CABANA Secondees

CABANA Secondees

Rebeca Campos-Sanchez

Rebeca Campos-Sanchez is a professor of Molecular Biology and Bioinformatics at the University of Costa Rica since 2005. Her PhD studies took her to The Pennsylvania State University where she worked on genomics and bioinformatics graduating in 2015. With the plan to continue working on genomics on return to Costa Rica, to her surprise bioinformatics was still exclusive to a small group of researchers with previous experience in the field or with strong international collaborators. Her goal since then has been to enlarge the community and consolidate this field by the creation of RedBioAplicada and supporting the Bioinformatics and Systems Biology Masters program. With that in mind Rebeca proposed the project she is currently developing with Cath Brooksbank and the training team at EMBL-EBI as part of the CABANA secondments.

The project’s title is ‘Developing data analysis resources for Costa Rica: e-Learning as an alternative and complement to lectures and workshops’. The project started as a local initiative to accelerate the learning process of Costa Rican students using tutorials written in Spanish and to evaluate if the English language is a barrier in the speed of learning. However, the project now has international connotations, the idea is that after testing the tutorials in a group of volunteers with different levels of bioinformatics experience, it will be made available to the Latin American community through the CABANA e-Learning platform. Eventually, the materials will be translated to other languages in the future. The first two tutorials to be published next year will be on transcriptomics using a reference genome and metagenomics applied to the challenge areas Sustainable Food Production and Protection of Biodiversity, respectively.

Guillermo Rangel

Guillermo Rangel is a Chemical Engineer and Microbiologist from the Universidad de los Andes (Bogota, Colombia), with a Master´s degree in Biological Sciences. During my Master’s degree, I developed a great interest in bacteriophage biology and evolutionary ecology, this led me to pursue a PhD degree on this field. In 2014 I began my PhD at University of Leicester (Leicester, UK) under the supervision of Professor Martha Clokie, undertaking research exploring the diversity of Streptococcus pneumoniae bacteriophages and providing insights into their role in pneumococcal virulence. During my PhD I developed an appreciation for the numerous opportunities that bioinformatics and big data analysis offer to the study of bacteriophage-host interactions at the microbiome level.

Viruses lack universally conserved marker genes and therefore require the application of alternative approaches for their taxonomic classification in metagenomic datasets. Previous work conducted by Dr. Alejandro Reyes’s research team at the Universidad de los Andes identified a subset of profile Hidden Markov Models (HMMs) that could serve as taxonomic markers for a wide range of currently known viral clades. My research secondment project, supervised by Dr. Rob Finn (EMBL-EBI) and Dr. Alejandro Reyes, is aimed at assessing the potential profile HMMs have for accurately classifying viral sequences from metagenomic datasets into their corresponding taxonomic clades. The output from this project is intended to contribute to the expansion of the analysis pipeline currently employed by MGnify, the open-source EBI’s metagenomic analysis tool developed by Dr. Rob Finn’s team. 

César Prada

César Prada Medina is a Ph.D. student at the University of São Paulo, Brazil, in the Department of Clinical Analysis, School of Pharmaceutical Sciences. After he obtained his Biology BSc, he worked at the Research Center for Tropical Diseases (CINTROP) in Colombia and began pursuing a Systems Biology career. Having merged this goal with his biomedical experience allowed his encounter with Helder Nakaya and his further adhesion to the Computational Systems Biology Laboratory.

Currently, his major research goal is to better characterize the physiopathological heterogeneity of the Juvenile Idiopathic Arthritis (JIA) disease. His investigation aims to reveal the leukocyte gene expression programs that drive the chronic inflammation in JIA patients. By combining statistical meta-analysis and network medicine principles, he hopes to contribute to approach a more personalized clinical practice on JIA patients. 

As a CABANA fellow, César is part of the Expression Atlas team where he aims to expand the Expression Atlas repository on JIA and to advance on a personalized prescription model based on patients’ gene expression profiles and inspired on the Open Target approach. “My time at the EMBL-EBI is also a great opportunity to learn about bioinformatics service standards as well as teaching skills on bioinformatic approaches; and certainly, this time will expand my collaboration network along through my CABANA fellow colleagues”.