Accelerated discovery of functional non-coding genomic variation using single molecule real-time (SMRT) sequencing.
Lead Research Organisation:
UNIVERSITY OF EXETER
Department Name: University of Exeter Medical School
Abstract
The last decade has seen tremendous advances in our understanding about the role of genetic variation in health and disease, driven largely by developments in technology for sequencing the genome. Genes involved in a spectrum of debilitating disorders and health-related traits have been identified, including many by researchers at the University of Exeter Medical School, and these discoveries are starting to directly impact upon clinical practice. Despite this success, however, many regions of the genome remain hidden to contemporary first- and second-generation sequencing approaches. These include highly complex stretches of repetitive DNA and regions harbouring other types of genetic variation such as deletions and duplications. Furthermore, because the sequencing reads generated by current approaches are relatively short, they cannot be used to examine the long-distance relationships between more distal variants, nor explore the extent to which different genes are expressed in different versions in health and disease. Finally, most focus in disease genetics has been on regions of the genome that actually encode specific genes, ignoring the role of regulatory variation occurring outside of these regions. Of note, current sequencing approaches cannot be used to directly detect the presence of non-sequence-based epigenetic modifications and explore their role in disease. In this application we are requesting funds to support the acquisition of "third generation" sequencing technology, which will enable us to fully characterise genomic complexity. We are also requesting funds to support the high-performance computing infrastructure needed to store and analyse this complex data. Our aim is to advance genomics research into diabetes, neurological and other medical conditions by defining functional genetic and epigenetic variation in non-coding regions of the human genome.
Technical Summary
We are requesting funds to develop our genomic sequencing infrastructure, primarily through the acquisition of a Pacific Biosciences single molecule real-time (SMRT) sequencing system, making us one of only a handful of institutes in Europe to have such capability. This system will enable us to assay, identify and analyse regions of the genome hidden from current methods for gene discovery, and facilitate research into the functional mechanisms involved in disease. The Pacific Biosciences RS II SMRT Sequencing System provides the highest consensus accuracy and longest read lengths of any sequencing technology; current average read-lengths are >8.5kb (with a maximum of ~50kb). SMRT sequencing will facilitate advances in disease characterisation, stratification and diagnosis via its unique utility for de novo assembly across highly complex regions of the genome, targeted re-sequencing, long-range phasing of genetic variation, and epigenomic analysis via the direct allele-specific detection of modified DNA bases. We will also develop our High-Performance Computing/Informatics Infrastructure to enable the storage, analysis, alignment, and assembly of SMRT sequencing data. This infrastructure investment will enable the world-leading genetic and epigenetic research groups at the University of Exeter Medical School to further develop their innovative program of clinical genomic research in human disease, with a specific focus on diabetes and neurological phenotypes.
Planned Impact
In addition to other scientists (especially other and research groups investigating the role of genetics in diabetes and neurological diseases) the data generated using the new sequencing infrastructure has the potential to impact on a number of other beneficiaries. These include patients, the pharmaceutical industry, health service providers, and academic groups investigating the causes of other disease phenotypes and functional genomics. Existing genetics research by Exeter groups has already made significant impact in terms of understanding the causes of disease and the mechanisms behind disease progression (see description in the Case for Support), with tangible patient benefit. For example, Professor Hattersley's group discovered that patients with neonatal diabetes caused by K-ATP channel mutations demonstrate a remarkable improvement in glycaemic control when sulphonylurea tablets replace insulin injections. Quality of life has also been improved for many patients with maturity onset diabetes of the young (MODY) who have either stopped treatment or transferred from insulin to sulphonylureas as a consequence of their genetic diagnosis. The ability of SMRT sequencing to interrogate regions of the genome hidden from second generation sequencing, in addition to epigenetic and transcriptomic variation, will identify additional pathways to disease that we hope to have similar impact on clinical diagnosis, prognosis, and treatment.
Organisations
- UNIVERSITY OF EXETER (Lead Research Organisation)
- Aarhus University (Collaboration)
- University College London (Collaboration)
- UK Biobank (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- Princeton University (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- Twist Bioscience (Collaboration)
- Eli Lilly & Company Ltd (Collaboration)
- Icahn School of Medicine at Mount Sinai (Collaboration)
- Cambridge Epigenetix (Collaboration)
- UNIVERSITY OF ESSEX (Collaboration)
- University of Virginia Medical Center (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
Publications
Laver TW
(2016)
Pitfalls of haplotype phasing from amplicon-based long-read sequencing.
in Scientific reports
Harrison J
(2016)
Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants.
in Genome announcements
Dunthorn M
(2017)
Meiotic Genes in Colpodean Ciliates Support Secretive Sexuality
Tennant RK
(2017)
Metagenomic Analysis of Silage.
in Journal of visualized experiments : JoVE
Dunthorn M
(2017)
Meiotic Genes in Colpodean Ciliates Support Secretive Sexuality.
in Genome biology and evolution
Pass DA
(2017)
Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.
in PLoS genetics
Sambles C
(2017)
Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii.
in MicrobiologyOpen
Jeffries AR
(2017)
Profiling Regulatory Variation in the Brain: Methods for Exploring the Neuronal Epigenome.
in Biological psychiatry
Title | Additional file 10: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S6. Phylogenetic relationship of 67 C. burnetii isolates based on partial genome content. A) Core genome-based tree determined by Roary, B) Core genome-based tree determined by BPGA, C) Accessory (binary) genome-based tree determined by Roary, and D) Pan genome-based tree determined by BPGA. Newick outputs of both BPGA and Roary pipelines were used to draw trees using FigTree, and Genomic Groups were color coded. All trees were rooted along the branch leading to GG IV (see Methods). (TIF 3891 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_10_of_Extensive_genome_analysis_of_Coxi... |
Title | Additional file 10: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S6. Phylogenetic relationship of 67 C. burnetii isolates based on partial genome content. A) Core genome-based tree determined by Roary, B) Core genome-based tree determined by BPGA, C) Accessory (binary) genome-based tree determined by Roary, and D) Pan genome-based tree determined by BPGA. Newick outputs of both BPGA and Roary pipelines were used to draw trees using FigTree, and Genomic Groups were color coded. All trees were rooted along the branch leading to GG IV (see Methods). (TIF 3891 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_10_of_Extensive_genome_analysis_of_Coxi... |
Title | Additional file 12: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S7. New gene plots after BPGA pan-genome subset analysis using groups of isolates according to their genomic group associations. Proteins annotated using PROKKA were used as input files. The protein similarity threshold for protein clustering was 90%. Genomic groups were assigned as seen in Fig. 1. Note that â newâ genes represent polymorphic variants due to the presence of SNPs in existing genes rather than newly acquired genes. (TIF 404 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_12_of_Extensive_genome_analysis_of_Coxi... |
Title | Additional file 12: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S7. New gene plots after BPGA pan-genome subset analysis using groups of isolates according to their genomic group associations. Proteins annotated using PROKKA were used as input files. The protein similarity threshold for protein clustering was 90%. Genomic groups were assigned as seen in Fig. 1. Note that â newâ genes represent polymorphic variants due to the presence of SNPs in existing genes rather than newly acquired genes. (TIF 404 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_12_of_Extensive_genome_analysis_of_Coxi... |
Title | Additional file 5: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S1. Phylogenetic relationship of 76 sequenced C. burnetii isolates based on core-SNPs. SNP-based phylogenetic relationship (left-hand side) and SNP density plot (right hand side) of all available C. burnetii genomes established with Parsnp and visualized with Gingr. SNPs are highlighted in magenta in the density plot, whereas highly conserved regions are highlighted with grey shading. The tree was rooted along the branch leading to GG IV (see Methods). (TIF 6933 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 5: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S1. Phylogenetic relationship of 76 sequenced C. burnetii isolates based on core-SNPs. SNP-based phylogenetic relationship (left-hand side) and SNP density plot (right hand side) of all available C. burnetii genomes established with Parsnp and visualized with Gingr. SNPs are highlighted in magenta in the density plot, whereas highly conserved regions are highlighted with grey shading. The tree was rooted along the branch leading to GG IV (see Methods). (TIF 6933 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 6: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S2. Novel SNP profiles and their position within the adaA region. SNP profiles (A) and sequence alignment of the in silico generated adaA regions (B) were obtained after progressive MAUVE alignment using strain RSA493 (GG I) as a reference. SNPorig = GG II-a, SNPV2 = GG II-b, SNPV3 = GG III. Note that the original SNP within the adaA CDS described by Frangoulidis et al. (PLoS ONE 8:e53440, 2013, doi: 10.1371/journal.pone.0053440) corresponds to position 2097 in the adaARef. region. Unique, identifying SNPs are highlighted as colored vertical lines in panel B). (TIF 1293 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_6_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 6: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S2. Novel SNP profiles and their position within the adaA region. SNP profiles (A) and sequence alignment of the in silico generated adaA regions (B) were obtained after progressive MAUVE alignment using strain RSA493 (GG I) as a reference. SNPorig = GG II-a, SNPV2 = GG II-b, SNPV3 = GG III. Note that the original SNP within the adaA CDS described by Frangoulidis et al. (PLoS ONE 8:e53440, 2013, doi: 10.1371/journal.pone.0053440) corresponds to position 2097 in the adaARef. region. Unique, identifying SNPs are highlighted as colored vertical lines in panel B). (TIF 1293 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_6_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 7: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S3. Summary of genotyping and phylogenetic analyses. The ParSNP tree obtained after whole-genome alignment (see Fig. 1) was complemented with data from in silico plasmid typing, Acute Disease Antigen A (adaA) typing, and Multi-Spacer Sequence (MST) typing. Assumed or published data (shown in brackets) was used when typing results were inconclusive or data was missing. (TIF 2679 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_7_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 7: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S3. Summary of genotyping and phylogenetic analyses. The ParSNP tree obtained after whole-genome alignment (see Fig. 1) was complemented with data from in silico plasmid typing, Acute Disease Antigen A (adaA) typing, and Multi-Spacer Sequence (MST) typing. Assumed or published data (shown in brackets) was used when typing results were inconclusive or data was missing. (TIF 2679 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_7_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 8: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S4. Phylogenetic relationship between MST20 (GG III) isolates. A maximum-parsimony tree was reconstructed based on 82 SNPs defined by Olivas et al. (Microb. Genom. 2016, 2(8):e000068) using RSA493 as a reference and to root the tree. MST20 sub-genotypes (GT_20.1-3) as defined by Olivas et al. are colour coded. (TIF 301 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_8_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 8: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S4. Phylogenetic relationship between MST20 (GG III) isolates. A maximum-parsimony tree was reconstructed based on 82 SNPs defined by Olivas et al. (Microb. Genom. 2016, 2(8):e000068) using RSA493 as a reference and to root the tree. MST20 sub-genotypes (GT_20.1-3) as defined by Olivas et al. are colour coded. (TIF 301 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_8_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 9: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S5. Core-Pan-genome plots and gene frequency plots for 67 C. burnetii genomes. Proteins annotated using PROKKA were used as input files for BPGA (A&C) and Roary (B&D) pan-genome analyses. The protein similarity threshold for protein clustering was 90% in all cases. Core-Pan-genome plots (A&B) and gene frequency plots (C&D) are shown. (TIF 368 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_9_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 9: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Figure S5. Core-Pan-genome plots and gene frequency plots for 67 C. burnetii genomes. Proteins annotated using PROKKA were used as input files for BPGA (A&C) and Roary (B&D) pan-genome analyses. The protein similarity threshold for protein clustering was 90% in all cases. Core-Pan-genome plots (A&B) and gene frequency plots (C&D) are shown. (TIF 368 kb) |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/Additional_file_9_of_Extensive_genome_analysis_of_Coxie... |
Description | AMP-CMD - Functional genomic annotations in human brain regions implicated in BMI and obesity |
Amount | £153,297 (GBP) |
Organisation | Foundation for the National Institutes of Health (FNIH) |
Sector | Charity/Non Profit |
Country | United States |
Start | 12/2022 |
End | 12/2024 |
Description | ARUK Project Grant |
Amount | £433,549 (GBP) |
Funding ID | ARUK-PG2018B-016 |
Organisation | Alzheimer's Research UK |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2019 |
End | 02/2022 |
Description | Accelerating genetic research in Exeter with the Illumina NovaSeq 6000 DNA Sequencing System |
Amount | £616,706 (GBP) |
Funding ID | 218247/Z/19/Z |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2019 |
End | 10/2020 |
Description | Building on Brains for Dementia Research (BDR): A UK Nervous Tissue Network (UKNTN) for the Twenty-first Century |
Amount | £1,855,571 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2022 |
End | 10/2025 |
Description | CASE STUDENTSHIP |
Amount | £100,000 (GBP) |
Funding ID | MR/P016227/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 08/2017 |
End | 09/2021 |
Description | Defining Best Practises for Data Science Education across Disciplines |
Amount | £16,191 (GBP) |
Organisation | Alan Turing Institute |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2023 |
End | 01/2024 |
Description | Developing a blood test for the early detection of ALS |
Amount | $100,000 (USD) |
Organisation | The ALS Association |
Sector | Charity/Non Profit |
Country | United States |
Start | 12/2022 |
End | 01/2025 |
Description | Developing a blood test for the early detection of neurodegenerative disease using cell-free DNA |
Amount | £68,339 (GBP) |
Organisation | Alzheimer's Research UK |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 04/2023 |
End | 05/2025 |
Description | Development of software to model multi-modal genomic data as an integrated system: application to understanding the gene regulatory landscape |
Amount | £823,688 (GBP) |
Funding ID | EP/V052527/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 11/2021 |
End | 10/2026 |
Description | Dysregulation of RNA processing as a driver in Amyotrophic Lateral Sclerosis |
Amount | £988,532 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 05/2024 |
End | 06/2027 |
Description | Establishment of a single cell isolation platform for identification of heavy and light1 chains in the antibody repertoire using PacBio sequencing" MRC Proximity to Discovery Grant, University of Exeter (S.Pagliara & K.Paszkiewicz, £137,427 |
Amount | £137,427 (GBP) |
Organisation | University of Exeter |
Sector | Academic/University |
Country | United Kingdom |
Start | 03/2016 |
End | 12/2016 |
Description | Exploring the role of epigenetic mechanisms in the manifestation of Huntington's disease |
Amount | £1,248,387 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2024 |
End | 03/2027 |
Description | NARSAD YOUNG INVESTIGATOR [EILIS HANNON] |
Amount | $70,000 (USD) |
Organisation | Brain & Behaviour Research Foundation |
Sector | Charity/Non Profit |
Country | United States |
Start | 01/2018 |
End | 12/2019 |
Description | Research grant |
Amount | £1,012,743 (GBP) |
Funding ID | MR/R005176/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 01/2018 |
End | 12/2020 |
Description | SFARI Research Grant |
Amount | $975,000 (USD) |
Organisation | Simons Foundation |
Sector | Charity/Non Profit |
Country | United States |
Start | 02/2018 |
End | 02/2021 |
Description | The Autism Prenatal Sex Differences (APEX) study |
Amount | $16,000,000 (USD) |
Organisation | Simons Foundation |
Sector | Charity/Non Profit |
Country | United States |
Start | 01/2022 |
End | 01/2027 |
Description | University of Exeter - SMRT Pump-priming funds |
Amount | £50,000 (GBP) |
Organisation | University of Exeter |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2016 |
End | 07/2016 |
Title | Barcoded and targeted cDNA library preparation for Oxford Nanopore Technologies sequencing |
Description | The NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module (NEB) was adapted for the purpose of adding Oxford Nanopore Technologies (ONT) compatible barcodes during reverse transcription of RNA. This is a useful process for multiplexing low input samples for ONT transcriptome library preparation. An optional step before ONT library preparation is the targeted enrichment of cDNA molecules using IDT hybridisation probes. Here we provide a protocol for this process based on the 'PacBio cDNA capture using IDT xGen Lockdown Probes' protocol. Using this approach, up to 100 samples can be barcoded with individual ONT barcodes via reverse transcription. Samples can then be pooled together and a cDNA PCR amplification performed. This allows sufficient material for cDNA enrichment and/or ONT ligation sequencing library preparation. |
Type Of Material | Technology assay or reagent |
Year Produced | 2024 |
Provided To Others? | Yes |
Impact | Requests for more information on our protocol. |
URL | https://www.protocols.io/view/barcoded-and-targeted-cdna-library-preparation-for-kqdg3xzwzg25/v1 |
Title | Fluorescence-activated nuclei sorting (FANS) on human post-mortem cortex tissue enabling the isolation of distinct neural cell populations for multiple omic profiling |
Description | Increased understanding of the functional complexity of the genome has led to growing recognition about the role of epigenetic/transcriptional variation in health and disease. Current analyses of the human brain, however, are limited by the use of "bulk" tissue, comprising a heterogeneous mix of different neural cell types. Because epigenetic processes play a critical role in determining cell type-specific patterns of gene regulation it is important to consider cellular composition in regulatory genomic studies of human post-mortem tissue, and there is a need for methods to purify populations of specific cell-types. Furthermore, the valuable nature of human post-mortem tissue means it is important to use methods that maximize the amount of genomic data generated on each sample. This protocol describes a method that uses fluorescence-activated nuclei sorting (FANS) to isolate and profile nuclei from multiple different human brain cell-types from frozen post-mortem tissue. This protocol can be used to robustly purify populations of neuronal (NeuN+ve), oligodendrocytes (SOX10+ve), microglia (IRF8+ve) and other glial origin nuclei (NeuN-ve/SOX10-ve/IRF8-ve) from adult post-mortem frozen brain, with each tissue sample yielding purified populations of nuclei amenable to simultaneous analysis of i) DNA modifications (via bisulfite sequencing / array), ii) histone modifications (via CUT&Run-seq), iii) open chromatin analysis (via ATAC-seq), and iv) gene expression (via RNA-seq). |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | This method for isolating purified nuclei populations from human cortex is being widely used by us and other groups to undertake work into the genomic underpinnings of disease. |
URL | https://www.protocols.io/view/fluorescence-activated-nuclei-sorting-fans-on-huma-bmh2k38e.html |
Title | Purification of human cortex excitatory neuron nuclei from fetal and postnatal tissue using fluorescent activated nuclei sorting (FANS) in combination with a SATB2 antibody. |
Description | Increased understanding of the functional complexity of the genome has led to growing recognition about the role of epigenetic/transcriptional variation in health and disease. Current analyses of the human brain, however, are limited by the use of "bulk" tissue, comprising a heterogeneous mix of different neural cell types. Because epigenetic processes play a critical role in determining cell type-specific patterns of gene regulation it is important to consider cellular composition in regulatory genomic studies of human post-mortem tissue, and there is a need for methods to purify populations of specific cell-types. This protocol builds on a previous protocol that uses fluorescence-activated nuclei sorting (FANS) to isolate and profile nuclei from multiple different human brain cell-types from frozen post-mortem tissue. Because NeuN is not an optimal marker for neuronal nuclei from fetal cortex, we have optimized a method using a SATB2 antibody to purify nuclei from excitatory neurons in both fetal and postnatal cortex. Purified populations of nuclei are amenable to simultaneous profiling of i) DNA modifications (via bisulfite sequencing / array), ii) histone modifications (via CUT&Tag), iii) open chromatin analysis (via ATAC-seq), and iv) gene expression (via RNA-seq). |
Type Of Material | Technology assay or reagent |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | This protocol has been used by several other groups and in our own work on the developing human brain. |
URL | https://www.protocols.io/view/purification-of-human-cortex-excitatory-neuron-nuc-b4efqtbn.html |
Title | Additional file 3: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S1. Details of B. thailandensis strain E555 genes and proteins. (XLSX 6051 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_3_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 3: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S1. Details of B. thailandensis strain E555 genes and proteins. (XLSX 6051 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_3_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 4: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S2. Gene expression results and details of the genes subjected to RT-qPCR analysis. (XLSX 15 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_4_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 4: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S2. Gene expression results and details of the genes subjected to RT-qPCR analysis. (XLSX 15 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_4_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 4: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Data File S1. Raw data for in silico MST genotyping and pan-genome analyses. Data Sheets A) Strain Overview; B) In silico MST genotyping results; C) Gene Sequence Identity Scores; D) BPGA results _ all strains; E) BPGA results _ Genomic-Group-specific proteins; F) Scoary output _ pan-GWAS significant associations; G) snippy output_merged vcf file; H) ParSNP output _ vcf file; I) MST20_SNP_Matrix. (XLSX 12334 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_4_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 4: of Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups |
Description | Data File S1. Raw data for in silico MST genotyping and pan-genome analyses. Data Sheets A) Strain Overview; B) In silico MST genotyping results; C) Gene Sequence Identity Scores; D) BPGA results _ all strains; E) BPGA results _ Genomic-Group-specific proteins; F) Scoary output _ pan-GWAS significant associations; G) snippy output_merged vcf file; H) ParSNP output _ vcf file; I) MST20_SNP_Matrix. (XLSX 12334 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_4_of_Extensive_genome_analysis_of_Coxie... |
Title | Additional file 5 of Islet-expressed circular RNAs are associated with type 2 diabetes status in human primary islets and in peripheral blood |
Description | Additional file 5. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Islet-expressed_circular_RNAs_are_... |
Title | Additional file 5 of Islet-expressed circular RNAs are associated with type 2 diabetes status in human primary islets and in peripheral blood |
Description | Additional file 5. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Islet-expressed_circular_RNAs_are_... |
Title | Additional file 5: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S3. Transcripts detected in vitro and in vivo. (XLSX 2144 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 5: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S3. Transcripts detected in vitro and in vivo. (XLSX 2144 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_5_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 6: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S4. Proteins detected in vitro and in vivo. (XLSX 1095 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_6_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 6: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S4. Proteins detected in vitro and in vivo. (XLSX 1095 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_6_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 7: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S5. Significantly regulated genes, capsule expression and all expression data. (XLSX 2279 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_7_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 7: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S5. Significantly regulated genes, capsule expression and all expression data. (XLSX 2279 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_7_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 8: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S6. Known virulence genes. (XLSX 208 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_8_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 8: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S6. Known virulence genes. (XLSX 208 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_8_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 9: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S7. Lists of genes in each group shown in Table 2. (XLSX 321 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_9_of_Burkholderia_thailandensis_strain_... |
Title | Additional file 9: of Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages |
Description | Table S7. Lists of genes in each group shown in Table 2. (XLSX 321 kb) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/Additional_file_9_of_Burkholderia_thailandensis_strain_... |
Title | Genetics of DNA methylation Consortium mQTL dataset |
Description | Cis and trans meta-analysis results from genome-wide scans of 420,509 DNA methylation sites |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | Therse data are being widely used by the wider research community. |
URL | http://mqtldb.godmc.org.uk/ |
Title | GitHub code for genomic studies on purified brain cell types |
Description | We have made all our analysis code available to other researchers on GitHub. |
Type Of Material | Computer model/algorithm |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Our code means that other groups can replicate our findings and apply our methods to their own projects. |
URL | https://github.com/ejh243/BrainFANS |
Title | Human and Mouse Brain Iso-seq and RNA-Seq |
Description | Visual database of brain isoforms from human and mouse cortex. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | The database has been accessed by multiple research groups and we have instigated a number of new collaborations from these data. |
URL | https://genome.exeter.ac.uk/build/index.html |
Title | Human and mouse cortex isoform database |
Description | tive splicing is a post-transcriptional regulatory mechanism producing multiple distinct mRNA molecules from a single pre-mRNA. Alternative splicing has a prominent role in the central nervous system, impacting neurodevelopment and various neuronal functions as well as being increasingly implicated in brain disorders including autism, schizophrenia and Alzheimer's disease. Standard short-read RNA-seq approaches only sequence fragments of the mRNA molecule, making it difficult to accurately characterize the true nature of transcript isoform diversity. In this study, we used long-read isoform sequencing (Iso-Seq) to generate full-length cDNA sequences and map transcript diversity in the human and mouse cortex. We identify widespread isoform diversity amongst expressed genes in the cortex, including many novel transcripts not present in existing genome annotations. Alternative splicing events were found to make a major contribution to isoform diversity in the cortex, with intron retention being a relatively common event associated with nonsense mediated decay and reduced expression. Of note, we found evidence for transcription from novel (unannotated genes) and fusion events between neighbouring genes. Although global patterns of isoform diversity were found to be generally similar between human and mouse cortex, we identified some notable exceptions. We also identified striking developmental changes in isoform diversity, with differential transcript usage between adult and fetal cortex. Finally, we found evidence for extensive isoform diversity in genes associated with autism, schizophrenia and Alzheimer's disease. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide this isoform level data as a resource to the scientific community. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | This is the largest database of cortex isoforms generated using long-read sequencing. The database has been widely accessed and used by other researchers in the field. |
URL | http://genome.exeter.ac.uk/BrainIsoforms.html |
Description | Collaboration with Cambridge Epigenetix |
Organisation | Cambridge Epigenetix |
Country | United Kingdom |
Sector | Private |
PI Contribution | Our lab is beta testing a new chemistry for profiling DNA methylation and DNA hydroxymethylation. |
Collaborator Contribution | We were provided with early access to a new kit, free of charge. |
Impact | Experiments ongoing. |
Start Year | 2023 |
Description | Collaboration with Eli Lilly & Co |
Organisation | Eli Lilly & Company Ltd |
Country | United Kingdom |
Sector | Private |
PI Contribution | We have begun working extensively with collaborators at Eli Lilly on projects spanning neuroscience, genomics, dementia and schizophrenia. We now have a joint grant funded and two CASE PhD students. |
Collaborator Contribution | Access to transgenic models and resources for research studies Access to laboratory facilities and compounds Co-funding of students |
Impact | We have submitted several grant applications, and have been funded by ARUK to undertake a joint project on rodent models of neuropathology. We have successfully applied for funding for two CASE PhD students [one MRC, one BBSRC] |
Start Year | 2016 |
Description | Collaboration with Gloria Sheynkman group |
Organisation | University of Virginia Medical Center |
Country | United States |
Sector | Hospitals |
PI Contribution | We are collaborating on validation of protein changes related to novel gene transcripts identified in human brain |
Collaborator Contribution | They are providing expertise and data to help us compare RNA and protein isoforms |
Impact | We are working on a joint publication. |
Start Year | 2021 |
Description | Collaboration with John Hardy and group, UCL |
Organisation | University College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We are working with John Hardy and his team on a collaboration to use long-read sequencing to map isoform diversity in Alzheimer's disease. |
Collaborator Contribution | We are sharing protocols, analysis pipelines and data. |
Impact | We aim to submit a new research grant in the next year. |
Start Year | 2023 |
Description | Collaboration with Olga Troyanskaya and team |
Organisation | Princeton University |
Country | United States |
Sector | Academic/University |
PI Contribution | We have established a collaboration with Olga Troyanskaya and her team. We are providing data and bioinformatics pipelines to the collaboration. |
Collaborator Contribution | They are using our data to generate deep-learning models for the prediction of cell-specific epigenetic states and alternative splicing of transcripts. |
Impact | The collaboration has just started but we are planning to develop models for predicting transcriptional states and epigenetic regulation using AI. |
Start Year | 2023 |
Description | Collaboration with Pinto group, Mount Sinai School of Medicine, New York |
Organisation | Icahn School of Medicine at Mount Sinai |
Country | United States |
Sector | Academic/University |
PI Contribution | We are working with the group of Dalila Pinto to create a database of isoform diversity and alternative splicing in the human and mouse brain. We have generated fetal cortex Pacific Biosciences Iso-Seq data as part of our MRC funding and mouse cortex iso-seq data as part of our ARUK funding. |
Collaborator Contribution | Our partner group have generated complementary datasets, including data on adult cortex samples. |
Impact | We are currently finalising a publication for submission. |
Start Year | 2019 |
Description | Collaboration with The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPsych) and Minerva consortia |
Organisation | Aarhus University |
Country | Denmark |
Sector | Academic/University |
PI Contribution | We are working extensively on DNA methylation analyses of dried blood spots collected at birth to identify molecular biomarkers of prenatal exposures and risk for developing psychiatric illness. |
Collaborator Contribution | We have played an integral role in analysing and generating DNAS methylation data from Danish blood spot data. I am a member of the Scientific Advisory Board for iPsych. |
Impact | We have been involved in several collaborative research projects, with several papers already published and other in preparation. |
Start Year | 2016 |
Description | Collaboration with The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPsych) and Minerva consortia |
Organisation | Icahn School of Medicine at Mount Sinai |
Country | United States |
Sector | Academic/University |
PI Contribution | We are working extensively on DNA methylation analyses of dried blood spots collected at birth to identify molecular biomarkers of prenatal exposures and risk for developing psychiatric illness. |
Collaborator Contribution | We have played an integral role in analysing and generating DNAS methylation data from Danish blood spot data. I am a member of the Scientific Advisory Board for iPsych. |
Impact | We have been involved in several collaborative research projects, with several papers already published and other in preparation. |
Start Year | 2016 |
Description | Collaboration with Twist Bioscience |
Organisation | Twist Bioscience |
Country | United States |
Sector | Private |
PI Contribution | We are collaborating with them on new applications for their DNA methylation profiling methods -- Exploring the utility of EM-Seq with a targeted methylation system for cfDNA biomarker discovery |
Collaborator Contribution | They are providing reagents for us to use. |
Impact | We are currently optimising the method and will be applying to clinical samples soon. |
Start Year | 2022 |
Description | Collaboration with Understanding Society cohort |
Organisation | University of Essex |
Department | Institute for Social and Economic Research, Essex |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have worked with Professor Kumari and Professor Schalkwyk to generate an extensive DNA methylation resource in the Understanding Society cohort. This resource is available to other researchers and is being used in many ongoing projects. |
Collaborator Contribution | They provided us with DNA samples for profiling from ~4500 individuals. This represents one of the largest DNA methylation resources available. |
Impact | 1/ a DNA methylation data resource that is being used by groups across the world 2/ multiple publications coauthored by us and other groups |
Start Year | 2019 |
Description | Collaboration with Understanding Society cohort |
Organisation | University of Essex |
Department | Institute for Social and Economic Research, Essex |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have worked with Professor Kumari and Professor Schalkwyk to generate an extensive DNA methylation resource in the Understanding Society cohort. This resource is available to other researchers and is being used in many ongoing projects. |
Collaborator Contribution | They provided us with DNA samples for profiling from ~4500 individuals. This represents one of the largest DNA methylation resources available. |
Impact | 1/ a DNA methylation data resource that is being used by groups across the world 2/ multiple publications coauthored by us and other groups |
Start Year | 2019 |
Description | Epigenetics in UK Biobank |
Organisation | UK Biobank |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | We are leading a consortium effort to raise funds to generate DNA methylation data in the UK Biobank cohort |
Collaborator Contribution | UK Biobank have provided networking opportunities with potential funders (commercial and non-commercial) |
Impact | I presented at the UK Bioabank annual conference in London and will be speaking at a fund-raising event in California in March 2024. |
Start Year | 2023 |
Description | Functional Genomics workgroup in the Psychiatric Genomics Consortium |
Organisation | University of Cambridge |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We are leading a sub-group on alternative splicing and epigenetics. This will establish an international collaborative research program. |
Collaborator Contribution | Providing data and analysis plans. |
Impact | We have established a new functional genomics working group within the PGC. I am on the management committee and leading a sub-group on alternative splicing. |
Start Year | 2023 |
Description | Functional Genomics workgroup in the Psychiatric Genomics Consortium |
Organisation | University of Edinburgh |
Department | Edinburgh Genomics |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We are leading a sub-group on alternative splicing and epigenetics. This will establish an international collaborative research program. |
Collaborator Contribution | Providing data and analysis plans. |
Impact | We have established a new functional genomics working group within the PGC. I am on the management committee and leading a sub-group on alternative splicing. |
Start Year | 2023 |
Description | Research collaboration with Anthony Vernon at KCL |
Organisation | King's College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Have hosted a PhD student in the lab numerous times to facilitate them generating data. |
Collaborator Contribution | Have provided the PhD student and funding for consumables |
Impact | The PhD student has generated data for their thesis. There have been conference abstracts |
Start Year | 2022 |
Title | Scripts for our RNA-seq analysis of tau and amyloid pathology |
Description | Scripts for our RNA-seq analysis of tau and amyloid pathology |
Type Of Technology | Software |
Year Produced | 2023 |
Impact | Other researchers have used these methods to process their own long-read sequencing data. |
Description | - London Calling, Oxford Nanopore Technologies Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Invited platform presentation at flagship ONT meeting in London. Title - Long read transcriptome sequencing reveals isoform diversity across human neurodevelopment and aging. |
Year(s) Of Engagement Activity | 2022 |
URL | https://londoncallingconf.co.uk/lc23 |
Description | 2017 WORKSHOP ON GENOMICS, CESKY KRUMLOV |
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 | The Workshop on Genomics was developed in response to the increasing demand for training on how to effectively analyze and manage data generated by modern sequencing technologies. The Workshop curriculum includes extensive coverage of fundamental techniques required of all studies utilizing modern sequence data. This includes management and modification of modern sequence data files, using the Unix command-line and editors to manipulate large data files, assembly and best practices for sequence data generation, management and analysis. The second-half of the Workshop is devoted to specific sub-disciplines within the genomic sciences. While these topics may change from year-to-year, efforts are made to devote significant amounts of time to techniques being used widely in the field (e.g. transcriptomics, genome assembly, metagenomics, population genomics). |
Year(s) Of Engagement Activity | 2017 |
URL | http://evomics.org/workshops/workshop-on-genomics/2017-workshop-on-genomics-cesky-krumlov/ |
Description | 2018 Paul Janssen Lecture at IoPPN |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | The Paul Janssen Lecture has been a regular feature of the academic calendar at the Institute of Psychiatry, Psychology & Neuroscience for nearly 20 years. Lecturers are chosen on the basis of their global eminence in the field of neuroscience with a focus on schizophrenia. The annual lecture is named in honour of Belgian pharmacologist Paul Janssen (1926-2003) noted for discovering various drugs important to psychiatry, such as haloperidol, and who founded Janssen - the pharmaceutical company which sponsors the event. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.kcl.ac.uk/ioppn/news/special-events/paul-janssen-lecture |
Description | Brain Awareness Week Public Lecture |
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 | As part of the inaugural Exeter Brain Awareness Week, I gave a public (lay) presentation on our research into genomics of schizophrenia. |
Year(s) Of Engagement Activity | 2018 |
URL | http://www.exeter.ac.uk/news/events/details/index.php?event=8040 |
Description | Brain Prize meeting - Lundbeck Foundation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I was invited to give a presentation at the Brain Prize meeting arranged by the Lundbeck Foubdation. I gave an overview of our work into the genomics of brain disorders. I have been subsequently approached by several groups with requests for data and collaboration. |
Year(s) Of Engagement Activity | 2021 |
URL | https://lundbeckfonden.com/en/the-brain-prize |
Description | British Society for Research on Aging Meeing - Keynote Lecture |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Professor Mill presented latest findings from brain genomics studies in context of ageing. |
Year(s) Of Engagement Activity | 2017 |
URL | http://bsra.org.uk/bsra-2017-university-exeter/ |
Description | Celebrating Diversity in Science Virtual Conference - Oral Presentation: Heterogeneity in purified neural populations: implications for post-mortem genomic studies. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | One of our team members gave a presentation at the Celebrating Diversity in Science Virtual Conference. This had a large impact, not only focused on scientific results but also discussing diversity in science. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.facebook.com/events/d41d8cd9/celebrating-diversity-in-science-virtual-conference/1922678... |
Description | Cold Spring Harbor Laboratories: Workshop on Autism Spectrum Disorders - Foetal Brain Development and Neuropsychiatric Disease |
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 presented our work on gene regulation in human brain development at this workshop in which attendees develop their knowledge of the field of research into ASD and the implications on clinical output. Wide range of experience from attendees, from various backgrounds of research. Attendees share their research and develop networking connections. |
Year(s) Of Engagement Activity | 2019 |
URL | https://meetings.cshl.edu/autism19 |
Description | College student visit |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | We hosted a college student thinking about applying for medicine at the RILD building. I demonstrated examples of medical research and organised a tour/chats with RILD colleagues. |
Year(s) Of Engagement Activity | 2024 |
Description | Developmental trajectories of DNA methylation in the human cortex: evidence for sex differences - Poster presentation at the Epigenomics of Common Diseases conference (Wellcome Connecting Science, Hinxton, UK |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation on our work into sex differences in the human brain. Led to new collaboration opportunities. |
Year(s) Of Engagement Activity | 2023 |
Description | Epigenomic and transcriptional signatures of progressive neuropathology in transgenic models of Alzheimer's disease - Oral presentation at the Wellcome Trust Epigenoics of Common Diseases meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented our first major findings from our study of gene regulation in mouse models of Alzheimer's disease pathology.There was considerable interest in this work from the audience with many questions and requests for additional information. |
Year(s) Of Engagement Activity | 2019 |
URL | https://coursesandconferences.wellcomegenomecampus.org/register/conferences/form1.aspx?e=771 |
Description | Epigenomics of Common Diseases Meeting - Wellcome Trust 2017 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Our group presented a series of posters and talks on data generated by our MRC funding. |
Year(s) Of Engagement Activity | 2017 |
URL | https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=638 |
Description | Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave a presentation on our long-read isoform sequencing approaches to explore alternative splicing in the brain |
Year(s) Of Engagement Activity | 2021 |
Description | Feature article on our research in British Neuroscience Association (BNA) Newsletter |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | The BNA interviewed me, and wrote a feature article on our work. |
Year(s) Of Engagement Activity | 2016 |
URL | https://www.bna.org.uk/publications/bna-bulletin/ |
Description | Functional characterisation of GWAS loci using epigenetic editing - Oral Presentation at Wellcome Trust Epigenomics of Common Disease Meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented our work on epigenetic editing of schizophrenia candidate genes nominated from our MRC-funded project. The talk instigated considerable debate and interest from novel collaborators. |
Year(s) Of Engagement Activity | 2019 |
URL | https://coursesandconferences.wellcomegenomecampus.org/register/conferences/form1.aspx?e=771 |
Description | International Molecular Pathology Symposium - Edinburgh |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Professor Mill gave an invited talk at the 2017 International Molecular Pathology Symposium. He discussed current advances in using genomics in molecular pathology. There was considerable discussion following the even and several new collaborations established. |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.ed.ac.uk/centre-genomic-medicine/news-events/news-2017/international-molecular-pathology... |
Description | Invited Lecture - Astex Pharmaceuticals. Global Lecture Series |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Invited to give an update of our research to a wide audience online. |
Year(s) Of Engagement Activity | 2021 |
URL | https://astx.com/ |
Description | Invited Lecture - Radboud University, Nijmegen |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Other audiences |
Results and Impact | Professor Mill was invited to give a lecture at Radboud University in Nijmegen, The Netherlands; hosted by Barbara Franke. He presented an overview of our work on epigenetic analyses of mental health including schizophrenia. He also gave an overview of novel genomic sequencing technologies. The lecture sparked considerable discussion and several new potential collaborations. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.ru.nl/english/people/franke-b/ |
Description | Invited seminar - Roche Pharmaceuticals, pRED, Neurosciences & Rare Disease. Invited Seminar |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Online virtual seminar to the pRED department at Roche. |
Year(s) Of Engagement Activity | 2021 |
Description | Invited seminar at Department of Psychiatry, University of Oxford |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | I gave an invited seminar to researchers at the University of Oxford Departmenty of Psychiatry. I presented an overview of our work on the genomics of schizophrenia and dementia. Following this seminar I visited the department in person, met with several researchers and discussed novel collaborations. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.psych.ox.ac.uk/ |
Description | Invited seminar at Roche Pharma |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I gave an invited seminar on genomics to the neuroscience genomics group at Roche. I presented an overview of our work and how this might inform drug discovery in the future. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.roche.com/ |
Description | Invited seminar at Sheffield Institute of Translational Neuroscience |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | I gave an invited seminar at SITRAN where I presented our work on genomic profiling in human neurodegenerative disease. The talk led to several new collaboration opportunities. |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.sheffield.ac.uk/sitran |
Description | Invited seminar at the UCL Dementia Research Institute |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | I gave an invited seminar to the UK Dementia Research Institute at UCL where I presented our research into the genomic basis of dementia and schizophrenia. As a result of this seminar, I have established several novel collaborations and disseminated information about our data resources to the wider community. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.ucl.ac.uk/uk-dementia-research-institute/ |
Description | Invited seminar for the Imperial College London Dementia Research Institute |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | I gave an invited seminar to the UK Dementia Research Institute where I presented our research into the genomic basis of dementia and schizophrenia. As a result of this seminar, I have established several novel collaborations and disseminated information about our data resources to the wider community. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.imperial.ac.uk/dementia-research-institute/seminars--events/2019-20-seminars/ |
Description | Invited speaker at the "Epigenetics in the Nervous System" meeting in Stockholm |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I gave an invited presentation at this international meeting sponsored by Abcam. There was considerable discussion and interest in our work, and several new collaborative opportunities arising from this are being explored. |
Year(s) Of Engagement Activity | 2018 |
URL | http://docs.abcam.com/pdf/events/stockholm-2018-program.pdf |
Description | Invited speaker at the 2018 International Human Epigenome Consortium (IHEC) meeting in Hong Kong |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I was an invited speaker at the 2018 IHEC meeting which brings together researchers from around the world working on epigenomics. I presented our ongoing work to leaders in the field and established new collaborations with other international groups. |
Year(s) Of Engagement Activity | 2018 |
URL | http://ihec-epigenomes.org/news-events/hong-kong-2018/ |
Description | Invited speaker at the virtual event Epigenetics - The Full Picture from Illumina International. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited presentation on our epigenomics work for Illumina seminar series |
Year(s) Of Engagement Activity | 2021 |
Description | Invited talk - Genome Institute of Singapore |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Professor Mill gave a presentation and established new collaborations at GIS and other institutions in Singapore. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.gis.a-star.edu.sg |
Description | Isoform diversity in the human cortex - SFARI Annual Meeting, New York |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I presented our work on RNA isoform diversity at the Simons Foundation in New York. This stimulated considerable interest, and interaction with research groups with whom we are now collaborating. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.sfari.org/events/ |
Description | Long-reads, single-cells and cream teas -- Third-generation sequencing meeting / workshop |
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 | We organised a day workshop and conference to launch our MRC Clinical Infrastructure project. It was a great success with atendees from across the UK and international speakers. Programme below: 1st September 2015, University of Exeter, U.K. Location: RILD Building, RD&E Hospital (directions here). To celebrate the launch of our MRC Clinical Infrastructure and our new Pacific Biosciences instrument, we'd like to invite you to a special one-day meeting. 09:00 - 09:45 Tea/coffee 09:45 - 10:00 Welcome 10:00 - 10:30 Introduction to PacBio, Steve Picton Pacific Biosciences 10:30 - 11:00 Introduction to Oxford Nanopore, James Brayer/Oliver Hartwell Oxford Nanopore Technologies 11:15 - 12:00 18 months of PacBio sequencing - John Kenny, Liverpool Centre for Genomic Research 12:00 - 13:00 Lunch 13:00 - 14:00 Single cell genomics at Joint Genome Institute, Tanja Woyke 14:00 -14:45 Evolutionary genomics with PacBio - Alistair Darby, University of Liverpool 14:45 - 15:30 Clinical and bacterial applications of long-read sequencing - Nick Loman, University of Birmingham 15:30 - 16:15 Tea/coffee 16:15 - 17:15 Genomics at the New York Genome Centre, Mike Zody 17:15 - 18:15 Genome Sciences at University Washington, School of Medicine, Evan Eichler Followed by an evening meal at the Cosy Club, Exeter. |
Year(s) Of Engagement Activity | 2015 |
URL | http://sequencing.exeter.ac.uk/long_reads_and_cream_teas/ |
Description | MRC Expert Group Meeting on Human Brain Research |
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 | We discussed optimal approaches for using human brain tissue in research |
Year(s) Of Engagement Activity | 2017 |
Description | Meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights 220 differentially methylated loci across cortex - Oral Presentation at Wellcome Trust Epigenomics of Common Diseases meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented our findings from a large EWAS meta-analysis of Alzheimer's disease. We are assessing parallel changes at the same loci in our study of regulatory genomic changes in mouse models of neuropathology, funded by ARUK. The presentation sparked considerable interest with many questions and opportunities for novel collaborations. |
Year(s) Of Engagement Activity | 2019 |
URL | https://coursesandconferences.wellcomegenomecampus.org/register/conferences/form1.aspx?e=771 |
Description | Multiple presentations and posters at the World Congress of Psychiatric Genetics in Glasgow |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Our group had several presentations at the 2018 WCPG meeting, disseminating results from our work into the genomics of schizophrenia. There was considerable interest in our data and we interacted with collaborators on the projects. |
Year(s) Of Engagement Activity | 2018 |
URL | https://wcpg2018.org |
Description | Multiple presentations at World Congress of Psychiatric Genetics |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented multiple findings at the World Congress of Psychiatric Genetics, including talks on microRNAs in schizophrenia, epigenetic analyses in schizophrenia, and novel methods for profiling purified nuclei populations. Our work reached an international audience and several collaborations on future projects. |
Year(s) Of Engagement Activity | 2020 |
URL | https://ispg.net/wcpg-2020/ |
Description | Multiple presentations at the Wellcome Trust Epigenomics of Common Diseases meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented our data in multiple presentations at the 2020 Epigenomics of Common Diseases meeting. This enabled us to disseminate our work to a wide scientific audience and also help foster novel collaborations. |
Year(s) Of Engagement Activity | 2020 |
URL | https://coursesandconferences.wellcomegenomecampus.org/register/conferences/form1.aspx?e=808 |
Description | Neurogenomics Seminar - Imperial College London |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Members of the team were invited to present our work at the online [international reach] Imperial College London neuogenomics seminar. Several hundred attendees joined the meeting and many questions were asked. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.youtube.com/watch?v=32_R9P_T0sQ |
Description | Oral presentation at ARUK Conferences, Harrogate, UK |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk at the annual ARUK meeting in Harrogate discussing my teams research into the epigenetics of Alzheimer's disease. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.alzheimersresearchuk.org/for-researchers/research-conference-2020/ |
Description | Oral presentation at Wellcome Trust Epigenomics of Common Diseases meeting - Pleiotropic effects of trait-associated genetic variation on DNA methylation: Utility for refining GWAS loci |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented our work on fine-mapping schizophrenia risk loci using epigenetic annotations. The talked sparked questions and considerable positive feedback on our work. |
Year(s) Of Engagement Activity | 2019 |
URL | https://coursesandconferences.wellcomegenomecampus.org/register/conferences/form1.aspx?e=771 |
Description | PacBio Global Summit - Using Iso-Seq to uncover AD-associated splicing variants in mouse model of tau pathology and human cortex |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A team member was invited to join this panel discussion on long-read sequencing for identifying novel isoforms / transcripts. This had a very broad international audience and resulted in several new collaborations. |
Year(s) Of Engagement Activity | 2020 |
URL | https://events.pacb.com/global-summit |
Description | Pacific Biosciences Long Read Sequencing - Exeter Engagement Day |
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 organised a day workshop in collaboration with Pacific Biosciences to promote long-read sequencing infrastructure in Exeter. There were numerous end-user presentations and discussions about novel applications and sequencing approaches. |
Year(s) Of Engagement Activity | 2019 |
URL | http://sequencing.exeter.ac.uk |
Description | Presentation at Academy of Medical Sciences meeting: The developing brain in health and disease - Molecular profiling of discrete cellular populations in post mortem human cortex |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We presented our method for isolating nuclei from specific neural cell populations from human cortex developed in our MRC project grant. This two day meeting hosted by the Academy of Medical Sciences highlighted the latest advances in the field and provided a unique space for researchers across disciplines to discuss the challenges and priorities for neurodevelopmental research. |
Year(s) Of Engagement Activity | 2019 |
URL | https://acmedsci.ac.uk/more/news/understanding-brain-development-what-next-for-research |
Description | Presentation at INSAR meeting, Montreal, Canada. Epigenetic pathways to neurodevelopmental phenotypes. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I was an invited speaker at a workshop on gene regulation in the brain in neurodevelopmental phenotypes (autism, schizophrenia). I presented work to a large audience on our findings related to gene expression, epigenetics and isoform diversity in the human cortex. The meeting involved teams from across the world and resulted in ongoing collaborations with researchers at Mount Sinai School of Medicine in New York. |
Year(s) Of Engagement Activity | 2019 |
URL | https://insar.confex.com/insar/2019/webprogram/start.html |
Description | Presentation at UK Biobank annual conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I gave a presentation on the promise of profiling DNA methylation in UK biobank. As a result of this we have established an academic consortium to pursue funding to achieve this goal. |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwj_rMDC8-uEA... |
Description | Presentation at World Congress of Psychiatric Genetics |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I gave a presentation about our work on alternative splicing in the developing brain and schizophrenia at the WCPG meeting in Montreal, Canada in October 2023. I had several requests for more information and collaboration. |
Year(s) Of Engagement Activity | 2023 |
URL | https://ispg.net/events/wcpg-2023-invitation-to-attend/ |
Description | Presentation on long-read genomics: 2016 Workshop on Genomics, Cesky Krumlov |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The Workshop on Genomics was developed in response to the increasing demand for training on how to effectively analyze and manage data generated by modern sequencing technologies. The Workshop curriculum includes extensive coverage of fundamental techniques required of all studies utilizing modern sequence data. This includes management and modification of modern sequence data files, using the Unix command-line and editors to manipulate large data files, assembly and best practices for sequence data generation, management and analysis. The second-half of the Workshop is devoted to specific sub-disciplines within the genomic sciences. While these topics may change from year-to-year, efforts are made to devote significant amounts of time to techniques being used widely in the field (e.g. transcriptomics, genome assembly, metagenomics, population genomics). |
Year(s) Of Engagement Activity | 2016 |
URL | http://evomics.org/workshops/workshop-on-genomics/2016-workshop-on-genomics-cesky-krumlov/ |
Description | Presentations at Alzheimer's Research UK 2022 meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | We presented several presentations detailing results from our research projects. |
Year(s) Of Engagement Activity | 2022 |
Description | Presentations at the Wellcome Trust Genomics of Brain Disorders Meeting, Cambridge |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | We had a series of presentations - oral talks and posters - presented on our work at this international meeting on the genomics of brain disorders. |
Year(s) Of Engagement Activity | 2018 |
URL | https://coursesandconferences.wellcomegenomecampus.org/our-events/genomics-of-brain-disorders-2018/ |
Description | Presentations at the World Congress of Psychiatric Genetics, Florence, Italy. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | We gave multiple presentations at the 2022 WCPG meeting in Florence, showcasing the results of our research projects. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.emedevents.com/c/medical-conferences-2022/world-congress-of-psychiatric-genetics-wcpg-20... |
Description | Seminar at OHSU in Portland, USA |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | I was invited to give a seminar at OHSU in Portland where I discussed our work to medics and researchers. I discussed ongoing research into psychiatric epigenetics and established several new collaborations. |
Year(s) Of Engagement Activity | 2018 |
Description | Symposium at 13th World Congress of Biological Psychiatry, Copenhagen |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Professor Mill was co-chair and a presenter at the ISBP meeting. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.wfsbp-congress.org/former-congresses/highlights2017.html |
Description | Talk at the Festival of Genomics |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I gave a presentation on the use of long-read RNA sequencing for characterising transcript variation in the human brain. |
Year(s) Of Engagement Activity | 2024 |
URL | https://festivalofgenomics.com/london/en/page/home |
Description | Training seminars in genomics / bioinfotrmatics |
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 Bioinformatics Support Service (EXBiSS) offers a number of advanced training courses aimed at developing the skills necessary to handle large scale high-throughput datasets from sequencing, mass-spectrometry and ecology. The course are available to PhD students, post-doctoral researchers and staff. As part of the current MRC funded grant, we established training in genomics and sequencing analysis. |
Year(s) Of Engagement Activity | 2015,2016 |
URL | http://www.exeter.ac.uk/biomedicalhub/training/ |
Description | Two selected oral presentations at the Wellcome Trust Epigenomics of Common Diseases meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | We had two platforms presenting work from this project at the Wellcome Trust Epigenomics of Common Diseases meeting. |
Year(s) Of Engagement Activity | 2016 |
URL | https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=594 |
Description | UK Pharmacogenetics and Stratified Medicine - Open Meeting - Invited Talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | Professor Mill gave an invited lecture on how epigenetic epidemiology might inform pharmacokinetic studies. There was considerable interest and many questions. |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.uk-pgx-stratmed.co.uk |
Description | Workshop on Schizophrenia and Related Disorders - Cold Spring Harbor |
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 | I taught on the Cold Spring Harbor Schizophrenia Workshop as an invited lecturer. This involved small-group teaching to leading postdocs and PhD students selected form around the world. The students were enthused about genomics in schizophrenia and there was very positive feedback. |
Year(s) Of Engagement Activity | 2018 |
URL | http://meetings.cshl.edu/schizophrenia18 |
Description | XXV World Congress of Psychiatric Genetics, Orlando |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | We had multiple presentations at the 2017 WCPG meeting. We networked extensively with collaborators and established several new projects. |
Year(s) Of Engagement Activity | 2017 |
URL | https://wcpg2017.org |