I am a computational biologist working at the interface of statistical modelling, machine learning, single-cell multiomics, and spatial transcriptomics, with transcriptional gene regulation as a unifying theme across my research. My work focuses on developing computational methods to understand how regulatory programs shape cellular identity, function and tissue organisation in health and disease. I collaborate closely with experimental biologists at the University of Manchester, cancer researchers at CRUK MI and beyond, embracing a strong team science approach. My group’s recent methodological contributions include scalable joint non-negative matrix factorisation methods for integrating single-cell multiomics data, approaches for factor discovery from spatial transcriptomics and histology, and the development of the AML single-cell atlas, which revealed age-related regulatory networks in t(8;21) acute myeloid leukemia. More recently, we have developed a deep learning framework to predict pathway activity directly from histopathology images, and we are exploring computational geography approaches to define spatial domains in tissues.

Alongside my research, I serve as Academic Lead for the Advanced Bioinformatics and Computation Core Facility within the Faculty of Biology, Medicine and Health. I am also Programme Director for the NHS-sponsored Higher Specialist Scientific Training (HSST) Clinical Bioinformatics doctoral programme, which trains clinical scientists working across the NHS genomics infrastructure. My teaching portfolio includes contributions to Machine Learning unit for the MSc in Health Data Science, as well as bespoke modules in genomics and clinical bioinformatics for the HSST programme.

I have a degree in Physics from the University of the Punjab (Lahore, Pakistan), followed by an MSc in Mathematical Modelling in Trieste, Italy. My Master’s research focused on developing methods to analyse codon usage bias in bacterial genomes, which is where I first developed a deep interest in biology. I later completed my PhD in Computer Science at the University of Kent, working on prediction of protein–protein and domain–domain interactions and developing new approaches that borrowed ideas from machine learning and statistical physics. Since then, I have continued working at this interdisciplinary boundary, building a research programme in biological network inference, with a more recent focus on integrating and analysing single-cell and spatial multiomics data.

Outside work, I am a keen cricketer, a fair-weather cyclist, and—more recently—a somewhat more serious runner. My running ambitions are steadily increasing, although my pace has not yet caught up with them.

Current PhD Students

• Mohammad Faiz Iqbal Faiz (BBSRC DTP, started 2025)
  Developing novel methods for identifying spatial domains and cell–cell interactions from spatial transcriptomics data

• Shin-Yu Kung (Bicentenary DTP, started 2025)
  Integration of multimodal datasets to understand adipose tissue responses to obesity

• Shangde Li (Bicentenary DTP, started 2025)
  Using single-cell multiomics to unravel cell fate decisions during early embryo development

• Toby Holdcroft (Bicentenary DTP, started 2025)
  Understanding congenital heart disease using single-cell genomics and machine learning

• Jacob Pope (BSF funded, started 2025)
  Single-cell genomics approaches to study circadian regulation in psoriasis

• Adriana Toutoudaki (HSST / DClinSci, Cambridge University Hospitals NHS Trust, started 2025)
  Clinical bioinformatics

• Muhammad Ahtazaz Ahsan (MRC CASE DTP, started 2024)
  Deep learning methods for predicting gene and pathway expression from histology images

• Grace Eckersley (MRC CASE, started 2024)
  Multiomics approaches to study metastatic breast cancer

• Emily Edwards (MRC DTP, started 2024)
  Gene regulatory landscapes in embryonic stem cells and oesophageal cancer cells

• Vrinda Sharma (MRC DTP, started 2024)
  Production of human immune cells for therapeutic applications

• Jessica Whittle (MRC DTP, started 2022)
  Single-cell multiomics approaches to study acute myeloid leukemia

Alumni

• Kamla Reddi (DClinSci, 2026) – ViaPath, London
• Ying Li (DClinSci, 2025) – Bioinformatics Scientist, NHS Blood and Transplant
• Magdalena Grudzien (PhD, 2025)
• Mueez Waqar (PhD, 2024) – Neurosurgery Resident, Salford Royal Hospital, Manchester
• Sanjeev Bhaskar (DClinSci, 2024) – NHSE GTAC Professional Lead & Clinical Genomics Bioinformatics Lead, Manchester
• Xin Ma (PhD, 2024) – Industry position, Shanghai
• William Morgans (PhD, 2024) – Postdoctoral Researcher, University of Manchester
• Louise Hunter (PhD, 2019) – PI / Clinical Senior Lecturer, University of Manchester