In both solid and haematopoietic cancers, recent clinical trials have revealed how new classes of immune-based cancer therapies, including immune checkpoint blockade, bispecific antibodies and chimeric antigen receptor therapy target key pathways of the immune and immune-interacting tumour microenvironment. Either alone or in combination with conventional chemotherapeutics, these interventions have led to unprecedented results in patients with previously untreatable advanced disease. However, in ongoing clinical trials less than 15% of patients with various cancer types respond to immunotherapy and for some patients these new treatments lead to life-threatening toxicities. There is therefore an urgent need to develop reliable tools for patient stratification in order to ensure that only those likely to benefit are given a specific treatment.
Our combined research groups are focused on understanding the tumour-immune cell cross talk in malignancies with particular emphasis on understanding mechanisms that underpin how cells from the immune system move within tumours. An additional area of interest is the immune response generated to infection in patients with solid and haematopoietic cancers, including SARS-Cov-2.
The Bionformatician/Computational Biologist post holder will contribute expertise in applying technologies of all types associated with the stratification of patients for immune-oncology treatments. As part of this job, the post holder will be using bioinformatic tools to create novel analytical pipelines for analysis of multidimensional data sets. The project involves (and not limited to) multi-omic (Genomics, single-cell RNAseq, ChIP- seq, Methyl-seq, metabolomics, and microbiomics) and mass-cytometry (CyTOF) data analysis of both blood samples and tissue biopsies. The individual will also be managing anonymised clinical databases and write relevant scripts to better organise and manage these. For this, there will be opportunities to work with teams based at our partner NHS sites utilising application frameworks such as CogStack allowing extracting of data from unstructured sources.
The Bionformatician/Computational Biologist post will be based at the Guy’s Hospital Campus and embedded within Dr Irshad’s team, part of the Comprehensive Cancer Centre (CCC) within the School of Cancer and Pharmaceutical Sciences. Defined deliverable projects will be in both Lymphoma/CLL (Dr Patten) and Breast Oncology (Dr Irshad) with an emphasis on generating common analytical pathways for these distinct malignancies. The post will be supported by a large bioinformatics infrastructure (> 1,000 CPU cores, 450 TB storage) integrated into the KCL high-performance computing setting. Bioinformatics support will be provided by the Integrative bioinformatics group at CCC. Interactions with wider colleagues, e.g. those based in the Breast Cancer Now Research Unit at KCL and the Breast Cancer Now Research Centre at the Institute of Cancer Research, London, both under the Directorship of Professor Andrew Tutt, and with those based in Department of Infectious Diseases in the School of Immunology and Microbial Sciences (Professor Mike Malim and Dr Rocio Martinez-Nunez) will be facilitated for relevant projects.
The Bionformatician/Computational Biologist post will be offered on an a fixed-term for 2 years
This is a full-time post – 100% full time equivalent
Specific Research Responsibilities for Bionformatician/Computational Biologist
• To work on the immunological and molecular profiling of patient cells, blood and tissue samples in collaboration with clinical and basic scientists and under the direction of the senior lecturer in Cancer & Pharmaceutical Sciences.
• To develop mechanistic insights derived from such profiling activities in collaboration with clinical and basic scientists
• To use a variety of technologies (including imaging) to investigate the functional immunological status of cancers and the influence of their microenvironments
• To create, implement and use analytical and bioinformatics tools to analyse and interpret multidimensional data.
• To establish the pipelines for collection of cells from cancer samples, enable the development of experimental protocols, and inform on sample size calculations for a larger study.
• To support grant writing, for maintaining the continual research in this domain.
• To promote research initiatives and original contributions to the research programmes of the CRUK King’s Health Partners Centre.
General Research Responsibilities:
• To contribute in experiment design, collect and analyse data
• To maintain careful permanent records of all experimental work
• To maintain appropriate databases, keeping accurate written and computerised records and to ensure that these records are stored in a secure place, and to maintain confidentiality of all electronically stored personal data in line with the provisions of the Data Protection Act.
• To attend and participate in the Centre’s academic activities.
• To keep up to date with scientific, clinical and professional issues, in particular developments in the specific subject area.
• To combine anonymised clinical and research data and generate predictive modelling for patient stratification.
• Abide by the Human Tissue Act regulations
• Comply with all data protection directives
• Ensure that research projects comply with ethics regulations
• Ensure appropriate confidentiality of records and information (written and verbal)
Communication & networking:
• Present research findings in regular internal meetings.
• Provide reports on progress.
• Maintain regular progress updates to the supervising group leaders
• Engender good lines of communication with all colleagues and collaborators.
• Participate in and develop research networks
• Maintain accurate written and electronic records of all work undertaken
• Draft conference papers and papers for publication
• Present findings to different audiences and attend relevant conferences
Analysis & research:
• Engage in internationally-leading research
• Publish the outcomes of research
• Help develop research objectives, projects and proposals
• Assess, interpret and evaluate outcomes of research
The above list of responsibilities may not be exhaustive, and the post holder will be required to undertake such tasks and responsibilities as may reasonably be expected within the scope and grading of the post.
Skills, knowledge, and experience
1. Knowledge of relevant platforms and techniques
2. Skills in statistical analysis of data/modelling in R or Python
3. Knowledge of computational biology
4. Develop novel tools using statistics, mathematics and machine learning approaches for the analysis of high dimensional data.
5. Ability to work within a team
6. Interest in the field of translation cancer research
7. Experience of working with complex datasets and database management
8. An independent thinker
1. Knowledge of immunology, any previous lab experience is advantageous.
2. Knowledge/skills in the use of platforms monitoring patient immunological and/or microenvironment status
3. Past peer-reviewed publication(s) that involves the analysis of genomics NGS data or bulk/single-cell transcriptomics data or CyTOF data
4. Experience in pipeline scripting, automation and management in HPC clusters
5. Ability to analyse data with existing publicly available and commercial software solutions (e.g. R/Bioconductor, UMAP, viSNE, SPADE, FlowJo, CytoBank suite).