Research Secondments

Research Secondments

CABANA’s research secondments are aimed at catalysing lasting collaborations between researchers in Latin America and bioinformatics groups in the UK, initially at EMBL-EBI.

  • Scientists from Latin America can apply for a secondment of 6 months to pursue a bioinformatics research project in the challenge areas of the CABANA project. These are communicable diseases, protecting biodiversity and food security   
  • The project should be designed in collaboration of the host of your choice listed below from EMBL-EBI or a host institution in Latin America
  • Our hosts have identified ideas for projects that span curiosity-driven research, software development, data curation and creation of bioinformatics training materials. It is important that your proposed research topic is aligned with the research interests of your selected host
  • Secondments are open to scientists at MSc. level and above
  • Secondees will be responsible for their health insurance while in the UK

Take a look at CABANA Secondees  

The outcomes of the secondments will be placed in the public domain:

  • Research papers will be published in open-access journals
  • Software will be licensed under open source licenses
  • Datasets will be made openly available (unless there are ethical reasons for controlling access) through public data resources and tools (including but not limited to those hosted by EMBL-EBI)
  • Training materials will be given a CC-BY-SA license and made freely available through EMBL-EBI’s eLearning resource, Train online

Secondment benefits

  • The opportunity to engage and connect with the bioinformatics research community in the UK including scientists at the University of Cambridge and the Wellcome Sanger Institute as well as EMBL-EBI
  • The opportunity to collaborate with  Latin American bioinformatics researchers in a different country
  • Return travel/to from home for secondment and after 3 months if required to visit family
  • A living expense allowance (LEA) of £1,000 per month less National Insurance Contributions (approx. 12.5 % per month). If the secondment is supported by other means, the LEA is reduced accordingly
  • A contribution of £450 per month towards accommodation
  • Secondment benefits (LEA) in Latin American universities and research institutes will be in line with host policy to the maximum of the EMBL-EBI benefits
  • The CABANA project will facilitate exempt vignette visa applications for secondments to EMBL-EBI. CABANA will not reimburse incidental costs such as postage and travel relating to the visa
  • Secondees will be responsible for applying for visas to all other institutions

The call for secondment places in 2019/2020 is now closed

  • Applicants will be notified in early March 2019

Take a look at CABANA Secondees  

Secondments between Latin American institutions are dependent on a signed agreement between the host and the home institution being received at the EMBL-EBI prior to the start.
Hosts are in the UK and Latin America

Secondment host in the UK (Click on their name for more details of their research interest and publication list):

Janet Thornton

(Available from August 2019)

Director Emeritus of EMBL-EBI and Senior Scientist

  • Using enzymes in biotechnology - design and evolution
  • Studying protein variation and disease, from a structural perspective

Sandra Orchard

Team Leader - Protein Function Content

  • Software development, text-mining and data filtering to provide a curation queue of papers containing human molecular interactions and protein complexes

Dominic Clark

Industry Programme Manager - Industry Programme office

  • Consultation with Latin American bioindustries, with the goal of providing industry support for bioinformatics in the region

Henning Hermjakob

(Available from July 2019)

Team Leader Molecular Networks - Hermjakob team

  • Curation of Human/Pathogen pathways in Reactome (ideally several six-month projects, each on a different disease theme)
  • The Omics Discovery Index: Efficient discovery of local and global omics datasets

Pedro Beltrao

Group Leader - Beltrao research group

Research projects on the theme of evolution of cellular networks, protein post-translational regulation, cancer genomics or genotype to phenotype mapping.

Rodrigo Lopez

Head of Web Production

  • Development of new web-based services or programmatic access to them


Maria Martin                     

Team Leader: Protein Function Development

In Collaboration with Sandra Orchard (above)

  • Computational annotation of protein sequences, data mining and analysis tools
  • Data integration technologies and format
  • Protein data visualization design and web technologies
  • Enzymes and biocatalysis services
  • Gene Ontology services and programmatic access

Irene Papatheodorou

(Available from September 2019)

Team Leader - Gene Expression

Projects related to:

  • Analysis or visualisation of bulk and single cell transcriptomics,
  • Linking gene expression to phenotypes,
  • Characterising cell types

Juan Antonio Vizcaino

Proteomics Team Leader - Vizcaino Team: Proteomics

  • Development of data integration approaches involving mass spectrometry proteomics data
  • Re-analysis of proteomics datasets to create an updated view of the proteome or metaproteome (e.g. for relevant Latin American pathogens, crops or livestock species)
  • Proteogenomics analysis and related genome annotation activities for relevant organisms in Latin America

Rob Finn

(Available from June 2019)

Team Leader, Sequence Families

  • Analysing metagenomics datasets from different ecological niches to understand the taxonomic and functional repertoire present and adaptation
  • Recovery of genomes from metagenomic datasets, identification and investigation  of novel proteins and pathways
  • Curation of Pfam entries for specific genomes of agricultural or disease relevance

Guy Cochrane

Team Leader, European Nucleotide Archive

  • Curating and adding value to data in the area of Zika and/or other currently relevant pathogens including bacterial pathogens

Paul Flicek

Senior Scientist and Team Leader, Vertebrate Genomics

  • Genomics of livestock species or endangered vertebrate species
  • Genomics of crops and pathogens

Cath Brooksbank

Head of the EMBL-EBI Training Programme

  • Development of training materials and training methods of relevance to CABANA's three challenges
  • Piloting remote participation in courses
  • Adaptation and translation of existing training materials for new target audiences such as undergraduates and schools

Daniel Zerbino

Team Leader, Genome Analysis

  • Defining regulatory elements from large epigenomic datasets
  • Defining cis-regulatory interactions from Hi-C and eQTL
  • GWAS functional analysis pipeline

Evangelia Petsalaki

Group Leader - Petsalaki research group

  • Topics related to network inference and data integration

Zamin Iqbal

Research Group Leader - Iqbal research group

  • Diagnostics and surveillance of drug resistance in tuberculosis, in S. America and across the world

Claire O’Donovan

Team Leader - O'Donovan team: Metabolomics

  • Identifying the Metabolomes of model organisms
  • Identifying the Metabolomes of commercial crops and their pathogens
  • Building a reference set of chemical compounds and their metabolomic context

Sameer Velankar

Team Leader, PDBe content and integration

  • enrichment of 3D macromolecular structures in the PDB with added-value annotations and analysis of assembled data sets
  • development of innovative web-based visualisation tools for 3D structure data

Alex Bateman

Senior Team Leader, Protein sequence resources

  • Computational characterisation of bacterial host interacting proteins.
  • Investigation of protein domain composition, discovery of novel protein domains, correlated mutation analysis and sequence analysis of host binding domains.

Thomas Keane

Team Leader, EGA and Archive Infrastructure

  • Rodent diversity, rodent genetics and genomics, environmental adaptation 

Andrew Leach

Head of Chemistry Services

  • Drug Discovery
  • Molecule design (Including structure-based design)
  • Cheminformatics, Computational chemistry, Chemogenomics 
  • Machine learning
  • Text mining

Sarah Morgan

Scientific Training Coordinator, EMBL-EBI

  • Development of training programmes and course curricula (both face to face and online)
  • Analysis of training quality and impact
  • New trainer development and mentoring

Alan Archibald

Genetics and Genomics, The Roslin Institute

  • Genome sequencing of farmed animals
  • Genome sequencing of Suina species
  • Phyologenomics
  • Genetics of complex traits

Claire Jenkins

Head of E. coli, Shigella, Yersinia and Vibrio Reference Service

  1. Public Health
  2. Gastrointestinal infections
  3. Whole genome sequencing

Kevin Howe

Team Leader, Eukaryotic Annotation

  • Vertebrate genome annotation and comparative genomics 
  • Genomics of helminths (parasitic worms)
  • Model organism genomics

Investigators from Latin American countries are warmly invited to apply for fellowships at the following locations:

Jan Kreuze

Centro Internacional de la Papa, Peru

  • Determining and monitoring plant-associated microbiome and/or pathogen populations to support sustainable food production 
  • Metagenomic biodiversity analysis in response to climate change in different agro-ecologies

Andrés Gatica

University of Costa Rica

  • Plant pathogens such as Hemileia Vastatrix
  • Comparative transcriptone profile of defense-related genes in coffee plants infected by  Xylella FastidiosaStudy of genes related to the flowering process in coffee:Towards improvemenst in a climate change scenarion
  • In vitro cultivation and mutants
  • Safety of genetically modified crops 

Selene Fernández

Centro de Investigación y de Estudios Avanzados - Cinvestav, Mexico

  • Development of time-efficient phylogenomic gene annotation methods for non model organisms.
  • Reconstruction of gene regulatory networks from high-throughput sequencing data.

Cei Abreu

Centro de Investigación y de Estudios Avanzados - Cinvestav, Mexico

  • Discovery of gene regulation motifs using high-throughput functional genomics experiments
  • Exploring signatures of selection across whole genomes

Alfredo Herrera Estrella

Centro de Investigación y de Estudios Avanzados - Cinvestav, Mexico

  • Study of gene regulation during tissue regeneration across kingdoms, using high-throughput functional genomics experiments
  • Search for signatures of domestication and introgression in crop plants native to Mexico

Maximo Rivarola

Bioinformatics Unit at the National Institute for Agricultural Technologies (CNIA-INTA), Argentina

  • Discovery of candidate genes involved in stress (biotic and abiotic) response in sunflower through NGS RNA-seq experiments.
  • Discovery of new markers linked to traits of interest using GBS (genotype by sequencing).

Marcelo Martí

University of Buenos Aires (UBA), Argentina

  • Developing of new high throughput docking techniques to identify new drug for infectious diseases.
  • From genomes to drugs: whole genome structural analysis

Adrián Turjanski

University of Buenos Aires (UBA), Argentina

  • Study of SNP on protein function by using structural bioinformatics tools
  • Study of Rare diseases by Whole Exome Sequencing and Whole Genome Sequencing techniques.

Dario Fernandez Doporto

University of Buenos Aires (UBA), Argentina

  • Reconstruction of metabolic networks from whole genome sequencing and RNA-seq data
  • Identification of new targets in tuberculosis and Klebsiella pneumoniae

Marco Cristancho

University of the Andes, Colombia

  • Development of molecular tags for Latin American endemic plants
  • Whole genome sequencing of the coffee rust pathogen

César Rodríguez

University of Costa Rica/CIET

  • Comparative microbial genomics
  • Antimicrobial resistance and genomic epidemiology of Clostridium difficile

Ricardo Fujita

Universidad de San Martín de Porres - Centro de Genética y Biología Molecular, Peru

  • Determination of ancestry and reconstructing pre-Columbian history of South American human populations with genomic markers
  • Genomic and Epigenomic changes in cancer tumours

Rebeca Campos

Universidad de Costa Rica (UCR) - Centro de Investigación en Biología Celular y Molecular

  • Description of the microbial gut community and its implication in the weight of infants from Costa Rica
  • Bioinformatics and Biostatistics Network applied to research and teaching (RedBioAplicada)
  • Developing e-Learning tutorials (written in Spanish and English) for CABANA on three data analysis pipelines: transcriptomics, genome assembly, and metagenomics. Currently recruiting two secondees for 2019.

Alejandro Reyes Muñoz

  • Development and optimization of bioinformatic pipelines for amplicon metagenomic data and viral shotgun metagenomic data.
  • Developing e-Learning tutorials (written in Spanish and English) for CABANA on metagenomic analysis

Please join the CABANA mailing list if you would like to be alerted when new opportunities open.