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 will join an EMBL-EBI group for 6 months to pursue a biounformatics research topic of their choice.
  • It is important that the research topic is alligned with the research topics of the Hosts pictured below.
  • Secondments are open to scientists at all career stages
  • Our partners have identified ideas for projects that span curiosity-driven research, software development, data curation and creation of bioinformatics training materials

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

  • Return travel/to from home for secondment and after 3 months if required to visit family
  • A living expense allowence (LEA) of £1,000 month less National Insurance Contributions (approx £38/month).If the secondment is supported by other means, the LEA is reduced accordingly
  • Contribution of £450 per month towards accommodation

Next application 

Call for secondees will be open on 10th September 2018 for placements in 2019. 

The form can be accessed and completed Here

Deadline for Applications Monday 10th October 2018 Midnight UK Time Contact ian@ebi.ac.uk if you have problems downloading the document

Please do not contact your Host before the closing date of the application. There will be opportunities to discuss and fine tune your proposal with your host, if shortlisted, after the application deadline.

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

Janet Thornton

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

Team Leader Molecular Networks - Hermjakob team

  • Establishment of a Reactome South America mirror
  • 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 intergration technologies and format
  • Protein data visualization design and web technologies
  • Enzymes and biocatalysis services
  • Gene Ontology services and programmatic access

Irene Papatheodorou

Expression Atlas Leader, Human Cell Atlas

  • Gene expression normalisation methods across plant experiments in Expression Atlas
  • On-the-fly overlap analysis between user-provided sets of genes and differential comparisons in Expression Atlas across species (using orthologues of user-provided genes)
  • Visualisation of the results thereof
  • Visualisation of clusters of gene co-expression within a baseline experiment and link to pathways

Juan Antonio Vizcaino

Proteomics Team Leader - Vizcaino Team: Proteomics

  • Proteogenomics analysis and annotation of pathogens, crop and livestock species or bacteria involved in food poisoning
  • Consistent reanalysis of public datasets in PRIDE that correspond to specific diseases, or of the gut metaproteome, to create a consistent view of how the proteome (or metaproteome) changes under different conditions

Rob Finn

Team Leader, Sequence Families

  • Analysing metagenomics datasets from different ecological niches to understand the taxonomic and functional repertoir 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

Also Clara Amid content supervisor and Ana Toribio placements supervisors

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

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

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

Co-investigator Organisation Topic
Jan Kreuze Centro Internacional de la Papa, Peru Determining and monitoring plant-associated microbiome and/or pathogen populations to support sustainable food production (through discovery and use of beneficial microorganisms, management of disease etc.)
Metagenomic biodiversity analysis in response to climate change in different agro-ecologies
Guilherme Oliveira Vale Technology Institute, Belem, Brazil Landscape genomics of endangered amazon plant species
Metagenomic landscapes in the amazon
Environmental signatures for monitoring and land recovery
Bioinformatics infrastructure for genomes of the amazon
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 EstrellaA Centro de Investigación y de Estudios Avanzados - Cinvestav, Mexico Study of gene regulation during tissue regeneration across kingdoms, using high-throughput functional genomics experiments
Exploiting Phaseolus vulgaris (common bean) biodiversity for crop improvement through the development of SNP-based markers using high-throughput sequencing, and a user-friendly database for marker-assisted breeding
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).
Identification of important hubs in gene regulatory networks from NGS data.
Exploring new methodologies and strategies in de novo transcriptomic assembly (in particular with plant crops with no genome assembly).
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 bioinformatic tools
Study of Rare diseases by Whole Exome Sequencing and Whole Genome Sequencing techniques.
Developing of bioinformatic tolos to identify new targets in pathogens with applications to Neglected Diseases.
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
Development of nanopore sequencing protocols for the rapid identification of human diseases in Latin American rural areas
Benilton Carvalho U. Campinas, Brazil Host mirrors to tools locally, and bioinformatics support for local researchers
Fine-tuning tools (such as our Bioconductor oligo package) and promoting its use through a possible integration with larger initiatives (e.g. Expression Atlas)
Develop and deploy a number of courses to be offered locally and regularly to the Latin American community
Assess the use of online services for real-time training
Create an infrastructure that would allow responsible genomic data sharing (accounting for privacy of individuals, for example)
Collaborate with the BIPMed initiative by providing tools and computational infra-structure to assist on the development of precision medicine in Brazil
Create and distribute a dataset that can be used as a reference for identification of common variants in the Brazilian population
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
Identification of genes and genetic variants by Next Generation Sequencing in native and admixed human populations.Impact on rare diseases, pharmaco- and immunogenomic analysis
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
Comparison of different library preparation protocols for sequencing by synthesis and its application to DNAs from diverse sources
Bioinformatics and Biostatistics Network applied to research and teaching (RedBioAplicada)
Detecting mutations in the coding region of the apolipoprotein CII gene (APO-C2), lipoprotein lipase cofactor gene (LPL) in a sample of patients with hypertrigliceridemia
Transcriptional profile of endogenous retroviruses (ERV) in primates: evolution at testis level and genome architecture impact in expression