Miguel Rocha

Associate Professor



Career

  • Since  2012: Associate Professor, Universidade do Minho
  • 2004 - 2012: Assistant Professor, Universidade do Minho

Qualifications

  • 2004: Doutoramento em Informática, Universidade do Minho

Roles and Responsibilities

  • Since  2015: Program Director, Master Program in Bioinformatics
  • 2013 - 2013: Member of the Scientific Steering Committee of the Research Unit, Computer Science and Technology Centre
  • 2010 - 2013: Director of Research Unit, Computer Science and Technology Centre
  • Since  2010: Member of the Scientific Steering Committee of Department, Department of Informatics
  • Since  2010: Member of Program Studies Steering Committee, Master Program in Bioinformatics - Biological Sciences
  • 2007 - 2010: Program Director, Master Program in Bioinformatics - Biological Sciences
  • 2005 - 2009: Associate Diretor of Research Unit, Computer Science and Technology Centre

Laboratory Management

Courses

  • Bioinformatics ( Master Program in Bioinformatics - TI )
  • Computation and Programming ( Integrated Master in Biological Engineering )
  • Bioinformatics ( Integrated Master in Biomedical Engineering )

Projects

Research Students


Recent Publications

1
Artificial intelligence in biological activity prediction
  • Advances in Intelligent Systems and Computing, 1005 (PACBB 2019), 164-172, 2019
2
Troppo - A Python framework for the reconstruction of context-specific metabolic models
  • Advances in Intelligent Systems and Computing, 1005 (PACBB 2019), 146-153, 2019
3
Predicting promoters in phage genomes using machine learning models
  • Advances in Intelligent Systems and Computing, 1005 (PACBB 2019), 105-112, 2019
4
Towards the reconstruction of integrated genome-scale models of metabolism and gene expression
  • Advances in Intelligent Systems and Computing, 1005 (PACBB 2019), 173-181, 2019
5
Comparison of pathway analysis and constraint-based methods for cell factory design
  • BMC Bioinformatics, 20(350), 2019
6
MOSCA: an automated pipeline for integrated metagenomics and metatranscriptomics data analysis
  • Advances in Intelligent Systems and Computing, 803 (PACBB 2018), 183-191, 2019
7
Metabolite integration pipeline for the improvement of human metabolic models
  • Advances in Intelligent Systems and Computing, 803 (PACBB 2018), 192-199, 2019
8
A review on metabolomics data analysis for cancer applications
  • Advances in Intelligent Systems and Computing, 803 (PACBB 2018), 157-165, 2019
9
HABIT - a webserver for interactive T cell neoepitope discovery
  • bioRxiv, (In Press), 2019
10
A model integration pipeline for the improvement of human genome-scale metabolic reconstructions
  • Journal of Integrative Bioinformatics, 16(1), 20180068, 2019
11
  • Cabral, Debora; Cardoso, Sara; Rocco, Silvana; Sforça, Maurício; Hengeltraub, Simone Fanan; Bauer, Cláudia; Rocha, Miguel; Maraschin, Marcelo
17α-ethinylestradiol analysis of endo- and exometabolome of Ulva lactuca (chlorophyta) by 1H-NMR spectroscopy and bioinformatics tools
  • Advances in Intelligent Systems and Computing, 803 (PACBB 2018), 216-223, 2019
12
  • Bauer, Claudia M.; Vilaça, Paulo; Ramlov, Fernanda; de Oliveira, Eva Regina; Cabral, Débora Q.; Schmitz, Caroline; Corrêa, Rafaela Gordo; Rocha, Miguel; Maraschin, Marcelo
In silico predictions for fucoxanthin production by the diatom Phaeodactylum tricornutum
  • Advances in Intelligent Systems and Computing, 803 (PACBB 2018), 139-148, 2019
13
  • 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
14
Methods for automated genome-scale metabolic model reconstruction
  • Biochemical Society Transactions, 46(4), 931-936, 2018
15
Utilitarian placement of composite services
  • IEEE Transactions on Network and Service Management, 15(2), 638-649, 2018
16
Development of an information retrieval tool for biomedical patents
  • Computer Methods and Programs in Biomedicine, 159, 125-134, 2018
17
A review of dynamic modeling approaches and their application in computational strain optimization for metabolic engineering
  • Frontiers in Microbiology, 9, 1690-1690, 2018
18
A critical evaluation of automatic atom mapping algorithms and tools
  • Advances in Intelligent Systems and Computing, 616 (PACBB 2017), 257-264, 2017
19
Development of text mining tools for information retrieval from patents
  • Advances in Intelligent Systems and Computing, 616 (PACBB 2017), 66-73, 2017
20
  • Lopes, Susane; Moresco, Rodolfo; Peruch, Luiz Augusto Martins; Rocha, Miguel; Maraschin, Marcelo
UV-Vis spectrophotometry and chemometrics as tools for recognition of the biochemical profiles of organic banana peels (Musa sp.) according to the seasonality in southern Brazil
  • Advances in Intelligent Systems and Computing, 616 (PACBB 2017), 289-296, 2017
Full List