Bioinformatics is the application of computational and statistical techniques for the analysis of data of biological origin, which also includes its organization and storage as well as the development of tools to manage them.
The volume of data currently generated by sequencing techniques promotes a constant development of methods to deal efficiently with numerous genomes and proteomes, without losing sight of the biologically relevant data.
At the Bioinformatic Unit we apply various tools to the comparative study of genomes on a global scale, as well as specific families of genes and proteins. Historically we have focused on bacteria, human pathogens and the human genome. We have also developed specific tools to deal with the new methodological challenges posed by the information explosion. These applications and developments have a place in genetics and biomedicine, and most recently in metagenomics, the genomic characterization of environmental samples.
The URUGENOMES project seeks to create local capacities in the area of human genomics and especially medical genomics. In this context, 50 genomes were sequenced, which are being analyzed from the point of view of population genomics (ancestry), and 30 other genomes of patients with rare diseases, which are analyzed in the context of medical genomics.
One of the areas in which the unit specializes is human transcriptomics. Several projects are currently being developed within this line. One of them is dedicated to the study of differentiation processes of stem cells to different cell types (adipogenesis, osteogenesis and cardiomyogenesis). Of special interest is the post transcriptional regulation that takes place during these processes. Another project within this research line aims to analyze the response of human cells to the infection of pathogens of different origins.
We seek to exploit data on protein structures, generated by X-ray crystallography and other techniques (NMR, cryo-electromicroscopy), in the functional understanding of protein families. Using three-dimensional structures and genomic sequences often provides clues about the function of a protein and, sometimes, generates functional hypotheses about whole families of ‘hypothetical’ genes (genes without known function).
Genomics and microbial evolution:
It seeks to understand the evolution of pathogens that affect livestock and domestic animals using phylodynamics; and fundamentally the discovery of the evolutionary forces that shape the genomes of zoonotic bacteria such as Campylobacter, Leptospira and Mycobacterium. Among the ongoing projects within this line, there is currently a Latin American joint effort to study the population dynamics of Clostridium difficile using genomic epidemiology approaches. Recently, one of the projects of this line seeks to analyze the dynamics of resistance to antibiotics in enterobacteria of urban environments through the application of metagenomics.
Statistical genetics and its application to evolution
NGS and microarrays data analysis:
- Genome Assembly
- Variant analysis
- Transcriptomic and ribosomal profile analyses
- Small RNAs data analysis
Sequence alignment and phylogenetic inference
Biostatistics and advice on specific software usage
Metagenomic data analyses and experimental design.
Dissemination conference of Genomics applied to Medicine. May 4, 2018. Organizer: Hugo Naya. Funded by: Inter-American Development Bank, project ATN / KK-14584-UR.
Course “Introduction to Medical Genomics”. March 5-9, 2018. Institut Pasteur de Montevideo. Organizer: Hugo Naya. Funded by: Inter-American Development Bank, project ATN / KK-14584-UR.
Genomic Medicine Conference. December 18-19, 2017. Institut Pasteur de Montevideo. Organizer: Hugo Naya. Funded by: Inter-American Development Bank, project ATN / KK-14584-UR.
“Hands on Metagenomics data analysis: tools for bioprospection in – environmental and clinical microbiology”. September 25-October 6, 2017. Funded by: UNU BIOLAC, French Cooperation, CAMPUS FRANCE and FOCEM.
“Deciphering regulator RNA functions by high-throughput sequencing”. December 4-8, 2017. Funded by: UNU BIOLAC, FOCEM, and private sponsors.
2018-2019 – “Tools development for the analysis of Uruguayan human genomes”. ANII. Lucía Spangenberg, María Inés Fariello
2016-2018 – “Identification of microRNAs regulating infection of human cells by Listeria monocytogenes”. PROGRAMS TRANSVERSAUX DE RECHERCHE – PTR Institut Pasteur, France. Javier Pizarro-Cerdá (H Naya)
2014-2017 – “Strengthening technical and human capacities for genomic services exports”. Financiación: Banco Interamericano de Desarrollo, proyecto ATN/KK-14584-UR. Responsable: Hugo Naya.
2014-2015 – “Estrogen receptor: Functional tissue-specific characterization of synonymous polymorphisms and translational kinetics in human cells”. Clemente Estable Fund- ANII. Responsible: Tamara Fernández
2016 – “Modulation of the ubiquitin-proteasome system by electrophiles and oxidants: study of molecular networks”. Clemente Estable Fund-ANII. Responsible: Horacio Botti. Collaborators: Gregorio Iraola, Álvaro Cabana, Martín Hugo, Marcelo Hill.
2016 – “Genomic evolution of Mycobacterium avium paratuberculosis in wild and production animals”. Clemente Estable Fund-ANII. Responsible: Pablo Fresia. Collaborators: Gregorio Iraola, Ignacio Ferres, Hugo Naya, Fernando Paolicci (INTA)
2017-2019 – Metagenomic Project – ANII (Gregorio Iraola)
2012-2015 – “Investigation of two Genetic and Molecular Mechanisms in Biofilmes of Leptospira”. CAPES Brazil funds. Responsible: A Schnadelbach / P Ristow. Participants: H. Naya
2013-2015 – “Transcriptional analysis in Leptospires forming biofilms”. ANII funds Responsible: H. Naya.