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Bioinformatics: Discovering non-protein-coding vulnerabilities in lung cancer with CRISPR-Cas9

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

About This PhD Project

Project Description

Are you a BSc or MSc graduate with computational / statistical background looking for a challenge in cancer genomics and CRISPR?

The Project: This project will develop and apply bioinformatic and statistical methods to the analysis of CRISPR-Cas9 high-throughput screens, and the cancer genes they discover. Finding therapeutic targets in cancer remains a grand challenge in biomedical research. Our genome contains many thousands of long noncoding RNA (lncRNA) genes representing a rich and unexplored source of drug targets. Our lab has adapted CRISPR-Cas9 technology to powerful screens for these cancer-causing lncRNAs. This approach rests on a foundation of informatic and statistical analyses. Furthermore, candidate lncRNAs are investigated by integrative analysis with diverse clinical and genomic datasets. Both are the objective of this PhD project. You will be trained and closely supported by highly-experienced experimentalists and bioinformaticians. There will also be ample opportunity to develop your own interests.

The Group: We are a diverse, interdisciplinary and fun team with a passion for research. We foster an open and collaborative working environment. We are funded by a prestigious Future Research Leaders grant. We are recognised internationally and have numerous links with other RNA researchers, including through our participation in GENCODE, NCCR “RNA & Disease” and the International Cancer Genome Consortium (ICGC). We enjoy clinical collaborations at the St Vincent’s Hospital. For more information see gold-lab.org and twitter.com/goldlab_bern.

The Person: We seek a motivated and thoughtful colleague to join our team. You should have a degree in a numerical subject (computer science, statistics etc) and familiarity with some of: Unix, R, python, machine learning.

Details: Start date September 2020, funded for 3 years. Tax-free stipend according to University scales, tuition fees covered.

The City: Dublin, the capital of Ireland, is a lively international city with numerous cultural, recreational and social possibilities.

To apply: Please send [1] a brief email explaining why you’re interested in the project and why you’re suitable, [2] your CV and [3] contact details of referee(s) to rory.johnson[at]ucd.ie with subject title: “Application UCD PhD”. Informal enquiries are also welcome. The position will be advertised until filled, and latest updates on the job availability will be posted at http://www.gold-lab.org/we-are-hiring, so please check before applying. 14/02/2020

References

Selected publications:
-Pan-cancer analysis of whole genomes. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature. 2020 Feb;578(7793):82-93.

-CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long noncoding RNAs. Bergadà-Pijuan J, Pulido-Quetglas C, Vancura A, Johnson R. Bioinformatics

-Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening. Esposito R, Bosch N, Lanzós A, Polidori T, Pulido-Quetglas C, Johnson R. Cancer Cell. 2019 Apr 15;35(4):545-557.

-High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R. Nat Genet. 2017 Dec;49(12):1731-1740.

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