Deliverables
Updated models publicly available on the DDDeCaF platform and as SBML exchangeable files
Pathway database with all ranking and analysis metricsDatabase containing the pathways and ranking metrics used
Report detailing the communication channels, such as the website and social media accounts
Project visuals and messagingReport detailing project visuals and messaging plaforms
Sustainability appraisal and risk assessment of 10 target moleculesPublications
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Author(s):
Weilandt, Daniel Robert
Published in:
2020
Publisher:
EPFL
DOI:
10.5075/epfl-thesis-7900
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
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
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
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
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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