Postdoc: infective competence of the human microbiome

Publiée le 22/03/2024

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Université du Luxembourg


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About us...

The Luxembourg Centre for Systems Biomedicine (LCSB) is an interdisciplinary research centre of the University of Luxembourg. We conduct fundamental and translational research in the field of Systems Biology and Biomedicine - in the lab, in the clinic and in silico. We focus on neurodegenerative processes and are especially interested in Alzheimer's and Parkinson's disease and their contributing factors.

The LCSB recruits talented scientists from various disciplines: computer scientists, mathematicians, biologists, chemists, engineers, physicists and clinicians from more than 50 countries currently work at the LCSB. We excel because we are truly interdisciplinary and together we contribute to science and society.

The University of Luxembourg has the following vacancy at the Luxembourg Centre for Systems Biomedicine (LCSB):Postdoctoral researcher focusing on the infective competence of the human microbiome in health and disease.

AREA: Computational and experimental study of gut microbiome-borne pathogenicity.

DESCRIPTION:

The Systems Ecology group at the LCSB is further expanding its research efforts on microbiomes and has an immediate opening for a highly motivated and talented postdoctoral researcher (entry- to advanced-level position) to work on the resolution of the role of microbiome-borne virulence factors, antibiotic resistance genes, and biosynthetic gene clusters in human health and disease using computational biology approaches.

The human microbiome represents a reservoir of pathogen-associated genes, more specifically virulence factors, including toxins, antimicrobial resistance genes and biosynthetic gene clusters. Studies focusing on the role of these infection-mediating genes are typically limited to specific pathogenic taxa and seldomly consider the overall infective competence represented by them in the context of the microbiome. Here, using a triptych approach leveraging in silico, in vitro and in vivo methods, we aim to specifically and systematically characterise and validate microbiome-borne VFs, implicated in human diseases, with a particular focus on their cytotoxicity and immunogenicity.

To achieve these aims, this project is a close collaboration between the Systems Ecology group (head: Paul Wilmes, Luxembourg, the Molecular Disease Mechanisms group (co-head: Elisabeth Letellier, Luxembourg), the EMBL-EBI's Microbiome Informatics team (head: Robert Finn, United Kingdom), and the Protein Expression and Purification Core Facility (head: Kim Remans, Germany). The current position will build on the computational solutions developed by the project partners, notably PathoFact and MGnify.

Your Role...

You will expand the the functionality of PathoFact through additional contextual information and a broader set of annotations and employ additional ML/AI-based methods to improve the identification of virulence factors as well as antibiotic resistance genes and biosynthetic gene clusters. You will, in collaboration with our project partner at EMBL-EBI, hosting and maintaining the MGnify pipeline, mature the software stack to enable easy deployment within MGnify pipelines. This will lead to computational solutions which will be applied to relevant datasets to establish a baseline of the prevalence and abundance of these microbiome-derived genes and to compare these aspects, thereby resolving the microbiome-borne pathogenic potential in a variety of diseases. You will closely interact with project partners at the University of Luxembourg and EMBL to advance from the identification of new virulence factors in silico to the assessment of the pathogenicity of these virulence factors in vitro and in vivo. You will furthermore support data management and analysis on servers of the group as well as the University of Luxembourg's High Performance Computing Cluster.

Important technical competencies and tasks include, but are not limited to:

  • Experienced in sequence-based and/or structure-based functional annotation of microbial genomes, including also metagenome-assembled genomes
  • Prior work with virulence factors (in silico/in vitro) is considered an asset
  • Implementation of reproducible computational workflows (using snakemake, nextflow, etc.)
  • Collaborative code development using Git and GitHub/GitLab
  • End-to-end processing (QC, preprocessing, processing, data analysis) of at least one of the following data types: metagenomics, metatranscriptomics, metaproteomics, metametabolomics, is considered an asset
  • Familiarity with UNIX/LINUX-based operating systems and shared compute infrastructure

What we expect from you…

  • A PhD in Biomedical Sciences, Biochemistry, Bioinformatics, Analytical Chemistry, Microbial Ecology, or related disciplines
  • Dry-laboratory experience
  • Experience in translating dry-lab experience to wet-lab experiments is considered an important asset
  • Previous experience in bioinformatic analysis of mixed microbial communities or Systems Biology datasets in at least one computer programming or scripting language (Python, R, Ruby, etc.) will be considered assets
  • A good working knowledge of basic statistical concepts
  • Team player
  • Highly reliable and precise work style
  • Great organizational skills and willingness to work independently in phases of potentially little guidance from supervisor
  • Prior supervision activities, e.g., undergraduate or graduate students, will be considered an asset
  • Excellent working knowledge of English

Here's what awaits you at the LCSB...

  • Excellent work environment with state-of-the-art infrastructure, laboratory and administrative support
  • Truly connected. We work together with hospitals and research institutes on a national and international level as well as industrial partners. Connection between science and society is very important to us. From our school lab - the Scienteens Lab - to the different outreach activities and collaborative partnerships with patient associations, we love to listen to society's needs and share our passion for science
  • Be part of a multicultural team. At the LCSB we have more than 50 nationalities. Throughout the year, we organise team-building events, networking activities and more

Find out more about us!

How to apply...

Applications should be submitted online and include:

  • A detailed curriculum vitae
  • List of publications, if applicable
  • Cover letter indicating your motivation for this position, relevant past experience and future interests
  • Name and addresses of two referees

Early application is highly encouraged, as the applications will be processed upon reception. Please apply formally through the HR system. Applications by email will not be considered.

The University of Luxembourg embraces inclusion and diversity as key values. We are fully committed to removing any discriminatory barrier related to gender, and not only, in recruitment and career progression of our staff.

General information:

  • Contract type: Fixed Term Contract 24 Month (may be extended up to 5 years)
  • Start date: June 2024
  • Work hours: Full Time 40.0 Hours per Week
  • Location: Belval
  • Job reference: UOL06274

The yearly gross salary for every Postdoctoral Researcher at the UL is EUR 83099 (full time)

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