Daniel Machado

Post-Doc


Career

  • 2013 - 2015: Invited Assistant Researcher, Universidade do Minho

Qualifications

  • 2012: PhD Program in Bioengineering, Universidade do Minho

Roles and Responsibilities

  • Since  2013: Guest Editor at Frontiers in Bioengineering and Biotechnology

Honors and Awards

  • 2011: Best Poster Award at 5th Annual Workshop on the Business-Government Interface: Systems and Synthetic Biology, Universidade do Minho, Braga. Title: Exploring the gap between dynamic and constraint-based models of metabolism.
  • 2015 - 2016: Genome-scale modeling of allosteric regulation in E. coli
  • 2013 - 2015: Systems Biology
  • 2011 - 2012: SYNBIOBACTHER - Synthetic biology approaches to engineer "therapeutic" bacteria
  • 2008 - 2012: Novel modelling formalisms and simulation tools in Computational Biosystems

Past Students


Recent Publications

1
  • Kang, Kang; Bergdahl, Basti; Machado, Daniel; Dato, Laura; Han, Ting-Li; Li, Jun; Villas-Boas, Silas; Herrgård, Markus J; Förster, Jochen; Panagiotou, Gianni
Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations
  • GigaScience, 8(4), giz015, 2019
2
  • Menden, Michael P.; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Yu, Thomas; Kang, Jaewoo; Jeon, Minji; Wolfinger, Russ; Nguyen, Tin; Zaslavskiy, Mikhail; Abante, Jordi; Abecassis, Barbara Schmitz; Aben, Nanne; Aghamirzaie, Delasa; Aittokallio, Tero; Akhtari, Farida S.; Al-lazikani, Bissan; Alam, Tanvir; Allam, Amin; Allen, Chad; de Almeida, Mariana Pelicano; Altarawy, Doaa; Alves, Vinicius; Amadoz, Alicia; Anchang, Benedict; Antolin, Albert A.; Ash, Jeremy R.; Aznar, Victoria Romeo; Ba-alawi, Wail; Bagheri, Moeen; Bajic, Vladimir; Ball, Gordon; Ballester, Pedro J.; Baptista, Delora; Bare, Christopher; Bateson, Mathilde; Bender, Andreas; Bertrand, Denis; Wijayawardena, Bhagya; Boroevich, Keith A.; Bosdriesz, Evert; Bougouffa, Salim; Bounova, Gergana; Brouwer, Thomas; Bryant, Barbara; Calaza, Manuel; Calderone, Alberto; Calza, Stefano; Capuzzi, Stephen; Carbonell-Caballero, Jose; Carlin, Daniel; Carter, Hannah; Castagnoli, Luisa; Celebi, Remzi; Cesareni, Gianni; Chang, Hyeokyoon; Chen, Guocai; Chen, Haoran; Chen, Huiyuan; Cheng, Lijun; Chernomoretz, Ariel; Chicco, Davide; Cho, Kwang-Hyun; Cho, Sunghwan; Choi, Daeseon; Choi, Jaejoon; Choi, Kwanghun; Choi, Minsoo; Cock, Martine De; Coker, Elizabeth; Cortes-Ciriano, Isidro; Cserzö, Miklós; Cubuk, Cankut; Curtis, Christina; Daele, Dries Van; Dang, Cuong C.; Dijkstra,Tjeerd; Dopazo,Joaquin; Draghici,Sorin; Drosou,Anastasios; Dumontier,Michel; Ehrhart,Friederike; Eid,Fatma-Elzahraa; ElHefnawi,Mahmoud; Elmarakeby,Haitham; vanEngelen,Bo; Engin, Hatice Billur; deEsch,Iwan; Evelo,Chris; Falcao, Andre O.; Farag,Sherif; Fernandez-Lozano, Carlos; Fisch,Kathleen; Flobak,Asmund; Fornari,Chiara; Foroushani, Amir B.K.; Fotso, Donatien Chedom; Fourches,Denis; Friend,Stephen; Frigessi,Arnoldo; Gao,Feng; Gao,Xiaoting; Gerold,JeffreyM.; Gestraud,Pierre; Ghosh,Samik; Gillberg,Jussi; Godoy-Lorite,Antonia; Godynyuk,Lizzy; Godzik,Adam; Goldenberg,Anna; Gomez-Cabrero,David; Gonen,Mehmet; deGraaf,Chris; Gray,Harry; Grechkin,Maxim; Guimera,Roger; Guney,Emre; Haibe-Kains,Benjamin; Han,Younghyun; Hase,Takeshi; He,Di; He,Liye; Heath,LenwoodS.; Hellton,KristofferH.; Helmer-Citterich,Manuela; Hidalgo,MartaR.; Hidru,Daniel; Hill,StevenM.; Hochreiter,Sepp; Hong,Seungpyo; Hovig,Eivind; Hsueh,Ya-Chih; Hu,Zhiyuan; Huang,JustinK.; Huang,R.Stephanie; Hunyady, László; Hwang,Jinseub; Hwang,TaeHyun; Hwang,Woochang; Hwang,Yongdeuk; Isayev,Olex; r; Don't Walk IV, Oliver Bear; Jack,John; Jahandideh, Samad; Ji,Jiadong; Jo,Yousang; Kamola,PiotrJ.; Kanev,GeorgiK.; Karacosta,Loukia; Karimi,Mostafa; Kaski,Samuel; Kazanov,Marat; Khamis,AbdullahM.; Khan,SuleimanAli; Kiani,NarsisA.; Kim,Allen; Kim,Jinhan; Kim,Juntae; Kim,Kiseong; Kim,Kyung; Kim,Sunkyu; Kim,Yongsoo; Kim,Yunseong; Kirk,PaulD.W.; Kitano,Hiroaki; Klambauer,Gunter; Knowles,David; Ko,Melissa; Kohn-Luque,Alvaro; Kooistra,AlbertJ.; Kuenemann,MelaineA.; Kuiper,Martin; Kurz,Christoph; Kwon,Mijin; vanLaarhoven,Twan; Laegreid,Astrid; Lederer,Simone; Lee,Heewon; Lee,Jeon; Lee,YunWoo; Leppäaho, Eemeli; Lewis,Richard; Li,Jing; Li,Lang; Liley,James; Lim,WengKhong; Lin,Chieh; Liu,Yiyi; Lopez,Yosvany; Low,Joshua; Lysenko,Artem; Machado,Daniel; Madhukar,Neel; Maeyer,DriesDe; Malpartida,AnaBelen; Mamitsuka,Hiroshi; Marabita,Francesco; Marchal,Kathleen; Marttinen,Pekka; Mason,Daniel; Mazaheri,Alireza; Mehmood,Arfa; Mehreen,Ali; Michaut,Magali; Miller,RyanA.; Mitsopoulos,Costas; Modos,Dezso; Moerbeke,MarijkeVan; Moo,Keagan; Motsinger-Reif,Alison; Movva,Rajiv; Muraru,Sebastian; Muratov,Eugene; Mushthofa,Mushthofa; Nagarajan,Niranjan; Nakken,Sigve; Nath,Aritro; Neuvial,Pierre; Newton,Richard; Ning,Zheng; Niz,CarlosDe; Oliva,Baldo; Olsen,Catharina; Palmeri,Antonio; Panesar,Bhawan; Papadopoulos,Stavros; Park,Jaesub; Park,Seonyeong; Park,Sungjoon; Pawitan,Yudi; Peluso,Daniele; Pendyala,Sriram; Peng,Jian; Perfetto,Livia; Pirro,Stefano; Plevritis,Sylvia; Politi,Regina; Poon,Hoifung; Porta,Eduard; Prellner,Isak; Preuer,Kristina; Pujana,MiguelAngel; Ramnarine,Ricardo; Reid,JohnE.; Reyal,Fabien; Richardson,Sylvia; Ricketts,Camir; Rieswijk,Linda; Rocha, Miguel; Rodriguez-Gonzalvez,Carmen; Roell,Kyle; Rotroff,Daniel; deRuiter,JulianR.; Rukawa,Ploy; Sadacca,Benjamin; Safikhani,Zhaleh; Safitri,Fita; Sales-Pardo,Marta; Sauer,Sebastian; Schlichting,Moritz; Seoane,JoseA.; Serra,Jordi; Shang,Ming-Mei; Sharma, Alok; Sharma, Hari; Shen, Yang; Shiga, Motoki; Shin, Moonshik; Shkedy, Ziv; Shopsowitz, Kevin; Sinai, Sam; Skola, Dylan; Smirnov, Petr; Soerensen, Izel Fourie; Soerensen, Peter; Song, Je-Hoon; Song, Sang Ok; Soufan, Othman; Spitzmueller, Andreas; Steipe, Boris; Suphavilai, Chayaporn; Tamayo, Sergio Pulido; Tamborero, David; Tang, Jing; Tanoli, Zia-ur-Rehman; Tarres-Deulofeu, Marc; Tegner, Jesper; Thommesen, Liv; Tonekaboni, Seyed Ali Madani; Tran, Hong; Troyer, Ewoud De; Truong, Amy; Tsunoda, Tatsuhiko; Turu, Gäbor; Tzeng, Guang-Yo; Verbeke, Lieven; Videla, Santiago; Consortium, AstraZeneca-Sanger Drug Combination DREAM
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
  • Nature Communications, 10(2674), 2019
3
  • Gonçalves, Emanuel; Sciacovelli, Marco; Costa, Ana S.H.; Tran, Maxine Gia Binh; Johnson, Timothy Isaac; Machado, Daniel; Frezza, Christian; Saez-Rodriguez, Julio
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells
  • Metabolic Engineering, 45, 149-157, 2018
4
Stoichiometric representation of gene–protein–reaction associations leverages constraint-based analysis from reaction to gene-level phenotype prediction
  • PLoS Computational Biology, 12(10:e1005140), 1-24, 2016
5
Current state and challenges for dynamic metabolic modeling
  • Current Opinion in Microbiology, 33, 97-104, 2016
6
A comparative analysis of dynamic models of the central carbon metabolism of Escherichia coli
  • IFAC-PapersOnLine, 49(26), 270-276, 2016
7
  • Monk, Jonathan M.; Koza, Anna; Campodonico, Miguel A.; Machado, Daniel; Seoane, Jose Miguel; Palsson, Bernhard O.; Herrgård, Markus J.; Feist, Adam M.
Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes
  • Cell Systems, 3(3), 238-251, 2016
8
Co-evolution of strain design methods based on flux balance and elementary mode analysis
  • Metabolic Engineering Communications, 2, 85-92, 2015
9
Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
  • Frontiers in Bioengineering and Biotechnology, 3(154), 2015
10
A kinetic model for curcumin production in Escherichia coli
  • BioSystems, 125, 16-21, 2014
11
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
  • PLoS Computational Biology, 10(4), 2014
12
Random sampling of elementary flux modes in large-scale metabolic networks
  • Bioinformatics, 28(18), i515-i521, 2012
13
Exploring the gap between dynamic and constraint-based models of metabolism
  • Metabolic Engineering, 14(2), 112-119, 2012
14
Modeling formalisms in systems biology
  • AMB Express, 1(45), 1-14, 2011
15
Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modeling
  • IET Systems Biology, 5(3), 157-163, 2011
16
Hybrid dynamic modeling of E. coli central metabolic network combining Michaelis-Menten and approximate kinetic equations
  • BioSystems, 100(2), 150-157, 2010
17
A critical review on modelling formalisms and simulation tools in computational biosystems
  • Lecture Notes in Computer Science, 5518, 1063-1070, 2009
18
Large scale dynamic model reconstruction for the central carbon metabolism of Escherichia coli
  • Lecture Notes in Computer Science, No. 5518, 1079-1083, 2009
Full List