How bugs in the gut affect ageing - using machine learning and networks to increase healthy lifespan
Lead Research Organisation:
University of East Anglia
Department Name: Graduate Office
Abstract
Ageing is a significant event in the general population not only due to the increasing proportion of elderly but also the prevalence of various age-associated disorders. Hence, it is essential to understand the mechanisms which either drive or slow down the ageing process. From a prognostic perspective, there exist very few tools which could predict beforehand the onset of ageing. Alterations in the gut microbiome have been observed in aged individuals compared to those displaying no ageing onset.
Machine Learning is a novel area of Artificial Intelligence wherein computers are allowed to learn rapidly from large datasets to discover the underlying complex patterns and signatures with minimal human interference. By combining systems biology approaches which capture the effects of the gut microbiota on host processes, the project aims to discover mechanistic explanations from the underlying hidden patterns identified by machine learning in metagenomic datasets from aged and healthy subjects.
Machine Learning is a novel area of Artificial Intelligence wherein computers are allowed to learn rapidly from large datasets to discover the underlying complex patterns and signatures with minimal human interference. By combining systems biology approaches which capture the effects of the gut microbiota on host processes, the project aims to discover mechanistic explanations from the underlying hidden patterns identified by machine learning in metagenomic datasets from aged and healthy subjects.
People |
ORCID iD |
| Tamas Korcsmaros (Primary Supervisor) |
Publications
Verstockt B
(2019)
DOP70 An integrated multi-omics biomarker predicting endoscopic response in ustekinumab treated patients with Crohn's disease
in Journal of Crohn's and Colitis
Verstockt B
(2019)
Su1909 - Predicting Endoscopic Response in Ustekinumab Treated Patients with Crohn's Disease Trhough an Integrated Multiomics Biomarker
in Gastroenterology
Treveil A
(2021)
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.
in PLoS computational biology
Seyed Tabib NS
(2020)
Big data in IBD: big progress for clinical practice.
in Gut
Potari-Gul L
(2021)
P020 Mapping the changing intercellular communication and its downstream effect in Ulcerative Colitis
in Journal of Crohn's and Colitis
Modos D
(2021)
DOP07 Ulcerative Colitis associated single nucleotide polymorphisms found in transcription factor binding sites effect key pathogenesis pathways and facilitate patient stratification
in Journal of Crohn's and Colitis
McKee AM
(2021)
Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth.
in iScience
Madgwick M
(2020)
P070 Machine learning approaches to identify IBD biomarkers from longitudinal microbiome data
in Journal of Crohn's and Colitis
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/S50743X/1 | 01/10/2018 | 31/12/2022 | |||
| 2116392 | Studentship | BB/S50743X/1 | 01/10/2018 | 30/11/2022 |
| Title | Singalink 3 |
| Description | Signaling networks represent the molecular mechanisms controlling a cell's response to various internal or external stimuli. Most currently available signaling databases contain only a part of the complex network of intertwining pathways, leaving out key interactions or processes. Hence, we have developed SignaLink3 (http://signalink.org/), a value-added knowledge-base that provides manually curated data on signaling pathways and integrated data from several types of databases (interaction, regulation, localisation, disease, etc.) for humans, and three major animal model organisms. SignaLink3 contains over 400 000 newly added human protein-protein interactions resulting in a total of 700 000 interactions for Homo sapiens, making it one of the largest integrated signaling network resources. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | This webtool provides a quick and easy interface with the large about PPI data which is open access for any users. |
| URL | http://signalink.org/ |
| Title | ViralLink |
| Description | ViralLink is a systems biology workflow which reconstructs and analyses networks representing the effect of viral infection on specific human cell types. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Provides an integrated pipeline to work with viral-host interactions on specific human cell types |
| URL | https://github.com/korcsmarosgroup/ViralLink |
| Title | earlham-sherlock/earlham-sherlock.github.io: First release of the official Sherlock platform |
| Description | First release. |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Sherlock is an open-source data platform to store, analyze and integrate bioinformatics data. Features include: - store all datasets in a redundant, organized cloud storage - convert all datasets to common, optimized file formats - execute analytical queries on top of data files - share datasets among different teams/projects - generate operational datasets for certain services or collaborators |
| URL | https://zenodo.org/record/4738516 |
| Title | korcsmarosgroup/iSNP: A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis |
| Description | A novel precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine the mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC) |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Impact | Provided an integrated pipeline to preform this systems medicine approach in a reproducible way. |
| URL | https://zenodo.org/record/6346651 |
| Description | Blog - 10 things you need to know about getting into machine learning |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | A blog for those interested in getting started in Machine Learning in bioinformatics |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/10-things-you-need-know-about-getting-machine-learning |
| Description | Blog - A PhD, is it worth it? Just ask our students |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | Blog answering questions and describing the first year of a PhD student and giving recommendations of what we wish we knew before we started. it was published on the Earlham Institutes website. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/phd-it-worth-it-just-ask-our-students |
| Description | How AI will help us to explore our microbiome |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Public engagement about how we can use AI to help us to explore our microbiome. This was short talk ~15 minutes |
| Year(s) Of Engagement Activity | 2019 |
| Description | Inside EI - Open Day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Open day for the general public and schools to visit a research institute and ask questions to researchers. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/open-day-2019 |