Cellular Genomics (CELLGEN): Consequences of somatic genome variation on traits
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
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.
Technical Summary
As a work package of the grant Cellular Genomics (CELLGEN) we will characterise somatic variation across the lifespan of organisms and determine how this influences traits
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- Oxford Nanopore Technologies (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- University of Sussex (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- UNIVERSITY OF MANCHESTER (Collaboration)
- Autonomous University of Madrid (Collaboration)
- University of Aberdeen (Collaboration)
- Johannes Gutenberg University of Mainz (Collaboration)
- Astrazeneca (Collaboration)
- QUADRAM INSTITUTE BIOSCIENCE (Collaboration)
- Technical University of Darmstadt (Collaboration)
- Tropic Biosciences Ltd (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
Publications
Etherington G
(2024)
Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features
in Yeast
Etherington GJ
(2024)
Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast.
in Yeast (Chichester, England)
Higgins J
(2024)
Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages.
in Annals of botany
Jibril A
(2023)
Plasma cell-derived mtDAMPs activate the macrophage STING pathway, promoting myeloma progression.
in Blood
Osorio-Guarin JA
(2024)
Genome-wide association analyses using multilocus models on bananas (Musa spp.) reveal candidate genes related to morphology, fruit quality, and yield.
in G3 (Bethesda, Md.)
Schindler D
(2023)
Design, construction, and functional characterization of a tRNA neochromosome in yeast.
in Cell
Shen A
(2023)
U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of C. elegans mRNAs.
in bioRxiv : the preprint server for biology
| Description | EDESIA DTP board |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.uea.ac.uk/research/research-with-us/postgraduate-research/latest-phds-and-research-stude... |
| Description | Boosting innovation in breeding for the next generation of legume crops for Europe |
| Amount | Ā£368,936 (GBP) |
| Funding ID | 10077978 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2023 |
| End | 02/2028 |
| Description | Connecting Research Culture Conference |
| Amount | Ā£59,558 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 05/2025 |
| Description | Earlham Institute and Tozer Seeds Limited KTP 23_24 R5 |
| Amount | Ā£176,013 (GBP) |
| Funding ID | 10102570 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2024 |
| End | 02/2027 |
| Title | Generation of Nanopore Q20+ long reads from seven triploid banana cultivars and three wild banana species |
| Description | ONT long reads generated by Transformative Genomics (GP) using R10 chemistry and P2 solo machine from fresh leave tissue: cv. Green Red (3n Red) cv. Pome (3n) cv Maia (3n Maia Maoli) cv. Guineo (3n) cv. Silver (3n Bluggloe) cv. curare (3n Plantain) cv. pelipita (3n Pelipita) M. ornata (2n WT) M. textilis (2n WT) M. velutina (2n WT) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | This dataset will be used in CELLGEN P 2.3 for Methods development: =ONT haplotype-resolved genome & epigenome =Pan-genome & Pan-epigenome variation graphs =Introgression and gene CNV analysis on the pangenome graph |
| Title | Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones |
| Description | File names indicate: The cell lines used (HeLa-S3 denoted as HeLa; hTert-RPE1 denoted as RPE1) as the first four characters of the file name; TE in the file name indicates that the sample was subjected to nCATS target enrichment sequencing (all other files are from genome-wide sequencing); BAM files include both alignment (to the GRCh38 human genome assembly) and BrdU modification probabilities in the mod.bam format; BED files list the location of left/right replication forks; initiation sites; termination sites as indicated. Experimental protocol: HeLa-S3 (adherent) and hTERT-RPE1 were maintained in DMEM Glutamax (HeLa-S3) or DMEM/F12 Glutamax (hTERT-RPE1, both Gibco), with the addition of 10% foetal bovine serum (Sigma) and 1% penicillin/streptomycin (Gibco). Cells were maintained at 70% confluency in 5% CO2 at 37 °C. Cells were treated with sequential addition of 0.5 µM BrdU every 2.5 minutes until 12 µM, followed by incubated for a further 1 hr at 12 µM BrdU High molecular weight genomic DNA extraction protocol For the target enrichment (TE; via nCATS) samples genomic DNA was prepared for sequencing with this protocol: dx.doi.org/10.17504/protocols.io.bmi5k4g6 Libraries were prepared with ONT Ligation Sequencing Kit (SQK-LSK109 or SQK-ULK001) Data processing steps: Basecalling was perform with guppy v6.1.5 Aligned reads to hg38 reference using minimap2 v2.17 Detected BrdU in reads using DNAscent v2.0.2 BrdU probabilities converted to mod.bam format with detect_to_modBAM script BrdU gradients, replication fork directions, replication initiation and replication termination sites identified with a custom Rscript |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | None. |
| URL | https://zenodo.org/doi/10.5281/zenodo.10827585 |
| Title | PRJEB62882: WGS from the 190 banana cultivars in the genebank used by the Colombian breeding programme |
| Description | Bananas and plantains (Musa spp.) are one of the most important crops worldwide. The cultivated varieties are vegetatively propagated, and their diversity is essentially fixed over time. Nevertheless, millennia of diversification and selection have led to hundreds of edible varieties. We aimed to characterise chromosomal exchanges and structural variation among lineages to understand shared foundational events and identify sources of allelic diversity in introgressed loci for genetic improvement. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | =Two publications in collaboration with the group =PhD project to explore PAV of NLR genes in this dataset =Discussion with another lab using a different technique to assess introgressions in the same species |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB62882 |
| Title | PRJEB86884: dosage-dependent phenotypic variation in allopolyploid banana cultivars |
| Description | This dataset includes Q20+ ONT (Nanopore) dataset generated from banana cultivars (varietal clonal lineages) and wild relatives with multiple subgenome compositions. We aim to investigate the association between copy-number variants (CNVs), homologous exchanges, gene dosage, and phenotypic variation in allopolyploid banana cultivars. The dataset serves also as the case to build new protocols for end-to-end ONT-based analysis of structural and epigenetic variation. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | Fusarium oxysporum f.sp. cubense (Foc) causes Panama disease in bananas. The new TR4 strain threatens the banana industry, particularly Cavendish (AAA) and Silk (AAB), which are highly susceptible. Resistance to TR4 exists in wild diploids (AA/BB), engineered cultivars, and some AAB/ABB varieties. In our CASE PhD with Tropic (2021-2025), we found that our cultivars respond differently to TR4 (unpublished) and analyzed NLR presence-absence variations among them. Limitations in short-reads and old single-haplotype references hinder accurate links to CNVs and dosage. However, this new long-read ONT dataset allows us to investigate the association between copy-number variants (CNVs), homologous exchanges, gene dosage, and phenotypic variation in allopolyploid banana cultivars. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB86884 |
| Title | Single cell RNA seq (10x) of immune cell in liver upon Slamonella typhimurium infection |
| Description | Single cell RNA seq (10x) of immune cell in liver upon Slamonella typhimurium infection in mice fed control or low protein diet |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Transcriptomic shifts in liver immune cells exposed to Salmonella typhimurium infection in animals fed control or low protein diet |
| Title | Single cell RNA sequencing of HSC, MkP, CFU-E including the lineage information recovered as RNA barcodes |
| Description | This dataset contains single cell RNA sequencing of blood stem cells, megakaryocytic progenitors, erythroid progenitors from control and platelet-depleted animals. Also lineage information-RNA barcodes are included in this dataset. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | This dataset enabled me to submit the manuscript, which is under revision. Furthermore, it allowed me to develop new collaborations with scientists from Australian National University and Cambridge University. |
| Description | Astrazeneca |
| Organisation | AstraZeneca |
| Department | Research and Development AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Analysis of long read bulk RNA-Seq for the detection of splicing variation in human cell lines under different conditions Additional collaborations with other groups at Astra Zeneca; Astra Zeneca visit to Earlham as part of Industry Seminar. |
| Collaborator Contribution | Experimental data (cell exposed to different compounds), sequencing data |
| Impact | Multidisciplinary collaboration combining molecular biologists and computational biologists |
| Start Year | 2023 |
| Description | CASE PhD with Tropic Biosciences |
| Organisation | Tropic Biosciences Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Our iCASE PhD project to answer fundamental questions on the diversity of immunity receptors in the Musa genus, and the relation of this diversity with genome composition and TR4 response. To contribute to developing resistant varieties, the project will build on genomic resources to identify candidate genes and alleles to facilitate future endeavours. |
| Collaborator Contribution | Tropic Biosciences is an NRP-based biotechnology company developing improved commercial varieties of banana and other tropical crops using CRISPR gene editing technologies. Tropic Biosciences has been developing novel Cavendish banana mutants that show resistance to TR4 or longer shelf lives. In addition to domain knowledge on banana and R genes, Tropic Biosciences will contribute their expertise on how to establish and propagate banana plantlets in CER control conditions, and how to perform fungal infection bioassays in banana plants. |
| Impact | One joint PhD studenship |
| Start Year | 2021 |
| Description | Collaboration - JS UEA |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration on the investigation of the implications of small RNAs during cardiomyocytes differentiation and implication of disruption We are analysing long read data from the iPSC, early differentiation, late differentiation |
| Collaborator Contribution | The collaborators provided cells for preparation of sequencing libraries and proteomic data |
| Impact | the collaboration is multidsiciplinary bringing together molecular biologists, cellular biologists, bioinformaticians |
| Start Year | 2024 |
| Description | Collaboration King College London |
| Organisation | King's College London |
| Department | Maurice Wohl Clinical Neuroscience Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Computational analyses of long read bulk and single cell data from human IPSCs with engineered mutation for Amyotrophic lateral sclerosis and derived neurons, bulk long reads RNA-Seq from mouse brains with human mutations for Amyotrophic lateral sclerosis |
| Collaborator Contribution | Generation of IPSC lines with causative mutations, generation of the mice lines with human mutation |
| Impact | The work is highly collaborative including clinicians, clinical geneticists, molecular biologists, cellular biologists, computational biologists |
| Start Year | 2023 |
| Description | Collaboration UEA Medical School |
| Organisation | University of East Anglia |
| Department | School of Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Computational analyses of long read data to assess polyAdenylation sites usage during cardiomyocytes maturation, both in wild type background and in cell lines with mutations for cardiac disorders |
| Collaborator Contribution | IPSC generation, cardiomyocytes maturation |
| Impact | Computational analyses of differential polyadenylation usage during cardiomyocytes maturation |
| Start Year | 2024 |
| Description | Earlham-Aberdeen collaboration |
| Organisation | University of Aberdeen |
| Department | School of Medical Sciences Aberdeen |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have trained a post-doc from the collaborators research group in experimental and computation technologies for single-molecule analysis of DNA replication. |
| Collaborator Contribution | The collaborators group have contributed technical expertise in the role of the Rif1 protein in regulation of DNA replication. |
| Impact | Ongoing collaboration. |
| Start Year | 2022 |
| Description | Earlham-Cai group engineering biology for synthetic chromosomes collaboration |
| Organisation | University of Manchester |
| Department | Manchester Institute of Biotechnology MIB |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Design, contribution of DNA parts and analysis of patterns of DNA replication for synthetic yeast chromosomes as part of Sc2.0. |
| Collaborator Contribution | Design, construction and analysis of synthetic yeast chromosomes. |
| Impact | Design, construction, and functional characterization of a tRNA neochromosome in yeast Daniel Schindler, Roy S.K. Walker, Shuangying Jiang, Aaron N. Brooks, Yun Wang, ..., Romain Koszul, Junbiao Dai, Lars M. Steinmetz, Jef D. Boeke, Yizhi Cai Cell · 01 Nov 2023 · doi:10.1016/j.cell.2023.10.015 Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome Yue Shen, Yun Wang, Tai Chen, Feng Gao, Jianhui Gong, ..., Junbiao Dai, Jef D. Boeke, Xun Xu, Yizhi Cai, Huanming Yang Science · 10 Mar 2017 · doi:10.1126/science.aaf4791 |
| Start Year | 2014 |
| Description | Earlham-Cardoso lab collaboration |
| Organisation | Technical University of Darmstadt |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Sharing of experimental and computational technologies for single molecule analysis of DNA replication |
| Collaborator Contribution | Sharing expertise in mouse DNA replication control. |
| Impact | Ongoing collaboration. |
| Start Year | 2022 |
| Description | Earlham-GDSC collaboration |
| Organisation | University of Sussex |
| Department | School of Life Sciences Sussex |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are contributing single-molecule expertise in DNA replication to our joint collaborative project to determine the role of Senataxins in protecting genome stability. This work is funded by a joint BBSRC grant. |
| Collaborator Contribution | The collaborators bring expertise in genome stability research and preliminary data on the role that Senataxins may play. |
| Impact | Ongoing collaboration. |
| Start Year | 2022 |
| Description | Earlham-Gutierrez collaboration |
| Organisation | Autonomous University of Madrid |
| Department | Centre for Molecular Biology Severo Ochoa |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Technical advice, nanopore sequencing and data analysis for detection of nascent DNA in material extracted from plant roots. |
| Collaborator Contribution | Plant growth optimisation and optimisation of high molecular weight DNA extraction. |
| Impact | None yet. |
| Start Year | 2023 |
| Description | Earlham-Ulrich group collaboration |
| Organisation | Johannes Gutenberg University of Mainz |
| Department | Institute of Molecular Biology (IMB), Mainz, Germany |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Sharing of genomic DNA resources for training R10 nanopore models for base analogue detection. |
| Collaborator Contribution | Incorporation of BrdU into yeast genomic DNA at various substitution levels (validated by MS) followed by R10 nanopore sequencing - data to be shared with Earlham for model training. |
| Impact | N/A |
| Start Year | 2023 |
| Description | Impact of low protein diet on liver function upon Salmonella infection |
| Organisation | Quadram Institute Bioscience |
| Department | Gut Health and Food Safety |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My team has performed FACS cell sorting and 10X analysis of immune cells in the liver. |
| Collaborator Contribution | Dr Beraza holds the project license enabling studies of the Salmonella infection and impact on liver function in M. musculus. Her team provided the expertise in immune cell isolation from the liver. |
| Impact | We have published the article: Low protein diet exerts protective effect on liver function upon Salmonella infection. Generated findings were a basis for a PhD project that will commence in October 2025 as a part of BBSRC DTP program. |
| Start Year | 2021 |
| Description | ONT Nanopore model training collaboration (betta) |
| Organisation | Oxford Nanopore Technologies |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are using protocols and pipelines shared by ONT to train computational models to detect base analogues in nanopore sequence data. |
| Collaborator Contribution | ONT have shared (under a developer agreement) protocols and pipelines (called 'betta') for nanopore model training. |
| Impact | This collaboration has resulted in a response mode grant award from BBSRC. |
| Start Year | 2023 |
| Description | Panhematopoietic clonal and molecular analysis using RNA-barcoding approach |
| Organisation | University of East Anglia |
| Department | School of Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I was performing FACS sorting of cells, isolated samples were included in published papers. |
| Collaborator Contribution | Dr Rushworth and his team provided wild type (C57Bl6, n=25) and PEPC Boy (n=20) mice and skills (intravenous injections). |
| Impact | Publications: 10.1172/JCI153157 10.1101/2022.05.16.491933 10.3389/fimmu.2022.1003006 10.1073/pnas.1913278116 10.1182/bloodadvances.2022007033 |
| Start Year | 2019 |
| Description | Tropic |
| Organisation | Tropic Biosciences Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We continue our collaboration with the biotech company Tropic related to their interest in improving copy number variation screening in order to further improve quality control in precision breeding of clonally propagated crops, such as banana. We contributed - Oxford Nanopore genome and epigenome sequencing Protocol and the variation analysis pipeline |
| Collaborator Contribution | Expertise in banana cell biology, tissue culture, micropropagation and production, samples of proprietary elite banana embryogenic cell lines developed at Tropic, expertise in genomic/bioinformatic analysis |
| Impact | Oxford Nanopore genome and epigenome sequencing Protocols New datasets |
| Start Year | 2023 |
| Description | Wellcome Trust Sanger Institute |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Computational analyses of single cell long read data (PacBio, ONT) for human IPSC and differentiated neuronal lineages (astrocytes, motor neurons) |
| Collaborator Contribution | Cells (IPSCs, derived neuronal lineages), sequencing data |
| Impact | The work is multidisciplinary bringing together cellular biologists, molecular biologists, and computational biologists |
| Start Year | 2023 |
| Title | Basecall2Assembly: v1.0 basecall and error correction pipeline for Nanopore Q20 reads |
| Description | Accurate basecalling of ONT nanopore reads is crucial for generating reliable and high-quality sequencing data for downstream analyses. Our SNAKEMAKE pipeline takes POD5 files with raw signals from the sequencer and generates corrected reads ready for haplotype-aware assembly. |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | In Oxford Nanopore Technology (ONT) sequencing, basecalling is the process of converting the electrical signals generated by DNA passing through a nanopore into a nucleotide sequence, while HERRO is a haplotype-aware error correction tool that improves the accuracy of ONT reads, particularly for ultra-long reads. HERRO uses a two-stage approach: all-vs-all alignment followed by haplotype-aware correction using a deep learning model, which helps to improve single-read accuracy. HERRO can improve the accuracy of ONT reads, leading to better genome assemblies and analyses. |
| URL | https://doi.org/10.5281/zenodo.15005310 |
| Title | Software and hands-on materials from EI nanopore modification course |
| Description | Software and hands-on materials associated with the nanopore modification course run by EI on 6-7 Feb 2024. Description of the course (copied from the course website) follows: "In this comprehensive two-day course, participants will learn how to use nanopore sequencing to detect DNA base modifications. Designed to be used to accompany the course and also for self-guided students. Click here to see the site generated from this github repository." |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Software and hands-on materials released to the public so that any person from anywhere in the world can follow along at their own pace. Also please see the entry associated with the corresponding training course run by EI. |
| URL | https://sathish-t.github.io/nanopore-mod-course/ |
| Title | scSQANTI |
| Description | https://github.com/ConesaLab/scSQANTI_devel |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | These developments enable users to assess data quality from single cell long read sequencing |
| URL | https://github.com/ConesaLab/scSQANTI_devel |
| Description | "Inside EI" instagram entry for EI Communications, 22nd June 2023. |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | EI Comms asked me to answer 3 simple questions for an "Inside EI" series of posts on Instagram. The questions were regarding my background and route into research, my current job and the things I enjoyed about working in research and at EI. This was written up and with a photo, the piece was put onto Instagram with a view to communicate to the peers and public about life at EI and the type of people that work at EI. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.instagram.com/p/CtyQHVBtc2D/?utm_source=ig_web_copy_link&igshid=MzRlODBiNWFlZA== |
| Description | "Inside EI" story on Instagram for the EI Comms team, May 2 2023. |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | EI Comms profiled me for an "Inside EI" post on Instagram. The inquiries delved into my personal and professional journey into research, my present role, and the aspects of research and working at EI that I find enjoyable. The responses, accompanied by a photo, were compiled and shared on Instagram with the aim of conveying insights to both colleagues and the public regarding the experiences at EI and the diverse individuals comprising the EI community. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.instagram.com/p/Cru0pcesmAS/?utm_source=ig_web_copy_link |
| Description | Analysing cell imaging data at scale with AI |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of the CellGen WP2, we wrote an article showcasing the partnership with the Earlham Institute and The Alan Turing Institute. The article focused on research being carried out by Sonia Fonseca, in the Wojtowicz Group at EI, and James Wilsenach at ATI, using an AI tool - FlowFI - to speed up the processing and analyses of cellular image data, primarily megakaryocytes. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/analysing-cell-imaging-data-scale-ai |
| Description | BBSRC Pioneer panel membership |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Membership of the BBSRC pioneer awards panel 2023 |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.ukri.org/opportunity/pioneer-awards-early-stage-frontier-bioscience-research/ |
| Description | BBSRC sLoLa Outlines panel |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Membership of the BBSRC strategic LoLa Committee. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.ukri.org/opportunity/strategic-longer-and-larger-slola-grants-frontier-bioscience-2023-t... |
| Description | CELLGEN project 2.1.1B working group |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Study participants or study members |
| Results and Impact | Regular meetings with our partner from UKHSA to discuss, plan and coordinate activities in CELLGEN project 2.1.1B. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Course co-organiser Single Cell Bioinformatics Course 2024 |
| 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 | Course on data analysis generated in single cell RNA sequencing experiments, 16 participants gained understanding in data analysis, interpretation and future directions in the single cell fields. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-bioinformatics-2024 |
| Description | Detection of DNA Base Modification using Nanopore Sequencing (06-07 Feb 2024) |
| 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 | In this new two-day online course, participants learnt how to use Oxford Nanopore Technologies (ONT) sequencing to detect DNA base modifications. The course covered experimental design, including important considerations for generating ultra-long Nanopore sequencing reads. Through a blend of lectures and hands-on sessions, attendees gained the skills necessary to analyse base modification profiles in various contexts. The course also explored relevant research case studies and practice visualising and manipulating base modification data using genome browsers and other tools. The course included: ā¢ Principles of base modification detection using Nanopore sequencing ā¢ Experimental considerations for generating ultra long Nanopore sequencing reads ā¢ Sequence alignment (minimap2) and data QC (pycoQC) ā¢ Hands-on experience with base modification detection (Nanopolish, DNAscent, Remora) ā¢ Visualisation and manipulation base modification data (IGV, modBAM) ā¢ Comparison of single molecule base modification detection approaches The course had 16 attendees including Undergraduates, Postgraduates, PhD Students, Post docs and Professors. The majority were from academic organisations, this included people from Australia, France, Kuwait, Spain and United States, alongside local and national attendees. Feedback was received from 12 attendees, all rated the trainers, overall quality, and organisation of the course as very good or excellent. 100% would recommend the course to others. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/detection-dna-base-modification-using-nanopore-sequencing |
| Description | EI Innovate 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration, specialising in agri-food, biotech, med-tech and public health. It provided plenty of networking opportunities and allowed us to gain insight into our ongoing collaborations, explain how our expertise and facilities can be accessed and discuss potential ideas for new collaborations. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | EI Innovate annual stakeholder engagement event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. EI Innovate events foster exciting and valuable conversations between academia and industry. An example of an exciting collaboration that resulted from a previous EI Innovate is the Hybrid Wheat Initiative, which connects 25 breeding companies and research institutes worldwide, to resolve the critical challenge of hybrid wheat. In 2023, we showcased our two new strategic programmes of research - Cellular Genomics and Decoding Biodiversity - and two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry. The programme included talks about Earlham expertise and capabilities, examples of collaborations, panel discussions, Innovation Showcase, exhibition, tours of the two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry, and networking. |
| Year(s) Of Engagement Activity | 2019,2020,2021,2022,2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | FTMA4, visit at MRC Stem cell institute, Cambridge |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | PDRA< RA and a group leader visited the lab at MRC Stem Cell Institute to gain practical knowledge and experience in new cell assays. Possibility of joint funding application. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Find My Future STEMM 2023 |
| 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 | FindMyFuture is an engagement event aimed at introducing Year 8 students to various STEMM careers. Members of EI chatted about their research and careers with the many students who visited our stand. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Hosting of MRes Evolution and Genomics student, LM |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Lucy Maddock is a UEA MRes student assigned to us from 15th January 2024 to carry out lab research project related to CELLGEN WP 2.2.3 looking at inducing ploidy changes in HAP1 cell cultures. She is here full time until September 2024 under my supervision. She requires to write up this project to be submitted as her masters research. Whilst here, Lucy will be embedded into the whole research culture - project work, lab meetings and journal clubs, seminars and other training. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.uea.ac.uk/course/postgraduate/mres-evolution-and-genomics |
| Description | Hosting of MRes Evolution and Genomics student, LM |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Lucy Maddock is a UEA MRes student assigned to us from 15th January 2024 to carry out lab research project related to CELLGEN WP 2.2.3 looking at inducing ploidy changes in HAP1 cell cultures. She is here full time until September 2024 under my supervision. She requires to write up this project to be submitted as her masters research. Whilst here, Lucy will be embedded into the whole research culture - project work, lab meetings and journal clubs, seminars and other training. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Hosting of Nuffield Research Placement Student (ML) at Earlham Institute, 24.07.23 - 03.08.23 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | The student came to gain work experience in the wet lab as part of the Nuffield Research Placement scheme for 2 weeks, where the goal was to generate NextGen sequencing libraries from cell pellets derived from yeast that had bee engineered to contain artificially, expanded short tandem repeats. This was completion of work from a pilot project of which the methods/data would be fed into progressing the work as part of the EI CELLGEN ISP. The NRP programme aims to provide engaging, hands-on research projects, where Year 12 students have the opportunity to make a meaningful contribution towards the work of a host organisation through a well-supervised but independent research collaboration relating to an area of science, quantitative social science, computing, technology, engineering or maths, or a combination of these disciplines. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.nuffieldresearchplacements.org/ |
| Description | Hosting of Nuffield Research Placement Student (RO) at Earlham Institute, 14.08.23 - 25.08.23 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | The student came to gain work experience in the wet lab as part of the Nuffield Research Placement scheme for 2 weeks, where the goal was to generate NextGen sequencing libraries from cell pellets derived from yeast that had bee engineered to contain artificially, expanded short tandem repeats. This was completion of work from a pilot project of which the methods/data would be fed into progressing the work as part of the EI CELLGEN ISP. The NRP programme aims to provide engaging, hands-on research projects, where Year 12 students have the opportunity to make a meaningful contribution towards the work of a host organisation through a well-supervised but independent research collaboration relating to an area of science, quantitative social science, computing, technology, engineering or maths, or a combination of these disciplines. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.nuffieldresearchplacements.org/ |
| Description | Hosting supervision of Nuffield Placement Student, EJ. |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Hosting of Nuffield Placement student, EJ, for 2 weeks. This involved carrying out a research project in the group. The placement also involved the student interacting with other areas at EI with other experiences such as journal clubs, lab meetings and delivering research presentations. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.nuffieldresearchplacements.org/ |
| Description | ISP all hands meetings FTMA4 |
| 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 | ISP all hands meeting allow the interaction amongst all the work package members. In addition to project and impact progress updates, workshops are held to drive discussion in areas such as IDEA, policy impact, futher funding opportunities and more. |
| Year(s) Of Engagement Activity | 2023,2024 |
| Description | Investigating accidents on the DNA highway |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Feature article on the Nieduszynski group's work on DNA replication. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/articles/investigating-accidents-dna-highway |
| Description | Invited seminar - Stockholm - What Your Are Missing Matters - Characterisation of novel splicing events across brain tissues and during development |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at a Oxford Nanopore Technology Event |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://nanoporetech.com/about/events/nanopore-days/nanopore-day-stockholm-2024#event-overview |
| Description | Invited speaker at Norwich Single Cell Symposium 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to talk about my research in front of an audience of around 80 experts on the topic, which sparked very interesting questions and conversations during networking sessions and had very positive feedback with potential for collaborations |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/norwich-single-cell-symposium-2024 |
| Description | Jacques-Monod conference on Transcription and Genome Maintenance 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Jacques-Monod conference 2024 was in France but has an international reach. This meeting has a focus on the various aspects of transcription and genome maintenance in all organisms. The conference was made up of session of short talks, posters, and keynote speakers. I presented a talk and a poster called "Single-molecule identification of replication fork pause sites around highly transcribed genomic loci using nanopore sequencing". Following my talk I had individuals reach out to learn more about the work we are doing. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://cjm3-2024.sciencesconf.org/?forward-action=index&forward-controller=index&lang=en |
| Description | Joint in person meeting with Carr group (University of Sussex) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | A two-day collaborator meeting at the University of Sussex, including the Carr group members. Each member of the extended project gave an oral presentation to update on research progress. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Leadership and Management Skills for Postdocs (hfp consulting), NBI, Norwich; 21st-23rd June 2023, |
| 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 | This was a 3 day workshop led by hfp consulting to learn tools/concepts regarding leadership and management skills. It was attended by postdocs, early career group leaders from across the NRP institutes (EI, JIC, TSL, QIB) from diverse backgrounds. The course was pitched perfectly with teaching based on flipcharts, simple models, interactive tasks, role playing and discussion. All participants were engaged, interacted really well with good energy and the response was overwhelmingly positive. The tools and concepts learnt will be highly useful in everyday working and personal life. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://hfp-consulting.com/services/#courses |
| Description | Lightning talk at Norwich Cancer Research Network Symposium 2024. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Based on my poster abstract, I was selected to give a 3 min-2 slide lightning talk about my research. It was an opportunity to highlight my work that is being carried out on the CellGen ISP, WP2, deliverable 2.2.1 and 2.2.3 and summarise my poster to the audience. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://cancerresearchnorwich.org.uk/ |
| Description | London Calling Meeting 2023 17th-19th May 2023 |
| 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 | The London Calling Meeting 2023 was a three-day hybrid event where scientists from different fields shared their latest research using nanopore sequencing. With a comprehensive list of events ranging from cancer research to transcriptome research, the conference offered a unique opportunity for attendees to learn about the latest developments in their field and beyond. The conference was organized around a series of events that cater to the diverse interests of researchers in different fields. The Masterclasses event covered a range of topics, from the basics of nanopore sequencing to more advanced topics such as machine learning and data analysis. In addition to attending the various events, I had the opportunity to network with fellow researchers, share my research, and discuss potential collaborations on new projects. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Low-protein diets offer protective effect during bacterial infection |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A news release based on a publication by Edyta Wojtowicz in partnership with the Quadram Institute, highlighting research looking into protein in diet and the immune system response. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/low-protein-diets-offer-protective-effect-during-bacterial-infection |
| Description | Norwich Nanopore Day (19 September 2024) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | The inaugural Norwich Nanopore Day offered a forum for researchers across the Norwich Research Park to discuss the latest developments and provide ample networking opportunities with other researchers to build a community of experts and initiate new collaborations. We brought together Norwich-based researchers who use nanopore sequencing technologies and those interested in discovering more about potential applications across a wide variety of species, together with expertise from Oxford Nanopore Technologies and New England Biolabs (with both also exhibiting). The event contained a programme of talks from scientists across the Norwich Research Park, and networking breaks. The event themes covered the application of nanopore sequencing in various protocols and systems including microbial, plant, animal and human health and disease. 94 people attended, including 13 speakers, with 10 attendees from Industry, 33 from EI and 45 from Academia outside of EI. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/events/norwich-nanopore-day-2024 |
| Description | Norwich Science Festival 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Save the Banana outreach activity to showcase EI's work on bananas. The Cavendish variety of bananas dominates the western world, accounting for around half of all bananas grown globally. These plants are a monoculture of genetic clones and the Cavendish is unable to adapt to change or threats. The pathogenic fungus Fusarium oxysporum f. sp. cubense, otherwise known as banana fusarium wilt or Panama disease, is devastating Cavendish plantations worldwide. Wild banana plants still grow in the tropics, and thousands of varieties are cultivated. De Vega and his Group are working to identify resistant plants. Once found, they will be examining the genome to find candidate resistance genes which could be edited into the Cavendish. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/bananas-are-brink-close-cousins-could-save-their-skins |
| Description | Norwich Science Festival 2025 |
| 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 | The Earlham Institute took two activities to the Norwich Science Festival, spending four days engaging people with our science. The first activity explored the soil microbiome and was linked to both the Decoding Biodiversity and Cellular Genomics ISPs, while the second looked at making medicines in plants and was just linked to Decoding Biodiversity. We engaged with hundreds of families, sparking an interest in our science and with many questions about related work. We also shared social posts about our attendance, which generated some positive engagement with our online followers. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://norwichsciencefestival.co.uk/ |
| Description | ON Helix New Horizons in Genetic Screening |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | 300 participants from private sector, NHS and academia attended ON Helix workshops over 4 days to discuss progress and challenges of personalised medicine, genetic screening to open up the discussion how to tackle new challenges the field encounters. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.onhelix.com/ |
| Description | PacBio webinar - Characterisation of transcript regulation in iPSCs and derived neuronal lineages |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at a webinar organised by PacBio on the use of novel libraries prep |
| Year(s) Of Engagement Activity | 2024 |
| Description | Participation in an open day or visit at my research institution - Hosting supervision of Nuffield Placement Student, MH. |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Hosting of Nuffield Placement student, MH, for 2 weeks. This involved carrying out a research project in the group. The placement also involved the student interacting with other areas at EI with other experiences such as journal clubs, lab meetings and delivering research presentations. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.nuffieldresearchplacements.org/ |
| Description | Pint of Science Norwich, 22nd May 2023 - "Our Body, From DNA to Diseases: Developing our Defences" theme, talk entitled "Why does my DNA keep repeating on me?" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | This talk was part of the national, annual Pint of Science festival and I gave a talk in the local branch of the participants (Norwich, Norfolk). The talk was 25 minutes long with 5 mins questions, with the aim to give an accessible insight into our research to the general public in a low-key, informal setting (local bar). There were good questions relating to the concepts/research that I described and feedback was very positive including "well-presented and clear" and appreciation for "sharing interesting work". |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://pintofscience.co.uk/event/from-dna-to-diseases-developing-our-defences |
| Description | Poster at Norwich Cancer Research Network (NCRN) symposium 2024 - Single-cell and spatial transcriptomics analysis of megakaryocytes in the healthy bone marrow |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster at Norwich Cancer Research Network (NCRN) symposium 2024, attended by around 100 scientists. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://cancerresearchnorwich.org.uk/ncrn-symposium-2024-please-register/ |
| Description | Poster presentation at CSHL DNA replication meeting - 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Presented a poster titled: Single molecule DNA replication dynamics of the human genome |
| Year(s) Of Engagement Activity | 2023 |
| Description | Poster presentation at the Molecular Haemopoiesis, 2024 |
| 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 | 250 researchers from around the world met to discuss most recent advance in molecular haematopoiesis and shared unpublished data. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Poster presentation of Norwich Cancer Research Network meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Presented a poster titled: Single molecule DNA replication dynamics of the human genome |
| Year(s) Of Engagement Activity | 2023 |
| Description | Poster presentations at Norwich Cancer Research Network Symposium 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Attendance at NCRN 2024 to present a poster - small meeting where researchers from NNUH, TSL, JIC, QIB, UEA came together to present/discuss research and to network. I was also awarded 3rd prize in the poster competition. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://cancerresearchnorwich.org.uk/ |
| Description | Presentation - Invited seminar - Norwich Cancer Research Network |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the CELLGEN ISP and Single cell genomics platform to the NCRN |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Invited talk -BioIndustry Association - Genomics Advisory Committee - Characterisation of novel potential targets through the characterisation of novel splicing events |
| 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 | Presentation as part of the Q1 genomics advisory committee meeting (BioIndusrty Association) |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation - Nucleic Acids Therapy Accelerator |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation to the research team of the Nucleic Acids Therapy Accelerator following meeting with Director at BIA meeting, discussion of interactions between NATA and EI, NATA showing interest in the platforms and services from EI. Discussion of potential collaborations with NATA around splicing regulation and setting up pilot projects |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation at Norwich Cancer research network |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | 20 scientists attended the presentation on new methods and their applications and how to implement them in their own research. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation at the Festival of Genomics and Biodata 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Presentation on RNA barcoding and its application to study the platelet biogenesis in different contexts. It sparked questions and the discussion on potential applications in other research groups and a potential interaction with the industrial partner. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://festivalofgenomics.com/london/en/page/home |
| Description | Presentation at the Innovation Showcase during EI Innovate 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | As part of the EI Innovate event in 2023, BDI team featured winners of the internal KEC Awards as part of the Innovation Showcase. JC, TB, JdV, WH, AH, JL presented their projects showcasing their KEC work - developing a spinout, a substantial collaboration, or a knowledge exchange activity with industry. EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | Presentation to John Innes Foundation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presented 'Data driven plant science' to John Innes Foundation Science subcommittee. This has helped secure continued funding for PGRs. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Quarterly Institution Strategic Programme Work package meetings |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | ISP work package meetings are hybrid and open to and involve all participants in the ISPs, including partners. The meetings include 1-3 oral presentations showcasing ongoing work and roundtable discussions on successes, barriers, and opportunities. |
| Year(s) Of Engagement Activity | 2023,2024,2025 |
| Description | Research group retreat |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | The whole research group participated in a retreat where each member gave an oral presentation that explored possible future research directions. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Researcher visit from Rijksuniversiteit of Groningen, Groningen, Netherlands |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar at EI on the history of clonal studies from bacteria to mammals, outlook into naturally occurring barcodes-possibilites and limitations. Discussion about new algorithms/pipelines to improve the analysis. Individual discussions on current practices and available pipelines. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Revised group website |
| 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 | Re-design of group website to raise external awareness of our research activities. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://dnareplicationlab.github.io/DNA-replication-group-website/ |
| Description | Scientists one step closer to rewriting world's first synthetic yeast genome |
| 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 | We press released new research about our involvement in engineering a chromosome entirely from scratch that will contribute to the production of the world's first synthetic yeast. The activity generated more than 10,000 impressions and almost 400 engagements on social. It was a joint study and the activity showcased our link to the other partners, helping to amplify the team science approach in this project. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/scientists-one-step-closer-rewriting-worlds-first-synthetic-yeast-gen... |
| Description | Single-cell show and tell |
| 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 | We organized the single-cell show and tell to showcase our equipment in the single-cell laboratories, talk about our workflows and provide some hands on lab experience to our colleagues within EI. We had 38 participants with different scientific and non-scientific backgrounds. The feedback was very positive, and most people would like to see other groups organize similar events. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Single-cell show-and-tell: Activity based tours of the EI single-cell labs |
| 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 | 40 staff from EI were given an interactive tour of the single-cell labs. We introduced them to the different platforms and concepts behind single-cell analysis. We hosted staff from operations, communications, business development and faculty, all staff at EI were invited. The event stimulated questions and discussion about both the biology and technology associated with single cell work. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Social post: Nuffield Foundation Students |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | We supported the Advanced Training programme by highlighting our support for the Nuffield Foundation Summer Research Placements. The aim of the post was to promote our support of the scheme for future applications. The post included details of the structure of the students time at EI, as well as quotes from EI staff who hosted the students. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.linkedin.com/posts/earlhaminstitute_nuffield-researchplacements-engineeringbiology-activ... |
| Description | Somatic variation in healthy organisms research project page |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Published a research webpage detailing the aims and activity from WP2 of the Cellular Genomics ISP - Somatic variation in healthy organisms. |
| Year(s) Of Engagement Activity | 2024,2025 |
| URL | https://www.earlham.ac.uk/research-project/somatic-variation-healthy-organisms |
| Description | Sphere Fluidics -Cambridge |
| 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 | PDRA, RA and Group Leader engaged with the industry-Sphere Fluidics to optimise bespoke microfluidc assays using their equipment. Obtained preliminary data for a grant application. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Starting point of DNA replication mystery solved - Professor Conrad Nieduszynski |
| 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 | Professional Practitioners |
| Results and Impact | Interview with Professor Conrad Nieduszynski to support publication and press release Starting point of DNA replication mystery solved |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://vimeo.com/manage/videos/1053392691 |
| Description | Talk to International Undergraduate Summer School |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | Gave a talk introducing the Earlham Institute, including the span of our research interests. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk to local business networking group TOAST at The Feed, Waterloo Park, Norwich. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | I presented a talk (previously presented at Pint of Science 2023) to a local business networking group about our project looking at engineering short tandem repeats in yeast. I had been approached by the chair of the group as they look to invite interesting speakers that are external to the group to give a talk. The group are Toast (https://www.toastnetworking.co.uk/) and meet once a week at 7.30am at the Feed Cafe to network and set up business relationships. At this particular meet, I spoke to around 20-25 people and my presentation sparked a good number of interesting questions. They asked if I would return again some time and also, they also asked if visiting EI as a group to see the labs and talk about our science (akin to an open day) was an option. So I felt this activity reached out to the general public, had a good, positive impact and showcased some of the work we do at EI. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Virtual participant at EMBO | EMBL Symposium. The ageing genome: from mechanisms to disease, 4th-7th June 2023. |
| 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 was attendance at a symposium focusing on the ageing genome with participants world-wide from a variety of inter-disciplinary laboratories. Attendance was pertinent as concepts, current/past research described in the presentations were related to the work that is being undertaken in the new CELLGEN ISP at EI. The symposium gave excellent background information in genomic instability, DNA damage and repair mechanisms, ageing and disease. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://iubmb.org/event/embo-embl-symposium-the-ageing-genome-from-mechanisms-to-disease/ |
| Description | Visit from NNUH clinicians to the Earlham Institute on 19 June 2023 |
| 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 | BDI team and IM of the Earlham Institute organised the visit from NNUH clinicians to the Earlham Institute. We held a workshop for researchers and clinicians to discuss their interests in developing potential collaborative projects that would utilise earlham expertise and capabilities and NNUH access to patients and patient data, and to the Norwich Biorepository. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Webinar 'Ask the PI' organised by International Society of Experimental Hematology (ISEH) |
| 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 | Small-group setting offers the perfect opportunity for trainees to learn about career transitions, gain expert insight, and build valuable connections.The event consisted of three rounds of breakout sessions, where participants got to meet and engage with multiple Junior Faculty for personalized conversations and insights on navigating their path to independence. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.iseh.org/page/2024NICAskthePIs |
| Description | Webinar: Optimizing Challenging Sample Types on the MerscopeĀ® Platform |
| 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 | Webinar about our experience using the Vizgen platform for spatial transcriptomics Merscope, with focus on challenging samples. Different research groups contacted EI after the webinar showing interest about the service provision side of our experience with Merscope. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://global-engage.com/product/optimizing-challenging-sample-types-on-the-merscope-platform/ |
| Description | Workshop and networking event between Earlham Institute and Oxford nanopore Technologies |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | 4 colleagues from ONT visited EI to expand a collaborative framework between ONT and Earlham, as part of collaborations with DECODE and CELLGEN ISPs. Key areas of the framework included last technological advances and protocols development in nanopore sequencing, data analyses, methylation and base modification, low input RNA seq and DNA base modifications, metagenomics and bacterial sequencing. Areas of interest for further collaboration and areas of joint research interests resulting in publications were identified. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Workshop for MRes students in Genomics and Evolution |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Workshop on capabilities enabled by single cell genomics, discussion of a selected scientific article. Critical assessment of the strengths and weaknesses of performed experiments. |
| Year(s) Of Engagement Activity | 2023 |