Search

Your search keyword '"Mary, A. (Arnaud)"' showing total 6 results
Start Over Author "Mary, A. (Arnaud)"
6 results on '"Mary, A. (Arnaud)"'

1. MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network.

Author

Pusa, T. (Taneli), Galvão Ferrarini, M. (Mariana), Andrade, R. (Ricardo), Mary, A. (Arnaud), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), Sagot, M.-F. (Marie-France), Pusa, T. (Taneli), Galvão Ferrarini, M. (Mariana), Andrade, R. (Ricardo), Mary, A. (Arnaud), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), and Sagot, M.-F. (Marie-France)

Abstract

MOTIVATION: Analysis of differential expression of genes is often performed to understand how the metabolic activity of an organism is impacted by a perturbation. However, because the system of metabolic regulation is complex and all changes are not directly reflected in the expression levels, interpreting these data can be difficult. RESULTS: In this work, we present a new algorithm and computational tool that uses a genome-scale metabolic reconstruction to infer metabolic changes from differential expression data. Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic activity. In other words, each reaction of the network is inferred to have increased, decreased, or remained unchanged in flux. In contrast to similar previous approaches, our method does not require a biological objective function and does not assign on/off activity states to genes. An implementation is provided and it is available online. We apply the method to three published datasets to show that it successfully accomplishes its two main goals: confirming or rejecting metabolic changes suggested by differentially expressed genes based on how well they fit in as parts of a coordinated metabolic change, as well as inferring changes in reactions whose genes did not undergo differential expression. AVAILABILITY AND IMPLEMENTATION: github.com/htpusa/moomin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Published
2020
Full Text
View/download PDF

2. MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network.

Author

Pusa, T. (Taneli), Galvão Ferrarini, M. (Mariana), Andrade, R. (Ricardo), Mary, A. (Arnaud), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), Sagot, M.-F. (Marie-France), Pusa, T. (Taneli), Galvão Ferrarini, M. (Mariana), Andrade, R. (Ricardo), Mary, A. (Arnaud), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), and Sagot, M.-F. (Marie-France)

Abstract

MOTIVATION: Analysis of differential expression of genes is often performed to understand how the metabolic activity of an organism is impacted by a perturbation. However, because the system of metabolic regulation is complex and all changes are not directly reflected in the expression levels, interpreting these data can be difficult. RESULTS: In this work, we present a new algorithm and computational tool that uses a genome-scale metabolic reconstruction to infer metabolic changes from differential expression data. Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic activity. In other words, each reaction of the network is inferred to have increased, decreased, or remained unchanged in flux. In contrast to similar previous approaches, our method does not require a biological objective function and does not assign on/off activity states to genes. An implementation is provided and it is available online. We apply the method to three published datasets to show that it successfully accomplishes its two main goals: confirming or rejecting metabolic changes suggested by differentially expressed genes based on how well they fit in as parts of a coordinated metabolic change, as well as inferring changes in reactions whose genes did not undergo differential expression. AVAILABILITY AND IMPLEMENTATION: github.com/htpusa/moomin. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Published
2020
Full Text
View/download PDF

3. BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Author

Dudnik, A. (Alexey), Almeida, A.F. (Filipa), Andrade, R. (Ricardo), Avila, B. (Barbara), Bañados, P. (Pilar), Barbay, D. (Diane), Bassard, J.-E. (Jean-Etienne), Benkoulouche, M. (Mounir), Bott, M. (Michael), Braga, A. (Adelaide), Breitel, D. (Dario), Brennan, R. (Rex), Bulteau, L. (Laurent), Chanforan, C. (Celine), Costa, I. (Inês), Costa, R.S. (Rafael), Doostmohammadi, M. (Mahdi), Faria, N. (Nuno), Feng, C. (Chengyong), Fernandes, A. (Armando), Ferreira, P. (Patricia), Ferro, R. (Roberto), Foito, A. (Alexandre), Freitag, S. (Sabine), Garcia, G. (Gonçalo), Gaspar, P. (Paula), Godinho-Pereira, J. (Joana), Hamberger, B. (Björn), Hartmann, A. (András), Heider, H. (Harald), Jardim, C. (Carolina), Julien-Laferriere, A. (Alice), Kallscheuer, N. (Nicolai), Kerbe, W. (Wolfgang), Kuipers, O.P. (Oscar), Li, S. (Shanshan), Love, N. (Nicola), Marchetti Spaccamela, A. (Alberto), Marienhagen, J. (Jan), Martin, C. (Cathie), Mary, A. (Arnaud), Mazurek, V. (Vincent), Meinhart, C. (Camillo), Méndez Sevillano, D. (David), Menezes, R. (Regina), Naesby, M. (Michael), Nørholm, M.H.H. (Morten), Okkels, F.T. (Finn), Oliveira, J. (Joana), Ottens, M. (Marcel), Parrot, D. (Delphine), Pei, L. (Lei), Rocha, I. (Isabel), Rosado-Ramos, R. (Rita), Rousseau, C. (Caroline), Sagot, M.-F. (Marie-France), Nunes dos Santos, C. (Claudia), Schmidt, M. (Markus), Shelenga, T. (Tatiana), Shepherd, L. (Louise), Silva, A.R. (Ana Rita), Henriques da Silva, M. (Marcelo), Simon, O. (Olivier), Stahlhut, S.G. (Steen Gustav), Solopova, A. (Ana), Sorokin, A. (Artem), Stewart, D. (Derek), Stougie, L. (Leen), Su, S. (Shang), Thole, V. (Vera), Tikhonova, O. (Olga), Trick, M. (Martin), Vain, P. (Philippe), Veríssimo, A. (André), Vila-Santa, A. (Ana), Vinga, S. (Susana), Vogt, M. (Michael), Wang, L. (Liangsheng), Wang, L. (Lijin), Wei, W. (Wei), Youssef, S. (Sandra), Neves, A.R. (Ana Rute), Forster, J. (Jochen), Dudnik, A. (Alexey), Almeida, A.F. (Filipa), Andrade, R. (Ricardo), Avila, B. (Barbara), Bañados, P. (Pilar), Barbay, D. (Diane), Bassard, J.-E. (Jean-Etienne), Benkoulouche, M. (Mounir), Bott, M. (Michael), Braga, A. (Adelaide), Breitel, D. (Dario), Brennan, R. (Rex), Bulteau, L. (Laurent), Chanforan, C. (Celine), Costa, I. (Inês), Costa, R.S. (Rafael), Doostmohammadi, M. (Mahdi), Faria, N. (Nuno), Feng, C. (Chengyong), Fernandes, A. (Armando), Ferreira, P. (Patricia), Ferro, R. (Roberto), Foito, A. (Alexandre), Freitag, S. (Sabine), Garcia, G. (Gonçalo), Gaspar, P. (Paula), Godinho-Pereira, J. (Joana), Hamberger, B. (Björn), Hartmann, A. (András), Heider, H. (Harald), Jardim, C. (Carolina), Julien-Laferriere, A. (Alice), Kallscheuer, N. (Nicolai), Kerbe, W. (Wolfgang), Kuipers, O.P. (Oscar), Li, S. (Shanshan), Love, N. (Nicola), Marchetti Spaccamela, A. (Alberto), Marienhagen, J. (Jan), Martin, C. (Cathie), Mary, A. (Arnaud), Mazurek, V. (Vincent), Meinhart, C. (Camillo), Méndez Sevillano, D. (David), Menezes, R. (Regina), Naesby, M. (Michael), Nørholm, M.H.H. (Morten), Okkels, F.T. (Finn), Oliveira, J. (Joana), Ottens, M. (Marcel), Parrot, D. (Delphine), Pei, L. (Lei), Rocha, I. (Isabel), Rosado-Ramos, R. (Rita), Rousseau, C. (Caroline), Sagot, M.-F. (Marie-France), Nunes dos Santos, C. (Claudia), Schmidt, M. (Markus), Shelenga, T. (Tatiana), Shepherd, L. (Louise), Silva, A.R. (Ana Rita), Henriques da Silva, M. (Marcelo), Simon, O. (Olivier), Stahlhut, S.G. (Steen Gustav), Solopova, A. (Ana), Sorokin, A. (Artem), Stewart, D. (Derek), Stougie, L. (Leen), Su, S. (Shang), Thole, V. (Vera), Tikhonova, O. (Olga), Trick, M. (Martin), Vain, P. (Philippe), Veríssimo, A. (André), Vila-Santa, A. (Ana), Vinga, S. (Susana), Vogt, M. (Michael), Wang, L. (Liangsheng), Wang, L. (Lijin), Wei, W. (Wei), Youssef, S. (Sandra), Neves, A.R. (Ana Rute), and Forster, J. (Jochen)

Abstract

BACterial Hosts for production of Bioactive phenolics from bERRY fruits (BacHBerry) was a 3-year project funded by the Seventh Framework Programme (FP7) of the European Union that ran between November 2013 and October 2016. The overall aim of the project was to establish a sustainable and economically-feasible strategy for the production of novel high-value phenolic compounds isolated from berry fruits using bacterial platforms. The project aimed at covering all stages of the discovery and pre-commercialization process, including berry collection, screening and characterization of their bioactive components, identification and functional characterization of the corresponding biosynthetic pathways, and construction of Gram-positive bacterial cell factories producing phenolic compounds. Further activities included optimization of polyphenol extraction methods from bacterial cultures, scale-up of production by fermentation up to pilot scale, as well as societal and economic analyses of the processes. This review article summarizes some of the key findings obtained throughout the duration of the project.

Published
2017
Full Text
View/download PDF

4. BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Author

Dudnik, A. (Alexey), Almeida, A.F. (Filipa), Andrade, R. (Ricardo), Avila, B. (Barbara), Bañados, P. (Pilar), Barbay, D. (Diane), Bassard, J.-E. (Jean-Etienne), Benkoulouche, M. (Mounir), Bott, M. (Michael), Braga, A. (Adelaide), Breitel, D. (Dario), Brennan, R. (Rex), Bulteau, L. (Laurent), Chanforan, C. (Celine), Costa, I. (Inês), Costa, R.S. (Rafael), Doostmohammadi, M. (Mahdi), Faria, N. (Nuno), Feng, C. (Chengyong), Fernandes, A. (Armando), Ferreira, P. (Patricia), Ferro, R. (Roberto), Foito, A. (Alexandre), Freitag, S. (Sabine), Garcia, G. (Gonçalo), Gaspar, P. (Paula), Godinho-Pereira, J. (Joana), Hamberger, B. (Björn), Hartmann, A. (András), Heider, H. (Harald), Jardim, C. (Carolina), Julien-Laferriere, A. (Alice), Kallscheuer, N. (Nicolai), Kerbe, W. (Wolfgang), Kuipers, O.P. (Oscar), Li, S. (Shanshan), Love, N. (Nicola), Marchetti Spaccamela, A. (Alberto), Marienhagen, J. (Jan), Martin, C. (Cathie), Mary, A. (Arnaud), Mazurek, V. (Vincent), Meinhart, C. (Camillo), Méndez Sevillano, D. (David), Menezes, R. (Regina), Naesby, M. (Michael), Nørholm, M.H.H. (Morten), Okkels, F.T. (Finn), Oliveira, J. (Joana), Ottens, M. (Marcel), Parrot, D. (Delphine), Pei, L. (Lei), Rocha, I. (Isabel), Rosado-Ramos, R. (Rita), Rousseau, C. (Caroline), Sagot, M.-F. (Marie-France), Nunes dos Santos, C. (Claudia), Schmidt, M. (Markus), Shelenga, T. (Tatiana), Shepherd, L. (Louise), Silva, A.R. (Ana Rita), Henriques da Silva, M. (Marcelo), Simon, O. (Olivier), Stahlhut, S.G. (Steen Gustav), Solopova, A. (Ana), Sorokin, A. (Artem), Stewart, D. (Derek), Stougie, L. (Leen), Su, S. (Shang), Thole, V. (Vera), Tikhonova, O. (Olga), Trick, M. (Martin), Vain, P. (Philippe), Veríssimo, A. (André), Vila-Santa, A. (Ana), Vinga, S. (Susana), Vogt, M. (Michael), Wang, L. (Liangsheng), Wang, L. (Lijin), Wei, W. (Wei), Youssef, S. (Sandra), Neves, A.R. (Ana Rute), Forster, J. (Jochen), Dudnik, A. (Alexey), Almeida, A.F. (Filipa), Andrade, R. (Ricardo), Avila, B. (Barbara), Bañados, P. (Pilar), Barbay, D. (Diane), Bassard, J.-E. (Jean-Etienne), Benkoulouche, M. (Mounir), Bott, M. (Michael), Braga, A. (Adelaide), Breitel, D. (Dario), Brennan, R. (Rex), Bulteau, L. (Laurent), Chanforan, C. (Celine), Costa, I. (Inês), Costa, R.S. (Rafael), Doostmohammadi, M. (Mahdi), Faria, N. (Nuno), Feng, C. (Chengyong), Fernandes, A. (Armando), Ferreira, P. (Patricia), Ferro, R. (Roberto), Foito, A. (Alexandre), Freitag, S. (Sabine), Garcia, G. (Gonçalo), Gaspar, P. (Paula), Godinho-Pereira, J. (Joana), Hamberger, B. (Björn), Hartmann, A. (András), Heider, H. (Harald), Jardim, C. (Carolina), Julien-Laferriere, A. (Alice), Kallscheuer, N. (Nicolai), Kerbe, W. (Wolfgang), Kuipers, O.P. (Oscar), Li, S. (Shanshan), Love, N. (Nicola), Marchetti Spaccamela, A. (Alberto), Marienhagen, J. (Jan), Martin, C. (Cathie), Mary, A. (Arnaud), Mazurek, V. (Vincent), Meinhart, C. (Camillo), Méndez Sevillano, D. (David), Menezes, R. (Regina), Naesby, M. (Michael), Nørholm, M.H.H. (Morten), Okkels, F.T. (Finn), Oliveira, J. (Joana), Ottens, M. (Marcel), Parrot, D. (Delphine), Pei, L. (Lei), Rocha, I. (Isabel), Rosado-Ramos, R. (Rita), Rousseau, C. (Caroline), Sagot, M.-F. (Marie-France), Nunes dos Santos, C. (Claudia), Schmidt, M. (Markus), Shelenga, T. (Tatiana), Shepherd, L. (Louise), Silva, A.R. (Ana Rita), Henriques da Silva, M. (Marcelo), Simon, O. (Olivier), Stahlhut, S.G. (Steen Gustav), Solopova, A. (Ana), Sorokin, A. (Artem), Stewart, D. (Derek), Stougie, L. (Leen), Su, S. (Shang), Thole, V. (Vera), Tikhonova, O. (Olga), Trick, M. (Martin), Vain, P. (Philippe), Veríssimo, A. (André), Vila-Santa, A. (Ana), Vinga, S. (Susana), Vogt, M. (Michael), Wang, L. (Liangsheng), Wang, L. (Lijin), Wei, W. (Wei), Youssef, S. (Sandra), Neves, A.R. (Ana Rute), and Forster, J. (Jochen)

Abstract

BACterial Hosts for production of Bioactive phenolics from bERRY fruits (BacHBerry) was a 3-year project funded by the Seventh Framework Programme (FP7) of the European Union that ran between November 2013 and October 2016. The overall aim of the project was to establish a sustainable and economically-feasible strategy for the production of novel high-value phenolic compounds isolated from berry fruits using bacterial platforms. The project aimed at covering all stages of the discovery and pre-commercialization process, including berry collection, screening and characterization of their bioactive components, identification and functional characterization of the corresponding biosynthetic pathways, and construction of Gram-positive bacterial cell factories producing phenolic compounds. Further activities included optimization of polyphenol extraction methods from bacterial cultures, scale-up of production by fermentation up to pilot scale, as well as societal and economic analyses of the processes. This review article summarizes some of the key findings obtained throughout the duration of the project.

Published
2017
Full Text
View/download PDF

5. A combinatorial algorithm for microbial consortia synthetic design

Author

Julien-Laferriere, A. (Alice), Bulteau, L. (Laurent), Parrot, D. (Delphine), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), Vinga, S. (Susana), Mary, A. (Arnaud), Sagot, M.-F. (Marie-France), Julien-Laferriere, A. (Alice), Bulteau, L. (Laurent), Parrot, D. (Delphine), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), Vinga, S. (Susana), Mary, A. (Arnaud), and Sagot, M.-F. (Marie-France)

Published
2016
Full Text
View/download PDF

6. A combinatorial algorithm for microbial consortia synthetic design

Author

Julien-Laferriere, A. (Alice), Bulteau, L. (Laurent), Parrot, D. (Delphine), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), Vinga, S. (Susana), Mary, A. (Arnaud), Sagot, M.-F. (Marie-France), Julien-Laferriere, A. (Alice), Bulteau, L. (Laurent), Parrot, D. (Delphine), Marchetti Spaccamela, A. (Alberto), Stougie, L. (Leen), Vinga, S. (Susana), Mary, A. (Arnaud), and Sagot, M.-F. (Marie-France)

Published
2016
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results