Matías Rodríguez

PhD Student

 

© Pixabay

Comparative Genomics
Institute of Bioinformatics
Niels Stensen Strasse 14
D-48149 Münster, Germany
Tel.: +49 251/83-50004
matidae@gmail.com

Nationality: Uruguayan Uy

 

Education

  • Since 2019:
    PhD studies in the Comparative Genomics Group, Institute of Bioinformatics, University of Münster, Germany
  • 2013 - 2018:
    Master of Science (M.Sc.) in Bioinformatics, University of the Republic, Montevideo, Uruguay
  • 2002 - 2013:
    Llicence (Lic.) in Biochemistry, University of the Republic, Montevideo, Uruguay
  • 2006 - 2012:
    System Analyst, Instituto BIOS, Uruguay

Work experience

  • 2017 - 2018:
    Technical Assistant, Molecular Biology Unit , Institut Pasteur of Montevideo, Uruguay
  • 2017:
    Internship, GENOPOM Laboratory, Dipartamento di Agraria, University of Naples Federico II, Itlay
  • 2016:
    Assistant, Biomathematics, Science Faculty, University of the Republic, Montevideo, Uruguay
  • 2014:
    Internship, Laboratory of Functional Genomics, Biotechnology Department, University of Verona, Italy
  • 2013 -2015:
    Assistant, Biomathematics, Science Faculty, University of the Republic, Montevideo, Uruguay
  • 2012 -2013:
    Technical Assistant, Molecular Biology Unit , Institut Pasteur of Montevideo, Uruguay
  • 2011:
    Assistant, Biomathematics, Science Faculty, University of the Republic, Montevideo, Uruguay

Supervisors

  • Prof. Dr. Wojciech Makałowski, Comparative Genomics Group, Institute of Bioinformatics, University of Münster, Germany
  •  
  •  

Research interests

  •  
  •  
  •  

PhD project description

Mobilome of Apicomplexa parasites

Apicomplexa protozoans are responsible for multiple pathologies of medical and veterinary importance. The study of transposable elements (TEs) across this phylum is a laborious task that has not been completely undertaken yet. Nevertheless, the investigations of active TEs, their presence or absence can help us to improve our understanding of the genomic organization and evolution of parasitism. My research will consist in a comprehensive mobilome analysis in these parasites. This will be done in the following manner:

I will start with the annotation of TE in all the Apicomplexa genomes available at Genbank. Due to the lack of the specific TE libraries for Apicomplexa, a de novo approach is the method of choice for this task. For manual annotation of TE consensus sequences I will use different pipelines and extensive manual curation using TE signatures and nucleotide composition. This will allow an exhaustive annotation of the mobilome in each Apicomplexa genome analyzed.

In a second stage, I will develop a genomic-centric relational database of Apicomplexa TEs, with all the annotated TEs features and ORFs along with the annotated genes. The Apicomplexa-specific TE taxonomy will also be stored and this basic information will be used for evolutionary analyses. A userfriendly web interface will be developed for access to this database.

Third, I will check for any exaptation events of TEs. This will be done by intersection of TE coordinates determined in the first stage of the project with coordinates of the annotated genes. The database of Apicomplexa TEs will enable easy search for TE exaptations and domestication. I will also perform GO analysis to check which of the protein categories are enriched in TE exaptations and investigate potential gene regulation by TEs in Apicomplexa genomes.

Publications

  • Rodríguez M, Makalowski W. (2022) Mobilome of Apicomplexa parasites. Genes 13(5):887. 10.3390/genes13050887 [doi]
  • Berná L, Rodríguez M, Chiribao ML, Parodi A, Rijo G, Alvarez-Valin F, Robello C (2018) Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microbial Genomics 4(5). 10.1099/mgen.0.000177 [doi]
  • Berná L, Chiribao ML, Greif G, Rodríguez M, Robello C, Alvarez-Valin F (2017) Transcriptomic analysis reveals that metabolic switch and surface remodeling are key processes for stage transition in Trypanosoma cruzi. PeerJ 5:e3017 10.7717/peerj.3017 [doi]
  • Greif G, Rodríguez M, Reyna-Bello A, Robello C, Alvarez-Valin F (2015) Kinetoplast adaptations in American strains from Trypanosoma vivax. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 773:69-82. 10.1016/j.mrfmmm.2015.01.008 [doi]
  • Greif G, Ponce de León M, Lamolle G, Rodríguez M, Piñeyro D, Tavares-Marques L, Reyna-Bello A, Robello C, Alvarez-Valín F (2013) Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax. BMC Genomics 14:149. 10.1186/1471-2164-14-149 [doi]