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  1. Employees

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Daniel Machado

Daniel Machado

Associate Professor
Department of Biotechnology and Food Science

daniel.machado@ntnu.no
Kjemi 3, 126, Gløshaugen
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About Research Publications Teaching Media

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

  • Bioinformatics
  • Biotechnology
  • Computational Biology
  • Metabolism
  • Modeling

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: 

  • 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.

Publications

  • Chronological
  • By category
  • See all publications in Cristin

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; Jaramillo Díaz, Patricia; Rivas-Torres, Gonzalo; Fernández-Mazuecos, Mario; Vargas, Pablo; McCauley, Ross; Petersen, Gitte; Santos-Bay, Luisa; Wales, Nathan; Catchen, Julian M.; Machado, Daniel; Nowak, Michael; Suh, Alexander; Sinha, Neelima R.; Rostgaard Nielsen, Lene; Seberg, Ole; Gilbert, Marcus Thomas Pius; Leebens-Mack, James H.; Rieseberg, Loren H.; Martin, Michael David. (2022) The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications. volum 13.
    Academic article
  • Machado, Daniel; Patil, Kiran R.. (2022) Reply to: Erroneous predictions of auxotrophies by CarveMe. Nature Ecology and Evolution.
    Letter to the editor
  • van den Berg, Naomi Iris; 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. volum 6 (7).
    Academic literature review

2021

  • 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
  • Blasche, Sonja; Kim, Yongkyu; Mars, Ruben A.T.; Machado, Daniel; Maansson, Maria; Kafkia, Eleni; Milanese, Alessio; Zeller, Georg; Teusink, Bas; Nielsen, Jens; Benes, Vladimir; Neves, Rute; Sauer, Uwe H.; Patil, Kiran R.. (2021) Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nature Microbiology. volum 6.
    Academic article
  • 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. volum 5.
    Academic article
  • Shechter, Ksenija Radic; Kafkia, Eleni; Zirngibl, Katharina; Gawrzak, Sylwia; Alladin, Ashna; Machado, Daniel; Lüchtenborg, Christian; Sévin, Daniel C.; Brügger, Britta; Patil, Kiran R.; Jechlinger, Martin. (2021) Metabolic memory underlying minimal residual disease in breast cancer. Molecular Systems Biology. volum 17.
    Academic article

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; Diener, Christian; Dräger, Andreas; Ebert, Birgitta E.; Edirisinghe, Janaka E.; Faria, José P.; Feist, Adam M.; Fengos, Georgios; Fleming, Ronan M.T.; García-Jiménez, Beatriz; Hatzimanikatis, Vassily; Van Helvoirt, Wout; Henry, Christopher S.; Hermjakob, Henning; Herrgård, Markus J.; Kaafarani, Ali; Kim, Hyun Uk; King, Zachary; Klamt, Steffen; Klipp, Edda; Koehorst, Jasper J; König, Matthias; Lakshmanan, Meiyappan; Lee, Dong-Yup; Lee, Sang Yup; Lee, Sunjae; Lewis, Nathan E.; Liu, Filipe; Ma, Hongwu; Moutinho Luz Machado, Carlos Daniel; Mahadevan, Radhakrishnan; Maia, Paulo; Mardinoglu, Adil; Medlock, Gregory L.; Monk, Jonathan M.; Nielsen, Jens; Nielsen, Lars Keld; Nogales, Juan; Nookaew, Intawat; Palsson, Bernhard O.; Papin, Jason A.; Patil, Kiran R.; Poolman, Mark; Price, Nathan D.; Resendis-Antonio, Osbaldo; Richelle, Anne; Rocha, Isabel; Sánchez, Benjamín J.; Schaap, Peter J.; Sheriff, Rahuman S. Malik; Shoaie, Saeed; Sonnenschein, Nikolaus; Teusink, Bas; Vilaça, Paulo; Vik, Jon Olav; Wodke, Judith A. H.; Xavier, Joana C.; Yuan, Qianqian; Zakhartsev, Maksim; Zhang, Cheng. (2020) MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. volum 38.
    Academic article

Journal publications

  • Cerca, José; Petersen, Bent; Lazaro-Guevara, José Miguel; Rivera-Colón, Angel G.; Birkeland, Siri; Vizueta, Joel; Li, Siyu; Li, Qionghou; Loureiro, João; Kosawang, Chatchai; Jaramillo Díaz, Patricia; Rivas-Torres, Gonzalo; Fernández-Mazuecos, Mario; Vargas, Pablo; McCauley, Ross; Petersen, Gitte; Santos-Bay, Luisa; Wales, Nathan; Catchen, Julian M.; Machado, Daniel; Nowak, Michael; Suh, Alexander; Sinha, Neelima R.; Rostgaard Nielsen, Lene; Seberg, Ole; Gilbert, Marcus Thomas Pius; Leebens-Mack, James H.; Rieseberg, Loren H.; Martin, Michael David. (2022) The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications. volum 13.
    Academic article
  • Machado, Daniel; Patil, Kiran R.. (2022) Reply to: Erroneous predictions of auxotrophies by CarveMe. Nature Ecology and Evolution.
    Letter to the editor
  • van den Berg, Naomi Iris; 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. volum 6 (7).
    Academic literature review
  • 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
  • Blasche, Sonja; Kim, Yongkyu; Mars, Ruben A.T.; Machado, Daniel; Maansson, Maria; Kafkia, Eleni; Milanese, Alessio; Zeller, Georg; Teusink, Bas; Nielsen, Jens; Benes, Vladimir; Neves, Rute; Sauer, Uwe H.; Patil, Kiran R.. (2021) Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nature Microbiology. volum 6.
    Academic article
  • 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. volum 5.
    Academic article
  • Shechter, Ksenija Radic; Kafkia, Eleni; Zirngibl, Katharina; Gawrzak, Sylwia; Alladin, Ashna; Machado, Daniel; Lüchtenborg, Christian; Sévin, Daniel C.; Brügger, Britta; Patil, Kiran R.; Jechlinger, Martin. (2021) Metabolic memory underlying minimal residual disease in breast cancer. Molecular Systems Biology. volum 17.
    Academic article
  • 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; Diener, Christian; Dräger, Andreas; Ebert, Birgitta E.; Edirisinghe, Janaka E.; Faria, José P.; Feist, Adam M.; Fengos, Georgios; Fleming, Ronan M.T.; García-Jiménez, Beatriz; Hatzimanikatis, Vassily; Van Helvoirt, Wout; Henry, Christopher S.; Hermjakob, Henning; Herrgård, Markus J.; Kaafarani, Ali; Kim, Hyun Uk; King, Zachary; Klamt, Steffen; Klipp, Edda; Koehorst, Jasper J; König, Matthias; Lakshmanan, Meiyappan; Lee, Dong-Yup; Lee, Sang Yup; Lee, Sunjae; Lewis, Nathan E.; Liu, Filipe; Ma, Hongwu; Moutinho Luz Machado, Carlos Daniel; Mahadevan, Radhakrishnan; Maia, Paulo; Mardinoglu, Adil; Medlock, Gregory L.; Monk, Jonathan M.; Nielsen, Jens; Nielsen, Lars Keld; Nogales, Juan; Nookaew, Intawat; Palsson, Bernhard O.; Papin, Jason A.; Patil, Kiran R.; Poolman, Mark; Price, Nathan D.; Resendis-Antonio, Osbaldo; Richelle, Anne; Rocha, Isabel; Sánchez, Benjamín J.; Schaap, Peter J.; Sheriff, Rahuman S. Malik; Shoaie, Saeed; Sonnenschein, Nikolaus; Teusink, Bas; Vilaça, Paulo; Vik, Jon Olav; Wodke, Judith A. H.; Xavier, Joana C.; Yuan, Qianqian; Zakhartsev, Maksim; Zhang, Cheng. (2020) MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. volum 38.
    Academic article

Teaching

Courses

  • BT8120 - Prokaryote Molecular Biology and Synthetic Biology
  • BT2100 - Computational Biotechnology

Media

Finding Genius Podcast

Harnessing the Ecology of Microbial Communities with Daniel Machado

2023

  • Poster
    Stallvik, Andrea; Moutinho Luz Machado, Carlos Daniel. (2023) Synthetic Microbial Communities for the Production of High-Value Compounds. 58th Norwegian Biochemical Society Meeting . Norwegian Biochemical Society; Ås, Norway. 2023-01-19 - 2023-01-22.

2022

  • Poster
    Burgos, Idun Maria Tokvam; Machado, Daniel. (2022) Modeling The Conversion Of Lignocellulose Into Medium-chain Carboxylates. ISME 18 . International Society for Microbial Ecology; Lausanne, Switzerland. 2022-08-14 - 2022-08-19.
  • Poster
    Teixeira, Miguel; Machado, Daniel. (2022) CarveMe roadmap: expanding genome-scale metabolic models’ reconstruction. ISME 18 . International Society for Microbial Ecology; Lausanne, Switzerland. 2022-08-14 - 2022-08-19.
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