Moonen, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Exploiting the Diversity of Saccharomycotina Yeasts To Engineer Biotin-Independent Growth of Saccharomyces cerevisiae - Anna K. Wronska, Meinske P. Haak, Ellen Geraats, Eva Bruins Slot, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Updated ATLAS of Biochemistry With New Metabolites and Improved Enzyme Prediction Power - Jasmin Hafner, Homa Mohammadi Peyhani, Anastasia Sveshnikova, Alan Scheidegger, Vassily Hatzimanikatis
The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability - Christoph S. Börlin, Jens Nielsen and Verena Siewers
Display of functional nucleic acid polymerase on Escherichia coli surface and its application in directed polymerase evolution - Mu‐En Chung, Kati Goroncy, Alisa Kolesnikova, David Schönauer, Ulrich Schwaneberg
The Transcriptome and Flux Profiling of Crabtree‐Negative Hydroxy Acid‐Producing Strains of Saccharomyces cerevisiae Reveals Changes in the Central Carbon Metabolism - Mathew M. Jessop‐Fabre, Jonathan Dahlin, Mathias B. Biron, Vratislav Stovicek, Birgitta E. Ebert, Lars M. Blank, Itay Budin, Jay D. Keasling, Irina Borodina
Directed evolution of VanR biosensor specificity in yeast - Vasil D'Ambrosio, Subrata Pramanik, Kati Goroncy, Tadas Jakočiūnas, David Schönauer, Mehdi D. Davari, Ulrich Schwaneberg, Jay D.Keasling, Michael K. Jensen
Regulatory control circuits for stabilizing long-term anabolic product formation in yeast - Vasil D'Ambrosio, Eleonora Dore, Roberto Di Blasi, Marcel van den Broek, Suresh Sudarsan, Jolanda ter Horst, Francesca Ambri, Morten O.A. Sommer, Peter Rugbjerg, Jay D.Keasling, Robert Mans, Michael K. Jensen
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism – 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
Publications
PAcMEN is a European training network, which offers excellent training in biotech research and innovation for 16 talented young scientists. PhD students will carry out cutting-edge research in metabolic engineering, modeling, systems and synthetic biology. In collaboration with industrial partners, they will create novel solutions for sustainable production of fuels and chemicals. The graduates will be prepared through research, business, and entrepreneurship training to launch their careers in industry or academia.
Systems Biology and Modeling
Research projects at Chalmers with Prof. Jens Nielsen
Research projects at EPFL with Prof. Vassily Hatzimanikatis
Research projects at SilicoLife with Dr. Simao Soares
Synthetic Biology and Protein Engineering
Research projects at DTU with Dr. Michael Krogh Jensen
Research projects at RWTH Aachen with Dr. Ulrich Schwaneberg
Research projects at SeSaM-Biotech
New Biorefinery Processes
Research projects at TU Delft with Prof. Jack Pronk
Research projects at DTU with Dr. Irina Borodina
Research projects at DTU with Prof. Uffe Hasbro Mortensen
This project has received funding from the European Union's Horizon 2020 research and innovation programme under the under the Marie Sklodowska-Curie grant agreement No 722287