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

  • 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


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
Analysing algorithms and data sources for the tissue-specific reconstruction of liver healthy and cancer cells
  • Interdisciplinary Sciences: Computational Life Sciences, 9(1), 36-45, 2017
2
Development of a framework for metabolic pathway analysis-driven strain optimization methods
  • Interdisciplinary Sciences: Computational Life Sciences, 9(1), 46-55, 2017
3
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
  • PLoS Computational Biology, 13(2), 1-25, 2017
4
Metabolomics of Ulva lactuca Linnaeus (Chlorophyta) exposed to oil fuels: Fourier transform infrared spectroscopy and multivariate analysis as tools for metabolic fingerprint
  • Marine Pollution Bulletin, 114(2), 831-836, 2017
5
Genome-wide semi-automated annotation of transporter systems
  • IEEE/ACM Transactions on Computational Biology and Bioinformatics, (In Press), 2017
6
  • Guinney, Justin; Wang, Tao; Laajala, Teemu D.; Winner, Kimberly Kanigel; Bare, J. Christopher; Neto, Elias Chaibub; Khan, Suleiman A.; Peddinti, Gopal; Airola, Antti; Pahikkala, Tapio; Mirtti, Tuomas; Yu, Thomas; Bot, Brian M.; Shen, Liji; Abdallah, Kald; Norman, Thea; Friend, Stephen; Stolovitzky, Gustavo; Soule, Howard; Ryan, Charles J.; Scher, Howard I.; Sartor, Oliver; Xie, Yang; Tero Aittokallio; Fang Liz Zhou; James C Costello; Catalina Anghel; Helia Azima; Robert Baertsch; Pedro J Ballester; Chris Bare; Vinayak Bhandari; Cuong C Dang; Maria Bekker-Nielsen Dunbar; Ann-Sophie Buchardt; Ljubomir Buturovic; Da Cao; Prabhakar Chalise; Junwoo Cho; Tzu-Ming Chu; R Yates Coley; Sailesh Conjeti; Correia, Sara; Ziwei Dai; Junqiang Dai; Philip Dargatz; Sam Delavarkhan; Detian Deng; Ankur Dhanik; Yu Du; Aparna Elangovan; Shellie Ellis; Laura L Elo; Shadrielle M Espiritu; Fan Fan; Ashkan B Farshi; Freitas, Ana Alão; Brooke Fridley; Christiane Fuchs; Eyal Gofer; Gopalacharyulu Peddinti; Stefan Graw; Russ Greiner; Yuanfang Guan; Jing Guo; Pankaj Gupta; Anna I Guyer; Jiawei Han; Niels R Hansen; Billy HW Chang; Outi Hirvonen; Barbara Huang; Chao Huang; Jinseub Hwang; Joseph G Ibrahim; Vivek Jayaswal; Jouhyun Jeon; Zhicheng Ji; Deekshith Juvvadi; Sirkku Jyrkkiö; Amin Katouzian; Marat D Kazanov; Shahin Khayyer; Dalho Kim; Agnieszka K Golinska; Devin Koestler; Kokowicz, Fernanda; Ivan Kondofersky; Norbert Krautenbacher; Damjan Krstajic; Luke Kumar; Christoph Kurz; Matthew Kyan; Michael Laimighofer; Eunjee Lee; Wojciech Lesinski; Miaozhu Li; Ye Li; Qiuyu Lian; Xiaotao Liang; Minseong Lim; Henry Lin; Xihui Lin; Jing Lu; Mehrad Mahmoudian; Roozbeh Manshaei; Richard Meier; Dejan Miljkovic; Krzysztof Mnich; Nassir Navab; Elias C Neto; Yulia Newton; Subhabrata Pal; Byeongju Park; Jaykumar Patel; Swetabh Pathak; Pattin, Alexandrina; Donna P Ankerst; Jian Peng; Anne H Petersen; Robin Philip; Stephen R Piccolo; Sebastian Pölsterl; Aneta Polewko-Klim; Karthik Rao; Xiang Ren; Rocha, Miguel; Rudnicki, Witold R.; Hyunnam Ryu; Hagen Scherb; Raghav Sehgal; Fatemeh Seyednasrollah; Jingbo Shang; Bin Shao; Howard Sher; Motoki Shiga; Artem Sokolov; Julia F Söllner; Lei Song; Josh Stuart; Ren Sun; Christopher J Sweeney; Nazanin Tahmasebi; Kar-Tong Tan; Lisbeth Tomaziu; Joseph Usset; Yeeleng S Vang; Roberto Vega; Vieira, Vítor; David Wang; Difei Wang; Junmei Wang; Lichao Wang; Sheng Wang; Yue Wang; Russ Wolfinger; Chris Wong; Zhenke Wu; Jinfeng Xiao; Xiaohui Xie; Doris Xin; Hojin Yang; Nancy Yu; Xiang Yu; Sulmaz Zahedi; Massimiliano Zanin; Chihao Zhang; Jingwen Zhang; Shihua Zhang; Yanchun Zhang; Zhu, Hongtu; Zhu, Shanfeng; Zhu, Yuxin
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
  • The Lancet Oncology, 18(1), 132-142, 2017
7
  • Faria, José Pedro; Davis, James J.; Edirisinghe, Janaka N.; Taylor, Ronald C.; Weisenhorn, Pamela; Olson, Robert D.; Stevens, Rick L.; Rocha, Miguel; Rocha, Isabel; Best, Aaron A.; DeJongh, Matthew; Tintle, Nathan L.; Parrello, Bruce; Overbeek, Ross; Henry, Christopher S.
Computing and applying atomic regulons to understand gene expression and regulation
  • Frontiers in Microbiology, 7(1819), 1-14, 2016
8
In vitro exposure of Ulva lactuca Linnaeus (Chlorophyta) to gasoline – Biochemical and morphological alterations
  • Chemosphere, 156, 428-437, 2016
9
An R package for the integrated analysis of metabolomics and spectral data
  • Computer Methods and Programs in Biomedicine, 129, 117-124, 2016
10
  • Uarrota, Virgílio Gavicho; Nunes, Eduardo da Costa; Peruch, Luiz Augusto Martins; Neubert, Enilto de Oliveira; Coelho, Bianca; Moresco, Rodolfo; Domínguez, Moralba Garcia; Sánchez, Teresa; Meléndez, Jorge Luis Luna; Dufour, Dominique; Ceballos, Hernan; Becerra Lopez-Lavalle, Luis Augusto; Hershey, Clair; Rocha, Miguel; Maraschin, Marcelo
Toward better understanding of postharvest deterioration: biochemical changes in stored cassava (Manihot esculenta Crantz) roots
  • Food Science & Nutrition, 4(3), 409-422, 2016
11
  • Uarrota, Virgílio Gavicho; Moresco, Rodolfo; Schmidt, Eder Carlos; Bouzon, Zenilda Laurita; Nunes, Eduardo da Costa; Neubert, Enilto de Oliveira; Peruch, Luiz Augusto Martins; Rocha, Miguel; Maraschin, Marcelo
The role of ascorbate peroxidase, guaiacol peroxidase, and polysaccharides in cassava (Manihot esculenta Crantz) roots under postharvest physiological deterioration
  • Food Chemistry, 197(Part A), 737-746, 2016
12
In silico constraint-based strain optimization methods: the quest for optimal cell factories
  • Microbiology and Molecular Biology Reviews, 80(1), 45-67, 2016
13
  • Uarrota, Virgílio Gavicho; Moresco, Rodolfo; Schmidt, Eder Carlos; Bouzon, Zenilda Laurita; Nunes, Eduardo da Costa; Neubert, Enilto de Oliveira; Peruch, Luiz Augusto Martins; Rocha, Miguel; Maraschin, Marcelo
Data supporting the role of enzymes and polysaccharides during cassava postharvest physiological deterioration
  • Data in Brief, 6, 503-506, 2016
14
Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data
  • Frontiers in Microbiology, 7(275), 1-11, 2016
15
Metabolic profiling and classification of propolis samples from Southern Brazil: An NMR-based platform coupled with machine learning
  • Journal of Natural Products, 79(1), 13-23, 2016
16
Extracting kinetic information from literature with KineticRE
  • Journal of Integrative Bioinformatics, 12(4), 282, 2015
17
Integrating data from heterogeneous DNA microarray platforms
  • Journal of Integrative Bioinformatics, 12(4), 281, 2015
18
  • Tomazzoli, Maíra Maciel; Neto, Remi Dal Pai; Moresco, Rodolfo; Westphal, Larissa; Zeggio, Amélia Regina Somensi; Specht, Leandro; Costa, Christopher; Rocha, Miguel; Maraschin, Marcelo
Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data
  • Journal of Integrative Bioinformatics, 12(4), 279, 2015
19
  • Moresco, Rodolfo; Uarrota, Virgílio Gavicho; Pereira, Aline; Tomazzoli, Maíra Maciel; Nunes, Eduardo da C.; Peruch, Luiz Augusto Martins; Gazzola, Jussara; Costa, Christopher; Rocha, Miguel; Maraschin, Marcelo
UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz)
  • Journal of Integrative Bioinformatics, 12(4), 280, 2015
20
  • Pojo, Marta; Gonçalves, Céline; Xavier-Magalhães, Ana; Oliveira, Ana Isabel; Gonçalves, Tiago; Correia, Sara; Rodrigues, Ana J.; Costa, Sandra; Pinto, Luísa; Pinto, Afonso A.; Lopes, José M.; Reis, Rui M.; Rocha, M.; Sousa, Nuno; Costa, Bruno M.
A transcriptomic signature mediated by HOXA9 promotes human glioblastoma initiation, aggressiveness and resistance to temozolomide
  • Oncotarget, 6(10), 7657-7674, 2015
Full List