Uni Münster Med. Fakultaet
NewickTreeModifier: a simple web page to prune and modify Newick trees
"The complete sequence of a human Y chromosome” by T2T Consortium has been published by Nature
"The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research” by Felix Manske, Lynn Ogoniak, Norbert Grundmann and Wojciech Makałowski has been published by Nucleic Acids Research.
"A Map of 3' DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes” by Reza Halabian and Wojciech Makałowski has been published by Biology.
"paPAML: An Improved Computational Tool to Explore Selection Pressure on Protein-Coding Sequences" by Lynn Ogoniak, Norbert Grundmann and others
"Mobilome of Apicomplexa Parasites" by Rodriguez and Makalowski has been published by Genes.
"Software evaluation for de novo detection of transposons" by Rodriguez and Makalowski has been published by Mobile DNA.
"From telomere to telomere: The transcriptional and epigenetic state of human repeat elements” by T2T consortium has been published by Science.
"Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing” by GRAID consortium that IoB is part of has been published by BMC Research Notes.
Congratulations to Reza and Matias on the excellent contribution on TE-driven DNA transductions in the human genome
"Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer" was published by MDPI

Matias Rodriguez

Matias R
I started a doctorate at the Institute of Bioinformatics, University of Münster, in April 2019 under the supervision of Prof. Wojciech Makałowski. I graduated as Lic. in Biochemistry (2013) and M.Sc in Bioinformatics (2018) from Universidad de la República (UdelaR), Uruguay.
Current project:
My research project consists in the identification and characterization of transposable elements (TEs) in all currently available apicomplexan genomes (64 genomes as of April 2019). The research involves developing a pipeline for an accurate classification and annotation of TEs and the evolutionary analysis of these elements considering their genomic context and their impact in the genome. For easy access to the results of this research I'm developing a database and web application along with interactive data visualizations.
I worked as research assistant at the Faculty of Science of UdelaR (2011-2016) in the assembly and annotation of two Trypanosoma vivax strains studying the genomic evolution and adaptation to the American continent. As part of this project I explored genome compartmentalization and gene expression during antigenic variation.
I also worked as technical assistant at the Institut Pasteur of Montevideo (2017-2018) in the assembly and annotation of three Trypanosoma cruzi strains and in the development of a web application to explore and visualize these assemblies.
- Functional Genomics Laboratory, Biotechnology Department, University of Verona, Italy, (June 2014) working with trypanosome RNAseq datasets.
- GENOPOM, Department of Agricultural Science, University of Naples Federico II, Italy, (October 2017) developing interactive plots for the analysis of tomato transposons.
I got a Master Program Grant from ANII (2014-2016) and a CSIC Research Grant (2014), both from Uruguay.
Since 2019 I've got funding from DAAD Research Grant/Doctoral Programmes in Germany for a four-year research plan.
  • Rodriguez M., Makałowski W. (2022) "Mobilome of Apicomplexa parasites" Genes 13(5), 887. doi.org/10.3390/genes13050887
  • Rodriguez M., Makałowski W. (2022) "Software evaluation for de novo detection of transposons" Mobile DNA 13(1). doi.org/10.1186/s13100-022-00266-2
  • Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., Altemose, N., Rhie, A., Core, L. J., Gerton, J. L., Makalowski, W., Olson, D., Rosen, J., Smit, A. F., Straight, A. F., Vollger, M. R., Wheeler, T. J., Schatz, M. C., Eichler, E. E., Phillippy, A. M., Timp, W., Miga, K. H., O’Neill, R. J. (2022) "From telomere to telomere: The transcriptional and epigenetic state of human repeat elements." Science 376(6588). doi.org/10.1126/science.abk3112
  • Greif G., Rodriguez M., Bontempi I., Robello C., Alvarez-Valin F. (2021) "Different kinetoplast degradation patterns in American Trypanosoma vivax strains: Multiple independent origins or fast evolution?" Genomics 113(2), 843-853 doi.org/10.1016/j.ygeno.2020.12.037
  • Berná L., Rodriguez 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 doi.org/10.1099/mgen.0.000177
  • Berná L., Chiribao ML., Greif G., Rodriguez 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:e3017doi.org/10.7717/peerj.3017
  • Greif G., Rodriguez, 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.doi.org/10.1016/j.mrfmmm.2015.01.008
  • Greif G., Ponce de León M., Lamolle G., Rodriguez 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.doi.org/10.1186/1471-2164-14-149
2022-06-07 18:30