We are seeking a motivated Master's student to push the boundaries in methods for geneset/signature analysis. Signature-based analyses are part of our core daily business for those in Biomics dealing with transcriptome analyses, yet at the moment there is no standard approach to solve the issue of multiple signatures purportedly representing the same state (a state: pathway status, drug response, or cell/tissue type). Gene expression signatures are also growing in importance with advances in cancer immunotherapy and reverse translation.
One approach based on the idea of "crowd-sourcing" is utilizing all available signatures for a given state. However, for this to work, signatures need to be labeled succinctly using standard ontology for both machine and human intelligence to make the best use of them. This is challenging considering that there are 5000+ public and internally-generated signatures, and the number is growing.
Your tasks will include:
Continue the development of a pipeline that provides standardized labels for all 5000+ signatures (e.g., all signatures representing activation of CD8 T-cells should be labeled as such)
Continue the development of an extension to the ?standard? signature analysis method (e.g. GSEA, multiGSEA, bioQC) able to give a call for whether a state (e.g., activation of CD8 T-cells) is seen in transcriptome profiles of interest, after considering the output from the standard method for all available signatures representing that state.
Develop a user interface for the above
Improve the interface for holistic querying of our signature database (GEMS)
Who you are:
You're someone who wants to influence your own development. You're looking for a company where you have the opportunity to pursue your interests across functions and geographies. Where a job title is not considered the final definition of who you are, but the starting point. You are highly self-motivated, passionate about working in a multinational company and you have good Python skills. Furthermore, you have:
Experience with natural language processing (NLP) methods
Intermediate to advanced programming level in Python. Familiarity (not necessarily similar level of expertise) with both Python and R would be preferable
Familiarity with MongoDB
Understanding of the concept of gene expression signatures, geneset analysis and signature database (e.g. GSEA, MSigDB)
Business-level proficiency in English (spoken and written)
What's to consider:
Send us your complete application merged into one PDF including CV and a Motivation Letter (including desired start date & duration)
A certificate of enrollment (if you are currently studying)
For non-EU/EFTA citizens: Certificate from the university stating that an internship is mandatory (required due to regulations). This letter we need already when submitting the application!
The starting date of this internship is ASAP or upon availability and it will run for 6 months. ?
??Are you ready to apply? We are looking for someone who thinks beyond the job offered - someone who knows that this position can be a rare springboard to many other opportunities at Roche. When applying for this position, already project yourself in the future. Think about what could come next and how you would like to build your future.
Roche embraces diversity and equal opportunity in a serious way. We are committed to building a team that represents a variety of backgrounds, perspectives, and skills. The more inclusive we are, the better our work will be.
If you still have questions then please check our FAQs and videos on careers.roche.ch/faq
