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The Computational Biology Lab (LBC) focuses on comparative and functional genomics of pathogens. Within these general areas of work, the aim of our research is to understand the genetic basis of complex phenotypes in bacteria and the evolution of multigene families in worms. In addition, we invest time in the development of bioinformatics tools and strategies for the application of deep sequencing and genome analysis.

Laboratorio de Biología Computacional

Laboratorio de Biología Computacional

Our Lab is part of the

Biotechnology Department


The Computational Biology Lab (LBC in Spanish) was established as an independent group in May 2016 and is part of the Biotechnology Department at the School of Medicine, Universidad de la República - Uruguay.

LBC’s main objective is to understand the basis of differential pathogenesis in bacteria and helminth using omic data as the main input. We have also invested some time in the development of bioinformatics tools and strategies for the analysis of sequenced data and to support other groups of researchers who need to apply deep sequencing or massive data analysis.

Our teams is currently formed by young research assistants, graduate students, and one postdoc. During these years many fruitful national and international collaborations were built, as a result, our group is participating in diverse and exciting research projects.

Research lines

Comparative genomics

One of the main goals of comparative genomics is the elucidation of the genetic basis of the phenotypic differences among species and strains. The genomic approach is of particular importance when analyzing complex phenotypes that depend on a combination of several genetic elements, such as pathogenicity, virulence, or symbiosis. The genomic variability may include several levels (rearrangements, presence/absence of genes, indels, or single nucleotide variants). We study these genomic traits and their evolutionary dynamics in pathogenic and nonpathogenic bacteria, including clinical and environmental isolates of Salmonella, Acinetobacter, and Shewanella, among others.

Study of gene duplications

The study of genomes confirmed that duplication is a powerful evolutionary mechanism, generating raw material for the acquisition of new functions in the cell. In many cases, the increase of copies in a family of genes has proven to be the result of an adaptive process. We have studied the evolution of gene families in Platyhelminthes and other phyla. Studies mainly include phylogenetic analyzes, gene structure identification, protein 3D prediction, and molecular distance estimations.

Functional genomics

Transcriptomic analysis, the analysis of the complete set of RNA transcripts, is nowadays the most commonly used approach in functional genomics. In our lab we apply RNA-seq to study the genome response to different conditions in a wide variety of organisms. Thus, we aim to identify novel genetic elements or interactions that contribute to produce the complex phenotype that characterize the pathogen when going through critical states relevant to its pathogenesis.


Characterization of cell factors involved in the bioremediation of organic compounds in Shewanella isolates.

The increasing pollution in the world is a serious problem with severe long-term consequences. The main sources of human-caused water pollution include mining, industry, livestock, and agriculture. In particular, the treatment and disposal of industrial waste requires complex processing that raises the costs of the final products.

Evolution of families of secretory proteins coding genes in Platyhelminthes

Parasitic flatworms generally have complex cycles involving various hosts, including humans and livestock species, and therefore have a great impact on human and animal health. Examples of species of this group of relevance are Echinococcus granulosus, Schistosoma mansoni, and Fasciola hepatica, among many others.

Functional and evolutionary genomics in Salmonella enterica, role of sRNA in lineage-specific pathogenicity

Salmonella enterica, a pathogen of birds and mammals, is distributed worldwide and has a considerable impact on human and animal health, being the main causal agent of foodborne infections. The different serotypes within the species show important differences in epidemic potential, virulence, and pathogenicity.

Genome wide association study (GWAS) in E. coli: an approach to the search for genetic markers of the Shiga toxin-producing pathotype (STEC)

Due to genetic changes, certain strains of E. coli have moved from commensals to pathogens. According to the pathogenic mechanisms involved, different pathotypes are recognized, one of them is STEC, a pathotype that produces Shiga toxins (Stxs).

Lab members

Principal Investigator


Andrés Iriarte

Associate Professor at the Biotech. Department.

Pathogens comparative genomics., Evolution of gene families., Evolution of codon and amino acid usage.

Postdoctorate fellows


German Matias Traglia

Postdoctoral student

Functional & comparative genomics of prokaryotes

PhD. students


Cecilia Rodriguez

PhD Student

Prokaryote transcriptomics, metabolomics and proteomics, Plant-bacteria interaction


Javier Calvelo

PhD student

Bioinformatics, Parasite transcriptomics


Paula Vico

PhD student

Genomics, Transcriptomics, Evolution, Toxin production in cyanobacteria

MSc. students


Hernan Juan

MSc student

Metagenomic of eukaryotes


Virginia Cantera

MSc student

Functional genomics of prokaryotes



Eugenio Jara


Bovine transcriptomics, Comparative genomics


Lucía Balestrazzi


Comparative genomics of prokaryotes


Mauricio Langleib


Comparative and functional genomics of platyhelminthes


Natalia Mannise


Molecular ecology, Environmental DNA, Metagenomics, DNA metabarcoding, Parasite studies


Pilar dos Santos


Genomics of Platyhelminthes


Sylvia Enid Vázquez Zeballos


Molecular markers for STEC, Resistance genes in bacteria

Selected Publications

SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

Background Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced.

Results In this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing.

Conclusions SLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation.

Biogeography of the cyanobacterium Raphidiopsis (Cylindrospermopsis) raciborskii: Integrating genomics, phylogenetic and toxicity data

Raphidiopsis (Cylindrospermopsis) raciborskii, a globally distributed bloom-forming cyanobacterium, produces either the cytotoxin cylindrospermopsin (CYL) in Oceania, Asia and Europe or the neurotoxin saxitoxin (STX) and analogues (paralytic shellfish poison, PSP) in South America (encoded by sxt genetic cluster) and none of them in Africa. Nevertheless, this particular geographic pattern is usually overlooked in current hypotheses about the species dispersal routes. Here, we combined genomics, phylogenetic analyses, toxicity data and a literature survey to unveil the evolutionary history and spread of the species. Phylogenies based on 354 orthologous genes from all the available genomes and ribosomal ITS sequences of the taxon showed two well-defined clades: the American, having the PSP producers; and the Oceania/Europe/Asia, including the CYL producers. We propose central Africa as the original dispersion center (non-toxic populations), reaching North Africa and North America (in former Laurasia continent). The ability to produce CYL probably took place in populations that advanced to sub-Saharan Africa and then to Oceania and South America. According to the genomic context of the sxt cluster found in PSP-producer strains, this trait was acquired once by horizontal transfer in South America, where the ability to produce CYL was lost.

Expansion of cap superfamily proteins in the genome of Mesocestoides corti: An extreme case of a general bilaterian trend

The CAP superfamily is a diverse group of proteins that are involved in different biological processes, yet their molecular functions are still incompletely understood. The α-β-α sandwich structure of the CAP domain is characteristic of this superfamily and several different domains may be found together with it. They are generally secreted proteins and in helminths many are secreted to the environment, and are related to the host-parasite interaction. In this work we mined cestode genomic data for members of this superfamily. Whereas in average 26 members with complete CAP domains were found in most cestodes, in Mesocestoides corti we strikingly found 271 members with complete domains, most of which show evidence of expression. We also found other truncated domains and putative pseudogenes. Interestingly, most of these genes were found in a monophyletic clade within a cestode-specific group of CAP domain containing proteins, and each cestode species has also developed independent duplications of these proteins. This pattern of extensive independent duplications can also be found in other parasitic and free-living flatworms, as well as in other metazoan phyla. Within the M. corti specific expansion, several sub-clades of these proteins showed evidence of evolution under positive selection. Our results suggest that the CAP domain containing proteins of animals evolve through a “birth and death” mechanism, and that different environmental pressures may drive this evolution in different species. In the case of helminth parasites, this could be related to the interaction between the parasite and the host, including mechanisms to evade and modulate the host immune system.

Contact us!

  • +5982 4871288 #1131
  • Dr. Alfredo Navarro 3051, Montevideo, UY 11600
  • Departamento de Desarrollo Biotecnológico. Piso 1 del Instituto, al fondo del corredor.
  • Lunes 8:00 AM a 18:00 PM
    Viernes 8:00 AM a 18:00 PM