MRC Human Genetics Unit
Medical Research Council Human Genetics Unit

Ava Khamseh Research Group

Biomedical Artificial Intelligence

Section: Biomedical Genomics

Dr Ava Khamseh, Lecturer in Biomedical AI
Dr Ava Khamseh, Lecturer in Biomedical AI

Research in a Nutshell 

One of the aims of biomedical genomics is to determine causal molecular interactions underlying biological processes. These interactions can be highly complex, involving many dependent variables constituting a given biological system of interest. Quantifying interactions, beyond extracting their magnitude, and moving towards obtaining information on their directionality requires well-designed experiments and/or large-scale individual-level biomedical data.

Currently, our research focuses on causal molecular interactions in the context of cancer & population biomedicine:

1. Cancer biology: Progression of cancer has been widely viewed as following Darwinian evolution, where cells acquiring somatic driver mutations are positively selected, leading to preferential expansions of clones carrying these mutations. Advances in high-throughput DNA- and RNA-sequencing have substantially increased our understanding of late-stage cancer. Yet we still lack a quantitative understanding of the necessary and sufficient early conditions and steps required for the evolution of normal cells into cancer cells.

We design experimental and computational models of early cancer to (i) capture mutational and transcriptional trajectories over time at single-cell resolution, and (ii) quantify how different driver mutation interactions lead to cooperation or competition amongst cells.

2. Population biomedicine: We develop machine learning techniques for applications to large-scale biomedical data, such as scRNA-seq and the UK Biobank. For example, we develop (non-)parametric probabilistic and neural network approaches to (i) extract higher-order interactions from gene expression data, and (ii) quantify causal interactions amongst DNA variants leading to physiological outcomes.

 

People

 
Dr Ava Khamseh Group Leader
Abel Jansma PhD student (jointly supervised with Chris Ponting and Luigi Del Debbio)

Contact

 ava.khamseh@igmm.ed.ac.uk

Website

https://edbiomed.ai/

Collaborations

  • Dr Luke Boulter, University of Edinburgh

  • Professor Chris Ponting, University of Edinburgh

  • Professor Martin Taylor, University of of Edinburgh

  • Dr Catalina Vallejos, University of Edinburgh

  • Professor Luigi Del Debbio, University of Edinburgh

  • Dr Sjoerd Beentjes, Hausdorff Center for Mathematics, Bonn

  • Dr Guido Cossu, Ascent Robotics, Tokyo

 

Scientific Themes

Understanding cancer initiation and evolution, probabilistic modelling for cancer, non-parametric probabilistic modelling and causal machine learning for large scale biomedical data, Targeted Learning

Technology Expertise

Single cell biology, cancer models