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The University of Southampton
Institute for Life Sciences

Insights Through Data

Technological advances have allowed scientists to gather large amounts of data about a vast array of organisms, cells and individual species. Our researchers are using mathematical and computational methods to understand large data sets relating to life sciences.

Image credit: Prof Ben MacArthur

While we can create and collect more data than ever before, it is not always easy to unlock the information it contains. To turn data into a major scientific and economic advantage is a challenge. To meet that challenge, we need to create analytic tools that allow us to use the data in a beneficial way.

Our mathematicians and computer scientists are working alongside other researchers in biological sciences, medicine, chemistry and physics to develop new ways of understanding complex datasets, so the information it contains can be used to benefit society.

We are investigating data from systems that span the full range of life on earth, from molecular dynamics inside cells, to ecosystems and evolutionary dynamics. We are particularly interested in using data to improve human health and wellbeing – from understanding better how our bodies fight cancer, to how our social networks affect our health.

Our work includes projects to develop new techniques for analysing single cell gene expression patterns; predicting clinical outcomes from heterogeneous clinical datasets; examining structural properties of networks and the ways in which network architecture relates to system behaviour; and using experimental methods and mathematical models to investigate molecular regulation of stem cell fate.

All of our work underpinned by the desire to take significant steps towards personalised medicine and to meet the biggest health challenges society faces today.

Related Staff Member

Image credit: Prof Ben MacArthur
Image credit: Prof Ben MacArthur

Key words

Complex datasets, Data, Interdisciplinary, Mathematical & Computational Methods, Networks

Please see a selection of postgraduate courses related to this subject area below. 


For the full range of undergraduate and postgraduate courses at the University of Southampton, please visit our courses webpages:  https://www.southampton.ac.uk/courses.page

MSc Data Science

This degree builds core areas of expertise: operating high-performance computing clusters & cloud-based infrastructures, devising & applying sophisticated Big Data analytics techniques.

MSc Computer Science

This one year degree includes modules from specialist programmes including artificial intelligence, cyber security, signal processing, software engineering, and web science and technology.

MSc Artificial Intelligence

This one year degree offers wide-ranging options including intelligent agents, complexity science, computer vision, robotics and machine learning techniques.

MSc in Statistics with Applications in Medicine

The MSc in Statistics with Applications in Medicine provides training in statistical methodology, with an emphasis on solving practical problems arising in the context of collecting and analysing medical data.

MSc Genomic Medicine

This programme explores the genomics & informatics of rare & common diseases, cancer & infectious diseases & the application for diagnostics & stratified medicine.

MSc Data and Decision Analytics

This programme is an ideal opportunity to provide yourself with the analytic skill set necessary for success in commercial companies or the public sector.

Image: Dr Jonathan West
Array of droplet reactors for single cell transcriptomics

Making connections for precision medicine

Researchers from across the Life Sciences are coming together in projects that will make personalised medicine a reality.  Microfluidic Engineers, systems biologists and doctors have combined digital fabrication and big data visualisation to develop single-cell analysis at a fraction of current costs.  With our super-efficient analytical pipeline we can now read the operating manuals of thousands of single cells simultaneously, monitor their behaviour in realtime, and computationally model them as cellular ecosystems of health and disease.  With unprecedented precision we can now map the landscapes of pathologies from allergy to cancer, supporting doctors making clinical decisions and giving patients the best possible treatment.

Contacts: Dr Jonathan WestDr Mat Rose-Zerilli, Dr Patrick Stumpf

https://dropletkitchen.github.io/

Cancer Cell Volume 32, Issue 6, 11 December 2017, Pages 777-791.e6 Antibody Tumor Targeting Is Enhanced by CD27 Agonists through Myeloid Recruitment Anna H. Turaj et al  https://www.sciencedirect.com/science/article/pii/S1535610817304713?via%3Dihub

Image: Prof Jacek Brodzki
Illustration of lung structure from CT scan data

Lung topology

Chronic Obstructive Pulmonary Disease (COPD) is a complex lung condition that affects more than 200 million people across the globe. It is the third leading cause of death worldwide.

Our researchers, supported by the EPSRC, have developed a new computational way of analysing CT scans of lungs, which could herald a breakthrough in the diagnosis and assessment of COPD and other lung diseases. The multi-disciplinary team of mathematicians, clinicians, and image specialists have devised a method for numerically describing the complicated three-dimensional structure of the lung using topology – a part of mathematics designed specifically for the study of complex shapes.

Using the method, the researchers have found that they could accurately distinguish the characteristics of patients’ lung function, the different stages of their condition and characteristics not detectable to the naked eye. It is hoped that the technology could lead to the real-world development of a valuable clinical tool for the early diagnosis of conditions like COPD and asthma.

Contacts: Prof Jacek Brodzki, Prof Ratko Djukanovic

Nature Scientific Reports paper

Life Sciences Respiratory theme

Life Sciences Imaging theme
 

Image: Prof Sarah Ennis Lab
Image: Prof Sarah Ennis Lab

Crohn's disease

At least 115,000 people have Crohn's Disease in the UK with up to one third being under 21 years old when their condition is diagnosed. It is the most common form of Inflammatory Bowel Disease in children and incidence rates are increasing. 

 Inflammation in the gut causes the symptoms - diarrhoea, abdominal pain and tiredness – but it is unclear what triggers this inflammation. It is thought that a combination of genetic and environmental factors are involved.

Our scientists are using next generation sequencing techniques to analyse patients’ genes, gene expression and the role the microbiome plays in triggering disease. The microbiome is the community of bacteria that live in the gut.

The study aims to assess how the microbiome interacts with the other factors to cause disease: including the children’s genetic susceptibility to developing Crohn’s disease, the activity of the children’s immune system and which genes are turned on or turned off.

Previous studies have tried to investigate the underlying causes of Crohn’s Disease, but to date none have examined the microbiome alongside genetic risk and gene expression over a long period of time in the same patients. 

Our research will improve the understanding of the cause of the disease and potentially lead to more effective therapies and new ways of predicting how severe the disease will be in individuals and how well they will respond to treatments. 

Contacts: Dr James AshtonProf Sarah Ennis 

Action Medical research
 

Identifying stem cells for regeneration

Ageing is often accompanied with illnesses and injuries associated with bones and joints. Diseases such as osteoporosis and arthritis cause pain, bone fractures, and can lead to immobility and distress. New treatments that enable the skeleton to heal more efficiently are urgently needed. Cell-based therapies are some of the most exciting and promising areas of treatments for bone disease, but despite intensive research no reliable methods to sufficiently enrich the rare bone stem cells, known as skeletal stem cells, which are needed for these strategies, have been developed.

Our mathematical scientists are working alongside the Bone and Joint Research Group, to tackle this challenge by combining stem cell biology, innovative chemistry and statistical methods to isolate bone stem cells. We are developing a novel single cell identification procedure that uses smart nano-probes to select stem cells from the bone marrow, and then explore their patterns of gene expression using next generation sequencing. Our nano-probes tag the cells, so that they can be isolated and examined further – for example, to assess their ability to make bone and cartilage for therapeutic application.

This exciting programme of research offers the ability to isolate the bone stem cell and provide substantially enriched, and potentially pure populations of bone stem cells, that are able to regrow human bone tissue.

Contacts: Prof Ben MacArthur, Prof Richard Oreffo

Life Sciences Repair and Stem Cell theme

 

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