Postdoctoral fellow, Oncology Computational Biology

Job reference:

Postdoctoral fellow, Oncology Computational Biology


Firm:

Novartis Institutes for BioMedical Research (NIBR)


Category:

External


Work city:

Basel


Work start:

01.01.2018


Created:

01.09.2017


Employment fraction:

100%


Type of contract:

Temporary


Job description

The Oncology Disease Area at the Novartis Institutes for BioMedical Research (NIBR), in collaboration with the Chemical Biology & Therapeutics department at NIBR, is looking for a Postdoctoral candidate trained in computational biology to join the Oncology Bioinformatics group in Basel.

Our team focuses on applying and developing computational approaches to gain a deeper understanding of the molecular mechanism of cancer and its response to therapies. We implement integrative methods to identify the somatic alterations driving oncogenesis leveraging multiple omics data sources. In particular our group employs a variety of computational approaches to analyze and interpret functional genomic data to elucidate cell autonomous cancer dependencies. This work has enabled the extensive exploration of gene essentiality in a multitude of cancer cell lines in Project DRIVE (McDonald, Cell, 2017) and highlighted the extensive representation of transcription factors (TF) among the top genes essential to cancer. In parallel the emergence of epigenomic technologies has led to the identification of regulatory elements critical for cell identity and tumorigenesis. These elements, called enhancers, are bound by TFs and play a key role in sustaining the oncogenic program in cancer.

The proposed project aims at leveraging internally generated data as well as the wealth of publicly available data to better understand TFs and their target enhancers. In particular we are interested in exploring the proliferative as well as transcriptional response upon knock-out of these enhancer elements. Performing this analysis using proliferation assays followed by bulk RNAseq remains a challenge requiring separate experiments for each potential enhancer. To address this challenge we plan to leverage the multiplexing capabilities of pooled CRISPR screens with single cell RNA-seq (scRNAseq) to understand the effect of enhancer knock-out on the transcriptome in a high-throughput fashion. The development of alternative and related projects is also possible.

Profile requirements

The successful candidate holds a PhD in a computationally intensive discipline such as Bioinformatics, Computer Science, Biostatistics or related field with a proven track record of scientific achievement as assessed by publications. Knowledge in cancer genomics and experience in next-generation sequencing data analysis are highly desirable. Experience in analyzing and interpreting epigenetics and/or single cell RNASeq data is an advantage. We are looking for a highly motivated and hard-working candidate with a good level of independence and creative thinking. The candidate will be able to access a wide range of expertise and resourcing within NIBR.

Applications will be collected via the NIBR-Postdoc website.

Position contact information

Name: Antoine de Weck

Address:
Novartis Institute for BioMedical Research Klybeckstrasse
Basel, Basel Stadt 4000
Switzerland

Phone: +41795273334

Email: antoine.deweck@novartis.com