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

Combinatorial Optimization of Succinate Production in Escherichia coli

Author(s): Vítor Pereira, Miguel Rocha
Published in: Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021), 2021, ISBN 978-3-030-86257-2
Publisher: Springer
DOI: 10.1007/978-3-030-86258-9_16

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, ISBN 978-3-030-23872-8
Publisher: Springer International Publishing
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, ISBN 978-3-030-23872-8
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-23873-5_20

Chapter 14 - A retrobiosynthetic approach for production, conversion, sensing, dynamic regulation and degradation of molecules

Author(s): Pablo Carbonell
Published in: New Frontiers and Applications of Synthetic Biology, 2022, Page(s) 205-214, ISBN 978-0-12-824469-2
Publisher: Academic Press
DOI: 10.1016/b978-0-12-824469-2.00024-5

Modulation of the cell wall protein Ecm33p in yeast Saccharomyces cerevisiae improves the production of small metabolites

Author(s): Verónica Ramos-Viana; Iben Møller-Hansen; Paul Kempen; Irina Borodina
Published in: FEMS Yeast Research, Issue 1, 2022, ISSN 1567-1356
Publisher: Blackwell
DOI: 10.1093/femsyr/foac037

Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules

Author(s): Francesco Del Carratore, Erik KR Hanko, Rainer Breitling, Eriko Takano
Published in: Current Opinion in Biotechnology, 2022, ISSN 1879-0429
Publisher: Elsevier
DOI: 10.1016/j.copbio.2022.102762

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Author(s): Omid Oftadeh, Pierre Salvy, Maria Masid, Maxime Curvat, Ljubisa Miskovic & Vassily Hatzimanikatis
Published in: Nature Communications, Issue 12, 2021, Page(s) 4790, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-25158-6

TFBMiner: A User-Friendly Command Line Tool for the Rapid Mining of Transcription Factor-Based Biosensors

Author(s): Erik K. R. Hanko, Tariq A. Joosab Noor Mahomed, Ruth A. Stoney, and Rainer Breitlin
Published in: ACS Synthetic Biology, 2023, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.2c00679

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Author(s): Subham Choudhury; Michael Moret; Pierre Salvy; Daniel Weilandt; Vassily Hatzimanikatis; Ljubisa Miskovic
Published in: Nature Machine Intelligence, Issue 1, 2022, ISSN 2522-5839
Publisher: Nature Group
DOI: 10.1101/2022.01.06.475020

New targets for drug design: importance of nsp14/nsp10 complex formation for the 3'-5' exoribonucleolytic activity on SARS-CoV-2.

Author(s): Margarida Saramago; Cátia Bárria; Vanessa G. Costa; Caio S. Souza; Sandra C. Viegas; Susana Domingues; Diana Lousa; Cláudio M. Soares; Cecília M. Arraiano; Rute G. Matos
Published in: The Febs Journal, Issue 1, 2021, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.15815

NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions

Author(s): Evangelia Vayena; Anush Chiappino-Pepe; Homa MohammadiPeyhani; Yannick Francioli; Noushin Hadadi; Meriç Ataman; Jasmin Hafner; Stavros Pavlou; Vassily Hatzimanikatis
Published in: PNAS, Issue 1, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1101/2022.02.10.479881

Engineering Saccharomyces cerevisiae for the de novo Production of Halogenated Tryptophan and Tryptamine Derivatives

Author(s): Nicholas Milne; Javier Sáez‐Sáez; Annette Munch Nielsen; Jane Dannow Dyekjær; Daniela Rago; Mette Kristensen; Tune Wulff; Irina Borodina
Published in: ChemistryOpen, Issue 1, 2023, ISSN 2191-1363
Publisher: Weinheim: Wiley-VCH-Verl.
DOI: 10.1002/open.202200266

Rational strain design with minimal phenotype perturbation

Author(s): Bharath Narayanan; Daniel Weilandt; Maria Masid; Ljubisa Miskovic; Vassily Hatzimanikatis
Published in: Nature Communications, Issue 1, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2022.11.14.516382

Metabolic Engineering of Saccharomyces cerevisiae for Rosmarinic Acid Production.

Author(s): Mahsa Babaei; Gheorghe Manuel Borja Zamfir; Xiao Chen; Hanne Bjerre Christensen; Mette Kristensen; Jens Nielsen; Jens Nielsen; Irina Borodina
Published in: ACS Synthetic Biology, Issue 6, 2020, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00048

Generative deep learning for targeted compound design

Author(s): Tiago J. C. Sousa; João Correia; Vitor Pereira; Miguel Rocha
Published in: Journal of Chemical Information and Modeling, Issue 61 (11), 2021, Page(s) 5343–5361, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.0c01496

Microbial production of the plant flavanone hesperetin from caffeic acid

Author(s): Erik K. R. Hanko; João Correia; Caio S. Souza; Alison Green; Jakub Chromy; Ruth Stoney; Cunyu Yan; Eriko Takano; Diana Lousa; Cláudio M. Soares; Rainer Breitling
Published in: BMC Research Notes, Issue 1, 2023, ISSN 1756-0500
Publisher: BioMed Central
DOI: 10.21203/rs.3.rs-2742541/v1

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Author(s): Asli Sahin; Daniel R. Weilandt; Vassily Hatzimanikatis
Published in: Nature Communications, Issue 1, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-38159-4

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol

Author(s): Mark S Dunstan, Christopher J Robinson, Adrian J Jervis, Cunyu Yan, Pablo Carbonell, Katherine A Hollywood, Andrew Currin, Neil Swainston, Rosalind Le Feuvre, Jason Micklefield, Jean-Loup Faulon, Rainer Breitling, Nicholas Turner, Eriko Takano, Nigel S Scrutton
Published in: Synthetic Biology, Issue 5 (1), 2020, ISSN 2397-7000
Publisher: Oxford University Press
DOI: 10.1093/synbio/ysaa012

An integrated yeast-based process for cis,cis-muconic acid production

Author(s): Guokun Wang; Guokun Wang; Aline Tavares; Simone Schmitz; Simone Schmitz; Lucas Gabriel Souza França; Hugo Almeida; João Cavalheiro; Ana Carolas; Süleyman Øzmerih; Lars M. Blank; Bruno Sommer Ferreira; Irina Borodina
Published in: Biotechnology and Bioengineering, Issue 7, 2021, ISSN 0006-3592
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.27992

Engineering the oleaginous yeast Yarrowia lipolytica for high-level resveratrol production

Author(s): Javier Sáez-Sáez; Guokun Wang; Eko Roy Marella; Suresh Sudarsan; Marc Cernuda Pastor; Irina Borodina
Published in: Metabolic Engineering, 2020, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2020.08.009

Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets

Author(s): Mahsa Babaei, Philip Tinggaard Thomsen, Marc Cernuda Pastor, Michael Krogh Jensen, and Irina Borodina
Published in: ACS Synthetic Biology, 2024, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.3c00396

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

Author(s): Irene Otero-Muras, Pablo Carbonell
Published in: Metabolic Engineering, Issue 63, 2020, Page(s) 61-80, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2020.11.012

Resveratrol Production from Hydrothermally Pretreated Eucalyptus Wood Using Recombinant Industrial Saccharomyces cerevisiae Strains.

Author(s): Carlos Costa; Iben Møller-Hansen; Aloia Romaní; José A. Teixeira; Irina Borodina; Lucília Domingues
Published in: ACS Synthetic Biology, Issue 6, 2021, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00120

Valorisation of wine wastes by de novo biosynthesis of resveratrol using a recombinant xylose-consuming industrial Saccharomyces cerevisiae strain

Author(s): Carlos E. Costa; Aloia Romaní; Iben Møller-Hansen; José A. Teixeira; Irina Borodina; Lucília Domingues
Published in: Green Chemistry, Issue 1, 2022, ISSN 1463-9270
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2gc02429b

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
Publisher: BioMed Central
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
Publisher: Academic Press
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
Publisher: Academic Press
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
Publisher: BioMed Central
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
Publisher: Oxford University Press
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
Publisher: Nature Publishing Group
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
Publisher: American Chemical Society
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
Publisher: Oxford University Press
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
Publisher: Elsevier
DOI: 10.1016/j.ifacol.2019.12.228

The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs

Author(s): Margarida Saramago; Vanessa Costa; Caio Souza; Cátia Bárria; Susana Domingues; Sandra Viegas; Diana Lousa; Cláudio Soares; Cecília Arraiano; Rute Matos
Published in: Microorganisms, Issue 1, 2022, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms10020342

In silico design and automated learning to boost next-generation smart biomanufacturing.

Author(s): Pablo Carbonell; Pablo Carbonell; Rosalind Le Feuvre; Eriko Takano; Nigel S. Scrutton
Published in: Synthetic Biology, Issue 5 (1), 2020, Page(s) ysaa020, ISSN 2397-7000
Publisher: Oxford University Press
DOI: 10.1093/synbio/ysaa020

Harnessing the yeast Saccharomyces cerevisiae for the production of fungal secondary metabolites

Author(s): Guokun Wang; Douglas B. Kell; Irina Borodina
Published in: Essays in Biochemistry, 2021, ISSN 0071-1365
Publisher: Portland Press, Ltd.
DOI: 10.1042/ebc20200137

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power

Author(s): Jasmin Hafner, Homa MohammadiPeyhani, Anastasia Sveshnikova, Alan Scheidegger, and 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

MEWpy: a computational strain optimization workbench in Python

Author(s): Vítor Pereira, Fernando Cruz, Miguel Rocha
Published in: Bioinformatics, Issue 37 (16), 2021, Page(s) 2494-2496, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab013

Expansion of EasyClone-MarkerFree toolkit for Saccharomyces cerevisiae genome with new integration sites

Author(s): Mahsa Babaei; Luisa Sartori; Alexey Karpukhin; Dmitrii Abashkin; Elena Matrosova; Irina Borodina
Published in: FEMS Yeast Research, Issue 3, 2021, ISSN 1567-1356
Publisher: Blackwell
DOI: 10.1093/femsyr/foab027

Combining multi-objective evolutionary algorithms with deep generative models towards focused molecular design

Author(s): Tiago J. C. Sousa; João Correia; Vitor Pereira; Miguel Rocha
Published in: Applications of Evolutionary Computation, Issue 24th International Conference, EvoApplications 2021, Held as Part of EvoStar 2021, Virtual Event, April 7–9, 2021, Proceedings, 2021, Page(s) 81-96, ISBN 978-3-030-72699-7
Publisher: Springer
DOI: 10.1007/978-3-030-72699-7_6

Variational Autoencoders and Evolutionary Algorithms for Targeted Novel Enzyme Design

Author(s): Miguel Martins; Miguel Rocha; Vitor Pereira
Published in: 2022 IEEE Congress on Evolutionary Computation (CEC), Issue 1, 2022, ISBN 9788070439876
Publisher: IEEE
DOI: 10.1109/cec55065.2022.9870421

Gene variant space for biosensor-based dynamic regulation

Author(s): Maria Guadalupe Camarena; Yadira Boada; Jesús Picó; Pablo Carbonell
Published in: Actas de las Jornadas de Automática, Issue yearly, 2021, ISBN 978-84-9749-804-3
Publisher: CEA-IFAC
DOI: 10.17979/spudc.9788497498043.485

Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design

Author(s): João Correia; Vítor Pereira; Miguel Rocha
Published in: GECCO '23: Proceedings of the Genetic and Evolutionary Computation Conference, Issue 1, 2023
Publisher: Association for Computing Machinery
DOI: 10.1145/3583131.3590413

Engineering microbial hosts for the production of aromatic compounds

Author(s): Saez Saez, Javier (PhD Student)Borodina, Irina (Main Supervisor)Babaei, Mahsa (Supervisor)Ingemann Jensen, Sheila (Supervisor)Morrissey, John (Examiner)Siewers, Verena (Examiner)
Published in: 2023
Publisher: DTU

Modeling biochemical reaction networks in complex intracellular environments

Author(s): Weilandt, Daniel Robert
Published in: 2020
Publisher: EPFL
DOI: 10.5075/epfl-thesis-7900

Symbolic Kinetic Models in Python (SKiMpy): Intuitive modeling of large-scale biological kinetic models

Author(s): Daniel R. Weilandt, Pierre Salvy, Maria Masid, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.17.476618

Developing an enzyme selection tool supporting multiple hosts contexts

Author(s): María Camarena, Pablo Carbonell
Published in: bioRxiv, 2021, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.09.09.459461

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

Author(s): Anastasia Sveshnikova, Homa MohammadiPeyhani, Vassily Hatzimanikatis
Published in: bioRxiv, 2021, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.12.06.471405

ATLASx: a computational map for the exploration of biochemical space

Author(s): Homa Mohammadi-Peyhani, Jasmin Hafner, Anastasia Sveshnikova, Victor Viterbo, Vassily Hatzimanikatis
Published in: bioRxiv, 2021, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.02.17.431583

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Author(s): Subham Choudhury; Bharath Narayanan; Michael Moret; Vassily Hatzimanikatis; Ljubisa Miskovic
Published in: bioRxiv, Issue 1, 2023
Publisher: bioRxiv
DOI: 10.1101/2023.02.21.529387

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