Dr. João Pedro Saraiva

Contact

Dr. João Pedro Leonor Fernandes Saraiva
Post doctoral associate

Working Group Microbial Systems Bioinformatics

João Pedro Saraiva

Department of Environmental Microbiology
Helmholtz Centre for Environmental Research - UFZ
Permoserstr. 15, 04318 Leipzig, Germany

Phone +49 341 235-1374
joao.saraiva@ufz.de


Scientific Career

09/2017 present

Post Doctoral Associate - Microbial Systems Bioinformatics group, Department of Environmental Microbiology, Helmholtz Center for Environmental Research - UFZ, Leipzig, Germany

02/2014 07/2017

PhD student- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll Institute, Network Modelling, Jena, Germany

01/2013 12/2013

Research Associate - Institute of Biotechnology and Bioengineering, University of Minho, Braga, Portugal


Education

PhD

2014
2017

Bioinformatics

Leibniz Institute for Natural Product Reasearch and Infection Biology, Hans Knöll Institute, Jena, Germany

MSc

2009
2012

Bioinformatics

Institute of Biotechnology and Bioengineering, Braga, Portugal
Dipl.

2000
2006

Biotechnology Engineering

Polytechnic Institute of Bragança, Bragança, Portugal

Research interests

My primary research interest is in the field of complex microbial systems. The advancements in high throughput sequencing technologies has greatly increased our ability to generate genomic data. This exponential increase in microbial big data now demands the development of novel concepts and strategies to better characterize and study microbial community composition and microbial interactions.

Developing and implementing novel concepts focused on microbial communities is the overall goal of my research. How to generate models that use (meta)genomic data to answer questions related to complex microbial communities and interspecies interactions is the main driver of my research activities. Because natural microbial communities are highly complex, answering these questions require careful design and planning to reflect its true scenario. I also use machine learning approaches that allows for the discovery of patterns in microbial communities composition and interactions.


Publications

  • Saraiva, J. et al. iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. Front. Microbiol. 10, 1283 (2019).
  • Rosado, P. M. et al. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J. 13, 921–936 (2019).
  • Saraiva, J. & Koenig, R. Infection-specific human immune responses: fungi vs. bacteria. in INFECTION 43, S10–S10 (SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY, 2015).
  • Leonor Fernandes Saraiva J. P., Zubiria-Barrera C., Klassert T. E., Lautenbach M. J. Blaess, M., Claus R. A., König R. (2017). Combination of Classifiers Identifies Fungal-Specific Activation of Lysosome Genes in Human Monocytes. Frontiers in Microbiology, 8, 2366
  • Saraiva JP, Oswald M, Biering A, Röll D, Assmann C, Klassert T, Blaess M, Czakai K, Claus R, Löffler J, Slevogt H, König R. (2017) Fungal biomarker discovery by integration of classifiers. BMC Genomics 18, 601.
  • Saraiva J, Oswald M, Biering A, Assmann C, Klassert T, Blaess M, Czakai K, Claus R, Löffler J, Slevogt H, König R (2016) Integrating classifiers across datasets improves consistency of biomarker predictions in sepsis. In: Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering, Magdeburg, 10/09/2016-10/12/2016, pp. 95-102.Elsevier ScienceDirect.