MICA: UK MEDical BIOinformatics partnership - aggregation, integration, visualisation and analysis of large, complex data (UK MED-BIO).
Lead Research Organisation:
Imperial College London
Department Name: School of Public Health
Abstract
This proposal brings together a group of leading multidisciplinary teams in medical, chemical, metabolic, statistical and computational sciences from across Imperial College London (ICL, lead institution) and its partners. These include the Institute of Cancer Research, the European Molecular Biology Laboratory-European Bioinformatics Institute, the Universities of Oxford, Swansea and Nottingham, and the MRC Clinical Sciences Centre and MRC Human Nutrition Research Centre, supported by strong partnerships and collaborative links with industry, the NHS and the National Institute for Health Research funded Biomedical Research Centres and Units. The proposal seeks support to build a DEDICATED INFRASTRUCTURE in data storage, aggregation, analysis and visualisation of diverse types of biomedical data. These come from standard clinical sources through to different types of information including from genetic analysis, and metabolic information, that help us to define patients or people studied in the general population using a holistic "systems medicine" framework. The GLOBAL AIM is to make major advances in understanding the causes and reasons for disease progression of common human diseases such as cancer, cardiovascular disease, respiratory disease and metabolic disorders such as type 2 diabetes and obesity. In this way we aim to create new disease diagnostics and prognostics aimed at the individual patient ("stratified medicine") through innovations in medical bioinformatics with powerful computing capability. The programme will create unprecedented capacity to i) DEVELOP powerful new approaches for computation and analysis of large-scale, complex, multi-source medical data; ii) INTEGRATE information linking multiple different types of biological information from analysis of blood and urine samples (e.g., metabolic, genomic, analysis of the microbial genome) to different diseases, disease progression and outcomes; hence to iii) help UNDERSTAND the causes and mechanisms of disease and improve individual disease classification for better patient treatments and safety; also to iv) TRANSFORM the training of the biomedical researchers of the future through creation of a seamless interdisciplinary environment spanning biomedicine, physical sciences, computing and engineering. In particular we will capitalise on computational expertise that has led to the development of a partnership in medical information infrastructure and service between universities and the pharmaceutical industry called eTRIKS, and related software platforms such as tranSMART, an "open source" solution for managing data and research knowledge in clinical studies. We also have world-leading expertise in metabolic "fingerprinting" and systems medicine approaches manifested in the MRC-NIHR National Phenome Centre located at ICL, and underpinned by excellence in genomics, computational sciences and advanced data modelling and visualisation. This project has a very broad collaboration with industrial sectors including major pharmaceutical companies, instrument vendors, IT and informatics companies. Our project covers the complete healthcare envelope of data generating activity and analysis from the level of basic measurement sciences through to the understanding of gene-environment interactions and disease mechanisms to the creation of knowledge systems for better clinical decision making based on detailed knowledge of individual patient biology. This application is strengthened by the decision of ICL to establish a major interdisciplinary centre for 'big data' at the new Imperial West campus, ensuring sustainability over the longer term. The project aims to deliver top class science, a robust informatics platform and in-depth scientific data and knowledge to contribute to the state of the art of UK and international medical research.
Technical Summary
UK MED-BIO brings together a multidisciplinary team in medical and computing science, statistical analysis, metabolic phenotyping and medical bioinformatics across Imperial College London (ICL, lead institution), Institute of Cancer Research, European Molecular Biology Laboratory-European Bioinformatics Institute, Universities of Oxford, Swansea and Nottingham, MRC Clinical Sciences Centre and MRC Human Nutrition Research - supported by strong industrial partnerships and collaborations. The aim is to bring together the necessary patient data, new omics technologies, computing and other resources, with dedicated infrastructure in data management, storage, integration, visualisation and analysis, to enable major advances in understanding the aetiopathogenesis of chronic human diseases. We have powerful world-leading expertise in metabolic phenotyping through the MRC-NIHR National Phenome Centre at ICL, and in innovative software infrastructure solutions through our leadership position in developing tranSMART and eTRIKS. We will provide unprecedented capacity to i) combine lifestyle/socio-demographic information, clinical data, and disease phenotypes from well characterised patient and population cohorts, with multi-omic information from analysis of linked biological samples; ii) develop powerful new approaches to integration/analysis of such large-scale, complex, multi-source medical data; hence iii) create new knowledge on disease aetiology, underlying biochemical pathways and mechanisms, leading to improved patient stratification, prevention and treatments; iv) transform the training/development of medical bioinformatics future leaders by providing a seamless interdisciplinary environment, bringing together researchers from biomedicine, physical sciences, computing and engineering. This application is strengthened by ICL's decision to establish a major interdisciplinary 'big data' centre at the Imperial West campus, ensuring sustainability over the long term.
Planned Impact
The UK MED-BIO project will provide important benefits in both the personalised and public healthcare arenas, associated medical research environments and the pharma/healthcare industry. Specific benefits include deeper understanding of gene-exposome interactions that underpin disease risks and mechanisms. This information can be used to inform future healthcare policy and help identify new potential therapeutic targets for a range of common diseases. Positive impacts include development of new monitoring and stratification models to augment clinical decision-making during the patient journey. Impacts can be summarised as:
1) Scientific and Clinical: The project has a clear focus on elucidating the aetiopathogenesis of chronic human disease, including cancer, cardio- metabolic and respiratory disease. By developing new systems medicine approaches linking multi-omics datasets (e.g., genomic/epigenomic, metagenomic, transcriptomic and metabolic) to disease phenotypes, progression and outcomes in patient and population cohorts, the project aims to make major scientific and clinical contributions to patient stratification and the development of new precision medicine approaches in real healthcare environments.
2) Methodological and Infrastructure: The computational methods developed for integrated analysis of multimodal data streams with large-scale data processing capacity will provide new tools in medical bioinformatics research and complex systems data and model visualisation. The further development and enhancement of platform technologies underlying the UK MED-BIO infrastructure, such as tranSMART and eTRIKS, in which ICL researchers have played a key developmental role, will enhance the capabilities of the medical bioinformatics community in general.
3) Knowledge: UK MED-BIO supports a new open science paradigm by dedicating specific resources to build a dissemination hub. We will work closely with EMBL-EBI to curate new large-scale research data for public access (e.g. from the MRC-NIHR National Phenome Centre) and to explore EMBL-EBI's public cloud dissemination mechanisms. Through our collaboration with content vendors, e.g. Thomson Reuters, the accuracy of knowledge in published medical databases will be validated.
4) Training: A key objective is to enhance the training of next generation medical informatics scientists by creation of a seamless interdisciplinary environment spanning biomedicine, physical sciences, computing and engineering. The training will be aligned with the ELIXIR-UK Node training activities. The new Imperial International Phenome Training Centre also offers a comprehensive multilevel training programme in omics modeling expressed through a series of courses in computational and systems medicine. We will explore the effective use of the dissemination hub to create a national informatics resource for biomedical research, coupled with focused training, for maximising dissemination and impacts.
5) Organisational: The continued major investments in biomedical research in multiple world class medical research facilities in London requires an advanced informatics infrastructure and networking mechanism across the distributed resources to form a virtual/scalable research environment. this can then be linked further to other national and international networks of medical bioinformatic activity.
1) Scientific and Clinical: The project has a clear focus on elucidating the aetiopathogenesis of chronic human disease, including cancer, cardio- metabolic and respiratory disease. By developing new systems medicine approaches linking multi-omics datasets (e.g., genomic/epigenomic, metagenomic, transcriptomic and metabolic) to disease phenotypes, progression and outcomes in patient and population cohorts, the project aims to make major scientific and clinical contributions to patient stratification and the development of new precision medicine approaches in real healthcare environments.
2) Methodological and Infrastructure: The computational methods developed for integrated analysis of multimodal data streams with large-scale data processing capacity will provide new tools in medical bioinformatics research and complex systems data and model visualisation. The further development and enhancement of platform technologies underlying the UK MED-BIO infrastructure, such as tranSMART and eTRIKS, in which ICL researchers have played a key developmental role, will enhance the capabilities of the medical bioinformatics community in general.
3) Knowledge: UK MED-BIO supports a new open science paradigm by dedicating specific resources to build a dissemination hub. We will work closely with EMBL-EBI to curate new large-scale research data for public access (e.g. from the MRC-NIHR National Phenome Centre) and to explore EMBL-EBI's public cloud dissemination mechanisms. Through our collaboration with content vendors, e.g. Thomson Reuters, the accuracy of knowledge in published medical databases will be validated.
4) Training: A key objective is to enhance the training of next generation medical informatics scientists by creation of a seamless interdisciplinary environment spanning biomedicine, physical sciences, computing and engineering. The training will be aligned with the ELIXIR-UK Node training activities. The new Imperial International Phenome Training Centre also offers a comprehensive multilevel training programme in omics modeling expressed through a series of courses in computational and systems medicine. We will explore the effective use of the dissemination hub to create a national informatics resource for biomedical research, coupled with focused training, for maximising dissemination and impacts.
5) Organisational: The continued major investments in biomedical research in multiple world class medical research facilities in London requires an advanced informatics infrastructure and networking mechanism across the distributed resources to form a virtual/scalable research environment. this can then be linked further to other national and international networks of medical bioinformatic activity.
Organisations
- Imperial College London (Lead Research Organisation)
- Northwestern University (Collaboration)
- Virginia Tech (Collaboration)
- Kaiser Permanente Washington Health Research Institute (Collaboration)
- UNIVERSITY OF READING (Collaboration)
- Charing Cross Hospital (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- QUEEN MARY UNIVERSITY OF LONDON (Collaboration)
- Thomson Reuters (Collaboration)
- St Mark's Hospital (Collaboration)
- UNIVERSITY OF WESTMINSTER (Collaboration)
- Imperial College Health Partners (Collaboration)
- Francis Crick Institute (Collaboration)
- HARVARD UNIVERSITY (Collaboration)
- Quadram Institute Bioscience (Collaboration)
- University College London (Collaboration)
- George Institute for Global Health (Collaboration)
- Erasmus MC (Collaboration)
- Brigham and Women's Hospital (Collaboration)
- The University of Texas at San Antonio (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- University of East Anglia (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- North West London Commissioning Hub (Collaboration)
- AstraZeneca (United Kingdom) (Collaboration, Project Partner)
- UNIVERSITY OF OXFORD (Collaboration)
- Farr Institute of Health Informatics Research (Collaboration)
- Imperial College Healthcare NHS Trust (Collaboration)
- University of Ioannina (Collaboration)
- Wake Forest University (Collaboration)
- National Cancer Institute (Collaboration)
- University of Massachusetts (Collaboration)
- SWANSEA UNIVERSITY (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- University of Leuven (Collaboration)
- European Commission (Collaboration)
- Erasmus University Rotterdam (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
- Bruker (United States) (Project Partner)
- Huawei Technologies (United Kingdom) (Project Partner)
- Waters Corporation (USA) (Project Partner)
- Thomson Reuters (United Kingdom) (Project Partner)
Publications
Herridge WP
(2020)
Bacteriophages of Klebsiella spp., their diversity and potential therapeutic uses.
in Journal of medical microbiology
Kraja AT
(2019)
Associations of Mitochondrial and Nuclear Mitochondrial Variants and Genes with Seven Metabolic Traits.
in American journal of human genetics
Tzoulaki I
(2018)
An Overview of Metabolic Phenotyping in Blood Pressure Research.
in Current hypertension reports
Toledano MB
(2018)
An international prospective cohort study of mobile phone users and health (COSMOS): Factors affecting validity of self-reported mobile phone use.
in International journal of hygiene and environmental health
Nalpas N
(2021)
An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome.
in Gut microbes
Asaria P
(2017)
Acute myocardial infarction hospital admissions and deaths in England: a national follow-back and follow-forward record-linkage study.
in The Lancet. Public health
Suzuki H
(2017)
Abnormal brain white matter microstructure is associated with both pre-hypertension and hypertension.
in PloS one
Letertre MPM
(2020)
A Two-Way Interaction between Methotrexate and the Gut Microbiota of Male Sprague-Dawley Rats.
in Journal of proteome research
Kuo C
(2017)
A Transcriptome-driven Analysis of Epithelial Brushings and Bronchial Biopsies to Define Asthma Phenotypes in U-BIOPRED
in American Journal of Respiratory and Critical Care Medicine
Kaakinen M
(2017)
A rare-variant test for high-dimensional data
in European Journal of Human Genetics
Sung YJ
(2018)
A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.
in American journal of human genetics
Stachulski AV
(2023)
A host-gut microbial amino acid co-metabolite, p-cresol glucuronide, promotes blood-brain barrier integrity in vivo.
in Tissue barriers
Dao MC
(2018)
A Data Integration Multi-Omics Approach to Study Calorie Restriction-Induced Changes in Insulin Sensitivity.
in Frontiers in physiology
Kaluarachchi M
(2018)
A comparison of human serum and plasma metabolites using untargeted 1H NMR spectroscopy and UPLC-MS.
in Metabolomics : Official journal of the Metabolomic Society
Boulieri A
(2020)
A Bayesian mixture modeling approach for public health surveillance.
in Biostatistics (Oxford, England)
| Description | Answering questions for parliamentary briefing document on the microbiome and human health |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| URL | https://researchbriefings.parliament.uk/ResearchBriefing/Summary/POST-PN-0574 |
| Description | E-infrastructure leadership council |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | Professor Robert Glen provided input from his experience of high performance computers and e-infrastructure in a report on entreprenerial academic policies as part of the e-infrastructure leadership council chaired by the Minister of Science and Technology. Professor Glen's contribution has had a big influence on high performance computers, networking and relevant skills training for UK leaderships and entrepreneurial advancements in these areas. |
| URL | https://www.gov.uk/government/groups/e-infrastructure-leadership-council |
| Description | MRC Discussion Workshop on Creating a National Health & Medical Bioinformatics - participation/contribution |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | MRC Framework for the Development, Design and Analysis of Stratified Medicine Research |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Invited to provide comments on draft - 'MRC Framework for the Development, Design and Analysis of Stratified Medicine Research' Dec 2015. |
| Description | MRC Strategic Meeting on "Challenges in Health and Biomedical Informatics in the UK"- participation/contribution |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Member of Office of Strategic Coordination for Health Research (OSCHR) sub Board on Health Informatics |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Panel member for BBSRC Tools and Resources Development Fund |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | Policy documents on Stratified Medicine Infrastructure and the second Farr Institute |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | Role as Imperial College London AHSC Director of Information Governance |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | In progress: positive impact on functions of HSCIC Data Governance Framework procedures to improve access for academic researchers to clinical data; improved streamlining of data processing via active feedback to senior HSCIC management. |
| Description | deNBI - the German National Network for Bioinformatics Infrastructures - evaluation panel member for round two |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | participation in working group - BBSRC Careers and development for non-faculty staff; also production of recommendations to BBSRC Council |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | ATHLETE: Advancing Tools for Human early Lifecourse Exposome research And Translation |
| Amount | £7,000,000 (GBP) |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 01/2020 |
| End | 12/2024 |
| Description | Alzheimer's Research UK Pilot Project |
| Amount | £46,518 (GBP) |
| Funding ID | ARUK-PPG2016B-6 |
| Organisation | Alzheimer's Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 08/2018 |
| Description | BRC/ITMAT Core Research Informatics Infrastructure |
| Amount | £97,395 (GBP) |
| Organisation | National Institute for Health Research |
| Department | NIHR Imperial Biomedical Research Centre |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2015 |
| End | 09/2017 |
| Description | CO-CONNECT: COVID - Curated and Open aNalysis aNd rEsearCh plaTform |
| Amount | £4,091,229 (GBP) |
| Funding ID | MR/V03488X/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2020 |
| End | 04/2022 |
| Description | Characterise and quantify the biological, social and environmental drivers of medium-term health outcomes following infection with SARS-CoV-2: national administrative data linkage to the REACT national community prevalence programme |
| Amount | £19,944,305 (GBP) |
| Funding ID | HDRUK2020.143 |
| Organisation | Health Data Research UK |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 06/2021 |
| Description | Creating a national platform for molecular studies of multiple conditions: HDRUK multiomics consortium |
| Amount | £1,088,606 (GBP) |
| Funding ID | CFC0107 |
| Organisation | Health Data Research UK |
| Sector | Private |
| Country | United Kingdom |
| Start | 04/2020 |
| End | 03/2022 |
| Description | Development of new immune-based treatments for Glioblastoma Multiforme (GBM) |
| Amount | £137,930 (GBP) |
| Organisation | HeadCase Cancer Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 03/2020 |
| Description | Diabetes UK |
| Amount | £500,000 (GBP) |
| Organisation | Diabetes UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 12/2023 |
| Description | Dietary methylamines as systems-level regulators of neuroinflammation |
| Amount | £5,000 (GBP) |
| Organisation | Alzheimer's Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 02/2021 |
| Description | Discover-Now Digital Innovation Hub at Imperial College London |
| Amount | £306,572 (GBP) |
| Organisation | United Kingdom Research and Innovation |
| Department | Industrial Strategic Challenge Fund |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2019 |
| End | 09/2023 |
| Description | EMBRACE: Engineering, Physical, Natural Sciences and Medicine: Bridging Research in Antimicrobial resistance: Collaboration and Exchange |
| Amount | £10,000 (GBP) |
| Organisation | Embrace UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 10/2016 |
| End | 07/2017 |
| Description | GutsUK Development Grant |
| Amount | £49,797 (GBP) |
| Organisation | GUTS UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2019 |
| End | 01/2022 |
| Description | HDR UK Respiratory Digital Innovation Hub |
| Amount | £1,016,410 (GBP) |
| Organisation | Health Data Research UK |
| Sector | Private |
| Country | United Kingdom |
| Start | 10/2019 |
| End | 08/2022 |
| Description | Health Data Research UK (HDR-UK) London - capital award |
| Amount | £772,637 (GBP) |
| Organisation | Health Data Research UK |
| Sector | Private |
| Country | United Kingdom |
| Start | 10/2018 |
| End | 03/2019 |
| Description | Health Data Research UK (HDR-UK) London - partner in University consortium |
| Amount | £6,910,861 (GBP) |
| Organisation | Health Data Research UK |
| Sector | Private |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 03/2023 |
| Description | Health Data Research UK (HDR-UK) substantive site award to Imperial College London as part of pan-London consortium |
| Amount | £6,900,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 02/2023 |
| Description | MRC-PHE Centre for Environment and Health, PPE/PPI Small Grants Scheme |
| Amount | £230 (GBP) |
| Organisation | Imperial College London |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 02/2018 |
| Description | NIHR Imperial Biomedical Research Centre (BRC) Institute for Translational Medicine and Therapeutics (ITMAT) Developing Capacity |
| Amount | £24,823 (GBP) |
| Organisation | Imperial College London |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2017 |
| End | 09/2018 |
| Description | Newton International Fellowship submission organised by Antonio J Berlanga-Taylor |
| Amount | £99,000 (GBP) |
| Organisation | Newton Fund |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 03/2022 |
| Description | PhenoMeNal H2020 |
| Amount | € 8,810,922 (EUR) |
| Funding ID | H2020 -EINFRA-1-2014 |
| Organisation | European Commission |
| Department | Horizon 2020 |
| Sector | Public |
| Country | European Union (EU) |
| Start | 09/2015 |
| End | 08/2018 |
| Description | UKRI Innovation/Rutherford Fund Fellowships (2 awarded) |
| Amount | £652,556 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 02/2021 |
| Title | System for sharing Consistent versioned public reference databases across UK Med-Bio and other Imperial HPC compute resources |
| Description | Many types of analysis require access to reference databases and curated datasets which frequently are large, requiring considerable download times and disk utilisation, and typically require indexing using a method appropriate for the desired analysis method. The indexing process itself will also frequently take over 12 hours for a mammalian genome. Frequently, the whole process can take 2-3 days, and is generally carried out by every researcher needing to carry out such analysis requiring reference datasets. To help reduce the overhead associated with obtaining and preparing reference datasets, we have established a centralised collection of reference datasets which are available to all bio-medical researchers across the college. These are accessible on UK Med-Bio, HPC and BDSG systems, and remotely via NFS and HTTP. Databases are automatically updated weekly where appropriate. The following datasets are currently available: Illumina iGenomes (reference database indexed for BWA, bowtie and bowtie2 searches; fasta format chromosome files; annotations as e.g. GTF files). A full list of the datasets available through iGenomes is available at http://support.illumina.com/sequencing/sequencing_software/igenome.html. Of these, we currently hold: Human GRCh37 (Ensembl annotation) Human GRCh38 (NCBI annotation) Mouse GRCm38 (Ensembl annotation) C. elegans WS220 (Ensembl annotation) E. coli K12 DH10B (Ensembl annotation) Human genome resources: Additional reference datasets for related to the Human genome 1000 genomes variant calls GATK resource bundle (including dbSNP, 1000 genomes, hapmap, gold standard indels preformatted for use with the Genome Analysis ToolKit (GATK) Kegg pathway databases - available to registered users only Blast databases: NCBI NR NCBI NT RefSeq Genomic Refseq RNA Refseq protein Uniprot Swissprot Uniprot Trembl |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | reduced replication of mainteinance effort |
| Title | 504 sequences used in phylogenetic analysis of MLST data |
| Description | Alignment file used to generate phylogenetic tree showing relationships among K. oxytoca complex species and different MLST sequence types. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/504_sequences_used_in_phylogenetic_analysis_of_MLST_data/14367... |
| Title | 504 sequences used in phylogenetic analysis of MLST data |
| Description | Alignment file used to generate phylogenetic tree showing relationships among K. oxytoca complex species and different MLST sequence types. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/504_sequences_used_in_phylogenetic_analysis_of_MLST_data/14367... |
| Title | Amino acid sequences for each protein encoded within the klebomycin biosynthetic gene cluster |
| Description | Twelve fasta files are provided - one for each protein sequence encoded within the kleboxymycin BGC. Each fasta file contains amino acid sequences for 88 genomes included in the study. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Associated with preprint - https://doi.org/10.1101/2020.07.24.215400 |
| URL | https://figshare.com/articles/Amino_acid_sequences_for_each_protein_encoded_within_the_klebomycin_bi... |
| Title | Batch effect exerts a bigger influence on experimental animal urinary metabolome and gut microbiota than uremia |
| Description | Looking at effects of medically induced chronic kidney disease in rats on microbiome and metabolome. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Publication - doi:10.1186/s40168-019-0738-y |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525754/ |
| Title | Cranberry study |
| Description | Shotgun metagenomic data generated for a feeding study where participants were fed cranberry extracts to look at effects on cognitive function and health. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Paper in preparation. Continuation of collaboration with colleagues at the University of East Anglia. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA681337 |
| Title | Determination of effects of propionate on gene expression in human cerebromicrovascular endothelial cell line hCMEC/D3 |
| Description | Data associated with paper published in 2018. Transcriptome - effect of propionate treatment on a model of the human blood-brain barrier. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Publication - https://pubmed.ncbi.nlm.nih.gov/29562936/ |
| URL | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5686/ |
| Title | Effect of Down Syndrome genotype on mouse microbiome |
| Description | Effect of Down Syndrome genotype on mouse microbiome. Metagenomes generated from mouse faecal samples. Associated with ERANET(MRC/ANR/BMBF/MINECO): The Gut Microbiome in Neuroinflammation and Neurodevelopmental Disorders (µNeuroInf). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Preprint publication available - https://doi.org/10.1101/2020.11.17.386938 |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA473429 |
| Title | Effect of Fmr1 knockout on mouse microbiome |
| Description | Faecal metagenomes generated from Fmr1 knockout and wild-type mice. Associated with ERANET(MRC/ANR/BMBF/MINECO): The Gut Microbiome in Neuroinflammation and Neurodevelopmental Disorders (µNeuroInf). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Publications in preparation. |
| URL | http://www.ncbi.nlm.nih.gov/bioproject/473224 |
| Title | Effect of GOS on the faecal microbiota in vitro |
| Description | 16S rRNA gene sequence data generated for in vitro fermentation vessels in presence and absence of prebiotic. 25 samples including negative control. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Useful information on influence of conditions in in vitro fermentation systems in presence and absence of prebiotic. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA472974 |
| Title | Effect of GOS on the in vitro faecal microbiota (6 metagenomes) |
| Description | Metagenomes derived from in vitro fermentation vessels after treatment with prebiotic. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Valuable information on species of bacteria likely to be involved in use of prebiotics in the human gut. |
| URL | http://www.ncbi.nlm.nih.gov/bioproject/472963 |
| Title | Effect of bariatric surgery on the faecal metagenome |
| Description | Clinical study looking at the effect of bariatric surgery on the faecal metagenome. Study carried out by Dr Nicholas Penney as part of clinical PhD. I processed and analysed the samples. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Publications (including clinical PhD thesis) in preparation. BioProject ID PRJNA473348. |
| URL | http://www.ncbi.nlm.nih.gov/bioproject/473348 |
| Title | Effect of enhanced environment on mouse microbiome |
| Description | Faecal metagenomes generated from control mice and mice kept in enriched environment. Associated with ERANET(MRC/ANR/BMBF/MINECO): The Gut Microbiome in Neuroinflammation and Neurodevelopmental Disorders (µNeuroInf). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Publications in preparation. |
| URL | http://www.ncbi.nlm.nih.gov/bioproject/473208 |
| Title | Effect of prebiotic feeding on rat model of kidney disease |
| Description | Shotgun metagenomic data derived from sham and nephrectomized rats fed prebiotics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Paper in preparation. Continued collaboration with the William Harvey Institute. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682232 |
| Title | Effect of subinhibitory concentration of ampicillin on human gut microbiota in vitro |
| Description | In vitro fermentation systems used to examine effect of sub-inhibitory concentration of ampicillin on human faecal microbiota. Metagenomes generated from samples taken before and during antibiotic treatment. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Publication in preparation. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA473225 |
| Title | Effects of gut-derived trimethylamines on an in vitro model of the blood-brain barrier |
| Description | Transcriptomic profiling of effects of TMA and TMAO on in vitro model of the human blood-brain barrier. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Preprint - https://doi.org/10.1101/2021.01.28.428430 |
| URL | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6662/ |
| Title | FLORINASH WGS human gut microbiome metagenomics dataset - fastq |
| Description | Data sets arising from the EU FLORINASH project. WGS human gut microbiome datasets. Raw metagenomic sequence data (with human-associated reads removed) have been deposited under study accession number PRJEB14215 (secondary accession number ERP015847). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Part of the dataset for a paper in press - Hoyles et al (2108) Molecular Phenomics and Metagenomics of Hepatic Steatosis in Non Diabetic Obese Women. Nature Medicine |
| URL | https://www.ebi.ac.uk/ena |
| Title | FLORINASH mouse hepatic steatosis study gut microbiome16s rRNA reads |
| Description | In this FLORINASH study faecal microbiota from control and steatotic patients (n = 3 per group) was transferred to C57BL6 mice (n=8 per donor) and followed for 15 days before evaluating hepatic steatosis. Data are deposited in European Nucleotide Archive SRA under study accession number PRJEB24891. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | This dataset is associated with a manuscript in press - Hoyles et al (2018) Molecular Phenomics and Metagenomics of Hepatic Steatosis in Non Diabetic Obese Women. Nature Medicine. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB24891 |
| Title | Fasta file of individual housekeeping genes for selected species |
| Description | Individual housekeeping genes (gapA, infB, mdh, pgi, phoE, rpoB, tonB) used in the K. oxytoca complex MLST scheme. Species sequences provided for include: K. huaxiensis, K. indica, K. spallanzanii and Raoultella spp. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Fasta_file_of_individual_housekeeping_genes_for_selected_speci... |
| Title | Fasta file of individual housekeeping genes for selected species |
| Description | Individual housekeeping genes (gapA, infB, mdh, pgi, phoE, rpoB, tonB) used in the K. oxytoca complex MLST scheme. Species sequences provided for include: K. huaxiensis, K. indica, K. spallanzanii and Raoultella spp. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Fasta_file_of_individual_housekeeping_genes_for_selected_speci... |
| Title | Figure_1.newick |
| Description | Newick file for Figure 1 in article. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Supplementary data for https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431098/ |
| URL | https://figshare.com/articles/Figure_1_newick/11635953/1 |
| Title | Kleb_phage_review_192_genomes.fasta |
| Description | Fasta file of genome sequences used to generate Figure 1. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Supplementary sequence data for https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431098/ |
| URL | https://figshare.com/articles/Kleb_phage_review_192_genomes_fasta/11635965/1 |
| Title | Klebsiella michiganensis encoding GES-5 |
| Description | WGS data from clinical isolates |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Publication - https://doi.org/10.1101/2020.07.24.215400 |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562720 |
| Title | MAGs.zip |
| Description | Metagenome-assembled genomes generated in study from data of Ward et al. (2016).Ward DV, Scholz M, Zolfo M, Taft DH, Schibler KR, Tett A, et al. Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. Cell Rep. 2016 Mar 29;14(12):2912-24. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Supplementary sequence data associated with https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371107/ |
| URL | https://figshare.com/articles/MAGs_zip/11923005/1 |
| Title | MLST similarity matrix |
| Description | Similarity matrix generated from a multiple-sequence alignment of the concatenated housekeeping-gene sequences of the 354 recognized sequence types of the K. oxytoca MLST scheme (as of 19 March 2021) against the corresponding regions of publicly available K. oxytoca complex and Raoultella spp. genomes (n=150). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/MLST_similarity_matrix/14368046 |
| Title | MLST similarity matrix |
| Description | Similarity matrix generated from a multiple-sequence alignment of the concatenated housekeeping-gene sequences of the 354 recognized sequence types of the K. oxytoca MLST scheme (as of 19 March 2021) against the corresponding regions of publicly available K. oxytoca complex and Raoultella spp. genomes (n=150). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/MLST_similarity_matrix/14368046/1 |
| Title | MSA of 169 blaOXY protein sequences |
| Description | Protein sequences (multiple-sequence alignment) of 169 blaOXY sequences associated with the phylogenetic tree presented in Supplementary Material. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/MSA_of_169_blaOXY_protein_sequences/14368214 |
| Title | MSA of 169 blaOXY protein sequences |
| Description | Protein sequences (multiple-sequence alignment) of 169 blaOXY sequences associated with the phylogenetic tree presented in Supplementary Material. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/MSA_of_169_blaOXY_protein_sequences/14368214/1 |
| Title | Microbiome of ME-CFS - UK cohort |
| Description | Faecal microbiome of ME-CFS patients and controls. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Detailed analysis of microbiome of ME-CFS patients and controls. Generated in collaboration with the Quadram Institute. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA478719 |
| Title | Microbiota of adult and aged mice |
| Description | Characterizing the difference in faecal microbiota of adult and aged mice, then looking at effects of FMT on microbiota and cognitive function. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Publication - doi:10.1186/s40168-020-00914-w |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA524024/ |
| Title | Prokka-annotated data of assemblies for BioProject PRJEB30858 |
| Description | BioProject |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Associated with preprint - https://doi.org/10.1101/2020.07.24.215400 |
| URL | https://figshare.com/articles/Prokka-annotated_data_of_assemblies_for_BioProject_PRJEB30858/11923014... |
| Title | RNA-seq of mouse brain tissue to investigate the integrity of the blood brain barrier to trimethylamine N-oxide |
| Description | Transcriptomic profiling of effects of TMAO on mouse brain after systemic exposure to the metabolite. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Preprint - https://doi.org/10.1101/2021.01.28.428430 |
| URL | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9869 |
| Title | Recovery of lactose-positive Enterobacteriaceae from preterm neonates |
| Description | Whole-genome sequences generated from bacteria isolated from faecal microbiota of preterm infants. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Preprint to be uploaded to bioRxiv once complete. |
| Title | Supplementary Material |
| Description | Supplementary Material detailing phenotypic and genomic characterization of the K. michiganensis clinical isolates that led to this study. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Supplementary_Material/14368652 |
| Title | Supplementary Material |
| Description | Supplementary Material detailing phenotypic and genomic characterization of the K. michiganensis clinical isolates that led to this study. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Supplementary_Material/14368652/1 |
| Title | Supplementary Material |
| Description | Supplementary material (Tables and Figures) for Chen et al. - Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Supplementary material associated with https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371107/ |
| URL | https://figshare.com/articles/Supplementary_Material/11925324/2 |
| Title | Supplementary Tables |
| Description | Supplementary Tables associated with the main paper. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Supplementary_Tables/14368562 |
| Title | Supplementary Tables |
| Description | Supplementary Tables associated with the main paper. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Supplementary_Tables/14368562/1 |
| Title | Supplementary_Figure_1.newick |
| Description | Newick file used to generate Supplementary Figure 1. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Supplementary figure from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431098/ |
| URL | https://figshare.com/articles/Supplementary_Figure_1_newick/11635971/1 |
| Title | Supplementary_Figure_1.pdf |
| Description | Supplementary Figure 1. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Supplementary figure for https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431098/ |
| URL | https://figshare.com/articles/Supplementary_Figure_1_pdf/11635962/1 |
| Title | Supplementary_Figure_1_genome_table_file.lst |
| Description | List of genomes used to create Figure 1. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Supplementary data for https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431098/ |
| URL | https://figshare.com/articles/Supplementary_Figure_1_genome_table_file_lst/11635950/1 |
| Title | Supplementary_Material.xlsx |
| Description | Supplementary Tables for processed transcriptomic data described in Stachulski et al. (2022). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Supplementary_Material_xlsx/18166706/1 |
| Title | Supplementary_Material.xlsx |
| Description | Supplementary Tables for processed transcriptomic data described in Stachulski et al. (2022). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Supplementary_Material_xlsx/18166706 |
| Title | Supplementary_Material.xlsx |
| Description | Supplementary Tables for processed transcriptomic data described in Stachulski et al. (2022). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/Supplementary_Material_xlsx/18166706/2 |
| Title | Supplementary_Tables_080121.xlsx |
| Description | Supplementary Material associated with preprint by Hoyles et al. XXXXX |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Supplementary material associated with https://doi.org/10.1101/2021.01.28.428430 |
| URL | https://figshare.com/articles/dataset/Supplementary_Tables_080121_xlsx/13549334/1 |
| Title | The long-term impact of distal feeding on patients with rectal cancer and formation of ileostomy |
| Description | Shotgun metagenomic data derived from faecal samples of patients undergoing distal feeding. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Paper in preparation. Established collaboration with group of Professor George Hanna at Imperial College London. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJEB38258 |
| Title | Transcription profiling by array of liver from patients with varying stages of non-alcoholic fatty liver disease |
| Description | Transcriptomic data associated with publication looking at the association between the microbiome and non-alcoholic fatty liver disease. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Nature Medicine paper. Funding from Diabetes UK and GutsUK. |
| URL | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4856/ |
| Title | consensus.zip |
| Description | Consensus sequence and associated files for Klebsiellla genomes encoding the kleboxymycin biosynthetic gene cluster. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Included in preprint - https://doi.org/10.1101/2020.07.24.215400 |
| URL | https://figshare.com/articles/consensus_zip/12357848/1 |
| Description | A systems biology approach to understanding cerebrovascular damage in diabetic kidney disease |
| Organisation | Queen Mary University of London |
| Department | William Harvey Research Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise on gut microbiota and its metabolites. Expertise in relation to neuroinflammation. Bioinformatics support. |
| Collaborator Contribution | Animal facilities. Expertise in relation to diabetic kidney disease. |
| Impact | Multi-disciplinary: computational biology, clinical studies, in vitro studies, neuroscience, immunology, microbiome, cognitive function, metabolomics Preparation of funding applications and manuscripts in progress |
| Start Year | 2017 |
| Description | Airwave collaboration with CIPHER and SAIL databank |
| Organisation | Swansea University |
| Department | Centre for Improvement in Population Health through E-records Research (CIPHER) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Airwave study cohort participant data and database and expertise in secure database management |
| Collaborator Contribution | Secure data linkage and data hosting in SAIL databank and expertise in processing and storage of electronic health data records |
| Impact | ongoing collaboration |
| Start Year | 2018 |
| Description | Airwave collaboration with DPUK - Dementia Platforms UK |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collection and provision of Airwave study data. Airwave data collected by the study team is being uploaded into the DPUK data portal so that it is available to other researchers. Collaboration with Prof Gallacher, PI of DPUK on pilot use of data including CSR pilot, collaborative grant applications and publications. |
| Collaborator Contribution | DPUK portal coordination and data access procedures |
| Impact | ongoing collaboration |
| Start Year | 2018 |
| Description | Airwave collaboration with DPUK and SAIL |
| Organisation | Swansea University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Provision of Airwave study data and expertise in database management and health data linkage |
| Collaborator Contribution | SAIL Databank is being used as a means of secure data processing and storage for study data |
| Impact | ongoing collaboration |
| Start Year | 2018 |
| Description | Bacteriophages as alternatives to antibiotics |
| Organisation | Charing Cross Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts |
| Collaborator Contribution | Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science |
| Impact | Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters) |
| Start Year | 2015 |
| Description | Bacteriophages as alternatives to antibiotics |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts |
| Collaborator Contribution | Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science |
| Impact | Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters) |
| Start Year | 2015 |
| Description | Bacteriophages as alternatives to antibiotics |
| Organisation | University of Reading |
| Department | Department of Food and Nutritional Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts |
| Collaborator Contribution | Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science |
| Impact | Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters) |
| Start Year | 2015 |
| Description | Bacteriophages as alternatives to antibiotics |
| Organisation | University of Westminster |
| Department | Biomedical Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | supervision of PhD students registered at the University of Westminster; expertise in phage biology and bioinformatics; assisting PhD students in preparing funding applications and manuscripts |
| Collaborator Contribution | Reading: co-supervision of PhD student, expertise in in vitro microbiology, lab facilities Quadram: co-supervision of PhD student, expertise in molecular biology Westminster: PhD student, expertise in phage biology and molecular biology; successful application for research funding to Microbiology Society Charing Cross: PhD student, expertise in antimicrobial resistance, microbiology and phage biology; successful application for research funding to Institute of Biomedical Science |
| Impact | Multi-disciplinary: bioinformatics, genome biology, basic laboratory science, microbiology, phage biology, molecular biology, microbial ecology Both PhD students have secured funding from societies to further their research posts tudents have presented work at Bacteriophage in Medicine, Food & Biotechnology meeting (posters) |
| Start Year | 2015 |
| Description | CFS/ME and the microbiome |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics (16S rRNA gene sequence analysis, metagenomics, development of virome pipeline); expertise in gut microbiome and virome, particularly in relation to isolation and characterization of phages; co-supervision of two PhD students |
| Collaborator Contribution | UEA: expertise in virology, immunology and pathology, two PhD students QUADRAM: expertise in gut microbiome, immunology, animal facilities, two PhD students co-supervised with UEA |
| Impact | Multi-disciplinary: computational biology, basic laboratory science, immunology, microbiology, biochemistry Invited review submitted to Alimentary Pharmacology and Therapeutics (see publications) Virome pipeline being built by associated student for addition to existing microbiome pipeline (SCAMP). |
| Start Year | 2016 |
| Description | CFS/ME and the microbiome |
| Organisation | University of East Anglia |
| Department | Norwich Medical School |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics (16S rRNA gene sequence analysis, metagenomics, development of virome pipeline); expertise in gut microbiome and virome, particularly in relation to isolation and characterization of phages; co-supervision of two PhD students |
| Collaborator Contribution | UEA: expertise in virology, immunology and pathology, two PhD students QUADRAM: expertise in gut microbiome, immunology, animal facilities, two PhD students co-supervised with UEA |
| Impact | Multi-disciplinary: computational biology, basic laboratory science, immunology, microbiology, biochemistry Invited review submitted to Alimentary Pharmacology and Therapeutics (see publications) Virome pipeline being built by associated student for addition to existing microbiome pipeline (SCAMP). |
| Start Year | 2016 |
| Description | CHARGE Consortium - collaboration - Cohorts for Heart and Aging Research in Genomic Epidemiology |
| Organisation | Erasmus MC |
| Country | Netherlands |
| Sector | Hospitals |
| PI Contribution | Contributing cohort data and epidemiological expertise, membership of steering committee and participated in scientific meetings, as part of joint collaboration and pooling of data for analysis. |
| Collaborator Contribution | Consortium facilitates genome wide association meta-analysis and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies and brings knowledge and skills in neuroscience, dementias and age-related diseases |
| Impact | continuing collaboration and planned joint publications |
| Start Year | 2017 |
| Description | CHARGE Consortium - collaboration - Cohorts for Heart and Aging Research in Genomic Epidemiology |
| Organisation | Kaiser Permanente Washington Health Research Institute |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | Contributing cohort data and epidemiological expertise, membership of steering committee and participated in scientific meetings, as part of joint collaboration and pooling of data for analysis. |
| Collaborator Contribution | Consortium facilitates genome wide association meta-analysis and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies and brings knowledge and skills in neuroscience, dementias and age-related diseases |
| Impact | continuing collaboration and planned joint publications |
| Start Year | 2017 |
| Description | CHARGE Consortium - collaboration - Cohorts for Heart and Aging Research in Genomic Epidemiology |
| Organisation | National Institutes of Health (NIH) |
| Department | National Heart, Lung, and Blood Institute (NHLBI) |
| Country | United States |
| Sector | Public |
| PI Contribution | Contributing cohort data and epidemiological expertise, membership of steering committee and participated in scientific meetings, as part of joint collaboration and pooling of data for analysis. |
| Collaborator Contribution | Consortium facilitates genome wide association meta-analysis and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies and brings knowledge and skills in neuroscience, dementias and age-related diseases |
| Impact | continuing collaboration and planned joint publications |
| Start Year | 2017 |
| Description | CHARGE Consortium - collaboration - Cohorts for Heart and Aging Research in Genomic Epidemiology |
| Organisation | National Institutes of Health (NIH) |
| Department | National Institute on Aging |
| Country | United States |
| Sector | Public |
| PI Contribution | Contributing cohort data and epidemiological expertise, membership of steering committee and participated in scientific meetings, as part of joint collaboration and pooling of data for analysis. |
| Collaborator Contribution | Consortium facilitates genome wide association meta-analysis and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies and brings knowledge and skills in neuroscience, dementias and age-related diseases |
| Impact | continuing collaboration and planned joint publications |
| Start Year | 2017 |
| Description | CHARGE Consortium - collaboration - Cohorts for Heart and Aging Research in Genomic Epidemiology |
| Organisation | University of Massachusetts |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Contributing cohort data and epidemiological expertise, membership of steering committee and participated in scientific meetings, as part of joint collaboration and pooling of data for analysis. |
| Collaborator Contribution | Consortium facilitates genome wide association meta-analysis and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies and brings knowledge and skills in neuroscience, dementias and age-related diseases |
| Impact | continuing collaboration and planned joint publications |
| Start Year | 2017 |
| Description | Collaboration with Farr and Crick Institute |
| Organisation | Farr Institute of Health Informatics Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration with Farr and Crick Institute |
| Collaborator Contribution | - |
| Impact | - |
| Start Year | 2016 |
| Description | Collaboration with Farr and Crick Institute |
| Organisation | Francis Crick Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration with Farr and Crick Institute |
| Collaborator Contribution | - |
| Impact | - |
| Start Year | 2016 |
| Description | Collaboration with University of Cambridge - High Performance Computing |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Professor Robert Glen is collaborating with University of Cambridge on a few calculation projects. |
| Collaborator Contribution | Use of their High Performance Computers |
| Impact | No outputs or outcomes to date |
| Start Year | 2015 |
| Description | Coriobacteriia of the human gut microbiota |
| Organisation | University of Reading |
| Department | School of Chemistry, Food and Pharmacy |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics, specific expertise in coriobacteria |
| Collaborator Contribution | DNA for sequencing, anaerobic microbiology, phenotyping |
| Impact | Manuscripts in preparation. |
| Start Year | 2016 |
| Description | DDN storage user group |
| Organisation | Farr Institute of Health Informatics Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Collaborator Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Impact | disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored. |
| Start Year | 2016 |
| Description | DDN storage user group |
| Organisation | Francis Crick Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Collaborator Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Impact | disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored. |
| Start Year | 2016 |
| Description | DDN storage user group |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Collaborator Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Impact | disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored. |
| Start Year | 2016 |
| Description | DDN storage user group |
| Organisation | University College London |
| Department | UCL Cancer Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Collaborator Contribution | Regular meetings sharing experiences and technical information regarding our use of DDN large scale high performance compute stoage systems for bio-medical data. Sharing methodologies and solutions for storage and use of bio-medical metadata to improve workflow fuctionality and assist with tracking standards-compliant metadata. |
| Impact | disciplines include bioinformatics, IT support and computer science. no specific outputs as yet. Ongoing sharing of information and expertise likely to speed up adoption of new technologies including use of iRODs for metadata-specific management of large volume bio-medical workflows. The possibl mechanisms for data sharing across different group's co-located systems (e.g. in JISC data centre Slough) are being explored. |
| Start Year | 2016 |
| Description | Development and Application of Novel Analytical Methods for Metabolite Structure Elucidation |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave cohort. |
| Collaborator Contribution | Optimisation of spectral data processing methods; metabolite identification; integration of complementary spectral data |
| Impact | No output yet. Multi-disciplinary: Analytical chemistry; Chemometrics / multivariate statistical analysis. |
| Start Year | 2016 |
| Description | Discover-NOW Health Data Research Hub |
| Organisation | Imperial College Health Partners |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Expertise in clinical epidemiology of common multifactorial diseases and assessment of environmental exposures and access to Small Area Health Statistics Unit health and environmental datasets. |
| Collaborator Contribution | Project and data hub coordination and liaison with healthcare providers and services. |
| Impact | ongoing collaboration |
| Start Year | 2020 |
| Description | Discover-NOW Health Data Research Hub |
| Organisation | Imperial College Healthcare NHS Trust |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | Expertise in clinical epidemiology of common multifactorial diseases and assessment of environmental exposures and access to Small Area Health Statistics Unit health and environmental datasets. |
| Collaborator Contribution | Project and data hub coordination and liaison with healthcare providers and services. |
| Impact | ongoing collaboration |
| Start Year | 2020 |
| Description | Discover-NOW Health Data Research Hub |
| Organisation | North West London Commissioning Hub |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Expertise in clinical epidemiology of common multifactorial diseases and assessment of environmental exposures and access to Small Area Health Statistics Unit health and environmental datasets. |
| Collaborator Contribution | Project and data hub coordination and liaison with healthcare providers and services. |
| Impact | ongoing collaboration |
| Start Year | 2020 |
| Description | EMBRACE pump-priming |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics (metagenomics); expertise in gut microbiome and in vitro experiments; preparation of successful funding application |
| Collaborator Contribution | Imperial (other depatments) mathematical modelling; antibiotic resistance; bioinformatics; metabolomics molecular biology; preparation of successful funding application READING: expertise in gut microbiome and in vitro experiments, access to in vitro fermentation equipment |
| Impact | Multi-disciplinary: computational biology, basic laboratory science, mathematical modeling, microbiology, molecular biology Successful application to EMBRACE pump-priming scheme (see further funding) |
| Start Year | 2016 |
| Description | EMBRACE pump-priming |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics (metagenomics); expertise in gut microbiome and in vitro experiments; preparation of successful funding application |
| Collaborator Contribution | Imperial (other depatments) mathematical modelling; antibiotic resistance; bioinformatics; metabolomics molecular biology; preparation of successful funding application READING: expertise in gut microbiome and in vitro experiments, access to in vitro fermentation equipment |
| Impact | Multi-disciplinary: computational biology, basic laboratory science, mathematical modeling, microbiology, molecular biology Successful application to EMBRACE pump-priming scheme (see further funding) |
| Start Year | 2016 |
| Description | EMBRACE pump-priming |
| Organisation | University of Reading |
| Department | Department of Meteorology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics (metagenomics); expertise in gut microbiome and in vitro experiments; preparation of successful funding application |
| Collaborator Contribution | Imperial (other depatments) mathematical modelling; antibiotic resistance; bioinformatics; metabolomics molecular biology; preparation of successful funding application READING: expertise in gut microbiome and in vitro experiments, access to in vitro fermentation equipment |
| Impact | Multi-disciplinary: computational biology, basic laboratory science, mathematical modeling, microbiology, molecular biology Successful application to EMBRACE pump-priming scheme (see further funding) |
| Start Year | 2016 |
| Description | Establishing a link between the gut-brain axis and Alzheimer's disease |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Computational biology Expertise in relation to gut microbiome and gut-derived microbial metabolites Expertise in computational chemistry and brain chemistry Preparation of manuscripts and funding applications |
| Collaborator Contribution | (QUODRAM) expertise in immunology and gut microbiome, animal facilities; preparation of manuscripts and funding applications (QMUL) expertise in neuroscience, inflammation, in vitro work; preparation of manuscripts and funding applications |
| Impact | Multi-disciplinary: in vitro cell biology, transcriptomics, bioinformatics, animal experiments Successful funding application to Alzheimer's Research UK Abstract accepted for Alzheimer's Research UK conference 2017 Two abstracts accepted for Alzheimer's Research UK conference 2018 Poster presentation at Linking Alzheimer's Disease with Type II Diabetes: challenges and solutions for food industry and healthcare professionals. University of Reading Oral presentation by McArthur at 13th World Congress on Inflammation (2017) One draft publication in preparation One preprint submitted to bioRxiv (currently under review after revision for Microbiome) McArthur, Hoyles and Glen have applied to Alzheimer's Research UK for a major grant award McArthur and Hoyles preparing funding applications to QMUL, and BBSRC McArthur and Hoyles invited to contribute to strategic plan for Quadram Institute |
| Start Year | 2016 |
| Description | Establishing a link between the gut-brain axis and Alzheimer's disease |
| Organisation | Queen Mary University of London |
| Department | Centre for Translational Medicine and Therapeutics |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Computational biology Expertise in relation to gut microbiome and gut-derived microbial metabolites Expertise in computational chemistry and brain chemistry Preparation of manuscripts and funding applications |
| Collaborator Contribution | (QUODRAM) expertise in immunology and gut microbiome, animal facilities; preparation of manuscripts and funding applications (QMUL) expertise in neuroscience, inflammation, in vitro work; preparation of manuscripts and funding applications |
| Impact | Multi-disciplinary: in vitro cell biology, transcriptomics, bioinformatics, animal experiments Successful funding application to Alzheimer's Research UK Abstract accepted for Alzheimer's Research UK conference 2017 Two abstracts accepted for Alzheimer's Research UK conference 2018 Poster presentation at Linking Alzheimer's Disease with Type II Diabetes: challenges and solutions for food industry and healthcare professionals. University of Reading Oral presentation by McArthur at 13th World Congress on Inflammation (2017) One draft publication in preparation One preprint submitted to bioRxiv (currently under review after revision for Microbiome) McArthur, Hoyles and Glen have applied to Alzheimer's Research UK for a major grant award McArthur and Hoyles preparing funding applications to QMUL, and BBSRC McArthur and Hoyles invited to contribute to strategic plan for Quadram Institute |
| Start Year | 2016 |
| Description | Farr@CIPHER/MED-BIO Partnership |
| Organisation | Swansea University |
| Department | Centre for Improvement in Population Health through E-records Research (CIPHER) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Airwave cohort - currently making use of UK Med-Bio computing technology - will seek to link their study data to the health records held in the SAIL Databank, a project which will both be attributed to CIPHER and Airwave, and also has been made possible by collaborating with Dementias Platform UK (DPUK), also led by Swansea University with regard to data sharing and linkage. UK Med-Bio have also suggested the install of their bespoke software in Swansea for the future manipulation of the multi-omics Airwave data. |
| Collaborator Contribution | farr@CIPHER are facilitating access for the Airwave Health Monitoring Study to linked health data currently held by the SAIL (Secure Anonymised Information Linkage) Databank at Swansea University. The Centre will have one one-year FTE post for analysis based on this with the Airwave cohort. CIPHER (via links to other organisations such as the SAIL Databank, Dementias Platform UK (DPUK) and Cloud Infrastructure for Microbial Bioinformatics (CLIMB)) will also be avaialble to host UK Med-Bio software and infrastructure for both the proposed linkage project and future collaborative work. |
| Impact | No major outcomes yet - work is ongoing yet but future impact could be associated with cultural (breaking barriers in data linkage) and policy and public services (linking health records to gain deeper understanding of participants' health)) |
| Start Year | 2016 |
| Description | Genome, metabolome and environmental-wide associations affecting blood pressure |
| Organisation | Imperial College London |
| Department | School of Public Health |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave, COMBI-BIO and UK Biobank cohorts. |
| Collaborator Contribution | Imperial: Genetic epidemiological analyses; biostatistics, epidemiological analyses; bioinformatics; metabolomics QMUL: Genetic epidemiological analyses; bioinformatics |
| Impact | Paper by Warren et al.; methods paper by Karaman et al. Multi-disciplinary: Clinical Genetics; Bioinformatics; Epidemiology; Biostatistics; Analytical Chemistry. |
| Start Year | 2016 |
| Description | Genome, metabolome and environmental-wide associations affecting blood pressure |
| Organisation | Queen Mary University of London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave, COMBI-BIO and UK Biobank cohorts. |
| Collaborator Contribution | Imperial: Genetic epidemiological analyses; biostatistics, epidemiological analyses; bioinformatics; metabolomics QMUL: Genetic epidemiological analyses; bioinformatics |
| Impact | Paper by Warren et al.; methods paper by Karaman et al. Multi-disciplinary: Clinical Genetics; Bioinformatics; Epidemiology; Biostatistics; Analytical Chemistry. |
| Start Year | 2016 |
| Description | Gut-brain axis - University of East Anglia |
| Organisation | University of East Anglia |
| Department | School of Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics and microbiome expertise for studies. |
| Collaborator Contribution | Facilitated animal cognitive work to complement ARUK-funded studies. |
| Impact | https://www.biorxiv.org/content/10.1101/866459v1 Two grant applications |
| Start Year | 2019 |
| Description | Gut-brain axis in cognitive impairment and ageing |
| Organisation | University of East Anglia |
| Department | Biomedical Research Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise on gut-derived microbial metabolites. Expertise with respect to neuroinflammation. Ongoing bioinformatics support. |
| Collaborator Contribution | Access to extensive collection of patient samples. Networking opportunities with relevant researchers. Access to germ-free animals and imaging facilities. |
| Impact | Multi-disciplinary: microbiology, biochemistry, immunology, systems biology, neuroscience, cognition. Introduction to a range of researchers working in the ageing/dementia field. Invitation to contribute to Quadram Institute research programme for the next five years. Two unsuccessful funding applications. |
| Start Year | 2016 |
| Description | Influence of microbial metabolites cognitive impairment associated with chronic kidney disease |
| Organisation | Queen Mary University of London |
| Department | William Harvey Research Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in gut microbiota and its metabolites. Metabolomics - analyses of samples and interpretation of data. Ongoing bioinformatics support for 16S rRNA gene sequencing work related to gut microbiota. |
| Collaborator Contribution | Animal facilities and brain samples. Clinical expertise relating to chronic disease. |
| Impact | Multi-disciplinary: microbiology, biochemistry, immunology, systems biology, neuroscience, renal biology. Networking opportunities and increased access to animal facilities. Several manuscripts in preparation. First manuscript to be submitted February 2019. |
| Start Year | 2016 |
| Description | Influence of the gut microbiome on cognitive function in ageing |
| Organisation | University of East Anglia |
| Department | Norwich Medical School |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics support for analyses of data generated from faecal microbial transplant experiments. |
| Collaborator Contribution | Animal models of cognitive function, metabolomics |
| Impact | Manuscript in preparation. Also investigating potential of incorporating blood-brain barrier work into the collaboration. |
| Start Year | 2018 |
| Description | KU Leuven - APOE collaboration |
| Organisation | University of Leuven |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | Metabolomics data analysis and statistical and epidemiological skills to interpret the data |
| Collaborator Contribution | Laboratory facilities to follow up and validate metabolomics findings in APOE knockout models and skills to interpret the results |
| Impact | ongoing collaboration |
| Start Year | 2019 |
| Description | MED-BIO : Astra Zeneca |
| Organisation | AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are discussing linking in AZ collaboration to other projects related to MED-BIO |
| Collaborator Contribution | AZ contacts are bringing expertise in large-scale data and sample handling with a focus on technological solutions. |
| Impact | ongoing collaboration |
| Start Year | 2015 |
| Description | MED-BIO : Thomson Reuters |
| Organisation | Thomson Reuters |
| Country | United States |
| Sector | Private |
| PI Contribution | We are discussing linking other potential projects into the MED-BIO consortium |
| Collaborator Contribution | TR is bringing industrial network contacts and leverage to the project and some new ideas on for example large scale dataset integration, multi-omic data analysis, and functional pathway scoring. |
| Impact | ongoing collaboration |
| Start Year | 2015 |
| Description | Manipulation of cellular vs humoral immunity to the intestinal microbiota and its potential for IBD therapy. |
| Organisation | Queen Mary University of London |
| Department | Wolfson Institute of Preventive Medicine |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Expertise in bioinformatics and gut microbiome; preparation of manuscripts and funding applications |
| Collaborator Contribution | St Marks: expertise in immunology and inflammatory bowel disease; preparation of manuscripts and funding applications Quadram: expertise in immunology, animal models and gut microbiome; preparation of manuscripts and funding applications Reading: expertise in gut microbiome and in vitro growth of bacteria; preparation of manuscripts |
| Impact | Multi-disciplinary: in vitro cell biology, immunology, microbiology, transcriptomics, bioinformatics, animal experiments funding application to MRC (unsuccessful) Abstract accepted for 12th Congress of ECCO, Inflammatory Bowel Diseases. Two abstracts accepted for British Society for Immunology Congress 2017 |
| Start Year | 2015 |
| Description | Manipulation of cellular vs humoral immunity to the intestinal microbiota and its potential for IBD therapy. |
| Organisation | St Mark's Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | Expertise in bioinformatics and gut microbiome; preparation of manuscripts and funding applications |
| Collaborator Contribution | St Marks: expertise in immunology and inflammatory bowel disease; preparation of manuscripts and funding applications Quadram: expertise in immunology, animal models and gut microbiome; preparation of manuscripts and funding applications Reading: expertise in gut microbiome and in vitro growth of bacteria; preparation of manuscripts |
| Impact | Multi-disciplinary: in vitro cell biology, immunology, microbiology, transcriptomics, bioinformatics, animal experiments funding application to MRC (unsuccessful) Abstract accepted for 12th Congress of ECCO, Inflammatory Bowel Diseases. Two abstracts accepted for British Society for Immunology Congress 2017 |
| Start Year | 2015 |
| Description | Manipulation of cellular vs humoral immunity to the intestinal microbiota and its potential for IBD therapy. |
| Organisation | University of Reading |
| Department | Department of Chemistry |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in bioinformatics and gut microbiome; preparation of manuscripts and funding applications |
| Collaborator Contribution | St Marks: expertise in immunology and inflammatory bowel disease; preparation of manuscripts and funding applications Quadram: expertise in immunology, animal models and gut microbiome; preparation of manuscripts and funding applications Reading: expertise in gut microbiome and in vitro growth of bacteria; preparation of manuscripts |
| Impact | Multi-disciplinary: in vitro cell biology, immunology, microbiology, transcriptomics, bioinformatics, animal experiments funding application to MRC (unsuccessful) Abstract accepted for 12th Congress of ECCO, Inflammatory Bowel Diseases. Two abstracts accepted for British Society for Immunology Congress 2017 |
| Start Year | 2015 |
| Description | Metabolic profiling of cardio-vascular disease GWAS hits |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave and UK Biobank cohorts. |
| Collaborator Contribution | Imperial: Chemometrics and metabolomics analyses Virginia Tech: Bioinformatics Wake Forest: Genetic epidemiology |
| Impact | Multi-disciplinary: Analytical Chemistry; Bioinformatics; Epidemiology |
| Start Year | 2016 |
| Description | Metabolic profiling of cardio-vascular disease GWAS hits |
| Organisation | Virginia Tech |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave and UK Biobank cohorts. |
| Collaborator Contribution | Imperial: Chemometrics and metabolomics analyses Virginia Tech: Bioinformatics Wake Forest: Genetic epidemiology |
| Impact | Multi-disciplinary: Analytical Chemistry; Bioinformatics; Epidemiology |
| Start Year | 2016 |
| Description | Metabolic profiling of cardio-vascular disease GWAS hits |
| Organisation | Wake Forest University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Bioinformatics; computational support by the UK Med-Bio bioinformatician. Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave and UK Biobank cohorts. |
| Collaborator Contribution | Imperial: Chemometrics and metabolomics analyses Virginia Tech: Bioinformatics Wake Forest: Genetic epidemiology |
| Impact | Multi-disciplinary: Analytical Chemistry; Bioinformatics; Epidemiology |
| Start Year | 2016 |
| Description | Metagenomics to study the bariatric surgery-associated microbiome |
| Organisation | Imperial College London |
| Department | Department of Surgery and Cancer |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics associated with the microbiome; expertise in gut microbiome. |
| Collaborator Contribution | Bariatric surgery, clinical data, gut microbiome |
| Impact | Multi-disciplinary: computational biology, clinical studies, metabonome, immunology, microbiome; cohort studies; surgical interventions. Manuscript(s) in preparation. |
| Start Year | 2017 |
| Description | Metagenomics to study the colorectal cancer mucosal microbiome |
| Organisation | Imperial College London |
| Department | Department of Surgery and Cancer |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics associated with the microbiome; expertise in gut microbiome. |
| Collaborator Contribution | Clinical samples and data, expertise in colorectal cancer, expertise in cancer-associated gut microbiome |
| Impact | Multi-disciplinary: computational biology, clinical studies, metabonome, immunology, microbiome; surgical studies. Abstract submitted to Digestive Disease Week (DDW) 2018. |
| Start Year | 2017 |
| Description | Microbial metabolites cause expression of brain-homing markers on dendritic cells |
| Organisation | St Mark's Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | Provided expertise on gut microbiota and microbial metabolites to colleagues working in the Antigen Presentation Research Group, Imperial College London. Ongoing bioinformatic support for in vitro and in vivo transcriptome studies. Expertise with respect to neuroinflammation. |
| Collaborator Contribution | Provided expertise in immunology and working with dendritic cells. |
| Impact | Multi-disciplinary: microbiology, biochemistry, systems biology, immunology, in vitro cell culture. Output: abstract submitted on dendritic cell homing to British Society of Immunology Congress 2017. |
| Start Year | 2017 |
| Description | Microbiome-associated metabolites and brain imaging |
| Organisation | University College London |
| Department | Centre for Advanced Bioimaging |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Immunohistochemistry, cell line work, range of metabolites to test. |
| Collaborator Contribution | MSc student, access to imaging facilities and animal models. Collaboration resulted from a discussion at the ARUK conference in London 2018. |
| Impact | MSc student project ongoing, expected publications. |
| Start Year | 2018 |
| Description | Molecular epidemiology of cardio-metabolic phenotypes |
| Organisation | Imperial College London |
| Department | School of Public Health |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Facilitation of analysis and storage of the LOLIPOP cohort: provision of access to high-performance computing resources; data storage, with expertise and support. |
| Collaborator Contribution | Bioinformatics: GWAS, EWAS, MWAS, TWAS on data from the LOLIPOP study. |
| Impact | Multiple papers in high impact journals, grant applications and presentations at meetings. Multi-disciplinary: computational biology, clinical studies, metabolomics, genomics, cardiology, cohort studies. |
| Start Year | 2016 |
| Description | PhenoMeNal |
| Organisation | European Commission |
| Department | Horizon 2020 |
| Country | European Union (EU) |
| Sector | Public |
| PI Contribution | PhenoMeNal - Electronic Infrastructure for Metabolomics, with Partners in 7 EU countries. H2020 funded (EUR 8M). MedBIO contribution: testing scalability of infrastructure and tools; computing with sensitive clinical data test case; local installation test case. |
| Collaborator Contribution | produced shareable workflows for metabolomics analyses |
| Impact | Interdisciplinary: computer science - chemistry - medicine. FULL Phenomenal Outputs detailed at http://phenomenal-h2020.eu/home/ .Main outputs from our collaboration are 'computing with sensitive clinical data' test case; 'workflow local installation' test case, including production of multiple trainining videos and deployment on YouTube. |
| Start Year | 2015 |
| Description | Quadram - infant microbiota |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Bioinformatics, expertise is gut microbiome, cultivation |
| Collaborator Contribution | PhD student to conduct data analyses, immunology, infant samples |
| Impact | Manuscripts in preparation. Will be submitted as pre-prints and to journals in due course. MinION manuscript available as a preprint already. |
| Start Year | 2016 |
| Description | Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease |
| Organisation | Erasmus University Rotterdam |
| Department | Department of Epidemiology |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods |
| Collaborator Contribution | Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis. |
| Impact | continuing collaboration |
| Start Year | 2018 |
| Description | Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease |
| Organisation | Farr Institute of Health Informatics Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods |
| Collaborator Contribution | Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis. |
| Impact | continuing collaboration |
| Start Year | 2018 |
| Description | Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease |
| Organisation | Harvard University |
| Department | Department of Epidemiology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods |
| Collaborator Contribution | Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis. |
| Impact | continuing collaboration |
| Start Year | 2018 |
| Description | Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease |
| Organisation | Northwestern University |
| Department | Feinberg School of Medicine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods |
| Collaborator Contribution | Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis. |
| Impact | continuing collaboration |
| Start Year | 2018 |
| Description | Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease |
| Organisation | University of Ioannina |
| Department | Department of Hygiene and Epidemiology |
| Country | Greece |
| Sector | Academic/University |
| PI Contribution | Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods |
| Collaborator Contribution | Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis. |
| Impact | continuing collaboration |
| Start Year | 2018 |
| Description | Serum metabolic signatures of atherosclerosis and subsequent cardiovascular disease |
| Organisation | University of Texas |
| Department | Health Science Center at Houston |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Epidemiological expertise in metabolomics data analysis and metabolic profiling and data interpretation and bioinformatics analysis methods |
| Collaborator Contribution | Contributing data from MESA and Rotterdam studies and expertise in clinical atherosclerosis. |
| Impact | continuing collaboration |
| Start Year | 2018 |
| Description | The Consortium of Metabolomics Studies (COMETS) and Airwave |
| Organisation | Brigham and Women's Hospital |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | Contributing data from the Airwave cohort to this consortium of 47+ international cohorts |
| Collaborator Contribution | Platform for sharing data to facilitate large-scale collaborative research e.g. meta-analysis and GWAS on the human metabolome |
| Impact | Publication Yu et al Am J Epidemiol 2019 https://doi.org/10.1093/aje/kwz028 . |
| Start Year | 2019 |
| Description | The Consortium of Metabolomics Studies (COMETS) and Airwave |
| Organisation | National Cancer Institute |
| Country | Lithuania |
| Sector | Hospitals |
| PI Contribution | Contributing data from the Airwave cohort to this consortium of 47+ international cohorts |
| Collaborator Contribution | Platform for sharing data to facilitate large-scale collaborative research e.g. meta-analysis and GWAS on the human metabolome |
| Impact | Publication Yu et al Am J Epidemiol 2019 https://doi.org/10.1093/aje/kwz028 . |
| Start Year | 2019 |
| Description | The association of socio-economic status and the metabolome |
| Organisation | Imperial College London |
| Department | Department of Physics |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Provision of access to high-performance computing resources and to software licences for data analyses of the Airwave cohort. |
| Collaborator Contribution | Analysis of influence of social and behavioral predictors on the metabolome. |
| Impact | Multi-disciplinary: social science; epidemiology; analytical chemistry; statistics and bioinfomatics; molecular biology. |
| Start Year | 2017 |
| Description | UK Biobank - association between sodium excretion and incident cardiovascular disease and mortality |
| Organisation | George Institute for Global Health |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Epidemiological expertise and knowledge of UK Biobank cohort data |
| Collaborator Contribution | Expertise in clinical trials and health effects of sodium consumption |
| Impact | continuing collaboration and scientific paper under submission |
| Start Year | 2018 |
| Description | Use of C. elegans as a model to study gut-brain axis |
| Organisation | Queen Mary University of London |
| Department | School of Biological and Chemical Science QMUL |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise in gut microbiota, gut-derived microbial metabolites and neuroinflammation. |
| Collaborator Contribution | C. elegans model, and facilities to run experiments related to ageing and the brain-gut axis. |
| Impact | Multi-disciplinary: microbiology, immunohistochemistry, immunology, neurobiology. Pilot work initiated to pursue research interests. |
| Start Year | 2017 |
| Title | BugBuilder |
| Description | BugBuilder is a pipeline for hands-free assembly and analysis of microbial genome sequences. It produces outputs suitable either for direct submission to sequence databases or for use in downstream finishing processes. It is configurable to work with most command-line assembly and scaffolding tools which are selectable at run-time, and supports all common sequence types used in microbial genome assembly.The BugBuilder workflow incorporates sequence pre-processing (quality assessment, read trimming, downsampling), contig assembly, scaffold assembly, annotation and generation of visualisations. Following assembly, validation processes can attempt to identify sequence misassemblies to facilitate genome finishing efforts.BugBuilder is intended to allow high-throughput automated analysis of microbial genome sequences, in addition to allow scientists without specialist knowledge to carry out assembly and annotation tasks. |
| Type Of Technology | Software |
| Year Produced | 2015 |
| Open Source License? | Yes |
| Impact | Originally designed to support a specific project, as part of MED-Bio infrastructure it has undergone extensive revision and enhancement to improve functionality and support additional analyses. BugBuilder has already been used on a variety of microbial genome projects to date for multiple collaborators and is available for download as a virtual machine. Its use has enabled researchers with little previous bioinformatics knowledge to undertake complex (previously very time-consuming) analyses effectively, reproducibly and rapidly. Data arising from its use has led to a number of publications including Florea M, Reeve B, Abbott J, Freemont PS, Ellis Tet al., 2016, Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582., Scientific Reports, Vol: 6, ISSN: 2045-2322. Software source and virual machine image are freely available via the URL below. |
| URL | http://www.imperial.ac.uk/bioinformatics-data-science-group/resources/software/bugbuilder/ |
| Title | Development of Galaxy workflow pipeline for analyzing metabonomics data |
| Description | Galaxy workflow pipeline for analyzing metabonomics data 3 different pipelines - 1 LC-MS (nearly done), 1 NMR, 1 GC-MS being developed |
| Type Of Technology | Webtool/Application |
| Year Produced | 2016 |
| Impact | This workflow is linked to Metabolights which is a database for Metabolomics experiments and derived information developed by EMBL-EBI. |
| Title | Metagenomics softwares |
| Description | Suite of metagenomics softwares in development |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | No notable impacts to report yet |
| Title | Research software engineer maintenance provided by Antonio J Berlanga-Taylor |
| Description | Provided updates throughout 2019 to maintain the development of a variety of websites dedicated to research related software engineering. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2019 |
| Impact | Following websites updated: • https://github.com/EpiCompBio (coordinator) • https://github.com/AntonioJBT/episcout (author and maintainer) • https://github.com/AntonioJBT/project_quickstart (author and maintainer) • https://github.com/cgat-developers (collaborator) |
| Title | SCAMP - Scaleable Metagenomics Pipeline |
| Description | SCAMP is a pipeline for assembly and analysis of metagenomes, allowing scaleble automated and reproducible analyses of whole microbiomes and other microbiomes. The system incorporates a number of third-party pre-published programs in a modular framework. It combines a number of well-known tools to provide a comprehensive analysis incorporating partitioning samples into reads derived from different phyla, relative species abundance determination, metagenome assembly, gene prediction, clustering of predicted genes, cluster abundance determination and gene characterisation. The software orchestrates the data management of the analysis process forming a loosely-coupled pipeline allowing different stages to be moved to appropriate computational resources. For example, some stages are embarrasingly parallel and can be optimally run on a compute cluster, whereas other components (i.e. metagenome assembly, gene clustering) require access to large amounts of memory which are typically found on standalone servers. The pipeline has been validated by reanalysing the data of Qin et al (2014, Nature 513, 59-64), and has been demonstrated to be capable of reproducing the results published in this study, while improving the contig assembly such that a number of additional genes were identified. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | The pipeline has already been used to analyse a large human gut microbiome dataset arising from an EU project - FLORINASH (The role of intestinal microflora in non-alcoholic fatty liver disease (NAFLD). These results form part of a paper currently in revision for Nature (Hoyles, Abbott et al). The pipeline can be used to analyse other microbiomes and allows fast processing of laarge datasets with reproducible documented procedures, parameters etc. This will also allow direct comparison of datasets arising from multiple sources. The pipeline is currently being run on Med-Bio hardware, but is being msde ready for distribution and a paper on the methodology is in preparation (Abbott, Hoyles, Butcher et al). |
| URL | http://www.imperial.ac.uk/bioinformatics-data-science-group/resources/software/scamp/ |
| Title | mzML2ISA & nmrML2ISA |
| Description | mzML2ISA & nmrML2ISA are Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Documetation is available from http://2isa.readthedocs.io/en/latest/ |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. Theses tools would be used and integrated within EMBL-EBI MetaboLights repository. |
| URL | https://github.com/ISA-tools |
| Description | -Lesley Hoyles - Invited talk - "Dietary methylamines, the gut microbiota and host health" Technical University of Munich, Freising, Germany |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave invited talk. Talk sparked many questions from and discussions with postgraduate students and academics present. Future collaborative work was discussed. |
| Year(s) Of Engagement Activity | 2016 |
| Description | 12th Invest in ME Research International ME Conference |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Patients, carers and/or patient groups |
| Results and Impact | Invited to attend meeting to discuss integrated systems biology approaches for ME/CFS research. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.investinme.eu/iimec12.shtml |
| Description | 6th Midlands Molecular Microbiology Conference, Nottingham |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented NAFLD work associated with Med-Bio Fellowship. |
| Year(s) Of Engagement Activity | 2019 |
| Description | A New Facet to the Gut-Brain Axis: Microbe-derived Metabolites and the Blood-Brain Barrier - King's College London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk to facilitate dissemination of research findings and networking. |
| Year(s) Of Engagement Activity | 2018 |
| Description | A New Facet to the Gut-Brain Axis: Microbe-derived Metabolites and the Blood-Brain Barrier - University of Roehampton |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk to facilitate dissemination of research and networking. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Academia/Industry Careers & Networking event - ARUK Oxford network |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Opportunity to present our work to researchers associated with the ARUK Oxford network. Prompted interesting discussions with other researchers, and led to providing bioinformatics support for one of the University of Reading students attending. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Antonio Berlanga - congress session chair, immunogenomics session, National Congress of Immunology, Mexican Society of Immunology |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This event led to another invitation in November 2016 to give a talk and continue the collaboration. As a result, working together on several research projects and planning a 2nd Genomics of Inflammation Workshop and Course (the first one was in 2015, Newton Fund). Applying for further funds for research and capacity building. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Antonio Berlanga - invited talk "Clinical applications of cellular and molecular inflammation", XXV National Forum on Health Research, Mexican Institute of Social Security |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited to establish an international collaboration in Genomics of Immunology. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Antonio Berlanga - workshop "Introduction to computational methods in biology: unix, command line and R", XXII National Immunology Conference, Mexico |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | We had an anonymous pre- and post- workshop survey which showed that: - 90% (of 11) participants thought the course met their expectations; - 82% replied that the quality of the instructors was excellent and the rest replied that it was very good; - All participants said they were motivated to continue learning. - A workshop participant (PhD student) is hoping to visit Imperial this summer to collaborate on a research project and continue developing data analysis skills. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Antonio J Berlanga-Taylor - Instructor for various software courses |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Instructor for two Software Carpentry Foundation courses held late 2019 and early 2020 increasing knowledge, skills and capabilities for postgraduate students and those interested in the area of software development. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Antonio J Berlanga-Taylor - Invited reviewer for CONCACyT |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited to act as a reviewer for CONACyT (Mexico) for the funding call 'Ciencia de Frontera 2019'. CONACyT (Consejo Nacional de Ciencia y Tecnología) is Mexico's entity in charge of the promotion of scientific and technological activities, setting government policies for these matters, and granting scholarships for postgraduate studies |
| Year(s) Of Engagement Activity | 2019 |
| Description | Antonio J Berlanga-Taylor - Invited reviewer for various original contributions/review articles |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Received invitations to review original contributions or review articles for BMJ Open (2019), PeerJ (2019) and Frontiers in Pediatrics (2019). |
| Year(s) Of Engagement Activity | 2019 |
| Description | Antonio J Berlanga-Taylor - Lecturer |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Lecturer for a range of selected topics within the Molecular and Genetic Epidemiology module (selected topics) for the masters in Epidemiology and Public Health at Imperial College London which sparked discussion and interest in the abovementioned topics. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Antonio J Berlanga-Taylor provided tutoring students obtaining their undergraduate and graduate degrees |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Provided 1:1 tutoring in the following degrees at Imperial College; MPH; MSc Epidemiology; MSc Health Data Analytics; BSc Global Health; leading to strengthened knowledge and understanding and successful attainment of degrees for 9 students. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Antonio J Berlanga-Taylor supervised activities supporting students obtaining postgraduate degrees |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Acted as either the main supervisor or co-supervisor for 6 students pursuing their masters or doctorate degrees resulting in one student receiving a merit overall and another sutdent receiving a distinction. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Are bacteria good for your brain? Linking gut microbes, blood and the brain's defences - LGBT+ STEMinar 2019, London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presenting work to a lay audience. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://lgbtsteminar2019.iopconfs.org/programme |
| Description | BBSRC 'careers for non-faculty research staff' |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Invited discussion group member - BBSRC 'careers for non-faculty research staff' led by Michael Ball - outcome led to creation and distribution of UK-wide questionnaire for non-faculty research staff and ongoing discussion on policy |
| Year(s) Of Engagement Activity | 2015 |
| Description | BBSRC China Partnering award (BB/M027635/1), CUDDEL - meeting UK 23-25 November 2016 workshop (Reza Salek) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Assisted with Workshops on hands on standards and data curation for metabolomics for participants in China partnering award. 16 participants. |
| Year(s) Of Engagement Activity | 2016 |
| Description | BBSRC Workshop to discuss Non-Faculty Researchers Careers and Recognition - (Sarah Butcher) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sarah Butcher was an invited attendee to BBSRC Workshop to discuss Non-Faculty Researchers Careers and Recognition in Manchester March 2017. The workshop was convened to discuss the outcomes of an earlier survey run by the BBSRC (which Dr Butcher helped to design), to collect information on careers of non-faculty staff. The workshop brought together representatives from BBSRC, other RCUK funders, and non-faculty staff from a variety of backgrounds to discuss ways of improving career progression, metrics and methods of recognition. Following the meeting Dr Butcher was invited by BBSRC to join a small working group following up on actions arising from the meeting. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.bbsrc.ac.uk/news/events/2017/1703-workshop-non-faculty-researcher-careers/ |
| Description | Big Data: Innovation in analysis, usability and curation' workshop Southampton |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Invited speaker for 'Big Data: Innovation in analysis, usability and curation' workshop Southampton 2015. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Bugs In Your Guts - personal blog on gut microbiology and the gut microbiota |
| 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 | Introducing the science associated with the gut microbiota and gut microbiology. |
| Year(s) Of Engagement Activity | 2016,2017,2018 |
| URL | http://bugs-in-your-guts.com |
| Description | Chair of Bio-HPC special interest area workshop at HPC summer school Imperial College september 2016 and 2017 (sarah Butcher) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Organised speakers for a half day workshop with discussion sessions on using high performance computing for bio-medical applications. Ensouraged discussion on shared experiences, and areas of joint interest iparticularly in the areas of scheduling and access to software. Started a mailing list to encourage sharing of information and expertise in bio-HPC use. |
| Year(s) Of Engagement Activity | 2016,2017 |
| Description | Combined CHARME, EMBnet and NETTAB Workshop, Reproducibility, standards and SOP in bioinformatics, November 24-26 2016 Rome (Reza Salek) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation on metabolomics data standards to workshop partcipants. |
| Year(s) Of Engagement Activity | 2016 |
| Description | EMBL-EBI, EMBO Practical Course on Metabolomics bioinformatics for life scientists, 13- 17 February 2016 (Reza Salek) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | teaching and training - hands on metabolomics data analysis course for researhers and postgraduate students. Participants learned how to produce and analyse metabolomics data; also learnt about public metbolomics resources such as Metabolights database. |
| Year(s) Of Engagement Activity | 2016 |
| Description | EMN Webinar Dr. Reza Salek (March 24, 2016) |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | British Metabolomics society - public webinar. "How close are we to metabolomics reproducibility? Data sharing, data standards and workflows for metabolomics " still available on the British Metabolomics Society web-site. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://metabolomicssociety.org/resources/videos/88-videos/218-2016-emn-webinars-public# |
| Description | EU Project Informatics Alignment Workshop (April 2015) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | The aims and objectives of the workshop were to: 1) Understand your project research objectives. 2) Understand the informatics needs to realise your research objectives. 3) Collect project informatics use cases. 4) Uncover synergies and propose collaborations between partners. 5) Report on the impact of project needs on the future eTRIKS / tranSMART roadmap. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.eventbrite.co.uk/e/eu-project-informatics-alignment-workshop-etriksimi-registration-1627... |
| Description | Ealing Primary Science Fair - The Ellen Wilkinson School for Girls, year 5 and 6 students, STEMNET Ambassador (Lesley Hoyles) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Assessed students' science projects, and awarded prizes for best biology, chemistry, physics and overall projects. Children were excited to show what they had done and were enthusiastic about future work. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Effects of gut-derived methylamines on the blood-brain barrier - ARUK Conference 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presented at ARUK Conference, Aberdeen March 2017 on our preliminary work. Invited to contribute review based on our work/ideas to Geriatrics (submission due November 2017). |
| Year(s) Of Engagement Activity | 2017 |
| Description | Effects of gut-derived trimethylamines on the blood-brain barrier, ARUK meeting London 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented work on effects of dietary methylamines on blood-brain barrier integrity. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Federation of Infection Societies, Edinburgh |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave a talk on microbiome-associated metabolites and their effects on host health. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Five-week after-school gut health science club, Primrose Hill Primary School |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | The presentations and activities we gave to the children over the first three weeks of the club improved their understanding of how the digestive system works, and encouraged lots of interesting questions and discussions. The children were able to present all they had learnt to their parents. All the parents reported the children had really benefitted from attending the club. We were particularly pleased to hear that some of the girls were know considering becoming scientists when they are older. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://wwwf.imperial.ac.uk/blog/gut-health-science-club/ |
| Description | Gave a talk on recent metagenomic work at "Integrating knowledge and approaches across microbiomes..." |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The aim of this one-day meeting, jointly hosted by the British Ecological Society, the Microbiology Society and the Society for Applied Microbiology, was to discuss approaches and findings from across a broad suite of environments and hosts. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.eventbrite.co.uk/e/integrating-knowledge-and-approaches-across-microbiomes-from-plants-t... |
| Description | Gut microbial dysfunction and its influence on the brain: Microbe-derived metabolites and the blood-brain barrier - University of Westminster |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk to disseminate research findings and facilitate networking. |
| Year(s) Of Engagement Activity | 2018 |
| Description | High Level Biology/Chemistry speaker Burlington Danes Academy, STEMNET Ambassador (Lesley Hoyles) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | keynote speaker for STEMNET schools meeting- promoting science. Talk was on the importance of the gut microbiome to human health and disease. Talk sparked lots of questions and discussion afterwards, as students didn't appreciate how important the gut microbiota is to host health. Considerable interest from students led to the visit being written-up by one of the students for the school newsletter. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Hosting International Phenome Centre meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | The MEDBIO working group hosts the international phenome centre meeting twice a year in 2015 and 2016 with policy makers, industry and academics participating in this meeting. The meetings have resulted in Singapore, Canada and China setting up phenome centres. |
| Year(s) Of Engagement Activity | 2015,2016 |
| Description | ILSI Europe Expert Group/Organizing Committee on 'Mechanistic Insights into the Gut-Brain Axis' |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Establishment of a working group to increase awareness of gut-brain axis, and to feed into future EU funding. |
| Year(s) Of Engagement Activity | 2019 |
| Description | INVEST IN ME RESEARCH BIOMEDICAL RESEARCH COLLOQUIUM - 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited to contribute to discussions on ME/CFS research because of my areas of research expertise. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.investinme.eu/brmec%20colloquiums.shtml |
| Description | ISBE (Infrastructure Systems Biology Europe) and UK MED BIO - workshop on High Performance Computing in Health Research |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Attendee on behalf of ISBE (Infrastructure Systems Biology Europe) and UK Med-BIO - workshop on High Performance Computing in Health Research (Brussels, October 2014) organised by the European Commission's Directorates-General for Research and Innovation and for Communications Networks, Content and Technology. The overall objective of this was to identify current and future health research needs for HPC and to explore mechanisms of addressing them through co-operation of relevant stakeholders. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Imperial College NIHR BRC Digital Health workshop - chair of session on Maximising capabilities in digital health technologies |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invitation to chair session to debate capacity building in digital health technologies to build on existing strengths and increase collaboration between academic researchers and clinicians and focus activities towards implementation of leading edge technologies with health applications. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Indian Institute of Science, Bangalore, India |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk at Institute. Visit and talk led to Royal Society International Exchange grant. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Integrated systems biology to study non-alcoholic fatty liver disease in obese women - Gut Microbiota for Health World Summit 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Invited talk allowed me to present my work to a wide audience, and to network. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Integrated systems biology to study non-alcoholic fatty liver disease in obese women - International Scientific Association for Probiotics and Prebiotics Students and Fellows Association Annual Meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation of Florinash work given at the ISAPP meeting to introduce concept of integrated microbiome research to industry figures. Led to me being invited to contribute to workshop, and to contributing to (in preparation) workshop write-up. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://isappscience.org/2017-annual-meeting/ |
| Description | Integrated systems biology to study non-alcoholic fatty liver disease in obese women - The 11th London Surgical Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Introducing integrated systems biology to surgeons, to demonstrate how clinical, host and microbiome data can allow us to identify disease biomarkers. Won prize for best poster. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Integrated systems biology to study non-alcoholic fatty liver disease in obese women - Translational Bioinformatics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Intended purpose was to present our integrated systems biology approach to characterizing host-microbiome interactions. No impacts have arisen from activity, as title of conference was misleading. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited talk - Data Science Meeting, Imperial College London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Talk was intended to share information on the kind of work I'm doing with other members of the College. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited talk - Institute of Biomedical Science Congress, Birmingham |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Intended purpose - To stimulate thinking. Talk encouraged lots of interesting questions and discussions from health professionals who knew little to nothing about gut microbiome research. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.meetbirmingham.com/organise-an-event/meet-birmingham-conference-guide-2017-18/ |
| Description | Invited talk - University of Warwick |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Purpose of talk was to share information. The talk encouraged lots of interesting questions and discussions from researchers who knew little to nothing about gut microbiome research in the context of liver disease. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited talk - Workshop on 'Data Science Challenges and Opportunities in Translational Medicine' (Sarah Butcher) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sarah Butcher gave an invited talk on the MED-Bio project as part of a one day workshop on Data Science Challenges and Opportunities in Translational Medicine'. The workshop included discussion sessions on the challenges of working with large multi-disciplinary datasets with input from international speakers. The talk led to requests for new collaborations with 2 separate research groups. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://saphir746.github.io/ITMAT-DSG-2017/ |
| Description | Invited to give talk at IMER BRMEC8 RESEARCH MEETING LONDON, 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave an invited talk to colloquium attendees - Integrated systems biology to understand the role of the gut microbiome in health and disease. Intended to introduce new concepts to ME-CFS research, and to highlight the work I've been doing during my Fellowship. Had many fruitful conversations, and identified potential funding streams. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.investinme.eu/BRMEC%20Colloquiums.shtml#brmec8 |
| Description | Korean Society for Laboratory Medicine - LMCE 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented microbiome-associated work from Med-Bio and ARUK grants. |
| Year(s) Of Engagement Activity | 2019 |
| Description | LGBT STEM |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Improving LGBT visibility in Science, Technology, Engineering and Mathematics |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://lgbtstem.wordpress.com/2017/08/17/an-interview-with-lesley-hoyles/ |
| Description | Lesley Hoyles - Invited speaker - "Integrated systems biology to study non-alcoholic fatty liver disease in obese women", Middlesex University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | invited speaker for departmental seminar. Sparked interesting questions and discussions among students and academics present in the audience. Also raised interest in potential collaborative work with colleagues in microbiology department. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Lesley Hoyles - invited talk "Use of next-generation sequencing in microbiome studies", University of Westminster |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | invited talk to MSc students. Students were surprised how important the microbiome was to host health, and had many questions about how to characterize the microbiome. Some of the students w.ere interested in pursuing PhD studies in microbiome research. |
| Year(s) Of Engagement Activity | 2016 |
| Description | London Farr Institute "Developing a Trusted Research Environment for London - a Meeting for Frontiers" |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop discussion to explore the idea of creating a national safe haven for clinical data accessible to academic researchers. |
| Year(s) Of Engagement Activity | 2015 |
| Description | MRC-HSCIC joint discussion meeting on HSCIC Data Services Platform |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Invited attendee on behalf of UK MED-BIO: MRC-HSCIC joint discussion meeting on HSCIC Data Services Platform (Des 2015), 1st and 2nd Farr - Medical Bioinformatics - ADRN - Jisc Annual Technical Leads Meeting (Jan 2015, 2016)- outputs were feeding requirements on e-infrastructure to support medical informatics to RCUK national eInfrastructure group. |
| Year(s) Of Engagement Activity | 2015,2016 |
| Description | MetaboInterview - Reza salek interview for |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Published in partnership between TMIC and the Metabolomics Society Issue 60 - August 2016 his issue featured an interview with Reza Salek. This section features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.metabonews.ca/Aug2016/MetaboNews_Aug2016.htm#MetaboInterviews |
| Description | Microbe-derived metabolites, the blood-brain barrier - Nottingham Trent University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk to facilitate dissemination of research findings and networking, to meet up with collaborators and discuss future research direction. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Microbiome R&D and Business Collaboration Forum: Europe, Rotterdam |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presented NAFLD work associated with Med-Bio Fellowship. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Microbiome-host interactions: protective effects of propionate upon the blood-brain barrier - Linking Alzheimer's Disease with Type II Diabetes: challenges and solutions for food industry and healthcare professionals. University of Reading |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Make food industry figures aware of the link between diet, the microbiome and cognitive function. |
| Year(s) Of Engagement Activity | 2018 |
| Description | New Scientist Live - Royal Society of Biology Ask A Biologist (Lesley Hoyles) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Keynote/Invited Speaker, answering questions posed by the generl public on "How do gut bacteria keep us healthy?". Members of the public were surprised how important gut bacteria were to their health and wellbeing. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://live.newscientist.com/ |
| Description | Nottingham Digestive Diseases Centre |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented NAFLD work to clinicians and associated staff at the Nottingham Digestive Diseases Centre. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Organising Hackathon workshop with workflow4metabolomics consortium |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | EBI is organising a Hackathon workshop in March 2016, inviting anyone who works on galaxy platform to learn from each other and to discuss what's missing for tools development. The outcome of which would be collaborative work |
| Year(s) Of Engagement Activity | 2016 |
| Description | Paul Elliott presentation to Imperial College London HPC Summer School on UK MED-BIO: A new platform for the analysis of omic data |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a presentation to the annual High Performance Computing Summer School at Imperial run by the HPC Group. It was particularly aimed at raising the profile of the project to highlight the resource that we are developing and excite interest in its use across the College and with collaborators. So we were aiming to reach out to HPC users in particular. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Presentation to 15th Annual Conference of The Metabolomics Society, June 23-27 2019, The Hague, NL |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented methods and results of work on a new cross-cohort matching in untargeted metabolomics to generate accurate within-dataset feature matching across multiple cohorts. The new approach addresses a key problem in metabolomics studies and promises to make analysis of large untargeted multi-cohort data sets a viable option. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://metabolomics2019.org/images/2019-Metabolomics_Abstract_9.pdf |
| Description | Presentation to 15th Annual Conference of The Metabolomics Society, The Hague, The Netherlands, June 23-27, 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented methods and results of work on a metabolomics analysis to identify and characterise metabolomic signatures associated with risk variants for coronary artery disease using samples from MESA, Rotterdam and Airwave cohort studies with the aim of producing new knowledge on the causal pathways linking genes to CVD. a new cross-cohort matching in untargeted metabolomics to generate accurate within-dataset feature matching across multiple cohorts. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://metabolomics2019.org/images/2019-Metabolomics_Abstract_9.pdf |
| Description | Press release and quote for Warren et al. Nature Genetics paper publication |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release accompanied publication of paper by Helen Warren et al. in Nature Genetics on "Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk: The UK Biobank Cardio-metabolic Traits Consortium Blood Pressure Working Group." P Elliott quoted ""Ultimately, blood pressure in the general UK population is too high, and we encourage everyone to maintain healthy lifestyles by eating properly and exercising enough, as this will reduce the risk of all sorts of diseases. However, our new findings may help doctors to identify earlier those who are most at risk of high blood pressure in mid-life and intervene to prevent that occurring." |
| Year(s) Of Engagement Activity | 2017 |
| Description | Press release re: JAMA publication on analysis to combine genetic results with patients' QRISK score to enhance knowledge of genetic variants linked to heart health |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release related to publication of JAMA paper on predictive accuracy of a Polygenic Risk Score for coronary artery disease resulted in a lot of interest within the research community and contacts to do comparative and further analyses. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.imperial.ac.uk/news/195398/gene-tests-heart-disease-risk-have/ |
| Description | Propionate has protective and anti-inflammatory effects on the blood-brain barrier - ARUK conference 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Allowed us to present our work on the interaction of the microbiome with host systems, and implications for neurodegenerative diseases. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Propionate has protective and anti-inflammatory effects on the blood-brain barrier - Dementia Symposium Imperial College London |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Dementia symposium held at Imperial College London to launch the Dementia Research Institute. Novel work presented to researchers who had not considered the gut microbiota and its metabolites could influence the blood-brain barrier and potentially contribute to health/disease. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Propionate has protective and anti-inflammatory effects on the blood-brain barrier - Exploring Human Host-Microbiome Interactions in Health and Disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented our work on propionate, which is available as a preprint and has been submitted for publication. Novel work not seen by members of the research community before. Led to many questions, and much interest in our work. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=637 |
| Description | ROIS International Workshop on Data Centric Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Invited speaker - ROIS (Research Organisation of Information and Systems) International Workshop on Data Centric Science, Feb 2015, Tokyo Japan, representing the Data Science Institute Imperial College. Also 1 day closed meeting with ROIS Institutes (together with Prof Yi-Ke Guo and Dr Martin Siegert, Grantham Institute) to discuss future collaborations and strengthening links with ROIS and Imperial through the Data Science Institute, in the areas of data-intensive sciences. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Regulatory effects of gut-derived methylamines on blood-brain barrier integrity - Exploring Human Host-Microbiome Interactions in Health & Disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Offered paper chosen for oral presentation to share our findings on dietary methylamines and the blood-brain barrier. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://coursesandconferences.wellcomegenomecampus.org/our-events/exploring-human-host-microbiome-in... |
| Description | Reza Salek - Talk Glasgow Poly-omics 10-11 August 2016, Metabolomics data analysis reproducibility: data sharing, data standards and workflows for metabolomics. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | gave talk -Metabolomics data analysis reproducibility: data sharing, data standards and workflows for metabolomics. to ~30 attendees. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Reza Salek - US NIHMetabolomics Common Funds, UCSD, San Diego, USA, 24-26 February 2016 - talk "Metabolomics Data sharing, MetaboLights and data standards." |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | gave presentation on Metabolomics Data sharing, MetaboLights and data standards to audiene of approx 60. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Sarah Butcher - key note speaker and co-presenter at European Bioinformatics Institute training workshop - Bioinformatics for Core Facilities - June 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training workshop - supported by the Core Faculities for the Life Sciences (CTLS) organisation, is aimed at aspiring, new and experienced managers of bioinformatics core facilities, or other facilities that support their users to analyse and interpret large biomolecular data sets. The course aims to introduce new ways of working, foster collaborations, as well as offer training support from experienced facility managers. As well as providing a keynote talk, I led several discussion areas, and also provided a seminar and discussion session for the back-to-back course Bioinformatics for PIs. Both courses were welll received, and are being run again in June 2018. In addition, an EMBO training grant has been submitted to enable the core facility course to be run in Turkey in 2019. |
| Year(s) Of Engagement Activity | 2017,2018 |
| URL | https://www.ebi.ac.uk/training/events/2017/bioinformatics-core-facility-managers |
| Description | Science and Engineering South Consortium - Research data management workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | Invited speaker for Science and Engineering South Consortium - Research data management workshop (March 2015, Imperial) |
| Year(s) Of Engagement Activity | 2015 |
| Description | Silvia Ottovani - poster at Cambridge Pancreatic Cancer Symposium 2017, Cambridge, United Kingdom |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | presented poster - TGF-ß regulating microRNAs as modulators of epithelial-to-mesenchymal transition, metastasis and stemness in pancreatic ductal adenocarcinoma. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Silvia Ottovani - poster at Non-coding RNAs in cancer and development. London, United Kingdom. May 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | presented a poster for discussion at the meeting Non-coding RNAs in cancer and development. London, United Kingdom. Poster title - TGF-ß regulating microRNAs as modulators of epithelial-to-mesenchymal transition, metastasis and stemness in pancreatic ductal adenocarcinoma. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Silvia Ottovani - poster presentation at meeting - Noncoding RNAs: Form, Function, Physiology. Keystone, Colorado, USA, Feb 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave poster presentation at international meeting - Noncoding RNAs: Form, Function, Physiology. Keystone, Colorado, USA. Poster title - TGF-ß induces miR-100 and miR-125b but blocks let-7a through co-regulation of lncRNA MIR100HG and LIN28B to mediate tumourigenesis in pancreatic ductal adenocarcinoma. The work has been written up for publication and is in review at present. |
| Year(s) Of Engagement Activity | 2018 |
| Description | UK Microbiome workshop - London 10 July 2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Innovate UK and the Microbiology Society organized a one-day workshop to facilitate academic-industrial engagement. "Identifying Cross Sectoral Challenges and Needs for Effective UK Microbiome Related Technology Exploitation" |
| Year(s) Of Engagement Activity | 2018 |
| Description | UK's Largest Careers Speed Networking Event for Young People, Lord's Cricket Ground (Lesley Hoyles) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | TeamLondon workshop facilitator for careers workshops aimed at school children. Schoolchildren came away with an overview of what jobs in a number of different sectors involve, and were made aware of opportunities they did not know were available to them for future careers -particularly in the sciences sector. Students left with increased awareness of careers available to them in science and other industries. |
| Year(s) Of Engagement Activity | 2017 |
| Description | University of Surrey, UK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Presented work to staff and students at University of Surrey Veterinary School. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Workshop facilitator - Regent High School Early Summer Fair |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Helped run school-organized activity for primary school children, arranged via STEMNET. Getting the students more interested in science using a fun activity. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Workshop on the e-Infrastructure part of the National Data Infrastructure |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Attendee on behalf of UK-MED BIO - 'Workshop on the e-Infrastructure part of the National Data Infrastructure' organised by the DiRAC National E-Infrastructure Project Directors Group Dec. 2014 (representing requirements for bio-medical compute and data storage) - output was feeding information on requirements to National E-Infrastructure Project Directors Group |
| Year(s) Of Engagement Activity | 2014 |
| Description | Workshop to advise researchers associated with the Indian microbiome project |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Part of invited panel of international researchers invited to attend workshop in Pune, India to advise the Indian microbiome project. |
| Year(s) Of Engagement Activity | 2018 |
| Description | eTRIKS-UBIOPRED-Clinical-Data-Analysis-Training - Professor Yi-KE Guo |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Professor Yi-Ke Guo conducted a series of web and face-to-face training to UbioPred scientists on clinical data analysis, AZ data anlysts and tranSMART users at NOVARTIS (UK), scientists (bioinformaticians, biologists, clinicians) at University of Southampton, GSK scientists etc. |
| Year(s) Of Engagement Activity | 2015,2016 |
| Description | invited talk (Reza Salek) at The CHARME of standardisation in life sciences workshop 21-22 June, Warsaw |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | gave invited tal on "Data sharing, standards and workflows in metabolomics; towards reproducibility in Metabolomics" at ELIXIR workshop in Warsaw, Poland. CHARME brings together various projects and collaborations in standardisation of life science data and facilitates information exchange, together with Elixir facilitators. CHARME will develop a framework to harmonise standards and formats in systems biology data. It will also act as a mediator between scientific standardisation efforts and relevant standardisation bodies and committees. The presented talk represented current staet of the art in data standards and sharing for metbolomics data. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://www.elixir-europe.org/news/charme-standardisation-life-sciences-21-22-june-warsaw |
| Description | webinar Dr Reza Salek - Metabolomics: molecules of life, an introduction. |
| 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 | The webinar gives an introductory tour of metabolomics. This webinar helps users to understand what metabolomics is and how it can be used to inform biological research. It also introduces the basics of the analytical technologies and data analysis methods commonly used in metabolomics Thwe webinar is available from the EBI training site. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.ebi.ac.uk/training/online/course/metabolomics-molecules-life-introduction?platform=hootsu... |
| Description | workshop facilitator for Turing House CoderDojo, coding club held once a term for children aged 7-11 (Lesley Hoyles) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | CoderDojo (https://coderdojo.com) Children got an introduction into coding in Scratch, python, arduino and html, and went away with worksheets to continue their learning at home in their own time. Children were enthusiastic about coding and wanted to learn more. |
| Year(s) Of Engagement Activity | 2016,2017,2018 |
| URL | https://turinghousecoderdojo.wordpress.com/ |