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

Applications are now open

The form can be accessed and completed Here

Deadline for Applications Monday 5th February 2018 Midnight GMT 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
  • Reference proteomes data sets relevant in health and disease, biotechnology and agriculture
  • Protein sequence web 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
  • Visualisation of pathway enrichment in differential experiments as a javascript Expression Atlas widget candidate to be displayed in Reactome
  • Exploring predictions on pathway deregulation via causal reasoning
  • Curation, analysis and identification of gene expression signatures of primary tumour data

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

Paul Kersey

Team Leader, Non-vertebrate Genomics

  • Genomics of crops and pathogens

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