COMPUTATIONAL SCIENTIST-POSTDOCTORAL SCIENTIST (IMMUNO-ONCOLOGY)

05 January 2021

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Interested?

All applications must include: A motivation letter, A full CV includingcontact details, a list of your publications and two contacts for furtherreferences. Apply online from KU Leuven website (please don't send these documents via email). For further information or in case of any doubts please don't hesitate to contact Prof. Abhishek D. Garg (abhishek.garg@kuleuven.be).

You can apply for this job no later than February 15, 2021 via the online application toolKU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR@kuleuven.be.

Ref. BAP-2021-31

Apply before 15 February 2021

The team of Prof. Abhishek D Garg (Department of Cellular & Molecular Medicine, KU Leuven), working in close collaboration with the clinical team of Prof. Sabine Tejpar (Department of Oncology, KU Leuven) is seeking, in this collaborative context, a suitable postdoctoral candidate with specialization in computational sciences approaches applied to biological hypothesis. Prof. Garg’s team aims to apply advanced computational approaches in the context of immuno-oncology, to tumour transcriptomics data generated in close collaboration with Prof. Tejpar, who is involved in conducting several cancer immunotherapy relevant clinical and preclinical trials, generating uniquely rich datasets in human and mouse models (see below)

The aim of Prof. Garg’s team, in collaboration with Prof. Tejpar, is to capitalize on multi-dimensional cancer patient datasets (tumour/lymph node/polyp bulk or single-cell RNAseq, TCR sequencing, microbiome 16S RNA or meta-transcriptome and others) and apply highly relevant computational biology/immunology and systems biology approaches to shed light on various clinically relevant immuno-oncology areas like effector functions or exhaustion of tumour-infiltrating lymphocytes, polarization of tumour-associated myeloid cells (DCs or macrophages), cross-talk between normal or tumorigenic tissue and last but not least, immunological cross-talk with environmental factors like gut microbiome.

The team of Prof. Garg currently has following ongoing research activities: (1) molecular & translational immunology underlying cellular immunotherapies, combinatorial regimens of chemotherapy and immune-checkpoint blockers; (2) computational immunology and bioinformatics pipelines (for exhausted/dysfunctional CD8+ T cells or type I interferon’s based biomarkers) and (3) throughput serum-based biomarker assessment in cancer patients to guide patient management, stratification and therapeutic decision-making relevant for immuno-oncology.

The team of Prof. Tejpar is focussing on detailed deconvolution and functional mapping of the gut immune response to malignant and pre-malignant lesions.

Both labs have multiple shared grants and a vast network of collaborators, both nationally and internationally, that provide additional expert framework for the activities.

Selected publications:

- Vanmeerbeek, I., Sprooten, J., De Ruysscher, D., Tejpar, S., Vandenberghe, P., Fucikova, J., Spisek, R., Zitvogel, L., Kroemer, G., Galluzzi L., & Garg AD (2020) Trial watch: chemotherapy-induced immunogenic cell death in immuno-oncology, OncoImmunology, 9:1, DOI: 10.1080/2162402X.2019.1703449.

- Garg, AD., Vandenberk, L., Van Woensel, M., Belmans, J., Schaaf, M., Boon, L., De Vleeschouwer, S., Agostinis, P. (2017). Preclinical efficacy of immune-checkpoint monotherapy does not recapitulate corresponding biomarkers-based clinical predictions in glioblastoma. OncoImmunology, 6 (4), Art.No. e1295903.

- Qian J, Olbrecht S, Boeckx B, Vos H, Laoui D, Etlioglu E, Wauters E, Pomella V, Verbandt S, Busschaert P, Bassez A, Franken A, Bempt MV, Xiong J, Weynand B, van Herck Y, Antoranz A, Bosisio FM, Thienpont B, Floris G, Vergote I, Smeets A, Tejpar S, Lambrechts D. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res. 2020 Sep;30(9):745-762. PMID: 32561858

- Lee HO, Hong Y, Etlioglu HE, Cho YB, Pomella V, Van den Bosch B, Vanhecke J, Verbandt S, Hong H, Min JW, Kim N, Eum HH, Qian J, Boeckx B, Lambrechts D, Tsantoulis P, De Hertogh G, Chung W, Lee T, An M, Shin HT, Joung JG, Jung MH, Ko G, Wirapati P, Kim SH, Kim HC, Yun SH, Tan IBH, Ranjan B, Lee WY, Kim TY, Choi JK, Kim YJ, Prabhakar S, Tejpar S, Park WY. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nat Genet. 2020 Jun;52(6):594-603. PMID: 32451460

- Guinney, J., Dienstmann, R., Wang, X., de Reyniès, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angelino, P., Bot, B.M., Morris, J.S., Simon, I.M., Gerster, S., Fessler, E., De Sousa E Melo, F., Missiaglia, E., Ramay, H., Barras, D., Homicsko, K., Maru, D., Manyam, G.C., Broom, B., Boige, V., Perez-Villamil, B., Laderas, T., Salazar, R., Gray, J.W., Hanahan, D., Tabernero, J., Bernards, R., Friend, S.H., Laurent-Puig, P., Medema, J.P., Sadanandam, A., Wessels, L., Delorenzi, M., Kopetz, S., Vermeulen, L., Tejpar, S. (2015). The consensus molecular subtypes of colorectal cancer. Nature Medicine, 21 (11), Art.No. 10.1038/nm.3967, 1350-6.

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Responsibilities

In your role as a postdoctoral scientist, you will focus on application and development of (advanced) computational and bioinformatics to cancer tumour expression data (bulk RNAseq,single-cell RNAseq and other advanced genetic datasets), in-sync with clinicalpatient data to ultimately derive results relevant for immuno-oncology andcancer immunotherapy. Eventually these analyses pipelines will also convergeinto integrate-multi-omics with other analyses modalities like gut microbiomeanalyses (16S RNA-seq), TCR sequencing data and/or antigenic peptidomics data,in collaboration with other labs working either in KU Leuven, Belgium orabroad.

Overall you will have the unique opportunity to shape as well as lead several immuno-oncology relevant computational/bioinformatics projects aiming to elaborate the intricatecross-talk between various immune cells and the tumour micro-environment in thecontext of clinical cancer immunotherapy including (but not limited to) immune-checkpoint blockers and advanced chemotherapy-based immunotherapy regimen. These research lines have a lot of translational potential for cancer patients, as the field of cancer immunotherapy is rapidly expanding but remainsin desperate need for novel molecular markers capable of guiding clinical decisions.

While spear heading these state-of-the-art research projects, you will also be expected to have good communication skills,a highly collaborative spirit and willingness to work in co-ordination with several different teams and clinicians.You will also be expected to provide advice, guidance and coordinate with PhD students or postdocs from within our teams or other collaborating teams on computational analyses in the context of immuno-oncology.

You are able to organize and troubleshoot yourwork independently, document it thoroughly and communicate results and experience with the team in a transparent and professional manner.

Profile

We are looking for a computational scientist/biologist/bioinformaticianwho is highly motivated, well organized and dynamic with a high level of independence and creative thinking for flexible and complex research approaches:

- You need to have a PhD with a topic in one of the following areas: Bioinformatics, computational sciences/biology, systems biology or similar.

- Experience with computational immunology is an added advantage.

- You should be able to demonstrate followingskills: Analysing and deciphering transcriptomic/genomic data, deriving systemsbiology-driven networks from omics data, proficiency with computational programming languages (e.g. R, Python,Bash, Snakemake, MATLAB or others), analysis of publicly available cancergenetic expression datasets (especially TCGA datasets and GEO datasets), andskills in application and development of statistical approaches to solving biologicalproblems (e.g. statistical testing, linear modelling, regression, machinelearning).

- A proven and successful publication track record in this field will be considered.

- High intrinsic motivation and a strongscientific curiosity.

- Ability to be inventive and to present novelideas in method development, data analysis and interpretation.

- Team player that can work independently and in a multidisciplinary (international) environment.

- Excellent oral and written Englishcommunication skills.

- Proactive, flexible, and problem-solving attitude.

- Experience in working with deadlines andbeing involved in multiple projects.

Offer

Duration: A full-time contract for one yearwith the possibility to extend (at least) 2 more years thereafter. You are stimulated to apply for a postdoctoral fellowship.

The position is immediately available.

(Early) access to state-of-the-art cancerpatient transcriptomics data.

A stimulating (international,multidisciplinary) research environment where quality, professionalism and team spirit are encouraged.

The ability to work on scientifically exceptional and high impact, state-of-the-art projects.

The opportunity to be part of a young anddynamic team (Prof. Garg) as well as work very closely with a world-renowned clinicians’ team (Prof. Tejpar) thereby providing a meaningful contribution to immuno-oncology research.

The KU Leuven is one of the most innovativeuniversities in Europe. Leuven is located 20 min. from Brussels, in the center of Europe.