Daniel Machado
About
Daniel Machado joined NTNU in September 2020 as Associate Professor of Computational Biology. He has a Bsc/Msc in Mathematics and Computer Science (University of Minho, Portugal) and PhD in Bioengineering and Biotechnology (MIT-Portugal Program).
Competencies
Research
Our research aims to unlock the potential of microbes to address multiple societal challenges. We use computational models to understand how microbes work together in their natural habitats. These so-called microbial communities are everywhere, with some playing an important role in the health of our bodies, and others in the health of our planet. We follow an interdisciplinary approach, combining computational models and biological data, which gives us the ability to design synthetic communities to apply in multiple biotechnological applications and create more sustainable industries.
For more information check our website:
Cell4Chem
SFI - Industrial Biotechnology:
ELIXIR Norway
Publications
2024
-
Stallvik, Andrea;
Moutinho Luz Machado, Carlos Daniel.
(2024)
Designing microbial consortia using metabolic modelling.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
-
Moutinho Luz Machado, Carlos Daniel.
(2024)
A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities.
mSystems
Academic article
2023
-
Melkonian, Chrats;
Zorrilla, Francisco;
Kjærbølling, Inge;
Blasche, Sonja;
Moutinho Luz Machado, Carlos Daniel;
Junge, Mette.
(2023)
Microbial interactions shape cheese flavour formation.
Nature Communications
Academic article
-
Røed, Elin Sandertun;
Moutinho Luz Machado, Carlos Daniel;
Márquez-Zavala, Elisa.
(2023)
Predicting Allosteric Regulation at Genome Scale.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
-
van Eggelen, Marieke Cecilia;
Moutinho Luz Machado, Carlos Daniel.
(2023)
Predicting metabolic fluxes from gene expression data using machine learning
.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
2022
-
van den Berg, Naomi Iris;
Machado, Daniel;
Santos, Sophia;
Rocha, Isabel;
Chacón, Jeremy;
Harcombe, William.
(2022)
Ecological modelling approaches for predicting emergent properties in microbial communities.
Nature Ecology and Evolution
Academic literature review
-
Machado, Daniel;
Patil, Kiran R..
(2022)
Reply to: Erroneous predictions of auxotrophies by CarveMe.
Nature Ecology and Evolution
Letter to the editor
-
Cerca, José;
Petersen, Bent;
Lazaro-Guevara, José Miguel;
Rivera-Colón, Angel G.;
Birkeland, Siri;
Vizueta, Joel.
(2022)
The genomic basis of the plant island syndrome in Darwin’s giant daisies.
Nature Communications
Academic article
-
Merkesvik, Jenny;
Moutinho Luz Machado, Carlos Daniel.
(2022)
Towards genotype—phenotype association: Leveraging multiple-source microbial data and genome annotations to infer trait attributes for the uncultured microbiome.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
-
Lien, Martin Eide;
Moutinho Luz Machado, Carlos Daniel.
(2022)
Metabolic network layout using biochemical coordinates
.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
2021
-
Blasche, Sonja;
Kim, Yongkyu;
Mars, Ruben A.T.;
Machado, Daniel;
Maansson, Maria;
Kafkia, Eleni.
(2021)
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community.
Nature Microbiology
Academic article
-
Machado, Daniel;
Maistrenko, Oleksandr M.;
Andrejev, Sergej;
Kim, Yongkyu;
Bork, Peer;
Patil, Kaustubh R..
(2021)
Polarization of microbial communities between competitive and cooperative metabolism.
Nature Ecology and Evolution
Academic article
-
Shechter, Ksenija Radic;
Kafkia, Eleni;
Zirngibl, Katharina;
Gawrzak, Sylwia;
Alladin, Ashna;
Machado, Daniel.
(2021)
Metabolic memory underlying minimal residual disease in breast cancer.
Molecular Systems Biology
Academic article
-
Alloul, Abbas;
Spanoghe, Janne;
Machado, Daniel;
Vlaeminck, Siegfried E..
(2021)
Unlocking the genomic potential of aerobes and phototrophs for the production of nutritious and palatable microbial food without arable land or fossil fuels.
Microbial Biotechnology
Academic article
2020
-
Lieven, Christian;
Beber, Moritz E.;
Olivier, Brett G.;
Bergmann, Frank T.;
Ataman, Meric;
Babaei, Parizad.
(2020)
MEMOTE for standardized genome-scale metabolic model testing.
Nature Biotechnology
Academic article
Journal publications
-
Moutinho Luz Machado, Carlos Daniel.
(2024)
A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities.
mSystems
Academic article
-
Melkonian, Chrats;
Zorrilla, Francisco;
Kjærbølling, Inge;
Blasche, Sonja;
Moutinho Luz Machado, Carlos Daniel;
Junge, Mette.
(2023)
Microbial interactions shape cheese flavour formation.
Nature Communications
Academic article
-
van den Berg, Naomi Iris;
Machado, Daniel;
Santos, Sophia;
Rocha, Isabel;
Chacón, Jeremy;
Harcombe, William.
(2022)
Ecological modelling approaches for predicting emergent properties in microbial communities.
Nature Ecology and Evolution
Academic literature review
-
Machado, Daniel;
Patil, Kiran R..
(2022)
Reply to: Erroneous predictions of auxotrophies by CarveMe.
Nature Ecology and Evolution
Letter to the editor
-
Cerca, José;
Petersen, Bent;
Lazaro-Guevara, José Miguel;
Rivera-Colón, Angel G.;
Birkeland, Siri;
Vizueta, Joel.
(2022)
The genomic basis of the plant island syndrome in Darwin’s giant daisies.
Nature Communications
Academic article
-
Blasche, Sonja;
Kim, Yongkyu;
Mars, Ruben A.T.;
Machado, Daniel;
Maansson, Maria;
Kafkia, Eleni.
(2021)
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community.
Nature Microbiology
Academic article
-
Machado, Daniel;
Maistrenko, Oleksandr M.;
Andrejev, Sergej;
Kim, Yongkyu;
Bork, Peer;
Patil, Kaustubh R..
(2021)
Polarization of microbial communities between competitive and cooperative metabolism.
Nature Ecology and Evolution
Academic article
-
Shechter, Ksenija Radic;
Kafkia, Eleni;
Zirngibl, Katharina;
Gawrzak, Sylwia;
Alladin, Ashna;
Machado, Daniel.
(2021)
Metabolic memory underlying minimal residual disease in breast cancer.
Molecular Systems Biology
Academic article
-
Alloul, Abbas;
Spanoghe, Janne;
Machado, Daniel;
Vlaeminck, Siegfried E..
(2021)
Unlocking the genomic potential of aerobes and phototrophs for the production of nutritious and palatable microbial food without arable land or fossil fuels.
Microbial Biotechnology
Academic article
-
Lieven, Christian;
Beber, Moritz E.;
Olivier, Brett G.;
Bergmann, Frank T.;
Ataman, Meric;
Babaei, Parizad.
(2020)
MEMOTE for standardized genome-scale metabolic model testing.
Nature Biotechnology
Academic article
Report
-
Stallvik, Andrea;
Moutinho Luz Machado, Carlos Daniel.
(2024)
Designing microbial consortia using metabolic modelling.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
-
Røed, Elin Sandertun;
Moutinho Luz Machado, Carlos Daniel;
Márquez-Zavala, Elisa.
(2023)
Predicting Allosteric Regulation at Genome Scale.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
-
van Eggelen, Marieke Cecilia;
Moutinho Luz Machado, Carlos Daniel.
(2023)
Predicting metabolic fluxes from gene expression data using machine learning
.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
-
Merkesvik, Jenny;
Moutinho Luz Machado, Carlos Daniel.
(2022)
Towards genotype—phenotype association: Leveraging multiple-source microbial data and genome annotations to infer trait attributes for the uncultured microbiome.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
-
Lien, Martin Eide;
Moutinho Luz Machado, Carlos Daniel.
(2022)
Metabolic network layout using biochemical coordinates
.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Masters thesis
Teaching
Courses
Knowledge Transfer
2024
-
PosterMarquez Zavala, Elisa; Di Bartolomeo, Francesca; Moutinho Luz Machado, Carlos Daniel. (2024) Automated Data Retrieval and Analysis for Enhanced Product Production. Centre for Digital Life Norway Norwegian Bioinformatics Days 2024 , Bergen, Norway 2024-05-28 - 2024-05-30
-
LectureBurgos, Idun Maria Tokvam; Øyås, Ove; Moutinho Luz Machado, Carlos Daniel. (2024) Elucidating the roles of bacteria in cellulose- and xylan-enriched communities with genome-scale metabolic models. Centre for Digital Life Norway Norwegian Bioinformatics Days 2024 , Bergen, Norway 2024-05-28 - 2024-05-30
-
PosterAlves Magalhaes Teixeira, Miguel; Moutinho Luz Machado, Carlos Daniel. (2024) Trust the universe - enlightening microbial metabolism with CarveMe’s new universal model. International Society for Microbial Ecology 19th International Symposium on Microbial Ecology , Cape Town, South Africa 2024-08-18 - 2024-08-23
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PosterStallvik, Andrea; Burgos, Idun Maria Tokvam; Moutinho Luz Machado, Carlos Daniel. (2024) Designing microbial consortia using metabolic modelling – possibilities and limitations. Centre for Digital Life Norway Norwegian Bioinformatics Days 2024 , Bergen, Norway 2024-05-28 - 2024-05-30
2023
-
PosterStallvik, Andrea; Moutinho Luz Machado, Carlos Daniel. (2023) Synthetic Microbial Communities for the Production of High-Value Compounds. Norwegian Biochemical Society 58th Norwegian Biochemical Society Meeting , Ås, Norway 2023-01-19 - 2023-01-22
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PosterAlves Magalhaes Teixeira, Miguel; Moutinho Luz Machado, Carlos Daniel. (2023) CarveMe roadmap: expanding genome-scale metabolic model reconstructions. International Society for Computational Biology ISMB/ECCB 2023 , Lyon, France 2023-07-23 - 2023-07-27
2022
-
PosterTeixeira, Miguel; Machado, Daniel. (2022) CarveMe roadmap: expanding genome-scale metabolic models’ reconstruction. International Society for Microbial Ecology ISME 18 , Lausanne, Switzerland 2022-08-14 - 2022-08-19
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PosterBurgos, Idun Maria Tokvam; Machado, Daniel. (2022) Modeling The Conversion Of Lignocellulose Into Medium-chain Carboxylates. International Society for Microbial Ecology ISME 18 , Lausanne, Switzerland 2022-08-14 - 2022-08-19