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Thoroughly Optimised Production Chassis for Advanced Pharmaceutical Ingredients


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Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling

Author(s): Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling
Published in: PLOS Computational Biology, Issue 16/7, 2020, Page(s) e1008039, ISSN 1553-7358
DOI: 10.1371/journal.pcbi.1008039

Multi-omics Study of Planobispora rosea, Producer of the Thiopeptide Antibiotic GE2270A

Author(s): Francesco Del Carratore, Marianna Iorio, Mercedes Pérez-Bonilla, Kamila Schmidt, Rosario Pérez-Redondo, Margherita Sosio, Sandy J. Macdonald, Ivan S. Gyulev, Areti Tsigkinopoulou, Gavin H. Thomas, Olga Genilloud, Antonio Rodríguez-García, Stefano Donadio, Rainer Breitling, Eriko Takano
Published in: mSystems, Issue 6/3, 2021, ISSN 2379-5077
DOI: 10.1128/msystems.00341-21

Structure and Function of an Elongation Factor P Subfamily in Actinobacteria

Author(s): Bruno Pinheiro, Christopher M. Scheidler, Pavel Kielkowski, Marina Schmid, Ignasi Forné, Suhui Ye, Norbert Reiling, Eriko Takano, Axel Imhof, Stephan A. Sieber, Sabine Schneider, Kirsten Jung
Published in: Cell Reports, Issue 30/13, 2020, Page(s) 4332-4342.e5, ISSN 2211-1247
DOI: 10.1016/j.celrep.2020.03.009

Synthetic biology approaches to actinomycete strain improvement

Author(s): Rainer Breitling, Martina Avbelj, Oksana Bilyk, Francesco Del Carratore, Alessandro Filisetti, Erik K R Hanko, Marianna Iorio, Rosario Pérez Redondo, Fernando Reyes, Michelle Rudden, Emmanuele Severi, Lucija Slemc, Kamila Schmidt, Dominic R Whittall, Stefano Donadio, Antonio Rodríguez García, Olga Genilloud, Gregor Kosec, Davide De Lucrezia, Hrvoje Petković, Gavin Thomas, Eriko Takano
Published in: FEMS Microbiology Letters, Issue 368/10, 2021, ISSN 1574-6968
DOI: 10.1093/femsle/fnab060

Fine-tuning the regulation of Cas9 expression levels for efficient CRISPR-Cas9 mediated recombination in Streptomyces

Author(s): Suhui Ye, Behnam Enghiad, Huimin Zhao, Eriko Takano
Published in: Journal of Industrial Microbiology and Biotechnology, Issue 47/4-5, 2020, Page(s) 413-423, ISSN 1367-5435
DOI: 10.1007/s10295-020-02277-5

Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries

Author(s): Andrew Currin, Neil Swainston, Mark S Dunstan, Adrian J Jervis, Paul Mulherin, Christopher J Robinson, Sandra Taylor, Pablo Carbonell, Katherine A Hollywood, Cunyu Yan, Eriko Takano, Nigel S Scrutton, Rainer Breitling
Published in: Synthetic Biology, Issue 4/1, 2019, ISSN 2397-7000
DOI: 10.1093/synbio/ysz025

Defining informative priors for ensemble modeling in systems biology

Author(s): Areti Tsigkinopoulou, Aliah Hawari, Megan Uttley, Rainer Breitling
Published in: Nature Protocols, Issue 13/11, 2018, Page(s) 2643-2663, ISSN 1754-2189
DOI: 10.1038/s41596-018-0056-z

Multi-Omics Analysis of the Effect of cAMP on Actinorhodin Production in Streptomyces coelicolor

Author(s): Katsuaki Nitta, Francesco Del Carratore, Rainer Breitling, Eriko Takano, Sastia P. Putri, Eiichiro Fukusaki
Published in: Frontiers in Bioengineering and Biotechnology, Issue 8, 2020, Page(s) 595552, ISSN 2296-4185
DOI: 10.3389/fbioe.2020.595552

Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

Author(s): Adam Amara, Eriko Takano, Rainer Breitling
Published in: BMC Genomics, Issue 19/1, 2018, ISSN 1471-2164
DOI: 10.1186/s12864-018-4905-5

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters

Author(s): Francesco Del Carratore, Konrad Zych, Matthew Cummings, Eriko Takano, Marnix H. Medema, Rainer Breitling
Published in: Communications Biology, Issue 2/1, 2019, ISSN 2399-3642
DOI: 10.1038/s42003-019-0333-6

Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships

Author(s): Francesco Del Carratore, Kamila Schmidt, Maria Vinaixa, Katherine A. Hollywood, Caitlin Greenland-Bews, Eriko Takano, Simon Rogers, Rainer Breitling
Published in: Analytical Chemistry, Issue 91/20, 2019, Page(s) 12799-12807, ISSN 0003-2700
DOI: 10.1021/acs.analchem.9b02354

Antibiotic export: transporters involved in the final step of natural product production

Author(s): Emmanuele Severi, Gavin H. Thomas
Published in: Microbiology, Issue 165/8, 2019, Page(s) 805-818, ISSN 1350-0872
DOI: 10.1099/mic.0.000794

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

Author(s): Kai Blin, Victòria Pascal Andreu, Emmanuel L C de los Santos, Francesco Del Carratore, Sang Yup Lee, Marnix H Medema, Tilmann Weber
Published in: Nucleic Acids Research, Issue 47/D1, 2018, Page(s) D625-D630, ISSN 0305-1048
DOI: 10.1093/nar/gky1060

A plasmid toolset for CRISPR‐mediated genome editing and CRISPRi gene regulation in Escherichia coli.

Author(s): Adrian J. Jervis, Erik K.R. Hanko, Mark S. Dunstan, Christopher J. Robinson, Eriko Takano, Nigel S. Scrutton
Published in: Microbial Biotechnology, Issue 14/3, 2021, Page(s) 1120-1129, ISSN 1751-7915
DOI: 10.1111/1751-7915.13780

Metabolomics tools for the synthetic biology of natural products

Author(s): Katherine A Hollywood, Kamila Schmidt, Eriko Takano, Rainer Breitling
Published in: Current Opinion in Biotechnology, Issue 54, 2018, Page(s) 114-120, ISSN 0958-1669
DOI: 10.1016/j.copbio.2018.02.015

Switchable foldamer ion channels with antibacterial activity

Author(s): Anna D. Peters, Stefan Borsley, Flavio della Sala, Dominic F. Cairns-Gibson, Marios Leonidou, Jonathan Clayden, George F. S. Whitehead, Iñigo J. Vitórica-Yrezábal, Eriko Takano, John Burthem, Scott L. Cockroft, Simon J. Webb
Published in: Chemical Science, Issue 11/27, 2020, Page(s) 7023-7030, ISSN 2041-6520
DOI: 10.1039/d0sc02393k

Molecular Biology Methods in Streptomyces rimosus, a Producer of Oxytetracycline

Author(s): Lucija Slemc, Špela Pikl, Hrvoje Petković, Martina Avbelj
Published in: Antimicrobial Therapies - Methods and Protocols, Issue 2296, 2021, Page(s) 303-330
DOI: 10.1007/978-1-0716-1358-0_18

Coupled Transcriptomics for Differential Expression Analysis and Determination of Transcription Start Sites: Design and Bioinformatics

Author(s): Antonio Rodríguez-García, Alberto Sola-Landa, Rosario Pérez-Redondo
Published in: Antimicrobial Therapies - Methods and Protocols, Issue 2296, 2021, Page(s) 263-278
DOI: 10.1007/978-1-0716-1358-0_16