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
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
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
Media
2023
-
PosterStallvik, 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
-
PosterBurgos, 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.
-
PosterTeixeira, 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.