Bioinformatician position

Leuven VIB-KU Leuven Center for Cancer Biology

07 Nov 2022

Leuven

VIB-KU Leuven Center for Cancer Biology

Peter Carmeliet Lab

Bio IT

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The laboratory of Angiogenesis and Vascular Metabolism headed by Prof. Peter Carmeliet is one of the laboratories of the Center for Cancer Biology (CCB), a research department of VIB (Flanders Institute for Biotechnology) located in the Oncology Faculty at the KU Leuven (Leuven, Belgium). The lab of Prof Carmeliet has an open position for a Bioinformatician.

We offer a vibrant international research environment where English is the preferred language in the laboratory, at meetings and at seminars. The Department employs >300 people and covers a range of different research areas within Biomedicine. The infrastructure at CCB is well sophisticated with modern laboratories, core and animal facilities.

Background project

The Laboratory of Angiogenesis and Vascular Metabolism headed by Prof. Peter Carmeliet focuses on the development of blood vessels (angiogenesis) and vascular heterogeneity in health and disease, with the ultimate aim to identify novel therapeutic pro-and anti-angiogenic strategies.

Current anti-angiogenesis therapies (AATs), by targeting the pro-angiogenic factor VEGF, suffer resistance and insufficient efficacy. The Carmeliet lab explores opportunities to overcome these limitations and to improve AAT by focusing on endothelial cell metabolism, endothelial heterogeneity and in particular, endothelial immunity. Recent projects, combining single-cell transcriptomics with bulk multi-omics (transcriptomics, (epi)-genomics, proteomics & metabolomics) revealed novel insights into endothelial cell metabolism and heterogeneity in health and disease that can help design novel AAT strategies.

For instance, endothelial cell-tailored computational genome-scale metabolic models (GEM) were built and successfully used to predict metabolic enzymes/pathways that are essential for endothelial cell growth. In addition, recent successful efforts in generating several single-cell transcriptome atlases of endothelial cells (ECs) from various tissues of preclinical models and clinical patient samples in health and disease revealed the existence of previously unknown endothelial cell subtypes, including ECs with a resident endothelial stem cell signature, and endothelial cells with a putative immuno-modulatory role (termed "IMECs"), key findings that will be further investigated. An important future focus will be to study in more depth the activities and role of these IMECs and to explore whether targeting IMECs can offer opportunities for "alternative immunotherapy".

The lab developed -and uses- innovative integrated approaches (e.g. single-cell (sc)RNA-sequencing, Artificial Intelligence(AI-)based tools, multi-omics analysis) to efficiently discover new, biologically important and therapeutically attractive targets. The ultimate goal is to bring promising validated scientific targets, upon translation, to the level of drug development. The project will be conducted in a multidisciplinary environment at the interface of an academic and clinical environment, where animal surgery expertise and clinical samples will be available.

The group

The lab of Peter Carmeliet started a twin lab, the laboratory for Angiogenesis and Vascular Heterogeneity, at the Department of Biomedicine at Aarhus University in Aarhus, Denmark (https://pure.au.dk/portal/da/pecar@biomed.au.dk) is closely intertwined with his lab at the VIB-KU Leuven, Belgium (https://carmelietlab.sites.vib.be/en). Both the Leuven and new Aarhus lab will function as one virtual lab, and synergistically combine their joint forces and focus to study similar fundamental questions in vascular biology and angiogenesis, and to develop more efficiently new vascular medicine. There will be frequent interactions and exchanges of junior/senior scientists and lab technicians between both labs, offering unique opportunities for multi-disciplinary training at both locations. Complementary settings and conditions at each location will create unprecedented extra-added opportunities to quantitatively and qualitatively increase the research output and translational development at a higher level.

Both the newly starting Aarhus and the Leuven lab apply their expertise and therapeutic focus to evaluate and deliver novel therapeutic concepts into clinical development with the ambition to change the life of patients with vasculature-related disorders. We use high-throughput multi-omics approaches (bulk and scRNAseq, spatial single-cell omics, scG&T, scATAC, etc.), as well as computational modelling and bioinformatics (e.g. artificial intelligence (AI), machine learning (ML)), both for hypothesis-generating and hypothesis-testing experiments. We recently developed an innovative AI-based tool to predict novel unknown genes in ECs, and to develop alternative therapies.

A major challenge of current medical research is to translate the obtained high-profile insights into new medicine. Big pharma is not interested in too early-stage scientific results (even when published in high-profile journals) because of the risk that these candidates are insufficiently validated for drug development, while academic scientists generally lack funds to bridge this gap ("the valley of death") by providing more validation. We aspire to not only discover new therapeutic targets but also to "bridge the valley of death" in order to improve drug development. Spinning out a start-up company belongs to future options (like we did in the past with Montis Biosciences; see https://www.montisbio.com).

Job Description

The lab is looking for a highly motivated Bioinformatician to help us to achieve the above-stated goals, i.e. (i) to discover new therapeutic targets (using bulk/single-cell multi-omics); and (ii) to bridge the valley of death.

We are looking for ambitious, dynamic and flexible candidates, willing to step into new adventures, daring to break new grounds outside of their comfort zone, passionate about opportunities to set up new technologies and facilities, not shy of diving into new fields, being primed and eager to become acquainted with new technologies (e.g., computational programming, artificial intelligence, etc.), and prepared to go the extra mile. Candidates should be able to either work independently (and troubleshoot practical work independently) under the leadership of Prof. Carmeliet, but also to team up with members of the lab (Leuven and Aarhus). In consultation with Prof. Carmeliet and his senior staff, you may be asked to run micro-projects, where you will have the freedom and responsibility to manage your projects, including supervising junior colleagues, planning daily agendas, managing budgets, writing papers, etc. You will mentor junior scientists daily, between multiple disciplines and ensure connectivity. You are sufficiently mature to interact with other colleagues via in-person and virtual meetings, communicate in a professional manner, and participate in seminars and grant/manuscript writing. You should be prepared to travel to the Aarhus lab for training and education, and for the exchange of expertise between the Aarhus and Leuven lab.

The main practical tasks consist of:

  • Leading and coordinating with the VIB & AU team members on the development of bioinformatics software platforms and implementation of new bioinformatics pipelines.
  • Leading the multi-omics data integration and development of novel multi-omics analyses, with the ultimate aim to identify novel ‘mystery’ genes.
  • Working independently in a multidisciplinary team in a biomedical sciences and transcriptomics/ (epi)-genomics/bioinformatics environment.
  • Function as a key person between the VIB and AU lab to transfer expertise and guide projects.
  • Drive projects to generate early hypotheses for innovative ideas.
  • Mentor junior scientists on a daily basis, between multiple disciplines and ensure connectivity.
  • Organize and troubleshoot work independently.
  • Communicate results in a professional manner (English) & participate in seminars and grant/manuscript writing

You will report directly to Prof. Peter Carmeliet.

Your profile

  • Candidates have a master’s in bioinformatics / Computer Science (advanced specialization area: artificial intelligence) or relevant experience (3-4 years) or a Ph.D. in bioinformatics/computer science (AI) or related fields – biology/ biomedicine expertise is an advantage, but not mandatory. A minimum of 3-4 years of research experience is requested.
  • Strong skills in working with algorithms, programming (mastering common computer languages and concepts), software design and development, computational biology, handling big biomedical datasets, automating data workflows and streamlining data transfer, using (commodity) web applications and algorithms, etc.
  • You have a publication record in peer-reviewed international journals.
  • Having experience in: (i) integrating single-cell multi-omics; (ii) computational programming in R (and other common computer languages); (iii) competence/interest in analysing and integrating complex omics- and clinical datasets are a plus. 
  • You are interested and motivated to work on ambitious projects in an open, dynamic, competitive and driven team.
  • You have excellent organizational and supervisory skills, you can work in a team as well as independently.
  • You have a strong ability to multi-task, meet timelines and work accurately.
  • You have good communication skills in spoken and written English.

We offer

  • The unique opportunity to work in a multidisciplinary international team and to contribute to the discovery and development of novel drug targets.
  • Access to, and training in, state-of-the-art technologies in biomedical research. The Leuven lab has multiple core facilities, with expertise in (single-cell) genomics/transcriptomics, bioinformatics, (stem) cell culture, FACS, metabolomics, animal surgery, mouse transgenesis, immunohistochemistry & in situ hybridisation (RNAscope) and imaging (https://vibcancer.be/expertise-centers).
  • Opportunities to interact with and become acquainted with start-up companies, involved in developing new vascular medicine and/or "big-biological data management companies" involved in target discovery. 
  • A dynamic working environment in which quality, professionalism and team spirit are encouraged. A stimulating scientific surrounding in a young, enthusiastic, motivated team (with English as the main language).
  • Training in project management (e.g., supervision of students, budget management). Excellent training conditions within a team of experts. Long-term career opportunities.
  • Starting as soon as possible.

How to apply?

Applications for this position should be submitted online. If you have questions about this position, please contact Prof. Peter Carmeliet: peter.carmeliet@kuleuven.be or Katie Van Geyte: katie.vangeyte@kuleuven.be.