Risultati finali
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
Pubblicazioni
Autori:
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
Pubblicato in:
Nature Microbiology, Numero 3/4, 2018, Pagina/e 514-522, ISSN 2058-5276
Editore:
Nature Publishing Group
DOI:
10.1038/s41564-018-0123-9
Autori:
René Verwaal, Nathalie Buiting-Wiessenhaan, Sacha Dalhuijsen, Johannes A. Roubos
Pubblicato in:
Yeast, Numero 35/2, 2018, Pagina/e 201-211, ISSN 0749-503X
Editore:
John Wiley & Sons Inc.
DOI:
10.1002/yea.3278
Autori:
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
Pubblicato in:
Microbiome, Numero 6/1, 2018, ISSN 2049-2618
Editore:
Springer Nature
DOI:
10.1186/s40168-018-0450-3
Autori:
Machado, Daniel; Herrgard, Markus; Rocha, Isabel
Pubblicato in:
PLoS Computational Biology, Numero 1, 2016, ISSN 1553-7358
Editore:
Public Library of Science
DOI:
10.1371/journal.pcbi.1005140
Autori:
Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen
Pubblicato in:
BMC Systems Biology, Numero 13/1, 2019, ISSN 1752-0509
Editore:
BioMed Central
DOI:
10.1186/s12918-018-0673-8
Autori:
Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
Pubblicato in:
Bioinformatics, 2018, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/bty499
Autori:
Daniel Machado, Sergej Andrejev, Melanie Tramontano, Kiran Raosaheb Patil
Pubblicato in:
Nucleic Acids Research, Numero 46/15, 2018, Pagina/e 7542-7553, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gky537
Autori:
Ilaria Massaiu, Lorenzo Pasotti, Nikolaus Sonnenschein, Erlinda Rama, Matteo Cavaletti, Paolo Magni, Cinzia Calvio, Markus J. Herrgård
Pubblicato in:
Microbial Cell Factories, Numero 18/1, 2019, ISSN 1475-2859
Editore:
BioMed Central
DOI:
10.1186/s12934-018-1052-2
Autori:
Carlos G Acevedo-Rocha, Luisa S Gronenberg, Matthias Mack, Fabian M Commichau, Hans J Genee
Pubblicato in:
Current Opinion in Biotechnology, Numero 56, 2019, Pagina/e 18-29, ISSN 0958-1669
Editore:
Elsevier BV
DOI:
10.1016/j.copbio.2018.07.006
Autori:
Douglas McCloskey, Julia Xu, Lars Schrübbers, Hanne B. Christensen, Markus J. Herrgård
Pubblicato in:
Metabolic Engineering, Numero 47, 2018, Pagina/e 383-392, ISSN 1096-7176
Editore:
Academic Press
DOI:
10.1016/j.ymben.2018.04.009
Autori:
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
Pubblicato in:
Nature, Numero 560/7717, 2018, Pagina/e 233-237, ISSN 0028-0836
Editore:
Nature Publishing Group
DOI:
10.1038/s41586-018-0386-6
Autori:
Xavier, Joana C.; Patil, Kiran Raosaheb; Rocha, Isabel
Pubblicato in:
Metabolic Engineering, 2017, ISSN 1096-7176
Editore:
Academic Press
DOI:
10.1016/j.ymben.2016.12.002
Autori:
Kristian Jensen, Joao G.R. Cardoso, Nikolaus Sonnenschein
Pubblicato in:
The Journal of Open Source Software, Numero 2/9, 2017, ISSN 2475-9066
Editore:
The Journal of Open Source Software
DOI:
10.21105/joss.00139
Autori:
Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
Pubblicato in:
Nucleic Acids Research, Numero 45/D1, 2017, Pagina/e D529-D534, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkw989
Autori:
Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
Pubblicato in:
Molecular Biology and Evolution, 2017, ISSN 0737-4038
Editore:
Oxford University Press
DOI:
10.1093/molbev/msx148
Autori:
Paula Jouhten, Jaime Huerta-Cepas, Peer Bork, Kiran Raosaheb Patil
Pubblicato in:
Metabolic Engineering, Numero 40, 2017, Pagina/e 1-4, ISSN 1096-7176
Editore:
Academic Press
DOI:
10.1016/j.ymben.2017.02.010
Autori:
Anne Sofie L?rke Hansen, Rebecca M. Lennen, Nikolaus Sonnenschein, Markus J Herrg?rd
Pubblicato in:
Current Opinion in Biotechnology, Numero 45, 2017, Pagina/e 85-91, ISSN 0958-1669
Editore:
Elsevier BV
DOI:
10.1016/j.copbio.2016.11.018
Autori:
Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha
Pubblicato in:
PLOS Computational Biology, Numero 14/11, 2018, Pagina/e e1006556, ISSN 1553-7358
Editore:
PLOS Computational Biology
DOI:
10.1371/journal.pcbi.1006556
Autori:
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
Pubblicato in:
Cell, Numero 179/5, 2019, Pagina/e 1068-1083.e21, ISSN 0092-8674
Editore:
Cell Press
DOI:
10.1016/j.cell.2019.10.014
Autori:
João G R Cardoso, Ahmad A Zeidan, Kristian Jensen, Nikolaus Sonnenschein, Ana Rute Neves, Markus J Herrgård
Pubblicato in:
Bioinformatics, Numero 34/13, 2018, Pagina/e 2319-2321, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/bty108
Autori:
Denis Shepelin, Anne Hansen, Rebecca Lennen, Hao Luo, Markus Herrgård
Pubblicato in:
Genes, Numero 9/5, 2018, Pagina/e 249, ISSN 2073-4425
Editore:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/genes9050249
Autori:
Thordis Kristjansdottir, Elleke F. Bosma, Filipe Branco dos Santos, Emre Özdemir, Markus J. Herrgård, Lucas França, Bruno Ferreira, Alex T. Nielsen, Steinn Gudmundsson
Pubblicato in:
Microbial Cell Factories, Numero 18/1, 2019, ISSN 1475-2859
Editore:
BioMed Central
DOI:
10.1186/s12934-019-1229-3
Autori:
Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
Pubblicato in:
BMC Bioinformatics, Numero 20/1, 2019, ISSN 1471-2105
Editore:
BioMed Central
DOI:
10.1186/s12859-019-2934-y
Autori:
Osvaldo D. Kim, Miguel Rocha, Paulo Maia
Pubblicato in:
Frontiers in Microbiology, Numero 9, 2018, ISSN 1664-302X
Editore:
Frontiers Media
DOI:
10.3389/fmicb.2018.01690
Autori:
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
Pubblicato in:
ACS Synthetic Biology, Numero 7/4, 2018, Pagina/e 1163-1166, ISSN 2161-5063
Editore:
American Chemical Society
DOI:
10.1021/acssynbio.7b00423
Autori:
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
Pubblicato in:
Gut, Numero 68/10, 2019, Pagina/e 1781-1790, ISSN 0017-5749
Editore:
BMJ Publishing Group
DOI:
10.1136/gutjnl-2018-317715
Autori:
Sofia Ferreira, Rui Pereira, Filipe Liu, Paulo Vilaça, Isabel Rocha
Pubblicato in:
Biotechnology for Biofuels, Numero 12/1, 2019, ISSN 1754-6834
Editore:
Biotechnology and Biofuels
DOI:
10.1186/s13068-019-1565-x
Autori:
Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Dias
Pubblicato in:
BMC Bioinformatics, Numero 20/1, 2019, ISSN 1471-2105
Editore:
BioMed Central
DOI:
10.1186/s12859-019-3038-4
Autori:
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
Pubblicato in:
BMC Biotechnology, Numero 19/1, 2019, ISSN 1472-6750
Editore:
BioMed Central
DOI:
10.1186/s12896-019-0529-3
Autori:
Oscar Dias, João Saraiva, Cristiana Faria, Mario Ramirez, Francisco Pinto, Isabel Rocha
Pubblicato in:
Frontiers in Microbiology, Numero 10, 2019, ISSN 1664-302X
Editore:
Frontiers Media
DOI:
10.3389/fmicb.2019.01283
Autori:
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
Pubblicato in:
The ISME Journal, Numero 14/5, 2020, Pagina/e 1247-1259, ISSN 1751-7362
Editore:
Nature Publishing Group
DOI:
10.1038/s41396-020-0600-z
Autori:
Vítor Vieira, Miguel Rocha
Pubblicato in:
Bioinformatics, Numero 35/24, 2019, Pagina/e 5361-5362, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/btz598
Autori:
Kristian Jensen, Valentijn Broeken, Anne Sofie Lærke Hansen, Nikolaus Sonnenschein, Markus J. Herrgård
Pubblicato in:
Metabolic Engineering Communications, Numero 8, 2019, Pagina/e e00087, ISSN 2214-0301
Editore:
Elsevier BV
DOI:
10.1016/j.mec.2019.e00087
Autori:
Josi Buerger, Luisa S. Gronenberg, Hans Jasper Genee, Morten O.A. Sommer
Pubblicato in:
Current Opinion in Biotechnology, Numero 59, 2019, Pagina/e 85-92, ISSN 0958-1669
Editore:
Elsevier BV
DOI:
10.1016/j.copbio.2019.02.014
Autori:
Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork
Pubblicato in:
Microbiome, Numero 7/1, 2019, ISSN 2049-2618
Editore:
Microbiome
DOI:
10.1186/s40168-019-0684-8
Autori:
Daniel R. Weilandt, Vassily Hatzimanikatis
Pubblicato in:
Biophysical Journal, Numero 117/2, 2019, Pagina/e 355-368, ISSN 0006-3495
Editore:
Biophysical Society
DOI:
10.1016/j.bpj.2019.06.017
Autori:
Pierre Salvy, Vassily Hatzimanikatis
Pubblicato in:
Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore:
Nature Publishing Group
DOI:
10.1038/s41467-019-13818-7
Autori:
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
Pubblicato in:
Nature Communications, Numero 10/1, 2019, ISSN 2041-1723
Editore:
Nature Publishing Group
DOI:
10.1038/s41467-019-11581-3
Autori:
Raphael Ferreira, Christos Skrekas, Alex Hedin, Benjamín J. Sánchez, Verena Siewers, Jens Nielsen, Florian David
Pubblicato in:
ACS Synthetic Biology, Numero 8/11, 2019, Pagina/e 2457-2463, ISSN 2161-5063
Editore:
American Chemical Society
DOI:
10.1021/acssynbio.9b00258
Autori:
Klaudia Ciurkot, Brenda Vonk, Thomas E. Gorochowski, Johannes A. Roubos, René Verwaal
Pubblicato in:
Journal of Visualized Experiments, Numero 147, 2019, ISSN 1940-087X
Editore:
MYJoVE Corporation
DOI:
10.3791/59350
Autori:
Anne P. Bali, David Lennox-Hvenekilde, Nils Myling-Petersen, Josi Buerger, Bo Salomonsen, Luisa S. Gronenberg, Morten O.A. Sommer, Hans J. Genee
Pubblicato in:
Metabolic Engineering, Numero 60, 2020, Pagina/e 97-109, ISSN 1096-7176
Editore:
Academic Press
DOI:
10.1016/j.ymben.2020.03.005
Autori:
Tuure Hameri, Georgios Fengos, Meric Ataman, Ljubisa Miskovic, Vassily Hatzimanikatis
Pubblicato in:
Metabolic Engineering, Numero 52, 2019, Pagina/e 29-41, ISSN 1096-7176
Editore:
Academic Press
DOI:
10.1016/j.ymben.2018.10.005
Autori:
Yu Chen, Jens Nielsen
Pubblicato in:
Proceedings of the National Academy of Sciences, Numero 116/35, 2019, Pagina/e 17592-17597, ISSN 0027-8424
Editore:
National Academy of Sciences
DOI:
10.1073/pnas.1906569116
Autori:
Meric Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
Pubblicato in:
PLOS Computational Biology, Numero 13/7, 2017, Pagina/e e1005444, ISSN 1553-7358
Editore:
Public Library of Science
DOI:
10.1371/journal.pcbi.1005444
Autori:
Meric Ataman, Vassily Hatzimanikatis
Pubblicato in:
PLOS Computational Biology, Numero 13/7, 2017, Pagina/e e1005513, ISSN 1553-7358
Editore:
Public Library of Science
DOI:
10.1371/journal.pcbi.1005513
Autori:
Benjamín J Sánchez, Cheng Zhang, Avlant Nilsson, Petri‐Jaan Lahtvee, Eduard J Kerkhoven, Jens Nielsen
Pubblicato in:
Molecular Systems Biology, Numero 13/8, 2017, Pagina/e 935, ISSN 1744-4292
Editore:
Nature Publishing Group
DOI:
10.15252/msb.20167411
Autori:
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
Pubblicato in:
Cell Systems, 2017, ISSN 2405-4712
Editore:
Elsevier Inc
DOI:
10.1016/j.cels.2017.09.002
Autori:
Paulo Maia, Isabel Rocha, Miguel Rocha
Pubblicato in:
Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '17, 2017, Pagina/e 1661-1668, ISBN 9781-450349390
Editore:
ACM Press
DOI:
10.1145/3067695.3082542
È in corso la ricerca di dati su OpenAIRE...
Si è verificato un errore durante la ricerca dei dati su OpenAIRE
Nessun risultato disponibile