Deliverables
Website and social media accounts The project website and the Social Media accounts will contain information on the aims partners work progress and current state of the project Month of Delivery M3 responsible partner DARWIN
Establishment of a limited number of SB chassis of reference Identification of target sequences genomewide analysis of relevant genetic determinants of the above mentioned species for specific performance scenarios and definition of streamlined genomes optimally adapted to each setting Accreditation of a minimum of 46 chassis extensible to about one dozen as hosts of engineered pathways for bioproduction or bioremediation The deliverable will make explicit the lowhanging fruits that can be reached out during the Project lifetime in terms of standardized platforms that can be established and which will become a benchmark for future additions to the collection Month of delivery M12 Responsible partner CSIC
Standards and ownership reportStandards and ownership report In this report we provide a detailed description of the activities carried out in WP5 and a discussion on responsibility in relation to knowledge infrastructures for synthetic biology Month of delivery M35 Responsible partner UiO
Review of standards in SB: detailing the gaps, challenges and opportunitiesReview of standards in synthetic biology detailing the gaps challenges and opportunities Month of delivery M20 Responsible partner IMPERIAL
Online repository of existing and novel biocontainment strategies.Online repository of existing and novel biocontainment strategies Month of Delivery M34 Responsible partner Biofaction
White paper of the BIOROBOOST projectWhite paper of the BIOROBOOST project The white paper will summarize all the advances conclusions and recommendations resulting from the project and will especially target the policy community Month of Delivery M34 responsible partner UVEG
White paper on exemplar metadata standards for use in biological metrologyD12 White paper on exemplar metadata standards and biological interdependencies for use in biological metrology Month of delivery M24 Responsible partner IMPERIAL EDIN ETH
Standardisation and multi-cellular systems reportStandardisation and multicellular systems report Month of delivery M34 responsible partner UEDINThe deliverables of this WP will include an overview of the modelling performed as well as recommendations
Standardisation and mammalian systems reportStandardisation and mammalian systems report Month of delivery M30 responsible partner UEDINThe deliverables of this WP will include an overview of the modelling performed as well as recommendations
Standardisation and yeast systems reportStandardisation and yeast systems report Month of delivery M28 responsible partner UEDIN The deliverables of this WP3 will include an overview of the modelling performed as well as recommendations
Report about incorporation efforts of safety relevant data and information in SB standardsReport about incorporation efforts of safety relevant data and information in SB standards Month of Delivery M24 Responsible partner Biofaction
A conceptual analysis of standardsA conceptual analysis of standards The first deliverable of WP4 is a description of an analytic framework for studying standards within the scope of the project The description will explain core theories how those together conceptualise standardisation and how the framework lends itself to the empirical research that will characterise WP4 and WP5 This document will serve all of those involved in these two work packages but it will also offer the rest of the project team a different perspective on the type of work that they are carrying out As such it plays both a functional role and a critical role Month of delivery M21 Responsible partner UEDIN
Workshop report about the initiation of the interface between science, industry and risk assessment authoritiesWorkshop report about the initiation of the interface between science industry and risk assessment authorities Month of Delivery Month of the first workshop plus 3 Months Responsible partner EMBO
A community map WP4 will also deliver a detailed description of relevant parties involved in the ongoing design and use of the standard The communities listed and described will form a representative set of people objects institutions and practices The map will describe key relationships between the different communities The map will be constructed using methods commonly employed in the social sciences Specifically the projects participants will serve as the first actors identified and then by investigating their connections the map will be expanded in steps Short qualitative interviews may be used to acquire greater detail about relations when necessaryThe map will serve several ends First overviews of social groups and their relationships are crucial to social scientific research It will support the rest of work carried out in WP4 which focuses on the social infrastructure that supports standards including relationships between people and their institutions Second it will contribute to WP5 and help link both packages We place value in working together in order to sustain an extended social scientific perspective Third it will function as a basis against with which to track changes in the network something which has both social scientific benefits and can help scientific practitioners to comprehend how their community is developing and what vital parties may be missing This deliverable will be made possible by the empirical data gathered which will also be taken up and expanded in WP5 Month of delivery M24 Responsible partner UEDIN
Upgraded SEVA platformUpgraded SEVA platform with genetic tools for the set of chassis adopted in BIOROBOOST and made accessible to the community through an automated on line requestretrievaldelivery system operating on an Open Source basis Month of delivery M12 Responsible partner CSIC
Tools for modelling chassis-implant and chassis-niche interplayTools for modelling chassisimplant and chassisniche interplay Implementation of complete genomic and metabolic models of each of the chassis and the interactions with implants and with selected environmental parameters specific of each application setting SBML will be used to record such parameter sets And also the extension of SBOL to include the description of chassis bacterial compartments that is not possible with current SBOL version Month of delivery M12 Responsible partner UNEW
Publications
Author(s):
Juan Antonio Garcia-Martin, Max Chavarría, Victor de Lorenzo, Florencio Pazos
Published in:
Biology Methods and Protocols, Issue 5/1, 2020, ISSN 2396-8923
Publisher:
Oxford University Press
DOI:
10.1093/biomethods/bpaa025
Author(s):
See-Yeun Ting, Esteban Martínez-García, Shuo Huang, Savannah K. Bertolli, Katherine A. Kelly, Kevin J. Cutler, Elizabeth D. Su, Hui Zhi, Qing Tang, Matthew C. Radey, Manuela Raffatellu, S. Brook Peterson, Víctor de Lorenzo, Joseph D. Mougous
Published in:
Cell Host & Microbe, Issue 28/2, 2020, Page(s) 313-321.e6, ISSN 1931-3128
Publisher:
Cell Press
DOI:
10.1016/j.chom.2020.05.006
Author(s):
Alba Iglesias, Adriel Latorre-Pérez, James E. M. Stach, Manuel Porcar, Javier Pascual
Published in:
Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher:
Frontiers Media
DOI:
10.3389/fmicb.2020.00645
Author(s):
Jacob Beal, Angel Goñi‐Moreno, Chris Myers, Ariel Hecht, María del Carmen Vicente, Maria Parco, Markus Schmidt, Kenneth Timmis, Geoff Baldwin, Steffi Friedrichs, Paul Freemont, Daisuke Kiga, Elena Ordozgoiti, Maja Rennig, Leonardo Rios, Kristie Tanner, Víctor Lorenzo, Manuel Porcar
Published in:
EMBO reports, Issue 21/5, 2020, ISSN 1469-221X
Publisher:
Nature Publishing Group
DOI:
10.15252/embr.202050521
Author(s):
Maarten Van Brempt, Jim Clauwaert, Friederike Mey, Michiel Stock, Jo Maertens, Willem Waegeman, Marjan De Mey
Published in:
Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher:
Nature Publishing Group
DOI:
10.1038/s41467-020-19446-w
Author(s):
Gonzalo Durante-Rodríguez, David Páez-Espino, Víctor de Lorenzo
Published in:
Frontiers in Microbiology, Issue 12, 2021, ISSN 1664-302X
Publisher:
Frontiers Media
DOI:
10.3389/fmicb.2021.641440
Author(s):
David R. Espeso, Elena Algar, Esteban Martínez-García, Víctor de Lorenzo
Published in:
BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
Publisher:
BioMed Central
DOI:
10.1186/s12859-020-3490-1
Author(s):
Sergi Valverde
Published in:
Mètode Revista
de difusió de la
investigació, Issue 11, 2020, ISSN 2174-9221
Publisher:
University of Valencia
DOI:
10.7203/metode.11.16112
Author(s):
A. David Páez‐Espino, Pablo I. Nikel, Max Chavarría, Víctor Lorenzo
Published in:
Environmental Microbiology, Issue 22/6, 2020, Page(s) 2230-2242, ISSN 1462-2912
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/1462-2920.14991
Author(s):
Juhyun Kim, Angel Goñi-Moreno, Víctor de Lorenzo
Published in:
mBio, Issue 12/1, 2021, ISSN 2150-7511
Publisher:
ASM Journals
DOI:
10.1128/mbio.03685-20
Author(s):
Pavel Dvořák, Jozef Kováč, Víctor Lorenzo
Published in:
Microbial Biotechnology, Issue 13/4, 2020, Page(s) 1273-1283, ISSN 1751-7915
Publisher:
Wiley_Society for applied microbiology
DOI:
10.1111/1751-7915.13574
Author(s):
Leila Satari, Alba Guillén, Àngela Vidal-Verdú, Manuel Porcar
Published in:
Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-020-73913-4
Author(s):
Jonathan Tellechea-Luzardo, Charles Winterhalter, Paweł Widera, Jerzy Kozyra, Víctor de Lorenzo, Natalio Krasnogor
Published in:
ACS Synthetic Biology, Issue 9/3, 2020, Page(s) 536-545, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.9b00400
Author(s):
John McCarthy
Published in:
Integrative Biology, Issue 13/8, 2021, Page(s) 210-220, ISSN 1757-9708
Publisher:
Oxford University Press
DOI:
10.1093/intbio/zyab013
Author(s):
Tomas Aparicio, Akos Nyerges, Esteban Martínez-García, Víctor de Lorenzo
Published in:
iScience, Issue 23/3, 2020, Page(s) 100946, ISSN 2589-0042
Publisher:
Elsevier
DOI:
10.1016/j.isci.2020.100946
Author(s):
Benjamin Schwan, Christian Abendroth, Adriel Latorre-Pérez, Manuel Porcar, Cristina Vilanova, Christina Dornack
Published in:
Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher:
Frontiers Media
DOI:
10.3389/fmicb.2020.00867
Author(s):
David R. Espeso, Pavel Dvořák, Tomás Aparicio, Víctor Lorenzo
Published in:
Microbial Biotechnology, 2020, ISSN 1751-7915
Publisher:
John Wiley & Sons
DOI:
10.1111/1751-7915.13678
Author(s):
Ángeles Hueso‐Gil, Belén Calles, Víctor Lorenzo
Published in:
Environmental Microbiology, Issue 22/8, 2020, Page(s) 3535-3547, ISSN 1462-2912
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/1462-2920.15126
Author(s):
Jacob Beal, Natalie G. Farny, Traci Haddock-Angelli, Vinoo Selvarajah, Geoff S. Baldwin, Russell Buckley-Taylor, Markus Gershater, Daisuke Kiga, John Marken, Vishal Sanchania, Abigail Sison, Christopher T. Workman
Published in:
Communications Biology, Issue 3/1, 2020, ISSN 2399-3642
Publisher:
Springer Nature Limited
DOI:
10.1038/s42003-020-01127-5
Author(s):
Elena Algar, Yamal Al‐Ramahi, Víctor Lorenzo, Esteban Martínez‐García
Published in:
ChemBioChem, Issue 21/22, 2020, Page(s) 3255-3265, ISSN 1439-4227
Publisher:
John Wiley & Sons Ltd.
DOI:
10.1002/cbic.202000330
Author(s):
Victor De Lorenzo
Published in:
Mètode Revista
de difusió de la
investigació, Issue 11, 2020, Page(s) 67-73, ISSN 2174-9221
Publisher:
University of Valencia
DOI:
10.7203/metode.11.15975
Author(s):
Javier Pascual, Sarah Hahnke, Christian Abendroth, Thomas Langer, Patrice Ramm, Michael Klocke, Olaf Luschnig, Manuel Porcar
Published in:
Microbiology Resource Announcements, Issue 9/27, 2020, ISSN 2576-098X
Publisher:
AMS Journals
DOI:
10.1128/mra.00507-20
Author(s):
Michele S. Garfinkel
Published in:
Mètode Revista
de difusió de la
investigació, Issue 11, 2020, Page(s) 99-103, ISSN 2174-9221
Publisher:
University of Valencia
DOI:
10.7203/metode.11.16103
Author(s):
Juli Peretó, Manuel Porcar
Published in:
Mètode Revista
de difusió de la
investigació, Issue 11, 2020, ISSN 2174-9221
Publisher:
University of Valencia
DOI:
10.7203/metode.11.15981
Author(s):
Alejandro Arce‐Rodríguez, Pablo I. Nikel, Belén Calles, Max Chavarría, Raúl Platero, Tino Krell, Victor Lorenzo
Published in:
Environmental Microbiology, Issue 23/3, 2021, Page(s) 1732-1749, ISSN 1462-2912
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/1462-2920.15422
Author(s):
Víctor de Lorenzo, Natalio Krasnogor, Markus Schmidt
Published in:
New Biotechnology, Issue 60, 2021, Page(s) 44-51, ISSN 1871-6784
Publisher:
Elsevier BV
DOI:
10.1016/j.nbt.2020.08.004
Author(s):
Markus Schmidt, Vladimir Kubyshkin
Published in:
ChemBioChem, 2020, ISSN 1439-4227
Publisher:
John Wiley & Sons Ltd.
DOI:
10.1002/cbic.202000758
Author(s):
Manuel Porcar, Juli Peretó
Published in:
Mètode Revista
de difusió de la
investigació, Issue 10, 2019, ISSN 2174-9221
Publisher:
Mètode Sciences Journal- University of Valencia
DOI:
10.7203/metode.10.13229
Author(s):
Manuel Porcar, Adriel Latorre‐Pérez, Esther Molina‐Menor, Martí Domínguez
Published in:
EMBO reports, Issue 20/7, 2019, ISSN 1469-221X
Publisher:
Nature Publishing Group
DOI:
10.15252/embr.201948401
Author(s):
Esther Molina‐Menor, Kristie Tanner, Àngela Vidal‐Verdú, Juli Peretó, Manuel Porcar
Published in:
Microbial Biotechnology, Issue September 2019, 2019, ISSN 1751-7915
Publisher:
Wiley
DOI:
10.1111/1751-7915.13475
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):
Martí Domínguez, Juli Peretó, Manuel Porcar
Published in:
Microbial Biotechnology, 2019, ISSN 1751-7915
Publisher:
society for applied microbiology
DOI:
10.1111/1751-7915.13522
Author(s):
Manuel Porcar, Juli Peretó
Published in:
Life Sciences, Society and Policy, Issue 14/1, 2018, ISSN 2195-7819
Publisher:
BMC - Springer Nature
DOI:
10.1186/s40504-018-0087-9
Author(s):
Sarah Hahnke, Christian Abendroth, Javier Pascual, Thomas Langer, Francisco M. Codoñer, Patrice Ramm, Michael Klocke, Olaf Luschnig, Manuel Porcar
Published in:
Microbiology Resource Announcements, Issue 8/46, 2019, ISSN 2576-098X
Publisher:
American Society for Microbiology
DOI:
10.1128/mra.01203-19
Author(s):
Cristina Vilanova, Manuel Porcar
Published in:
Microbial Biotechnology, Issue 12/1, 2019, Page(s) 8-10, ISSN 1751-7915
Publisher:
Society for Applied Microbiology
DOI:
10.1111/1751-7915.13326
Author(s):
Manuel Porcar
Published in:
Life, Issue 9/1, 2019, Page(s) 5, ISSN 2075-1729
Publisher:
MDPI
DOI:
10.3390/life9010005
Author(s):
Matthew Crowther, Lewis Grozinger, Matthew Pocock, Christopher P. D. Taylor, James A. McLaughlin, Göksel Mısırlı, Bryan A. Bartley, Jacob Beal, Angel Goñi-Moreno, Anil Wipat
Published in:
ACS Synthetic Biology, 2020, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.9b00470
Author(s):
Thomas Decoene, Sofie L. De Maeseneire, Marjan De Mey
Published in:
PLOS ONE, Issue 14/11, 2019, Page(s) e0224476, ISSN 1932-6203
Publisher:
Public Library of Science
DOI:
10.1371/journal.pone.0224476
Author(s):
Ruud Stoof, Alexander Wood, Ángel Goñi-Moreno
Published in:
ACS Synthetic Biology, Issue 8/9, 2019, Page(s) 2007-2016, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.9b00022
Author(s):
Angel Goñi-Moreno, Fernando de la Cruz, Alfonso Rodríguez-Patón, Martyn Amos
Published in:
Life, Issue 9/1, 2019, Page(s) 14, ISSN 2075-1729
Publisher:
MDPI
DOI:
10.3390/life9010014
Author(s):
Göksel Mısırlı, Renee Taylor, Angel Goñi-Moreno, James Alastair McLaughlin, Chris Myers, John H. Gennari, Phillip Lord, Anil Wipat
Published in:
ACS Synthetic Biology, Issue 8/7, 2019, Page(s) 1498-1514, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.8b00532
Author(s):
Martina Carrillo, Marcel Wagner, Florian Petit, Amelie Dransfeld, Anke Becker, Tobias J. Erb
Published in:
ACS Synthetic Biology, Issue 8/11, 2019, Page(s) 2451-2456, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.9b00220
Author(s):
Kristie Tanner, Christopher P. Mancuso, Juli Peretó, Ahmad S. Khalil, Cristina Vilanova, Javier Pascual
Published in:
International Journal of Systematic and Evolutionary Microbiology, Issue 70/3, 2020, Page(s) 1814-1821, ISSN 1466-5026
Publisher:
Society for General Microbiology
DOI:
10.1099/ijsem.0.003977
Author(s):
Esteban Martínez-García, Angel Goñi-Moreno, Bryan Bartley, James McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo
Published in:
Nucleic Acids Research, Issue 48/D1, 2019, Page(s) D1164-D1170, ISSN 0305-1048
Publisher:
Oxford University Press
DOI:
10.1093/nar/gkz1024
Author(s):
Hueso-Gil, Ángeles, Nyerges, Ákos, Pál, Csaba, Calles, Belén, de Lorenzo, Víctor
Published in:
ACS Synthetic Biology, Issue December 3, 2019, 2019, Page(s) 104–114, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.9b00375
Author(s):
Belén Calles, Ángel Goñi‐Moreno, Víctor Lorenzo
Published in:
Molecular Systems Biology, Issue 15/12, 2019, ISSN 1744-4292
Publisher:
Nature Publishing Group
DOI:
10.15252/msb.20188777
Author(s):
Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, Víctor Lorenzo
Published in:
Environmental Microbiology, Issue 22/1, 2019, Page(s) 45-58, ISSN 1462-2912
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/1462-2920.14814
Author(s):
Elena Velázquez, Víctor de Lorenzo,Yamal Al-Ramahi
Published in:
ACS Synthetic Biology, Issue August 16, 2019, 2019, Page(s) 2186–2193, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.9b00293
Author(s):
Alberto Sánchez-Pascuala, Lorena Fernández-Cabezón, Víctor de Lorenzo, Pablo I. Nikel
Published in:
Metabolic Engineering, Issue 54, 2019, Page(s) 200-211, ISSN 1096-7176
Publisher:
Academic Press
DOI:
10.1016/j.ymben.2019.04.005
Author(s):
Esteban Martínez-García, Víctor de Lorenzo
Published in:
Current Opinion in Biotechnology, Issue 59, 2019, Page(s) 111-121, ISSN 0958-1669
Publisher:
Elsevier BV
DOI:
10.1016/j.copbio.2019.03.012
Author(s):
Sofía Fraile, María Briones, Mónica Revenga-Parra, Víctor de Lorenzo, Encarnación Lorenzo, Esteban Martínez-García
Published in:
ACS Synthetic Biology, Issue 10/8, 2021, Page(s) 2049-2059, ISSN 2161-5063
Publisher:
American Chemical Society
DOI:
10.1021/acssynbio.1c00227
Author(s):
Pablo Schyfter
Published in:
Mètode Revista
de difusió de la
investigació, Issue 11, 2020, ISSN 2174-9221
Publisher:
University of Valencia
DOI:
10.7203/metode.11.16013
Author(s):
Kristie Tanner, Esther Molina‐Menor, Adriel Latorre‐Pérez, Àngela Vidal‐Verdú, Cristina Vilanova, Juli Peretó, Manuel Porcar
Published in:
Microbial Biotechnology, Issue 13/6, 2020, Page(s) 1819-1830, ISSN 1751-7915
Publisher:
John Wiley & Sons
DOI:
10.1111/1751-7915.13620
Author(s):
Özlem Akkaya, Tomás Aparicio, Danilo Pérez‐Pantoja, Víctor Lorenzo
Published in:
Environmental Microbiology, Issue 23/3, 2021, Page(s) 1608-1619, ISSN 1462-2912
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/1462-2920.15384
Author(s):
Huseyin Tas, Lewis Grozinger, Ruud Stoof, Victor de Lorenzo, Ángel Goñi-Moreno
Published in:
Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher:
Nature Publishing Group
DOI:
10.1038/s41467-020-20656-5
Author(s):
Marko Storch, Matthew C Haines, Geoff S Baldwin
Published in:
Synthetic Biology, Issue 5/1, 2020, ISSN 2397-7000
Publisher:
Oxford University Press
DOI:
10.1093/synbio/ysaa010
Author(s):
Pavel Dvořák, Carlos Alvarez‐Carreño, Sergio Ciordia, Alberto Paradela, Víctor Lorenzo
Published in:
Environmental Microbiology, Issue 23/8, 2021, Page(s) 4418-4433, ISSN 1462-2912
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/1462-2920.15628
Author(s):
Gonzalo Durante-Rodríguez, Belén Calles, Víctor Lorenzo, Pablo Nikel
Published in:
BIO-PROTOCOL, Issue 10/14, 2020, ISSN 2331-8325
Publisher:
Bio-protocol
DOI:
10.21769/bioprotoc.3688
Author(s):
Pablo I. Nikel, Tobias Fuhrer, Max Chavarría, Alberto Sánchez-Pascuala, Uwe Sauer, Víctor de Lorenzo
Published in:
The ISME Journal, Issue 15/6, 2021, Page(s) 1751-1766, ISSN 1751-7362
Publisher:
Nature Publishing Group
DOI:
10.1038/s41396-020-00884-9
Author(s):
Jennifer S. Hallinan, Anil Wipat, Richard Kitney, Simon Woods, Ken Taylor, Angel Goñi‐Moreno
Published in:
Engineering Biology, Issue 3/2, 2019, Page(s) 25-31, ISSN 2398-6182
Publisher:
John Wiley & Sons
DOI:
10.1049/enb.2019.0001
Author(s):
Tomás Aparicio, Víctor de Lorenzo, Esteban Martínez-García
Published in:
Horizontal Gene Transfer - Methods and Protocols, Issue 2075, 2020, Page(s) 383-398, ISBN 978-1-4939-9876-0
Publisher:
Springer US
DOI:
10.1007/978-1-4939-9877-7_27
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