Senior Bioinformatician (Genomics)

Salary for this Role:

From £51,345 per annum with benefits, subject to skills and experience

Job Title:

Senior Bioinformatician (Genomics)

Reports to:

Samra Turajlic [C]

Closing Date:

08/Jan/2025 23.59 GMT

Job Description:

Senior Bioinformatician (Genomics) – MANIFEST Research Platform / Cancer Dynamics Laboratory

Reports to: Prof. Samra Turajlic, Cancer Dynamic Laboratory Group Leader and MANIFEST Consortium Lead,

Contract term: This is a full-time, fixed term (4 years) position on Crick terms and conditions of employment.

The role will be placed in Cancer Dynamics Laboratory (Turajlic Lab) and will support the MANIFEST research platform led by Prof. Samra Turajlic

The Research Group & Project

THE MANIFEST RESEARCH PLATFORM

Harnessing the immune system to treat cancer has revolutionised survival outcomes for many patients. Immune checkpoint inhibitor therapies which unleash the brakes from immune cells to kill cancer cells, have become standard of care for many cancer subtypes. The success of existing, emerging and future immunotherapies and their routine use in the NHS is dependent on the appropriate tools, data and technology to rationalise their use and manage their side effects. Nevertheless, almost no biomarkers today can effectively distinguish responders from non-responders, predict toxicity, or guide treatment choices.

An exciting Senior Bioinformatician post is available in the Cancer Dynamics Laboratory. The post holder would work across multiple on-going projects of the lab, including a dedicated role within the MANIFEST project (“Multiomic ANalysis of Immunotherapy Features Evidencing Success and Toxicity”), a newly formed ambitious multi-stakeholder consortium involving academic, industry and NHS partners to deliver deep multiomic profiling for patients with cancer undergoing immunotherapy. The MANIFEST consortium represents a diverse group of UK-wide experts in cancer research and clinical care comprising major NHS trusts, academic institutes and universities, and industry partners. This grant is funded by the UK Office of Life Sciences (OLS) and the Medical Research Council (MRC).

MANIFEST addresses the critical challenge in cancer treatment: predicting how patients will respond to immunotherapy. By integrating multiomic data and innovative methodologies, this platform aims to enhance treatment precision and effectiveness.

More information about research interests and on-going projects of Cancer Dynamics Laboratory can be found here: https://www.crick.ac.uk/research/labs/samra-turajlic.

More information about MANIFEST can be found here: https://www.manifest-io.org.uk/about.

Summary of the role

The successful candidate will join the bioinformatics team at the Cancer Dynamics Laboratory. This role will involve leveraging data from the MANIFEST, TRACERx Renal (http://tracerx.co.uk/studies/renal/), and PEACE (https://clinicaltrials.gov/study/NCT03004755, renal cancer and melanoma) studies. The primary responsibility of the post-holder will be to perform bioinformatics discovery analyses aimed at identifying genomic and transcriptomic features that influence responses and resistance to immunotherapy. This analysis will be complemented by integrating various multiomic data types, including immunopeptidome, spatial imaging, and pathology data, among others. The post holder will interact closely with the machine learning team that aims to integrate several features for building a robust model to predict response to immunotherapy.

The post holder will report to the Group Leader, Samra Turajlic, and will interact closely with other laboratory staff from the MANIFEST platform and Software Engineering and AI STP at the Crick, as well as with post-docs, students, scientists, technicians from the lab, and scientific partners of MANIFEST.

Within this role, there will be several opportunities for personal development including access to relevant training and courses, interactions with scientific partners and Key Opinion Leaders across the MANIFEST platform as well as opportunities for training and secondment in different research environments across the UK within the MANIFEST consortium. 

Key Responsibilities

These include but are not limited to:

• To work within the bioinformatics team of the Cancer Dynamics lab, and collaborating with other groups at the Institute, academic, clinical and industry partners of MANIFEST.

• To conduct analyses of genomic and transcriptomic data, using established pipelines.

• To analyse DNA sequencing data, identifying somatic mutations, copy number aberrations, and neoantigens.

• To analyse RNA sequencing data, performing immune deconvolution and identifying gene expression signatures.

• To evaluate and provide state-of-the-art tools, databases, protocols and methods necessary for the analysis of above-mentioned biological data.

• To liaise and coordinate between the project collaborators which include clinicians, cancer biologists, machine learning experts and mathematical modellers.

• To document all analyses in an accurate, timely and clearly presented manner, and use this to prepare data summaries and reports as and when required.

• To understand the relevant literature (cancer biology, cancer genomics and cancer immunology) sufficiently to perform analyses and propose novel ideas.

• To attend, and report research results at regular group meetings.

• To contribute to the broader research programme of Turajlic lab intellectually and practically.

• To write and present work to MANIFEST stakeholders as required.

• To engage in relevant MANIFEST programme workflows with academic, NHS and industry partners.

• Any other duties appropriate to the scope and grade of the post. The job description may be subject to review and amendment in consultation with the post holder as job duties change/develop.

Person Specification

The post holder should embody and demonstrate our core Crick values: bold, open, collegial, in addition to the following:

Essential skills/experience

• Masters or higher degree in bioinformatics or a relevant discipline with extensive analytical component (or equivalent experience).

• Prior experience or skills in cancer genomics

• Fluent in shell scripting and at least one of the following programming languages: R or Python

• A strong foundation in bioinformatics and good computational skills

• Good understanding of statistical approaches for omics data analysis

• Experience working with high performance compute clusters and large-scale datasets

• Experience working/managing data from large-scale multiomic studies

• Ability to manage projects setting timelines, analysing, presenting, and writing up the conclusions

• Excellent presentation skills

• Excellent inter-personal skills and commitment to teamwork

• Pro-active in innovation and problem solving

Desirable skills/experience

• Prior experience in Cancer Immuno-genomics

• Understanding of techniques and challenges in neoantigen identification

• Prior experience in immune deconvolution from transcriptomics data

• Knowledge of cancer immunology and/or cancer evolution

• Previous experience of multidisciplinary working

• Experience with any workflow management framework like Nextflow or snakemake

• Understanding of best practices in data management, governance and documentation

About Us

At the Crick, we conduct research at the forefront of biomedical research. We combine rigour with an open and collaborative culture, and are outward-looking, reflecting our status as a partnership of six organisations aiming to pool knowledge, ideas and resources.

We have a wide research portfolio with no divisions or departments, bringing biomedical researchers together with clinicians, physical scientists and applied scientists from our pharmaceutical partners.

We aim to attract the most talented researchers and support them to tackle innovative research questions. Our science technology platforms provide our researchers with access to state-of-the-art technology and expertise.

We provide an excellent learning environment with dedicated education programmes in public engagement with science, education and personal development, and a postdoc training programme that prepares scientists for leadership roles in science.

• If you are interested in applying for this role, please apply via our website.

• All offers of employment are subject to successful security screening and continuous eligibility to work in the United Kingdom.

• If you require a visa to work in the UK we will help support your application should you be successful

Find out what benefits the Crick has to offer:

For more information on our great pay and benefits package please click here: https://www.crick.ac.uk/careers-and-study/life-at-the-crick/pay-and-benefits

Equality, Diversity & Inclusion:

We welcome applications from all backgrounds. We are committed to providing equal employment opportunities, regardless of ethnicity, nationality, gender, sexual orientation, gender identity, religion, pregnancy, age, disability, or civil partnership, marital or family status. We particularly welcome applications from people who are Minority Ethnic as they are currently underrepresented in the Crick at this level.

Diversity is essential to excellence in scientific endeavour. It increases breadth and perspective, leading to more innovation and creativity. We want the Crick to be a place where everyone feels valued and where diversity is celebrated and seen as part of the foundation for our Institute’s success.

The Crick is committed to creating equality of opportunity and promoting diversity and inclusivity. We all share in the responsibility to actively promote dignity, respect, inclusivity and equal treatment and it is our aim to ensure that these principles are reflected and implemented in all strategies, policies and practices.

Read more on our website: https://www.crick.ac.uk/careers-and-study/life-at-the-crick/equality-diversity-and-inclusion