Machine learning and systems biology approaches to study the gut microbiome
Developing a machine learning-based analytical pipeline using systems biology approaches to identify microbiome-related features implicated in ageing.
Biography
Matthew is a BBSRC iCASE PhD student where together with BenevolentAI, Matthew is developing machine learning (ML) and systems biology approaches to investigate the role of the microbiome during the ageing process.
By harnessing the power of ML, these approaches will be used to identify prognostic indicators from metagenomics and metatranscriptomics data. Combining ML-based features with host-microbiome interactions and systems biology, we aim to improve our understanding of how the microbiota contributes to our health.
Matthew started his research at the Earlham Institute during the second year of undergraduate studies where he was introduced to systems biology. As an intern within the Korcsmáros Group, he developed an algorithm to identify and contextualise autophagy-related proteins within a molecular interaction network.
This experience led to his final year research project, in which he created an integrated network-medicine and ML pipeline to identify prognosis indicators in ulcerative colitis. These short-term projects gave him the motivation and passion to further explore the capabilities of ML within life sciences.
Publications
Related reading.
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01 July 2022
Science
FEATURE
The genetic machinery that drives biodiversity
Thanks to new technologies and novel approaches to big data, researchers are revealing new secrets into the genetic processes that power Cichlid evolution.
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23 March 2022
Science
FEATURE
On the origin of errors: the causes and consequences of mistakes during DNA replication
DNA replication is a simple enough concept. Copy, divide, rest, repeat. While the basic idea is straightforward, the actual machinery governing the process of replication remains something of an enigma.
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11 February 2022
Science
FEATURE
| 10 min READ
Why is genome annotation important?
Genome annotation is no simple feat, but it’s incredibly important in identifying the functional elements of DNA. Building the appropriate tools and pipelines is key.
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04 February 2022
Science
Technology
FEATURE
| 5 min READ
Why cloud computing is important for data-driven bioscience research
Access to powerful compute resources via our cloud computing infrastructure enables bioscience research, collaboration, and innovation.
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10 December 2021
Science
FEATURE
| 15 min READ
How bioinformatics can crack the complex case of protist biodiversity
Protists defy taxonomic classification and wow us with their weirdness on a daily basis. They’ve been excruciatingly difficult to study but, thanks to single-cell genomics and bioinformatics being carried out at the Earlham Institute, we’re finally decoding their abundant biodiversity.
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25 November 2021
Science
FEATURE
| 8 min READ
The dramatic effects genomics will have on our future world
Fish and chips, fabrics, personalised medicine and coffee. These are just some of the things you might have Earlham Institute researchers to thank for in the decades to come.
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04 November 2021
Science
FEATURE
| 8 min READ
The inextricable link between climate change and biodiversity.
Why conservation must be at the forefront of the conversation.
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28 October 2021
Science
FEATURE
| 10 min READ
Hidden Biodiversity: How genomics can save nature’s secrets before they’re lost forever
Genomics offers a way to understand nature’s secrets like never before. In revealing them, this branch of science highlights the multitude of ways we might nurture and benefit from, rather than destroy, biodiversity.
28 September 2022
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European consortium launched to reverse biodiversity loss through genomics research
A quantum leap in the use of genomics is needed to reverse unprecedented species loss and ecosystem degradation, according to a new pan-European consortium of leading research organisations.
22 September 2022
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Tracking bacterial evolution in real time spots emergence of antimicrobial resistance
Single-cell genomics technology could transform understanding of how bacterial populations evolve and combat the growing issue of antibiotic resistance
29 June 2022
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Big Data initiative awarded £6.3 million as part of major UKRI investment in research infrastructure
UK Research and Innovation has awarded £6.3 million of new funding to support the development of BioFAIR, a collaborative virtual infrastructure that will support the sharing and management of life science data.
13 May 2022
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Not all looks rosy for the pink pigeon
Boosting numbers of the once critically endangered pink pigeon may not be enough to save it from extinction in the future, according to a major study on the iconic species.
02 May 2022
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Coronavirus jams communication signals to immune cells in the gut
A computer model could help to reveal how some infectious diseases - including COVID-19 - trigger an overactive immune response in certain patients, which can drive inflammation and lead to serious complications or even death.
28 April 2022
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Precision medicine tool finds hidden genetic connections that could personalise IBD treatment
People with Inflammatory Bowel Disease (IBD) develop the condition due to distinct and different mechanisms, determined by their genetics. Researchers and clinicians from the Quadram Institute, the Earlham Institute, the Norfolk and Norwich University Hospital and University of East Anglia with collaborators in Cambridge, London and Leuven (Belgium), have found that natural genetic variation appears to influence the development of IBD.
14 March 2022
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Deciphering gut microbiome ‘chatter’ to combat IBD
Scientists at the Earlham Institute, Quadram Institute and University of East Anglia on the Norwich Research Park, have developed a new computational biology method to better understand IBD for targeted clinical treatments.
20 January 2022
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New legislation granted to progress plant gene editing in UK
Following the UK’s departure from the EU, DEFRA has put into place new legislation to cut bureaucracy for gene editing in plant research.