Research Associate in Topological Data Analysis for Cell Biology

Research Associate in Topological Data Analysis for Cell Biology

SALARY: From £39,500 per annum (depending on skills and experience)

LOCATION: Didcot, Oxfordshire

JOB TYPE: 2 Year Fixed Term Contract (with the possibility of extension)

The Rosalind Franklin Institute (the Franklin) is a technology institute established by the UK Government as a unique centre committed to advancing tools that are needed to transform healthcare in the future.

The Institute brings together researchers in life and physical sciences, and engineering, to develop a spectrum of tools which we will use to image, interpret and intervene in biological systems. These insights will speed up the discovery of new medicines, help find new diagnostics and contribute to a deeper understanding of human health and disease. Our Science Strategy seeks to focus the Franklin’s research and unite our researchers around our Technology Innovation Challenges and Life Science Challenges.

This is an exciting research opportunity to join the VirtuAI Cell project which aims to develop a virtual mapping of intracellular contents of biological cells. This leads to the ultimate goal of running in-silico cell simulations that use such mappings to model how the dynamics of intracellular contents may modulate in response to various types of cell disturbances; e.g., due to the injection of a drug molecule;

or the intracellular growth of cancer promoting mutations, the checking of which one could model to predict new routes towards preventative cancer.

The Research Associate will develop and apply persistent homology to automatically classify cellular structure in experimental 2-D microscopy and 3-D tomography data, to help build a virtual mapping of biological cells. The role-holder will use persistent homology to represent and classify biomedical structure and explore how such structural representations can track over multi-scale image resolutions. The work may also involve applying topological data analysis (TDA) to assist with the design, construction and deployment of new feature engineering and optimisation strategies for the machine-learning (ML) modelling of cellular data.

More generally, this role offers a great opportunity for an expert in persistent homology to become a valued member of a highly interdisciplinary, challenge-focused project team that aims to solve a global research challenge.

As a Research Associate at the Franklin, you will bring scientific knowledge and skills to deliver a specific research project and/or you will bring independent, creative science, or specific skills to a team delivering a project or program. Through this work, you will build scientific independence, develop new science and leadership skills, and establish a growing reputation externally.

As a Research Associate, you will:

• Employ persistent homology to represent and classify structures in cell biology, using experimental data from 2-D microscopy images and 3-D tomograms
• Analyse and interpret results from persistent homology in liaison with experts in cell biology
• Apply persistent homology to track structural representations of biocellular species over multi-scale image resolutions
• Use persistent homology to track structural representations of biocellular species over time
• Curate large volumes of simulated data to help develop persistent homology for cell biology
• Apply TDA to assist ML modellers with the feature engineering and optimisation of cellular data
• Create data representations using TDA to help make more efficient ML models for cell biology
• Perform or supervise data annotation for training and evaluation purposes where necessary
• Plan data acquisitions with experimentalists who conduct them, analyse and interpret results and supervise delivery of outputs (e.g. research report, patent application) in a scientific/technology area of interest.
• Work within a project team, contributing to wider projects around key Challenges.
• Lead major contributions to outputs from research including papers, patents and both internal and external presentations.
• Support and develop others including day-to-day supervision of students or visitors in areas…