ARETE Project


Using lateral gene transfer of antimicrobial resistance genes in environmental and agri-food contexts with bioinformatics approaches.

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Interested in Lateral Transfer of Antimicrobial Resistance?


We are hiring postdocs, grad students and developers.

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Project Activities


Genetic Elements of Transmission

Profiling AMR transmission by improved detection of mobile genetic elements.
A) Environmental plasmid reconstruction.
B) Genomic Island delineation.
C) Mobilome CARD curation.
D) Clustering mobile elements.

Mapping Pathways of Transmission

Using phylogentic methods to identify horizontal transfer events and identifying ecological factors behind it.
A) Phylogenetic analysis.
B) Inferring gene transfers.
C) Ecological mapping of transmission.

ARETE Pipeline Development

Development of pipeline consolidating new and improved methods.

Available Positions


Beiko Lab in Dalhousie University (Halifax, Nova Scotia, Canada) is seeking 3 postdoctoral fellows:

ARETE Postdoctoral Fellow #1

Position ID 2019-06

Project will be building on existing tools (e.g., RSPR) to infer phylogenetic trees and perform large-scale inference of LGT. Key challenges include robust, large-scale phylogenomic inference, and synthesizing different lines of evidence to build a comprehensive picture of gene transfer in large genomic datasets. This position requires someone with a background in either bioinformatics or computer science.
Key technical skills include:

  • Phylogenetics
  • Microbial genomics and evolution
  • Some programming (Python sufficient; C++ an asset)

ARETE Postdoctoral Fellow #2

Position ID 2019-07

Project involves developing methods to map inferred LGT events into an ecological context. This will include the association of events with specific habitat parameters (e.g., geographic location, habitat type, specific patterns of antibiotic usage), as well as “gene-ecology” methods that examine the distributional dynamics of microbial genes and map these into traditional ecological frameworks (e.g., this work). This position requires an individual with a background in bioinformatics and/or ecology.
Key technical skills include:

  • Microbial ecology
  • Community ecology / metacommunity theory
  • Data analysis skills in R/Python

AMRtime Postdoctoral Fellow

Position ID 2019-08

This fellow will work to extend existing work in the inference of antimicrobial-resistance genes from metagenomic data (e.g., AMRtime) using rapid homology filtering and search alongside machine-learning methods to assign metagenomic sequences to specific classes of AMR genes The fellow will augment AMRtime with new models to better detect novel AMR variants that fall outside currently defined strict criteria for detection. Extending these models will require a combination of methods that encompass taxonomic assignment, sensitive homology search, mobile-element detection, and phylogenetics to differentiate legitimate AMR matches from homologs that do not confer a resistance phenotype.

All postdoctoral fellows will collaborate with other members of the project team, and be expected to give conference presentations and prepare journal articles based on their work. There will be opportunities to gain project-management experience through the ARETE project.

Please send a CV and statement of research interests to Elvira Mitraka. Applicants should indicate the position ID in the email subject header. Review of applications will begin on April 20, 2019. To receive full consideration, please submit your application by this deadline. Applications received after April 20 may also be considered.

Let's Get In Touch!


Interested in applying for a position or collaboration in any of these areas? Let's talk!