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Predictive and Accelerated Metabolic Engineering Network

Deliverables

A new validated method for FACS-based screening of engineered proteins

A new validated method for FACS-based screening of engineered proteins

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.

Publications

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
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
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
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
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
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
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
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
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
DOI: 10.1093/femsyr/foy128

A bioinformatic pipeline to analyze ChIP-exo datasets


Published in: ISSN 2396-8923
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
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
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
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
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
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
DOI: 10.1038/s41467-019-13818-7

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
DOI: 10.1007/978-1-4939-9736-7_19

Datasets