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  1. Ansatte

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Daniel Machado

Last ned pressefoto
Last ned pressefoto
Foto: Kai T. Dragland / NTNU

Daniel Machado

Førsteamanuensis
Institutt for bioteknologi og matvitenskap

daniel.machado@ntnu.no
Kjemi 3, 126, Gløshaugen
Twitter Google Scholar
Om Forskning Publikasjoner Undervisning Formidling

Om

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).

Kompetanseord

  • Computational Biology
  • Metabolism
  • Modeling

Forskning

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: 

  • Machado Lab

Cell4Chem

Designing synthetic microbial communities for conversion of lignocellulose waste products into medium-chain carboxylates

SFI - Industrial Biotechnology:

A research-based innovation centre aiming to boost the competitiveness of the Norwegian biotech industry

ELIXIR Norway

ELIXIR Norway is a national node of ELIXIR, the pan-European infrastructure for biological information, supporting life science research and its translation to medicine, environment, the bioindustries and society.

Publikasjoner

  • Kronologisk
  • Etter kategori
  • Alle publikasjoner i Nasjonalt vitenarkiv (NVA)

2026

  • Marquez Zavala, Elisa; Di Bartolomeo, Francesca; Machado, Daniel. (2026) A database of over 15,000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products. Metabolic Engineering
    Vitenskapelig artikkel

2025

  • Burgos, Idun Maria Tokvam; Øyås, Ove; Perret, Stéphanie; Fierobe, Henri Pierre; Moutinho Luz Machado, Carlos Daniel. (2025) Genome-scale metabolic modeling of Ruminiclostridium cellulolyticum: a microbial cell factory for valorization of lignocellulosic biomass. mSystems
    Vitenskapelig artikkel
  • Landro, Benjamin; Moutinho Luz Machado, Carlos Daniel. (2025) Making Transporters Transparent for Identification and Characterization. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • Hudgins, Eliah; Moutinho Luz Machado, Carlos Daniel. (2025) Predicting microbial traits from genome annotations. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave

2024

  • Moutinho Luz Machado, Carlos Daniel. (2024) A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities. mSystems
    Vitenskapelig artikkel
  • Stallvik, Andrea; Moutinho Luz Machado, Carlos Daniel. (2024) Designing microbial consortia using metabolic modelling. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave

2023

  • Røed, Elin Sandertun; Moutinho Luz Machado, Carlos Daniel; Márquez-Zavala, Elisa. (2023) Predicting Allosteric Regulation at Genome Scale. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • Eggelen, Marieke Cecilia van; Machado, Daniel; Moutinho Luz Machado, Carlos Daniel; Burgos, Idun Maria Tokvam. (2023) Predicting metabolic fluxes from gene expression data using machine learning. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • Melkonian, Chrats; Zorrilla, Francisco; Kjærbølling, Inge; Blasche, Sonja; Moutinho Luz Machado, Carlos Daniel; Junge, Mette; Sørensen, Kim Ib; Andersen, Lene Tranberg; Patil, Kiran R.; Zeidan, Ahmad A.. (2023) Microbial interactions shape cheese flavour formation. Nature Communications
    Vitenskapelig artikkel

2022

  • Cerca, José; Petersen, Bent; Lazaro-Guevara, José Miguel; Rivera-Colón, Angel G.; Birkeland, Siri; Vizueta, Joel; Li, Siyu; Li, Qionghou; Loureiro, João; Kosawang, Chatchai. (2022) The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications
    Vitenskapelig artikkel
  • Lien, Martin Eide; Moutinho Luz Machado, Carlos Daniel. (2022) Metabolic network layout using biochemical coordinates. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • 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
    Masteroppgave
  • Machado, Daniel; Patil, Kiran R.. (2022) Reply to: Erroneous predictions of auxotrophies by CarveMe. Nature Ecology and Evolution
    Kommentar
  • Berg, Naomi Iris van den; Machado, Daniel; Santos, Sophia; Rocha, Isabel; Chacón, Jeremy; Harcombe, William; Mitri, Sara; Patil, Kiran R.. (2022) Ecological modelling approaches for predicting emergent properties in microbial communities. Nature Ecology and Evolution
    Vitenskapelig oversiktsartikkel

2021

  • Machado, Daniel; Maistrenko, Oleksandr M.; Andrejev, Sergej; Kim, Yongkyu; Bork, Peer; Patil, Kaustubh R.; Patil, Kiran R.. (2021) Polarization of microbial communities between competitive and cooperative metabolism. Nature Ecology and Evolution
    Vitenskapelig artikkel
  • 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
    Vitenskapelig artikkel
  • Shechter, Ksenija Radic; Kafkia, Eleni; Zirngibl, Katharina; Gawrzak, Sylwia; Alladin, Ashna; Machado, Daniel; Lüchtenborg, Christian; Sévin, Daniel C.; Brügger, Britta; Patil, Kiran R.. (2021) Metabolic memory underlying minimal residual disease in breast cancer. Molecular Systems Biology
    Vitenskapelig artikkel
  • Blasche, Sonja; Kim, Yongkyu; Mars, Ruben A.T.; Machado, Daniel; Maansson, Maria; Kafkia, Eleni; Milanese, Alessio; Zeller, Georg; Teusink, Bas; Nielsen, Jens. (2021) Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nature Microbiology
    Vitenskapelig artikkel

2020

  • Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.; Chauhan, Siddharth; Correia, Kevin. (2020) MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology
    Vitenskapelig artikkel

Tidsskriftspublikasjoner

  • Marquez Zavala, Elisa; Di Bartolomeo, Francesca; Machado, Daniel. (2026) A database of over 15,000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products. Metabolic Engineering
    Vitenskapelig artikkel
  • Moutinho Luz Machado, Carlos Daniel. (2024) A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities. mSystems
    Vitenskapelig artikkel
  • Burgos, Idun Maria Tokvam; Øyås, Ove; Perret, Stéphanie; Fierobe, Henri Pierre; Moutinho Luz Machado, Carlos Daniel. (2025) Genome-scale metabolic modeling of Ruminiclostridium cellulolyticum: a microbial cell factory for valorization of lignocellulosic biomass. mSystems
    Vitenskapelig artikkel
  • Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.; Chauhan, Siddharth; Correia, Kevin. (2020) MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology
    Vitenskapelig artikkel
  • Cerca, José; Petersen, Bent; Lazaro-Guevara, José Miguel; Rivera-Colón, Angel G.; Birkeland, Siri; Vizueta, Joel; Li, Siyu; Li, Qionghou; Loureiro, João; Kosawang, Chatchai. (2022) The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications
    Vitenskapelig artikkel
  • Machado, Daniel; Maistrenko, Oleksandr M.; Andrejev, Sergej; Kim, Yongkyu; Bork, Peer; Patil, Kaustubh R.; Patil, Kiran R.. (2021) Polarization of microbial communities between competitive and cooperative metabolism. Nature Ecology and Evolution
    Vitenskapelig artikkel
  • 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
    Vitenskapelig artikkel
  • Shechter, Ksenija Radic; Kafkia, Eleni; Zirngibl, Katharina; Gawrzak, Sylwia; Alladin, Ashna; Machado, Daniel; Lüchtenborg, Christian; Sévin, Daniel C.; Brügger, Britta; Patil, Kiran R.. (2021) Metabolic memory underlying minimal residual disease in breast cancer. Molecular Systems Biology
    Vitenskapelig artikkel
  • Blasche, Sonja; Kim, Yongkyu; Mars, Ruben A.T.; Machado, Daniel; Maansson, Maria; Kafkia, Eleni; Milanese, Alessio; Zeller, Georg; Teusink, Bas; Nielsen, Jens. (2021) Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nature Microbiology
    Vitenskapelig artikkel
  • Melkonian, Chrats; Zorrilla, Francisco; Kjærbølling, Inge; Blasche, Sonja; Moutinho Luz Machado, Carlos Daniel; Junge, Mette; Sørensen, Kim Ib; Andersen, Lene Tranberg; Patil, Kiran R.; Zeidan, Ahmad A.. (2023) Microbial interactions shape cheese flavour formation. Nature Communications
    Vitenskapelig artikkel
  • Machado, Daniel; Patil, Kiran R.. (2022) Reply to: Erroneous predictions of auxotrophies by CarveMe. Nature Ecology and Evolution
    Kommentar
  • Berg, Naomi Iris van den; Machado, Daniel; Santos, Sophia; Rocha, Isabel; Chacón, Jeremy; Harcombe, William; Mitri, Sara; Patil, Kiran R.. (2022) Ecological modelling approaches for predicting emergent properties in microbial communities. Nature Ecology and Evolution
    Vitenskapelig oversiktsartikkel

Studentoppgave eller avhandling

  • Røed, Elin Sandertun; Moutinho Luz Machado, Carlos Daniel; Márquez-Zavala, Elisa. (2023) Predicting Allosteric Regulation at Genome Scale. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • Eggelen, Marieke Cecilia van; Machado, Daniel; Moutinho Luz Machado, Carlos Daniel; Burgos, Idun Maria Tokvam. (2023) Predicting metabolic fluxes from gene expression data using machine learning. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • Lien, Martin Eide; Moutinho Luz Machado, Carlos Daniel. (2022) Metabolic network layout using biochemical coordinates. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • 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
    Masteroppgave
  • Stallvik, Andrea; Moutinho Luz Machado, Carlos Daniel. (2024) Designing microbial consortia using metabolic modelling. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • Landro, Benjamin; Moutinho Luz Machado, Carlos Daniel. (2025) Making Transporters Transparent for Identification and Characterization. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave
  • Hudgins, Eliah; Moutinho Luz Machado, Carlos Daniel. (2025) Predicting microbial traits from genome annotations. Norges teknisk-naturvitenskapelige universitet
    Masteroppgave

Undervisning

Emner

  • BT8120 - Prokaryot molekylærbiologi og syntetisk biologi
  • TBT4508 - Bioinformatikk og Biopolymere materialer, fordypningsemne
  • TBT4507 - Bioinformatikk og Forsøksplanlegging og dataanalyse, fordypningsemne

Formidling

Finding Genius Podcast

Harnessing the Ecology of Microbial Communities with Daniel Machado

2025

  • Konferanseposter
    Hudgins, Eliah; Moutinho Luz Machado, Carlos Daniel. (2025) Predicting Microbial traits from genome annotations. 60th NBS contact meeting

2024

  • Foredrag
    Burgos, 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. Norwegian Bioinformatics Days 2024
  • Konferanseposter
    Stallvik, Andrea; Burgos, Idun Maria Tokvam; Moutinho Luz Machado, Carlos Daniel. (2024) Designing microbial consortia using metabolic modelling – possibilities and limitations. Norwegian Bioinformatics Days 2024
  • Konferanseposter
    Marquez Zavala, Elisa; Di Bartolomeo, Francesca; Moutinho Luz Machado, Carlos Daniel. (2024) Automated Data Retrieval and Analysis for Enhanced Product Production. Norwegian Bioinformatics Days 2024
  • Konferanseposter
    Alves Magalhaes Teixeira, Miguel; Moutinho Luz Machado, Carlos Daniel. (2024) Trust the universe - enlightening microbial metabolism with CarveMe’s new universal model. 19th International Symposium on Microbial Ecology
  • Foredrag
    Marquez Zavala, Elisa; Di Bartolomeo, Francesca; Moutinho Luz Machado, Carlos Daniel. (2024) Can you outsmart nature? Level Up your Cell Factories with ELISER. Joint conference of the 15th Globe Industrial Microbiology Congress (GIM) & Metabolic Engineering Summit (MES 2024)

2023

  • Konferanseposter
    Stallvik, Andrea; Moutinho Luz Machado, Carlos Daniel. (2023) Synthetic Microbial Communities for the Production of High-Value Compounds. 58th Norwegian Biochemical Society Meeting
  • Konferanseposter
    Alves Magalhaes Teixeira, Miguel; Moutinho Luz Machado, Carlos Daniel. (2023) CarveMe roadmap: expanding genome-scale metabolic model reconstructions. ISMB/ECCB 2023

2022

  • Konferanseposter
    Teixeira, Miguel; Machado, Daniel. (2022) CarveMe roadmap: expanding genome-scale metabolic models’ reconstruction. ISME 18
  • Konferanseposter
    Burgos, Idun Maria Tokvam; Machado, Daniel. (2022) Modeling The Conversion Of Lignocellulose Into Medium-chain Carboxylates. ISME 18

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