Daniel Machado
About
Daniel Machado joined NTNU in September 2020 as Associate Professor of Computational Biology.
Background
- Bsc/Msc in Mathematics and Computer Science (2006, University of Minho, Portugal)
- PhD in Bioengineering and Biotechnology (2012, MIT-Portugal Program)
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 details please visit our group's webpage: Machado lab
Projects / Collaborations
Competencies
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 D; 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 (1).
- 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).
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.
- 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.
- 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.
- 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.
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.
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 D; 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 (1).
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.