To develop cutting-edge epigenomics and computational technologies

Lead Research Organisation: Babraham Institute
Department Name: UNLISTED

Abstract

With the development of methods for genome-wide mapping of DNA methylation, histone modifications, chromatin accessibility and conformation, high-throughput sequencing has revolutionised the study and our understanding of epigenetics. In this ISPG, we have been at the forefront of methods development, including techniques for identification of new DNA modifications71,72, and low-cell and single-cell epigenomic methods, such as scBS-seq and scM&T-seq23,24. Integral to our IPSG objectives is the adoption and development of state-of-the-art techniques to enable us to interrogate epigenomic dynamics during the lifecourse – to reveal the epigenomes of rare cells (as in early embryos), to uncover cell-to-cell heterogeneity in epigenetic states during key lineage decision making events, and to measure the extent of heterogeneity as a function of ageing – and to integrate multiple parameters towards modelling epigenetic states and transitions. This objective is very much embedded within overall technology development at BI, and through our Sanger Institute/EBI Single Cell Genomics Centre links. This establishes a collaborative Cambridge environment that is hugely conducive to the development of novel epigenomics and computational methods. In addition, we shall extend interactions with industrial collaborators, such as Cambridge Epigenetix Ltd., in particular for developing targeted sequencing, and to commercialise IP we expect to develop in this area.
 
Description This award aims to develop new epigenomics and computational methods as important enabling capabilities for various projects within the Epigenetics ISPG. A key advance has been in single-cell multi-omic methods, notably the development of a method for genome-wide mapping of DNA methylation, chromatin accessibility and transcriptomes in parallel in single cells (scNMT-seq, Objective 6.2; PMID 29472610). These methods provide important underpinning technology for our studies of epigenetic heterogeneity during ageing (PMID: 31554804); epigenetic mechanisms in key lineage decision events during mammalian post-implantation development and gastrulation (PMID: 31827285); and human iPSC differentiation, revealing links between methylation and splicing regulation (PMID 30031774; PMID 30744673). In parallel, we have developed mechanistic biophysical modelling of DNA and transcriptional dynamics in single cells during the transition out of pluripotency, leading to discovery of genome-scale oscillations in DNA methylation (Objective 6.5; PMID 30031774). Important methodological improvements have also been made in the identification of biases affecting DNA methylation data in whole-genome bisulphite sequencing protocols (PMID 29544553). We have made advances in quantitative ultra low-cell ChIP-seq methods for mammalian cells (Objective 6.1; PMID 29472610), with which we are systematically investigating the extent of intergenerational transmission of epigenetic information, including changes associated with maternal diet. In the yeast system, we have developed methods for increased throughput of ageing cell purification, optimised for mRNA-seq, and implemented spike-in normalised low-cell number ChIP methodology for ageing yeast cells (Objective 6.1; PMID 30274593), allowing for the first time routine assessment of epigenetic changes with age. Advances in yeast also include analysis at a single-cell level of chromosomal mutations accrued during ageing (Objective 6.3; PMID 28654659) and genome-wide analysis of extrachromosomal DNA accumulation with age (Objective 6.1; PMID 31794573). We have launched a community driven global effort and successfully merged and extended a Caenorhabditis elegans whole-genome metabolic reconstruction model into a re-optimised version: WormJam. This model is being used in combination with mathematical modelling to predict metabolic fluxes in C. elegans (Objective 6.5; PMID 30488036). In parallel, we have described a multi-omics systems biology tool to study the metabolic changes that occur during ageing in C. elegans. Focusing on time series transcriptomics and metabolomic samples taken from sterile and normal lived animals in combination with Flux balance analysis, we find that the standard methods do not accurately predict in vivo measured fluxes nor age-related changes associated with central carbon metabolism. We present a novel Flux Balance Analysis method where we combined biomass production and targeted metabolomics information to generate an objective function that is more suitable for aging studies (Objective 6.5; PMID: 30788345).
Exploitation Route Many of the technological advances we are making under this award are being adopted by the scientific community, notably those investigating epigenetic mechanisms in development, in ageing and in disease processes; for example, epigenetic heterogeneity is likely to be an important factor in diseases such as cancer and chronic degenerative conditions. We are disseminating the outcomes of our research through scientific publications, presentations at international meetings, organisation of conferences (e.g. The Ageing Cell, 2017), and also to wider audiences (e.g., Royal Society Summer Exhibition, 2018). We are also hosting training visits in these techniques to equip other investigators (>20 visitors since the beginning of the award), and intend to seek commercial partners.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Enhancer DNA methylation dynamics during early mammalian development
Amount £300,000 (GBP)
Funding ID 215912/Z/19/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2019 
End 08/2023
 
Description Flagship
Amount € 1,000,000 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 02/2019 
End 03/2020
 
Description Investigator Award
Amount £2,600,000 (GBP)
Funding ID 210754/Z/18/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2018 
End 09/2023
 
Description Special initiative
Amount £10,000,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 04/2024
 
Title A protocol for high-throughput quantitative RT-qPCR in single C. elegans using nanofluidic technology 
Description high throughput protocol for fast and reliable determination of gene expression levels in single or pooled C. elegans samples utilizing nanofluidics real time polymerase chain reaction. 
Type Of Material Biological samples 
Year Produced 2020 
Provided To Others? Yes  
Impact Help other C elegans reserachers with the measurement of rare transcripts from single worm samples. 
 
Title C elegans Metabolic Reconstruction Model 
Description Merged and re-annotated C elegans Metabolic Reconstruction Model 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact This is a great improvement to the C elegans research community 
 
Title Novel method to study metabolic fluxes during ageing 
Description The novel method has been christened "Metab_FBA" and it is a novel flux balance analysis method to study ageing samples 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact This development is a step forward for the field of metabolism and ageing in multicellular model organisms 
 
Title Oxidative bisulfite sequencing 
Description Chemical method for sequencing of hydroxymethylation commercialised by Cambridge Epigenetix. 
Type Of Material Technology assay or reagent 
Year Produced 2013 
Provided To Others? Yes  
Impact Use in several publications. 
URL http://www.cambridge-epigenetix.com
 
Title PCR Bayes 
Description Novel algorithm to quantify expression and biological variability of steady state transcripts 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact This is a novel tool which extends the capabilities of C elegans researchers to quantitate biological noise in single worms 
 
Title Single cell multi-omics (scNMT-seq) 
Description Single cell triple-omics which records the transcriptome, methylome, and chromatin accessibility from the same single cell 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact This method was applied to the first real biology question in 2019 on an investigation of mouse gastrulation (Argelaguet et al 2019 Nature). The joint first author Stephen Clark was awarded the researcher of the year award 2019 by the Cambridge Independent newspaper. 
 
Title Single cell triple-omics 
Description Single cell triple-omics combining transcriptome, methylome, and chromatin accessibility from the same single cell. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact This method was just published. 
 
Title Ultra-low cell histone modification profiling 
Description Optimised method for ultra-low cell native ChIP-seq for histone modifications, exemplified by use in 250 mouse oocytes (see Hanna et al. 2019 Nat. Struct. Mol. Biol.) 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact This is providing us with major new capability in profiling histone modifications reproducibly and quantitatively in biological samples such as mouse oocytes and mouse pre-implantation and early post-implantation embryos, and is now being applied for a variety of research questions by the group. We are also using the method in a number of collaborators and have trained others in the method. 
 
Title Single-cell parallel analysis of DNA methylation, chromatin accessibility, RNA expression in mouse ES cells 
Description Single-cell analysis of DNA methylation, chromatin accessibility, RNA expression of mouse ES cells by method of scNMT-seq. scNMT-seq comprises parallel analysis of DNA methylation by bisulphite sequencing, or chromatin accessibility by NOME-seq, and RNA expression by RNA-seq. The database contains scNMT-seq datasets from 70 serum-grown and 16 2i-grown mouse ES cells, and 38 ES cells undergoing differentiation. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Too early to say, as method is very recently published. The method is being used by our groups to profile changes in DNA methylation and chromatin accessibility, and their correlation with gene expression, during mouse gastrulation. 
URL https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109262
 
Title We submit every year hundreds to thousands of new database entries these are all linked to the publications associated with the grants 
Description please see above 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact please see above 
 
Title Webtool for integration of high-throughput datasets and their rapid analysis 
Description Generation of a webtool allowing rapid data analysis of high-througput sequencing datasets. 
Type Of Material Computer model/algorithm 
Year Produced 2018 
Provided To Others? No  
Impact Webtool allows to upload and integrate multiple datasets of different nature (such as ChIP-seq, RNA-seq, DNA methyaltion profiles) and allows to perform rapid multivariate analyses on them to find co-occpuancy, mutual exclusion etc 
 
Title copper response in yeast 
Description Response of yeast to copper treatment by RNAseq and replication fork stalling 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact data re-use 
URL https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86283
 
Description Active Motif DNA modification antibody 
Organisation Active Motif
Country United States 
Sector Private 
PI Contribution Commercialisation of DNA modification antibodies we have made
Collaborator Contribution Commercialisation of DNA modification antibodies we have made
Impact Commercially available antibodies
Start Year 2016
 
Description Alex Meissner 
Organisation Harvard University
Department Department of Stem Cell and Regenerative Biology
Country United States 
Sector Academic/University 
PI Contribution Epigenomics and single cell multi-omics sequencing
Collaborator Contribution Crispr mouse mutants and protocols
Impact Several datasets.
Start Year 2019
 
Description Austin Smith 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Epigenomics and multi-omics sequencing
Collaborator Contribution Human and mouse pluripotent stem cells
Impact Several collaborative publications.
Start Year 2013
 
Description Benjamin Simons 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Single cell multi-omics datasets.
Collaborator Contribution Modelling methods for multi-omics datasets.
Impact Two collaborative publications, two joint grants. Multi-disciplinary between biology and theoretical physics.
Start Year 2014
 
Description Collaboration with Alvaro Rada-Iglesias 
Organisation University of Cantabria
Country Spain 
Sector Academic/University 
PI Contribution Single cell multi-omics
Collaborator Contribution In vitro PGCLC model
Impact First datasets have been obtained. A training visit has taken place.
Start Year 2019
 
Description Development of computational methods for the quantification of biological variability 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Development of an algorithm based on Bayesian statistics that quantifies variability in steady state levels of mRNA from nanofluidics-based PCR.
Collaborator Contribution Development of an algorithm based on Bayesian statistics that quantifies variability in steady state levels of mRNA from nanofluidics-based PCR.
Impact It is a multi-disciplinary collaboration involving high end PCR technology and statistical modelling.
Start Year 2015
 
Description Gastrulation team 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Conceived of the project and lead partner. Contributing single cell multi-omics and embryology.
Collaborator Contribution Helped to conceive of the project and several experimental and computational contributions.
Impact First publication Mohammed et al 2017. Experimental embryology, single cell biology, computation, modelling, epigenetics.
Start Year 2014
 
Description Human Cell Atlas 
Organisation Broad Institute
Country United States 
Sector Charity/Non Profit 
PI Contribution Contributed to formulating the white paper of the Human Cell Atlas.
Collaborator Contribution Conceived the project and brought the international consortium together.
Impact The white paper was published Regev et al 2017. It involves single cell biologists and computational and modelling scientists.
Start Year 2016
 
Description Janet Thornton 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Conceived of the study and provided computational work.
Collaborator Contribution Helped with computational work.
Impact Publications Herranz et al 2017, 2019. Wetlab epigenetics and computational.
Start Year 2016
 
Description Jenny Nichols mouse and human embryology 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Single cell multi-omics, mutants of epigenetic regulators.
Collaborator Contribution Mouse and human embryos
Impact Several collaborative publications and two joint grants. Multi-disciplinary between epigenetics, multi-omics, embryology, stem cell research.
Start Year 2014
 
Description John Marioni 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Development of single cell multi-omics and application in several biological systems including mouse and human embryos and pluripotent stem cells.
Collaborator Contribution Development of computational methods for single cell multi-omics.
Impact Several collaborative publications and a joint grant. Multi-disciplinary between wet and dry lab multi-omics approaches.
Start Year 2013
 
Description Jurkowski 
Organisation University of Stuttgart
Country Germany 
Sector Academic/University 
PI Contribution Helped with reagents and interpretation.
Collaborator Contribution Conceived and conducted study.
Impact Publication Stepper et al 2017. Involves biochemists, epigeneticists.
Start Year 2016
 
Description MRC EASIH 
Organisation University of Cambridge
Department Cambridge Institute for Medical Research (CIMR)
Country United Kingdom 
Sector Academic/University 
PI Contribution increased opportunities for deep sequencing using alternative platforms such as Roche 454 and ABI Solid
Collaborator Contribution MRC East Anglia Sequencing and Informatics Hub established in 2009
Impact see above
Start Year 2009
 
Description Manuel Serrano 
Organisation Institute for Research in Biomedicine (IRB)
Country Spain 
Sector Academic/University 
PI Contribution Epigenetics and multi-omics sequencing and computation
Collaborator Contribution Mouse model of age rejuvenation by Yamanaka factors
Impact Several datasets. Multi-disciplinary between epigenetics and mouse models of tissue rejuvenation.
Start Year 2017
 
Description Meri Huch 
Organisation Max Planck Society
Department Center for Systems Biology Dresden
Country Germany 
Sector Charity/Non Profit 
PI Contribution Single cell multi-omics
Collaborator Contribution Mouse model of liver regeneration
Impact Several datasets. Multi-disciplinary between epigenetics, multi-omics, disease modelling.
Start Year 2017
 
Description Millipore DNA modification antibodies 
Organisation Merck
Department MilliporeSigma
Country United States 
Sector Private 
PI Contribution Commercialisation of DNA modification antibodies we have made
Collaborator Contribution Commercialisation of DNA modification antibodies we have made
Impact DNA modification antibodies
Start Year 2011
 
Description Rakyan for mouse rDNA 
Organisation Queen Mary University of London
Department Blizard Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Development of mouse rDNA CNV assay
Collaborator Contribution Mouse models and project lead
Impact None yet...
Start Year 2016
 
Description Richard Gilbertson epigenetics of childhood cancer 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution We carry out multi-omics sequencing
Collaborator Contribution Model of childhood cancer in mice
Impact Sequencing results. Collaboration is betten epigenetics and cancer biology.
Start Year 2018
 
Description Romain Barres 
Organisation University of Copenhagen
Country Denmark 
Sector Academic/University 
PI Contribution Single cell multi-omics
Collaborator Contribution Human sperm from obese and control subjects
Impact Several datasets. Multi-disciplinary between epigenetics, multi-omics, human cohorts.
Start Year 2016
 
Description Single-cell epigenomic profiling of spermatogonial stem cells 
Organisation Yokohama City University
Country Japan 
Sector Academic/University 
PI Contribution Our group is providing expertise in single-cell methylation and expression profiling methods.
Collaborator Contribution Their group is responsible for framing the project and experimental design and for providing isolated mouse spermatogonial stem cells.
Impact Hosted visit by post-doc from collaborating group to initiate single cell methylation/transcription profiling. Joint grant awarded: Royal Society International Exchange Award IEC\R3\170052 (March 2018 March 2020): Analysis of spermatogonial stem cell maintenance and differentiation system by the state-of-the-art single-cell technology.
Start Year 2016
 
Description Steffen Rulands 
Organisation Max Planck Society
Department Max Planck Institute for the Physics of Complex Systems
Country Germany 
Sector Academic/University 
PI Contribution Single cell multi-omics datasets
Collaborator Contribution Modelling approaches for single cell multi-omics datasets
Impact One collaborative publication. Multi-disciplinary between biology and theoretical physics.
Start Year 2015
 
Description XIMBIO DNA modification antibodies 
Organisation Cancer Research Technology (CRT)
Country United Kingdom 
Sector Private 
PI Contribution Commercialisation of DNA modification antibodies we have made
Collaborator Contribution Commercialisation of DNA modification antibodies we have made
Impact DNA modification antibodies
Start Year 2016
 
Title Consortium agreement 
Description Consortium agreement between the Babraham Institute and the Max Delbrück Centre on LifeTime EU 
IP Reference  
Protection Protection not required
Year Protection Granted 2019
Licensed No
Impact The LifeTime consortium is now up and running as a Coordination and Support Action supported by the EU
 
Title Consultancy agreement 
Description Consultancy with the Sanger Institute 
IP Reference  
Protection Protection not required
Year Protection Granted 2016
Licensed No
Impact Many collaborative publications
 
Title Exclusive license agreement 
Description Antibodies against DNA modifications 
IP Reference  
Protection Protection not required
Year Protection Granted 2016
Licensed No
Impact Income to the Institute
 
Title Non-exclusive license agreement 
Description Antibodies against DNA modifications 
IP Reference  
Protection Protection not required
Year Protection Granted 2016
Licensed Commercial In Confidence
Impact Income to the Institute
 
Title Non-exclusive license agreement 
Description Antibodies against DNA modifications 
IP Reference  
Protection Protection not required
Year Protection Granted 2011
Licensed Commercial In Confidence
Impact Income to the Institute
 
Company Name CHRONOMICS LIMITED 
Description The company provides a sequencing based test of DNA methylation age for sputum samples 
Year Established 2017 
Impact The company is working with hundreds of human subjects to assess the effect of lifestyle factors on human ageing
 
Description 15th International Curie Course on Epigenetics - Paris 
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
Year(s) Of Engagement Activity 2019
 
Description 2019 Keystone Symposia on Single Cell Biology - Colorado 
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
Year(s) Of Engagement Activity 2019
 
Description 3rd Revolutionizing Next-Generation Sequencing Conference - Belgium 
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
Year(s) Of Engagement Activity 2019
 
Description Babraham Schools day 2018 
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 Experiments on epigenetics for local 6th form schools
Year(s) Of Engagement Activity 2018
 
Description Babraham Schools' Day 
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 As part of the annual Babraham Schools' Day, my group hosted 5 GCSE and 5 A level students for half-day practical sessions in the lab.
Year(s) Of Engagement Activity 2018
 
Description Biology of Aging Gordon Research Conference - Maine, USA 
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
Year(s) Of Engagement Activity 2019
 
Description Computational Modeling in Biology Network 
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 I created COMBINE to coordinate the development of standards in computational systems biology. The initiative includes several workshops a year (discussion of future standards, implementation of current standards, and end-user training), diffusion lists, social media dissemination.
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015,2016,2017,2018
URL http://co.mbine.org
 
Description Distinguished Lecture Speaker - University of Pennsylvania 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Invited talk
Year(s) Of Engagement Activity 2019
 
Description EMBL Conference: Chromatin and Epigenetics - Heidelberg 
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
Year(s) Of Engagement Activity 2019
 
Description GENIE network of C elegans researchers 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Joining this pan european network has allowed us to attend conferences, network with other C elegans labs across Europe and obtaining funding to organise a workshop on C elegans metabolic reconstruction.
Year(s) Of Engagement Activity 2015,2016,2017,2018
 
Description GENiE workshop "Extending the consensus representation of C. elegans metabolism" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact https://www.helmholtz-muenchen.de/genie-workshop-2017/program/index.html
Year(s) Of Engagement Activity 2018
URL https://www.helmholtz-muenchen.de/genie-workshop-2017/program/index.html
 
Description Genome editing workshop 
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 Workshop about Crispr genome editing at the Cambridge Science Festival
Year(s) Of Engagement Activity 2019
 
Description IMP Research Institute of Molecular Pathology - Vienna 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Invited talk
Year(s) Of Engagement Activity 2019
 
Description Invited speaker invitation - Grand Rapids, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Invited talk
Year(s) Of Engagement Activity 2019
 
Description Life2019 Conference - Netherlands 
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
Year(s) Of Engagement Activity 2019
 
Description Local community visit - Pampisford Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A society from the local community - the Pampisford Society - visited the Institute because of interest in finding out about the nature of the research conducted at the Institute. As well as a tour of some of the research facilities, including a virtual tool of the animal facilities, and presentations on the Institute, there were two research talks given, one by myself. The talk covered how we profile epigenetic marks in gametes and early embryos, and how we seek to understand possible effects of lifestyle (diet) and age on the transmission of epigenetic marks from parents to offspring. There was considerable interest in this area of research.
Year(s) Of Engagement Activity 2017
 
Description Nine invited presentations at international meetings, including EMBO, FASEB, Keystone, American Association for Cancer Research 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Conference presentations about our research
Year(s) Of Engagement Activity 2018
 
Description Organisation of C.elegans Cambridge local area meetings 
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 An audience of about 10-15 science labs from around the Cambridge area attend these events, including many PhD students and postdocs. The aim of these meetings is dissemination of techniques and science as well as networking.
Year(s) Of Engagement Activity 2015,2017,2018
 
Description Partcipation in The Future of Ageing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact A representative of the Casanueva lab attended a debate on the future of gein at London School of Economics geared towards general public.
Year(s) Of Engagement Activity 2018
 
Description Partnership Award from Royal Society 
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 My lab obtained funding to organise a short course for about 50 students in local high-schools to teach them how to work with the nematode C elegans.
Year(s) Of Engagement Activity 2016
 
Description Presentation to the EMBL-EBI Industry program 
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 EMBL-EBI Industry program, representing pharma and agri-food industry, on the use of genome scale metabolic models for personalised medicine.
Year(s) Of Engagement Activity 2018
 
Description Savile Club epigenetics talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation about epigenetics at the London Savile Club
Year(s) Of Engagement Activity 2018
 
Description Sophianum School collaboration - Technasium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact The Babraham Institute is continuing to coordinate activities supporting its commitment as a signatory of the Concordat on Openness on Animal Research. Institute staff, including animal unit managers, have been working closely with a school in the Netherlands to prepare and launch the Institute's contribution to the national 'Technasium' education programme, which aims to draw together students and industry.

Two projects, developed in collaboration with the Institute's Public Engagement team and teachers from the Sophianum School in Gulpen, will challenge students to research and design systems to improve the efficiency and safety of animal care systems. A third project will require the students to research how legislation regulating the use of animals in science, as well as public opinion, can vary throughout Europe and the world.

A two-day visit on 19th & 20th May will kick-start a 10-week programme for the 15-year old students, who will work in teams and compete to design the best solutions to the challenges. The Institute's animal technicians will monitor student progress by commenting on YouTube videos posted fortnightly by the teams. Regular video calls into the animal unit and the Institute's laboratories will allow live discussion between the students, the animal technicians and the scientists who use animals as part of their research.

The challenge projects will finish in July, with the winning Sophianum team coming to the Babraham Institute as part of their prize. The students will visit Institute animal facilities and will get a chance to see the award-winning camera system which displays live feeds from the facility - allowing groups to appreciate first-hand both the animal care environment and the nature of working within an animal research unit.

This pilot project will also involve sixth-form students at the school who will learn about the Institute's research and take part in workshops to discuss the ethics of the use of animals in science. The Institute has been running ethics workshops for secondary and sixth form students since 2005, with contributions from Understanding Animal Research, the European Animal Research Association and the Institute of Animal Technology.

The success of the Technasium project will be evaluated by both the Institute and Sophianum School, with a view to developing future challenges.
Year(s) Of Engagement Activity 2017,2018
 
Description Sophianum poster workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact A scientific poster workshop for the Sophianum school in the Netherlands
Year(s) Of Engagement Activity 2019
 
Description Sophianum sixth form project judging 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Sixth form students wrote scientific projects which were then judged
Year(s) Of Engagement Activity 2019
 
Description Sophianum visit to BI 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact School visit by dutch school classes
Year(s) Of Engagement Activity 2019
 
Description St Catharines Society Visit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A presentation and discussion at the St Catherine's society
Year(s) Of Engagement Activity 2019
 
Description SysMod 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I organised the 2nd meeting of the ISCB Community of Special Interest SysMod. Up to 270 people attended depending on the talk.
Year(s) Of Engagement Activity 2017
 
Description Talk at Cambourne Library 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact 15 general audience attended an Epigenetics presentation and discussion
Year(s) Of Engagement Activity 2018
 
Description Teacher workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk to sixth-form teachers as part of 'Twilight Teacher Session', held at the Wellcome Trust Sanger Institute, Hinxton. The remit of the event was to inform teachers about state-of-the-art DNA sequencing technologies and their applications. It comprised a tour of sequencing facilities at the Sanger and a talk from a Sanger scientist and from myself, in which I presented current progress in single-cell sequencing methods and their applications in reproductive medicine. The workshop also discussed teaching aids that could be used to illustrate current sequencing capabilities.
Year(s) Of Engagement Activity 2017
 
Description UKRI launch 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact UKRI launch event 2018
Year(s) Of Engagement Activity 2018
 
Description WT/EBI course in silico systems biology 
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 organised this one-week course, and gave presentations entitled: "What is Systems Biology? Where does it come from?", "The many faces of modelling in biology", "Modelling in systems biology, a few challenges", "From art to engineering: two decades of standards and tools towards digital organisms", "Modelling chemical kinetics" plus a tutorial on stochastic simulations of biological systems.
Year(s) Of Engagement Activity 2017
 
Description Weert College ethics workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact This was a scientific ethics workshop for a school in the Netherlands
Year(s) Of Engagement Activity 2019
 
Description Weert College presentation judging 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Students were making scientific presentations which were then judged
Year(s) Of Engagement Activity 2019
 
Description Wellcome Genome Campus Cell Fate Workshop 
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 This was an invitation only workshop organised by us on the Hinxton campus which brought together some of the international leaders working on cell fate biology and pathology.
A meeting report was produced subsequently.
Year(s) Of Engagement Activity 2018
 
Description Wellcome Trust Workshop on NEURONAL MATURATION: London 
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
Year(s) Of Engagement Activity 2019
 
Description Whittlewomen 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation to local women's group
Year(s) Of Engagement Activity 2019
 
Description Women's Institute visit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Visit by members of the Women's Institute for a discussion and workshop on Epigenetics
Year(s) Of Engagement Activity 2019
 
Description eLife Community Webinar - Refreshing approaches to researcher evaluation 
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 I animated a webinar discussing various ways to bypass the traditional publication-based evaluation of researchers.
Year(s) Of Engagement Activity 2017