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Modular cell factories for the production of 100 compounds from the shikimate pathway


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Comparison of pathway analysis and constraint-based methods for cell factory design

Author(s): Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
Published in: BMC Bioinformatics, Issue 20/1, 2019, ISSN 1471-2105
DOI: 10.1186/s12859-019-2934-y

Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers

Author(s): Christopher J. Robinson, Pablo Carbonell, Adrian J. Jervis, Cunyu Yan, Katherine A. Hollywood, Mark S. Dunstan, Andrew Currin, Neil Swainston, Reynard Spiess, Sandra Taylor, Paul Mulherin, Steven Parker, William Rowe, Nicholas E. Matthews, Kirk J. Malone, Rosalind Le Feuvre, Philip Shapira, Perdita Barran, Nicholas J. Turner, Jason Micklefield, Rainer Breitling, Eriko Takano, Nigel S. Scrutton
Published in: Metabolic Engineering, Issue 60, 2020, Page(s) 168-182, ISSN 1096-7176
DOI: 10.1016/j.ymben.2020.04.008

Metabolic engineering of Saccharomyces cerevisiae for the de novo production of psilocybin and related tryptamine derivatives

Author(s): N. Milne, P. Thomsen, N. Mølgaard Knudsen, P. Rubaszka, M. Kristensen, I. Borodina
Published in: Metabolic Engineering, Issue 60, 2020, Page(s) 25-36, ISSN 1096-7176
DOI: 10.1016/j.ymben.2019.12.007

Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose

Author(s): Gheorghe M. Borja, Angelica Rodriguez, Kate Campbell, Irina Borodina, Yun Chen, Jens Nielsen
Published in: Microbial Cell Factories, Issue 18/1, 2019, ISSN 1475-2859
DOI: 10.1186/s12934-019-1244-4

CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models

Author(s): Vítor Vieira, Miguel Rocha
Published in: Bioinformatics, Issue 35/24, 2019, Page(s) 5361-5362, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz598

Pathways to cellular supremacy in biocomputing

Author(s): Lewis Grozinger, Martyn Amos, Thomas E. Gorochowski, Pablo Carbonell, Diego A. Oyarzún, Ruud Stoof, Harold Fellermann, Paolo Zuliani, Huseyin Tas, Angel Goñi-Moreno
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-13232-z

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

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, 2019, ISSN 2397-7000
DOI: 10.1093/synbio/ysz025

Efficient learning in metabolic pathway designs through optimal assembling

Author(s): Pablo Carbonell, Jean-Loup Faulon, Rainer Breitling
Published in: IFAC-PapersOnLine, Issue 52/26, 2019, Page(s) 7-12, ISSN 2405-8963
DOI: 10.1016/j.ifacol.2019.12.228

Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression

Author(s): Fernando Cruz, Diogo Lima, José P. Faria, Miguel Rocha, Oscar Dias
Published in: Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, Issue 1005, 2020, Page(s) 173-181
DOI: 10.1007/978-3-030-23873-5_21

Artificial Intelligence in Biological Activity Prediction

Author(s): João Correia, Tiago Resende, Delora Baptista, Miguel Rocha
Published in: Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, Issue 1005, 2020, Page(s) 164-172
DOI: 10.1007/978-3-030-23873-5_20