Resultado final
Novel enzyme and pathway candidates publicly available
Metabolic interaction simulation software publically available
First version of the database providing novel functional and enzyme annotations
Genomic/metagenomic gene catalog database
Multiple genomic and metagenomic resources will be mined to produce a normalized gene catalog database EMBL inhouse STRING and eggNOG databases currently providing proteinprotein interactions and orthology information for more than 3600 qualityfiltered genomes will be used to obtain data from fully sequenced organisms Additionally 2000 human gut samples and 240 ocean samples will be exploited to extract gene pools from unculturable organisms The expected size of the final database is estimated to be over 50M sequences Given the amount and heterogeneity of the source data optimal database design and administration will be critical Therefore this task will be carried out with the technical support of biobyte Solutions P9
Algorithms for optimization using model with protein synthesis and secretionLarge-scale kinetic models of relevant production hosts
Cloud hosting solution for web-services on CSC compute infrastructure
Models for quantitative simulation of protein secretion
Results of optimization for selected case-studies
Interactive pathway visualization components are available on the DeCaF platform
A toolbox for integration of metabolomics data into thermodynamically-curated GEMs
A toolbox for integration of metabolomics data into thermodynamicallycurated GEMs
Community design software publically availableIntegration of gene and pathway mining components from WP2
Models for quantitative simulation of protein secretion by fungi
Models for quantitative simulation of protein secretion by bacterial hosts
Community model reconstruction pipeline publically available
Thermodynamically-curated GEMs with integrated metabolomics data
Software for designing synthetic microbial communities
Identifier translation service for metabolite, enzyme, gene, protein and reaction identifiers
Software for simulating metabolic interactions in microbial communities
General metaheuristics-based optimization framework
Functional annotation of gene catalog
Upload and access control system for processed omics data
Web-based cell factory and community design platform (DeCaF) hosted on CSC infrastructure
Algorithms for optimization using community models
Consortium-wide repository of methods, algorithms, software, and web-services that can be deployed as docker containers
Large-scale kinetic models of one fungal organism with integrated enzyme biosynthesis module
Models for yeast, E. coli and two other microorganisms that accounts for protein content
Large-scale kinetic models of one bacterial organism with integrated enzyme biosynthesis module
Algorithms for optimization using large-scale kinetic models
Integration of the visualization components with public data sources is implemented
Functional annotation pipeline established
Bioinformatics pipeline for building community metabolic models
Annual workshop
Periodic newslettersAnnual newsletters distributed every 12 months
Technology Transfer Activities, including training to SMEs1st annual DeCaF workshop
Annual workshops
3rd annual DeCaF workshopAnnual workshop
Project website: the report will provide a functional description of the project website, its main sections and how the access to the private area is implemented.Project website: the report will provide a functional description of the project website, its main sections and how the access to the private area is implemented
Press release about the launching of the projectFirst version of data management plan as required by Open Research Data Pilot
Publicaciones
Autores:
Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu, Martina Klünemann, Michael Kuhn, Marco Galardini, Paula Jouhten, Aleksej Zelezniak, Georg Zeller, Peer Bork, Athanasios Typas, Kiran Raosaheb Patil
Publicado en:
Nature Microbiology, Edición 3/4, 2018, Página(s) 514-522, ISSN 2058-5276
Editor:
Nature Publishing Group
DOI:
10.1038/s41564-018-0123-9
Autores:
René Verwaal, Nathalie Buiting-Wiessenhaan, Sacha Dalhuijsen, Johannes A. Roubos
Publicado en:
Yeast, Edición 35/2, 2018, Página(s) 201-211, ISSN 0749-503X
Editor:
John Wiley & Sons Inc.
DOI:
10.1002/yea.3278
Autores:
Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Robert Hayward, Sofia K. Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R. Jackson, Qinghong Li, Peer Bork
Publicado en:
Microbiome, Edición 6/1, 2018, ISSN 2049-2618
Editor:
Springer Nature
DOI:
10.1186/s40168-018-0450-3
Autores:
Machado, Daniel; Herrgard, Markus; Rocha, Isabel
Publicado en:
PLoS Computational Biology, Edición 1, 2016, ISSN 1553-7358
Editor:
Public Library of Science
DOI:
10.1371/journal.pcbi.1005140
Autores:
Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen
Publicado en:
BMC Systems Biology, Edición 13/1, 2019, ISSN 1752-0509
Editor:
BioMed Central
DOI:
10.1186/s12918-018-0673-8
Autores:
Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
Publicado en:
Bioinformatics, 2018, ISSN 1367-4803
Editor:
Oxford University Press
DOI:
10.1093/bioinformatics/bty499
Autores:
Daniel Machado, Sergej Andrejev, Melanie Tramontano, Kiran Raosaheb Patil
Publicado en:
Nucleic Acids Research, Edición 46/15, 2018, Página(s) 7542-7553, ISSN 0305-1048
Editor:
Oxford University Press
DOI:
10.1093/nar/gky537
Autores:
Ilaria Massaiu, Lorenzo Pasotti, Nikolaus Sonnenschein, Erlinda Rama, Matteo Cavaletti, Paolo Magni, Cinzia Calvio, Markus J. Herrgård
Publicado en:
Microbial Cell Factories, Edición 18/1, 2019, ISSN 1475-2859
Editor:
BioMed Central
DOI:
10.1186/s12934-018-1052-2
Autores:
Carlos G Acevedo-Rocha, Luisa S Gronenberg, Matthias Mack, Fabian M Commichau, Hans J Genee
Publicado en:
Current Opinion in Biotechnology, Edición 56, 2019, Página(s) 18-29, ISSN 0958-1669
Editor:
Elsevier BV
DOI:
10.1016/j.copbio.2018.07.006
Autores:
Douglas McCloskey, Julia Xu, Lars Schrübbers, Hanne B. Christensen, Markus J. Herrgård
Publicado en:
Metabolic Engineering, Edición 47, 2018, Página(s) 383-392, ISSN 1096-7176
Editor:
Academic Press
DOI:
10.1016/j.ymben.2018.04.009
Autores:
Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund, Jennifer L. Anderson, Nadejda A. Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema, Mia R. Maltz, Sunil Mundra, Pål Axel Olsson, Mari Pent, Sergei Põlme, Shinichi Sunagawa, Martin Ryberg, Leho Tedersoo, Peer Bork
Publicado en:
Nature, Edición 560/7717, 2018, Página(s) 233-237, ISSN 0028-0836
Editor:
Nature Publishing Group
DOI:
10.1038/s41586-018-0386-6
Autores:
Xavier, Joana C.; Patil, Kiran Raosaheb; Rocha, Isabel
Publicado en:
Metabolic Engineering, 2017, ISSN 1096-7176
Editor:
Academic Press
DOI:
10.1016/j.ymben.2016.12.002
Autores:
Kristian Jensen, Joao G.R. Cardoso, Nikolaus Sonnenschein
Publicado en:
The Journal of Open Source Software, Edición 2/9, 2017, ISSN 2475-9066
Editor:
The Journal of Open Source Software
DOI:
10.21105/joss.00139
Autores:
Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
Publicado en:
Nucleic Acids Research, Edición 45/D1, 2017, Página(s) D529-D534, ISSN 0305-1048
Editor:
Oxford University Press
DOI:
10.1093/nar/gkw989
Autores:
Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Publicado en:
Molecular Biology and Evolution, 2017, ISSN 0737-4038
Editor:
Oxford University Press
DOI:
10.1093/molbev/msx148
Autores:
Paula Jouhten, Jaime Huerta-Cepas, Peer Bork, Kiran Raosaheb Patil
Publicado en:
Metabolic Engineering, Edición 40, 2017, Página(s) 1-4, ISSN 1096-7176
Editor:
Academic Press
DOI:
10.1016/j.ymben.2017.02.010
Autores:
Anne Sofie L?rke Hansen, Rebecca M. Lennen, Nikolaus Sonnenschein, Markus J Herrg?rd
Publicado en:
Current Opinion in Biotechnology, Edición 45, 2017, Página(s) 85-91, ISSN 0958-1669
Editor:
Elsevier BV
DOI:
10.1016/j.copbio.2016.11.018
Autores:
Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha
Publicado en:
PLOS Computational Biology, Edición 14/11, 2018, Página(s) e1006556, ISSN 1553-7358
Editor:
PLOS Computational Biology
DOI:
10.1371/journal.pcbi.1006556
Autores:
Guillem Salazar, Lucas Paoli, Adriana Alberti, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sánchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller, Margaux Carmichael, Céline Dimier, Joannie Ferland, Stefani
Publicado en:
Cell, Edición 179/5, 2019, Página(s) 1068-1083.e21, ISSN 0092-8674
Editor:
Cell Press
DOI:
10.1016/j.cell.2019.10.014
Autores:
João G R Cardoso, Ahmad A Zeidan, Kristian Jensen, Nikolaus Sonnenschein, Ana Rute Neves, Markus J Herrgård
Publicado en:
Bioinformatics, Edición 34/13, 2018, Página(s) 2319-2321, ISSN 1367-4803
Editor:
Oxford University Press
DOI:
10.1093/bioinformatics/bty108
Autores:
Denis Shepelin, Anne Hansen, Rebecca Lennen, Hao Luo, Markus Herrgård
Publicado en:
Genes, Edición 9/5, 2018, Página(s) 249, ISSN 2073-4425
Editor:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/genes9050249
Autores:
Thordis Kristjansdottir, Elleke F. Bosma, Filipe Branco dos Santos, Emre Özdemir, Markus J. Herrgård, Lucas França, Bruno Ferreira, Alex T. Nielsen, Steinn Gudmundsson
Publicado en:
Microbial Cell Factories, Edición 18/1, 2019, ISSN 1475-2859
Editor:
BioMed Central
DOI:
10.1186/s12934-019-1229-3
Autores:
Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
Publicado en:
BMC Bioinformatics, Edición 20/1, 2019, ISSN 1471-2105
Editor:
BioMed Central
DOI:
10.1186/s12859-019-2934-y
Autores:
Osvaldo D. Kim, Miguel Rocha, Paulo Maia
Publicado en:
Frontiers in Microbiology, Edición 9, 2018, ISSN 1664-302X
Editor:
Frontiers Media
DOI:
10.3389/fmicb.2018.01690
Autores:
João G. R. Cardoso, Kristian Jensen, Christian Lieven, Anne Sofie Lærke Hansen, Svetlana Galkina, Moritz Beber, Emre Özdemir, Markus J. Herrgård, Henning Redestig, Nikolaus Sonnenschein
Publicado en:
ACS Synthetic Biology, Edición 7/4, 2018, Página(s) 1163-1166, ISSN 2161-5063
Editor:
American Chemical Society
DOI:
10.1021/acssynbio.7b00423
Autores:
Falk Hildebrand, Lucas Moitinho-Silva, Sonja Blasche, Martin T Jahn, Toni Ingolf Gossmann, Jaime Huerta-Cepas, Rajna Hercog, Mechthild Luetge, Mohammad Bahram, Anna Pryszlak, Renato J Alves, Sebastian M Waszak, Ana Zhu, Lumeng Ye, Paul Igor Costea, Steven Aalvink, Clara Belzer, Sofia K Forslund, Shinichi Sunagawa, Ute Hentschel, Christoph Merten, Kiran Raosaheb Patil, Vladimir Benes, Peer Bork
Publicado en:
Gut, Edición 68/10, 2019, Página(s) 1781-1790, ISSN 0017-5749
Editor:
BMJ Publishing Group
DOI:
10.1136/gutjnl-2018-317715
Autores:
Sofia Ferreira, Rui Pereira, Filipe Liu, Paulo Vilaça, Isabel Rocha
Publicado en:
Biotechnology for Biofuels, Edición 12/1, 2019, ISSN 1754-6834
Editor:
Biotechnology and Biofuels
DOI:
10.1186/s13068-019-1565-x
Autores:
Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Dias
Publicado en:
BMC Bioinformatics, Edición 20/1, 2019, ISSN 1471-2105
Editor:
BioMed Central
DOI:
10.1186/s12859-019-3038-4
Autores:
Bruna S. Fernandes, Oscar Dias, Gisela Costa, Antonio A. Kaupert Neto, Tiago F. C. Resende, Juliana V. C. Oliveira, Diego M. Riaño-Pachón, Marcelo Zaiat, José G. C. Pradella, Isabel Rocha
Publicado en:
BMC Biotechnology, Edición 19/1, 2019, ISSN 1472-6750
Editor:
BioMed Central
DOI:
10.1186/s12896-019-0529-3
Autores:
Oscar Dias, João Saraiva, Cristiana Faria, Mario Ramirez, Francisco Pinto, Isabel Rocha
Publicado en:
Frontiers in Microbiology, Edición 10, 2019, ISSN 1664-302X
Editor:
Frontiers Media
DOI:
10.3389/fmicb.2019.01283
Autores:
Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas S. B. Schmidt, Simone S. Li, João F. Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
Publicado en:
The ISME Journal, Edición 14/5, 2020, Página(s) 1247-1259, ISSN 1751-7362
Editor:
Nature Publishing Group
DOI:
10.1038/s41396-020-0600-z
Autores:
Vítor Vieira, Miguel Rocha
Publicado en:
Bioinformatics, Edición 35/24, 2019, Página(s) 5361-5362, ISSN 1367-4803
Editor:
Oxford University Press
DOI:
10.1093/bioinformatics/btz598
Autores:
Kristian Jensen, Valentijn Broeken, Anne Sofie Lærke Hansen, Nikolaus Sonnenschein, Markus J. Herrgård
Publicado en:
Metabolic Engineering Communications, Edición 8, 2019, Página(s) e00087, ISSN 2214-0301
Editor:
Elsevier BV
DOI:
10.1016/j.mec.2019.e00087
Autores:
Josi Buerger, Luisa S. Gronenberg, Hans Jasper Genee, Morten O.A. Sommer
Publicado en:
Current Opinion in Biotechnology, Edición 59, 2019, Página(s) 85-92, ISSN 0958-1669
Editor:
Elsevier BV
DOI:
10.1016/j.copbio.2019.02.014
Autores:
Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Publicado en:
Microbiome, Edición 7/1, 2019, ISSN 2049-2618
Editor:
Microbiome
DOI:
10.1186/s40168-019-0684-8
Autores:
Daniel R. Weilandt, Vassily Hatzimanikatis
Publicado en:
Biophysical Journal, Edición 117/2, 2019, Página(s) 355-368, ISSN 0006-3495
Editor:
Biophysical Society
DOI:
10.1016/j.bpj.2019.06.017
Autores:
Pierre Salvy, Vassily Hatzimanikatis
Publicado en:
Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor:
Nature Publishing Group
DOI:
10.1038/s41467-019-13818-7
Autores:
Hongzhong Lu, Feiran Li, Benjamín J. Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, Petre Mihail Anton, Dimitra Lappa, Christian Lieven, Moritz Emanuel Beber, Nikolaus Sonnenschein, Eduard J. Kerkhoven, Jens Nielsen
Publicado en:
Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor:
Nature Publishing Group
DOI:
10.1038/s41467-019-11581-3
Autores:
Raphael Ferreira, Christos Skrekas, Alex Hedin, Benjamín J. Sánchez, Verena Siewers, Jens Nielsen, Florian David
Publicado en:
ACS Synthetic Biology, Edición 8/11, 2019, Página(s) 2457-2463, ISSN 2161-5063
Editor:
American Chemical Society
DOI:
10.1021/acssynbio.9b00258
Autores:
Klaudia Ciurkot, Brenda Vonk, Thomas E. Gorochowski, Johannes A. Roubos, René Verwaal
Publicado en:
Journal of Visualized Experiments, Edición 147, 2019, ISSN 1940-087X
Editor:
MYJoVE Corporation
DOI:
10.3791/59350
Autores:
Anne P. Bali, David Lennox-Hvenekilde, Nils Myling-Petersen, Josi Buerger, Bo Salomonsen, Luisa S. Gronenberg, Morten O.A. Sommer, Hans J. Genee
Publicado en:
Metabolic Engineering, Edición 60, 2020, Página(s) 97-109, ISSN 1096-7176
Editor:
Academic Press
DOI:
10.1016/j.ymben.2020.03.005
Autores:
Tuure Hameri, Georgios Fengos, Meric Ataman, Ljubisa Miskovic, Vassily Hatzimanikatis
Publicado en:
Metabolic Engineering, Edición 52, 2019, Página(s) 29-41, ISSN 1096-7176
Editor:
Academic Press
DOI:
10.1016/j.ymben.2018.10.005
Autores:
Yu Chen, Jens Nielsen
Publicado en:
Proceedings of the National Academy of Sciences, Edición 116/35, 2019, Página(s) 17592-17597, ISSN 0027-8424
Editor:
National Academy of Sciences
DOI:
10.1073/pnas.1906569116
Autores:
Meric Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
Publicado en:
PLOS Computational Biology, Edición 13/7, 2017, Página(s) e1005444, ISSN 1553-7358
Editor:
Public Library of Science
DOI:
10.1371/journal.pcbi.1005444
Autores:
Meric Ataman, Vassily Hatzimanikatis
Publicado en:
PLOS Computational Biology, Edición 13/7, 2017, Página(s) e1005513, ISSN 1553-7358
Editor:
Public Library of Science
DOI:
10.1371/journal.pcbi.1005513
Autores:
Benjamín J Sánchez, Cheng Zhang, Avlant Nilsson, Petri‐Jaan Lahtvee, Eduard J Kerkhoven, Jens Nielsen
Publicado en:
Molecular Systems Biology, Edición 13/8, 2017, Página(s) 935, ISSN 1744-4292
Editor:
Nature Publishing Group
DOI:
10.15252/msb.20167411
Autores:
Olga Ponomarova, Natalia Gabrielli, Daniel C. Sévin, Michael Mülleder, Katharina Zirngibl, Katsiaryna Bulyha, Sergej Andrejev, Eleni Kafkia, Athanasios Typas, Uwe Sauer, Markus Ralser, Kiran Raosaheb Patil
Publicado en:
Cell Systems, 2017, ISSN 2405-4712
Editor:
Elsevier Inc
DOI:
10.1016/j.cels.2017.09.002
Autores:
Paulo Maia, Isabel Rocha, Miguel Rocha
Publicado en:
Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '17, 2017, Página(s) 1661-1668, ISBN 9781-450349390
Editor:
ACM Press
DOI:
10.1145/3067695.3082542
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