Earlham Institute UKRI Innovation Fellowships: BBSRC Flexible Talent Mobility Accounts
Lead Research Organisation:
Earlham Institute
Department Name: Directorate Office
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
People |
ORCID iD |
| Neil Hall (Principal Investigator) |
Publications
Bohar B
(2022)
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists
in F1000Research
Bohar B
(2021)
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists.
in F1000Research
Brooks-Warburton J
(2022)
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis.
in Nature communications
Concia L
(2020)
Wheat chromatin architecture is organized in genome territories and transcription factories.
in Genome biology
Dumur T
(2019)
Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions.
in Nucleus (Austin, Tex.)
Mistry JJ
(2019)
ROS-mediated PI3K activation drives mitochondrial transfer from stromal cells to hematopoietic stem cells in response to infection.
in Proceedings of the National Academy of Sciences of the United States of America
| Description | We have developed new software for use in personalized medicine which ioverlays SNP data onto gene networks (iSNP) Our single cell analysis work has beed used for preliminary data for a successful wellcome Trust fellowship. We have also developed tools for the analysis of insect microbiomes that is being applied to the development of insect protein for animal feed. We have made links with academic and industrial collaborators in Germany to develop genomic tools to study immunity genes in Sugar Beet |
| Exploitation Route | These various project have built strong links with industry and international groups and they will continue after the award. |
| Sectors | Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Description | We have used this funding to develop new collaborations with industry as well as academic groups internationally. We have developed pipeline for the analysis of microbiomes that affect productivity in the food industry. Developed new software for the integration of data that can be applied to personalised medicine - this software is being developed for a spinout. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Description | Membership of Future Leaders Fellowship Panel |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Unravelling key regulators of thrombopoiesis using a novel RNA based clonal and molecular approaches |
| Amount | £300,000 (GBP) |
| Funding ID | 213731/Z/18/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2019 |
| End | 05/2023 |
| Title | Sherlock - big data analytics platform for bioinformatics data |
| Description | The Sherlock tool is utilizing standard, open source big data technologies (like S3, Presto and docker) in order to execute simple analytical SQL queries on top of the integrated bioinformatics data organized into an S3-based data lake. |
| Type Of Material | Data analysis technique |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The method will help to increase the productivity of data heavy bioinformatics projects, easing the data cleaning, filtering and integration related tasks which are usually the first steps in each complex bioinformatics pipeline. Github link : https://github.com/NetBiol/sherlock |
| Description | Collaboration: Evolvability of constrained systems - the effects of genome duplication in a ligand-receptor model |
| Organisation | Okinawa Institute of Science and Technology |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | We hosted Stefano Pascarelli (Okinawa Institute of Science and Technology, Japan) for two months (Sept to Nov 2018) to work on a collaborative project looking at the evolvability of constrained systems. Owing to our expertise in vertebrate genomics and molecular evolution, we were able to share fish genomic data generated as part of other ongoing projects for the purpose of studying the effects of genome duplication in a ligands-receptor model in vertebrate genomes, fishes in particular. Furthermore, the use of our high-performance computing was beneficial for reconstructing large phylogenies and multiple sequence alignments. |
| Collaborator Contribution | Given Stefano's experience of protein engineering and evolution, he could apply techniques to 1) Analyse the evolution of EGFR in vertebrates using phylogentic approaches; 2) analyse the structural comparison of EGFR 3D models of duplicated vertebrate genes; and 3) analyses of the molecular docking for PPI prediction of the previous point models with human ligands. |
| Impact | This is a multi-disciplinary colloboration leveraging genomic, proteomic and transcriptomic data and using systems biology, phylogenetic and molecular evolution techniques to study the EGFR ligand system and it's evolution in vertebrates. As such, the collaboration formed a vital aspect of Stefano's PhD thesis (which he successfully defended) and involved the analysis of EGFR duplications across fish lineages and it's impact on phenotypic diversity. Furthermore, it has enabled him to develop hypothesis and aims for future collaborative grant applications aimed at unveiling the functional novelty produced by gene duplication. This will involve better understanding the molecular traces of evolution at the fine-grained, functional protein residue level in a system of duplicated genes. |
| Start Year | 2018 |
| Description | KWS Harnessing wild sugar beet diversiy |
| Organisation | KWS Group |
| Country | Germany |
| Sector | Private |
| PI Contribution | Knowledge of the wild and agricultural beet rust pathosystem combined with NGS expertise meant that we could put together PhD proposal which offered an opportunity to be able to develop new methods which could help identify novel pathogen resistance directly in wild hosts. |
| Collaborator Contribution | KWS provided input to the project design have promised significant resource (cost and in kind) to allow controlled trials and sequencing to take place. KWS have also granted access to the use of their labs for cloning and other biotechnology. |
| Impact | This collaboration resulted in a successful PhD iCASE application which will begin later 2019. |
| Start Year | 2018 |
| Description | Livestock gut microbiome 'fingerprinting' with Entomics |
| Organisation | Entomics Biosystems |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We have been working with Entomics to apply nanopore sequencing and metagenomic analysis approaches to understanding salmon fish microbiomes and the effect of different feeding regimes. We have brought nanopore sequencing and bioinformatics knowledge to the partnership. |
| Collaborator Contribution | Entomics have expertise in developing livestock feeds |
| Impact | Sequencing datasets and preliminary analysis. An application for further funding from the FTM to expand the research. |
| Start Year | 2018 |
| Description | Feature article on genomics in the Easton Daily Press |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | The Article was to cover the research activity at the Earlham Institute and at the Norwich Research park and how it would impact the general public |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited speaker Nordic Beet Research (Denmark) |
| 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 | Invited to the the NBR in Denmark to discuss how ash dieback invasions can teach us about how agricultural pathogen invaders in sugar beet rust. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited speaker: Aarhus University (Denmark) |
| 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 the Aarhus University departmental seminar series to talk about ash dieback invasions and sugar beet rust experiments. |
| Year(s) Of Engagement Activity | 2018 |