Statistical Genomics and the Analysis of High Dimensional Data

Lead Research Organisation: MRC Biostatistics Unit

Abstract

To better understand multifactorial diseases such as cancer, diabetes and cardiovascular diseases, and to ultimately better target treatments to individuals, researchers are using new biotechnologies that measure genetic code at extremely high resolution as well as downstream functional mechanisms essential to the maintenance of human health, and study designs that combine extensive questionnaires, genotyping and biobanks. However, the amount and diversity of information collected render their analysis difficult and statisticians are faced with the challenge of developing efficient dimension reduction approaches that can discover important predictors and patterns among a vast array of possibilities. Our programme proposes to develop a range of improved statistical techniques and algorithms for finding important combinations of features in large genetic and genomics datasets that characterise or predict health outcomes and for carrying out integrative analyses to characterise heterogeneous disease processes. The new methods will be accompanied by the development of freely available software and will be used in a number of collaborative projects to improve understanding of the regulation of genes and immunological response, to study gene-environment interactions and to develop biomarker-based prognostic signatures.

Technical Summary

Motivated by important biomedical collaborations, the broad aim of this programme is to enrich the statistical toolkit that is commonly used in genomics analyses by developing and implementing new analytical strategies for integrative and translational genomics, as well as for the analysis of data rich genetic epidemiological studies. The core of the proposed models and inference will be embedded within state of the art statistical developments in Bayesian modelling and computations, although analogous penalised approaches will also be investigated and compared to Bayesian implementations.

We will focus on modelling and computational strategies where the multidimensional (e.g. complex multiple-phenotype) and multivariate aspects (many explanatory features) of complex data sets are exploited at key steps of the analysis strategy. In order to perform dimension reduction, we will investigate sparse regression approaches, i.e. the finding of well supported models involving only a small number of important features, as well as the formulation of flexible clustering structures that can uncover major patterns of variability in large sets of genomic or epidemiological biomarkers. One important focus will be build structural links between different sources of data using context specific (e.g. epidemiological, biological) information, hierarchical relationships and informative priors based on substantive knowledge. Model uncertainty will be taken into account as part of the Bayesian modelling process.

We will use the methods to search for new associations and structures in a range of exemplar case studies demonstrating multiple facets of the applicability of the novel methods that will be developed. In particular, we will investigate gene expression profiling for autoimmune diseases, biomarkers for predicting small-for-gestational age infants, prognostic scoring for progression free survival in breast cancer, gene-environment interactions for Type 2 diabetes and integrative genomics of coronary heart disease. The algorithms that are developed will be made efficient by integrating new parallel computing techniques and novel software architecture that enormously reduce computing time. The computer programmes implemented will be open source and made publicly available.

Publications

10 25 50
 
Description Research Committee of the Health Effects Institute, Boston, US (2005 - 2013)
Geographic Reach North America 
Policy Influence Type Membership of a guidance committee
 
Description • Conseil Scientifique de l'ANSES (Agence Française de Sécurité sanitaire de l'alimentation, l'environnement et du travail) (2010 - 2018)
Geographic Reach Asia 
Policy Influence Type Membership of a guidance committee
 
Description EU FP7
Amount € 228,275 (EUR)
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 10/2013 
End 03/2020
 
Description INSERM
Amount € 112,393 (EUR)
Organisation National Institute of Health and Medical Research (INSERM) 
Sector Public
Country France
Start  
 
Description KCL- Spector- A systems based approach to integrating genetic and longitudinal omics data to support diagnosis and prediction of common chronic disease
Amount £143,160 (GBP)
Funding ID MR/M004422/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start  
 
Description MRC- MRP- Newcombe- Method development for Mendelian randomisation using summary statistics (MR)
Amount £152,934 (GBP)
Funding ID MR/N027493/1 
Organisation Medical Research Council (MRC) 
Department MRC/NIHR Methodology Research Programme
Sector Academic/University
Country United Kingdom
Start  
 
Description Research Collaboration - GSK
Amount £184,401 (GBP)
Organisation GlaxoSmithKline (GSK) 
Sector Private
Country Global
Start 01/2015 
End 12/2017
 
Description Research Collaboration - Papworth
Amount £130,855 (GBP)
Organisation Papworth Hospital NHS Foundation Trust 
Sector Public
Country United Kingdom
Start 09/2014 
 
Description A BIOMARKER AND PATHWAY DISCOVERY PROGRAMME IN INFLAMMATORY DISEASE 
Organisation University of Cambridge
Department School of Clinical Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Co- investigator on a research grant awarded by the MRC ref_MR/L019027/1 Co- supervision of a clinical research student Provide statistical input into the project
Collaborator Contribution Co-ordinated an MRC grant application ref MR/L019027/1 Clinical research student Provide intellectual input into the project
Impact Work of the clinical research student is ongoing and no outputs are reported here as yet
Start Year 2013
 
Description A systems based approach to integrating genetic and longitudinal omics data to support diagnosis and prediction of common chronic disease 
Organisation King's College London
Department Department of Medical & Molecular Genetics
Country United Kingdom 
Sector Academic/University 
PI Contribution Co Investigator on a research grant to the MRC- ref MR/M004422/1 Will provide statistical input to the project
Collaborator Contribution Awarded MRC grant ref ref MR/M004422/1 Other collaborators will provide intellectual input and data
Impact Awarded grant from the MRC
Start Year 2014
 
Description A toolbox for missing confounders in observational studies 
Organisation Imperial College School of Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution TBC
Collaborator Contribution TBC
Impact TBC
Start Year 2017
 
Description BRC- Cambridge renewal 
Organisation National Institute for Health Research
Department NIHR Biomedical Research Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution TBC
Collaborator Contribution TBC
Impact TBC
Start Year 2014
 
Description Immuno-psychiatry: a consortium to test the opportunity for immunotherapeutics in psychiatry 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Co supervisor on a grant application to the MRC- ref MR/L014815/1 Day to day supervision of a researcher based at BSU Providing statistical input to the project
Collaborator Contribution Project coordinator and was awarded an MRC research grant ref MR/L014815/1 Provides data and intellectual input into the project
Impact The researcher only recently started work on this and so no outputs are available yet
Start Year 2014
 
Description Integrative statistical methods for discovering the genetic basis of rare diseases 
Organisation University of Cambridge
Department Department of Haematology
Country United Kingdom 
Sector Academic/University 
PI Contribution Supervision of a doctoral student Providing statistical guidance on this project
Collaborator Contribution co supervision of the doctoral student Providing data and intellectual input to the project
Impact The doctoral student has just successfully completed his first year but as yet no outputs can be recorded. The project is proceeding well
Start Year 2014
 
Description Large-scale integrative studies of risk factors in coronary heart disease: from discovery to application 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Co- investigator on a MRC grant application ref MR/L003120/1 Providing statistical input into the project
Collaborator Contribution Coordinated the application for and was awarded an MRC research grant refMR/L003120/1 Will provide data and intellectual input into the project
Impact The grant was awarded recently and no outputs can be recorded as yet
Start Year 2013
 
Description Modelling single cell expression 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Day- to day supervision of a researcher based at BSU Providing statistical input into the project
Collaborator Contribution Provided the funds for and co-supervises the researcher working in the BSU Provides data and intellectual input into the project
Impact the research project is well underway and but no outputs as yet have been recorded
Start Year 2013
 
Description The Regression Discontinuity Design: a novel approach to evaluating the effect of drugs and treatments in primary care 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution co investigator on an MRC grant ref MR/K014838/1 Provided statistical input into the project
Collaborator Contribution Co-ordinated and was succesfully awarded an MRC grant ref MR/K014838/1 Will co-ordinate and provide statistical and intellectual input into the project
Impact No outputs as yet from this project but the collaboration has previously produced several publications
Start Year 2011
 
Title BASiCS 
Description BASiCS is an R package for the analysis of single-cell RNA-sequencing (scRNA-seq) datasets, where gene expression profiles of individual cells are quantified using Next Generation Sequencing. These experiments are prone to high levels of unexplained technical noise, creating new challenges regarding normalisation and the separation of technical from biological signal. Unlike previous step-wise approaches, BASiCS is an integrated Bayesian hierarchical model that incorporates built-in normalisation and quantifies technical artefacts by borrowing information from spike-in genes that that are artificially introduced to each cell's lysate and thence theoretically present at the same amount in this sample. Current downstream analyses implemented in BASiCS include a probabilistic approach to: (i) identify highly and lowly variable genes within a single-population of cells and (ii) compare gene expression patterns between 2 or more populations of cells. While traditional differential expression tools are limited to detecting changes in overall expression, BASiCS is also able to highlight genes undergoing changes in cell-to-cell heterogeneity but whose overall expression is unchanged. Control experiments and case studies suggests this can lead to novel biological insights that are not captured by previous methods. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact BASiCS is accompanied by two methodological papers: Vallejos, Marioni and Richardson (2015, Plos Comp Bio) and Vallejos, Richardson and Marioni (2016, in revision for Genome Biology). BASiCS has been already used in several case studies including the comparison of gene expression patterns between CD4+ T cells across different related mouse species, during ageing and activation of naive cells (Martinez-Jimenez, Eling et al, 2016, in preparation). Additional high-impact outcomes are expected from a collaboration with Anne Ferguson-Smith lab (University of Cambridge). The software is freely available in github (http://github.com/catavallejos/BASiCS) and will soon be submitted to Bioconductor (one of the most popular repositories of open source software for bioinformatics) to improve visibility and impact. 
URL https://github.com/catavallejos/BASiCS
 
Title PReMiuM 
Description PReMiuM is a broadly-applicable, open-source software package that allows the detection of groups (clusters) of similar patients/individuals. It has been designed to enable the identification of groups that are particularly associated with having a high risk of disease. The package is fully described in an article in the Journal of Statistical Software [1] and is freely available from the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/PReMiuM/index.html 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact The software has been applied to a variety of health-related datasets and problems, including: (i) analysing the effect of occupational exposure to organic solvents on lung cancer risk [2]; (ii) determining multi-pollutant exposure profiles associated with term low birth weight [3]; (iii) analysing the health effects of simultaneous exposure to physical and chemical properties of airborne particles [4]; and (iv) analysing blood pressure differences associated with ideal versus actual diets [5]. [1] Liverani, S., Hastie, D. I., Azizi, L., Papathomas, M., & Richardson, S. (2015). PReMiuM: An R Package for Profile Regression Mixture Models Using Dirichlet Processes. Journal of Statistical Software, 64(7).10.18637/jss.v064.i07 [2] Mattei, F., Liverani, S., Guida, F., Matrat, M., Cenée, S., Azizi, L., et al. (2016). Multidimensional analysis of the effect of occupational exposure to organic solvents on lung cancer risk: the ICARE study. Occupational and Environmental Medicine.10.1136/oemed-2015-103177 [3] Coker, E., Liverani, S., Ghosh, J. K., Jerrett, M., Beckerman, B., Li, A., et al. (2016). Multi-pollutant exposure profiles associated with term low birth weight in Los Angeles County. Environment International, 91, 1-13.10.1016/j.envint.2016.02.011 [4] Pirani, M., Best, N., Blangiardo, M., Liverani, S., Atkinson, R. W., & Fuller, G. W. (2015). Analysing the health effects of simultaneous exposure to physical and chemical properties of airborne particles.10.1016/j.envint.2015.02.010 [5] Molitor, J., Brown, I. J., Chan, Q., Papathomas, M., Liverani, S., Molitor, N., et al. (2014). Blood pressure differences associated with Optimal Macronutrient Intake Trial for Heart Health (OMNIHEART)-like diet compared with a typical American Diet. Hypertension, 64(6), 1198-1204. 10.1161/HYPERTENSIONAHA.114.03799 
URL http://cran.r-project.org/web/packages/PReMiuM/index.html
 
Title R2 GUESS 
Description R2 GUESS software R2GUESS is an R package wrapping the original C++ source code developed in GUESS (Graphical Processing Unit Evolutionary Stochastic Search). In addition to providing an user-friendly interface of the original C++ code automating its parametrisation, and data handling, R2GUESS also incorporates many features to explore the data, to extend statistical inferences from the native algorithm such as effect size estimation, significance assessment of the association through False Discovery Rate, and to visualize outputs from the algorithm. The C++ code is entirely object-oriented and open-source. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact R2GUESS has been used either as an intermediate tool in a larger pipeline for fine mapping (DOI: 10.1371/journal.pgen.1005272) or to detect associations in complex highly correlated data sets (DOI: 10.1016/j.celrep.2014.07.032). 
URL http://cran.r-project.org/web/packages/R2GUESS/index.html
 
Title R2BGLiMS 
Description R2BGLiMS is an R interface to BGLiMS (Bayesian Generalised Linear Model Selection); a Java package for fitting survival, logistic, and summary data Bayesian models under Reversible Jump model selection. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact The software helped identify several potentially novel protein markers of breast cancer survival[1]. It is also currently being used to help fine-map several genes associated with prostate cancer in collaboration with the ICR (Sutton), and to explore metabolites associated with type 2 diabetes, in collaboration with the MRC Epidemiology unit (Cambridge). [1] Newcombe, P. J., Ali, H. R., Blows, F. M., Provenzano, E., Pharaoh, P. D., Caldas, C. & Richardson, S. Weibull regression with Bayesian variable selection to identify prognostic tumour markers of breast cancer survival. Stat. Methods Med. Res. DOI: 10.1177/0962280214548748 (2014). dos:10.1177/0962280214548748 
URL https://github.com/pjnewcombe/R2BGLiMS
 
Title R2HESS 
Description R2HESS (R to Hierarchical Evolutionary Stochastic Search) performs joint multivariate regression analysis for high-dimensional data sets with hundreds of thousands of genetic markers, thousands of phenotypes and with a large number of individuals (sample size). It is able to detect marginal associations (rejecting the null hypothesis of no association) for each genotype-phenotype pair as well as to identify master regulators, i.e. genetic control points that regulate many phenotypes at the same time. A distinct feature of R2HESS is the ability to analyse high-dimensional phenotypes (gene expression, metabolites, etc) measured over different conditions/tissues/cell types. The software has an R interface that allows users to manipulate and input the data from the widely used R environment. Besides the statistical association between large data sets, the software performs automatically Bayesian False Discovery Rate calculation, Monte Carlo Markov Chain convergence checks and other diagnosis tests in order to automate user experience. The C++ code is entirely object-oriented and open-source, allowing community-based alteration and improvements. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact R2HESS has been successful used as the key discovery tool in a system genetics approach to uncover the genetic regulations of human temporal lobe epilepsy (doi:10.1038/ncomms7031). 
URL http://www.mrc-bsu.cam.ac.uk/software/r2hess_1-0-tar/
 
Description 26th Annual MASAMB Workshop, Cambridge, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Internationally recognized researchers attended the Workshop, which sparked questions and discussion after the talk.
Year(s) Of Engagement Activity 2016
URL http://www.cl.cam.ac.uk/events/masamb2016
 
Description Armitage Lectures 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Annual workshop and lecture created and hosted by the MRC Biostatistics Unit, to honour the immense contributions of Professor Peter Armitage who was at the unit from 1947 to 1961, and whose work is recognised throughout the world as achieving a successful balance between methodological rigour and applied commonsense, to which all statisticians aspire. An eminent medical statistician visits for a week and works with members of the unit. The highlight is the Armitage Lecture, where more than 100 delegates attend. This event raises the unit research profile and creates new collaborations.
Year(s) Of Engagement Activity 2011,2012,2013,2014,2015
URL https://www.mrc-bsu.cam.ac.uk/news-and-events/armitage-lectureships-and-workshops/
 
Description BSU Open 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 Unit held open day as part of MRC Festival of Medical Research.

The aim of the open day was to welcome secondary school students and members of the general public to come to the unit, find out about the research the unit does, and to take part in activities that illustrate BSU research, with the overall theme being 'Fun with statistics'. An open day of this format was a first for the unit and overall it was a very successful event. There were 40 attendees over a 4 hour event. All attendees pre-booked and were split into 4 groups for a 1 hour session comprising of an introduction, participation in hands-on activities, and a brief careers talk. The small groups and length of session allowed for quality engagement between the scientists and the audience.

Feedback from the attendees was very positive, and the wider MRC Festival activities that took place in Cambridge demonstrated the benefits in delivering these types of events.
Year(s) Of Engagement Activity 2016
URL http://www.mrc-bsu.cam.ac.uk/bsu-open-day-2016-why-are-statistics-important/
 
Description Big Biology Day 
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 Participation in Big Biology Day, organised by Hills Road Sixth Form College in Cambridge - a one day annual 'science festival' event open to memebers of the general public to participate in a range of biology based hands-on activities for all ages.

BSU presented a stand with three hands-on, interactive activities, each communicating a simple statistical method or idea, linked to the unit's research themes.
Year(s) Of Engagement Activity 2016
URL http://www.hillsroad.ac.uk/college-life/events/2016/10/15/default-calendar/big-biology-day
 
Description Bright Club (Cambridge) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Paul Kirk, Senior Statistician, took part in Bright Club as part of the Cambridge Science Festival, combining statistical research and comedy in a 10 minute talk, demonstrating that science can be accessible to wide variety of audiences.
Year(s) Of Engagement Activity 2017
 
Description Cambridge Science Festival 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Each year BSU participate in Cambridge Science Festival - members of the general public explore and discuss issues of scientific interest and concern, through a series of different events. The event also aims to raise aspirations by encouraging young people to consider a career in science, technology, engineering or mathematics.

BSU take part over two full days - 'Science Saturday' and the 'Cambridge Biomedical Campus' day. The unit presents a stand with 4 - 5 interactive activities that each communicate a basic statistical method or idea, representing one of the four research themes in the unit. Each year a new activity is developed and delivered requiring scientific input from staff across the unit. Over the two days, BSU engage with approximately 500 adults and children who visit the festival.


Raising the profile of the Unit in the region
Increase in request for further information
Audience asked for more opportunities for communication and interaction with the public health researchers
This event contributed to raise the profile of Biostatistics in medical research
This event contributed to enhance the methodological quality of medical research developed by BSU staff
This event contributed to enable Best Research for Best Health
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
URL http://www.cam.ac.uk/science-festival
 
Description Chair of Scientific Committee of the Medical Research Council Conference on Biostatistics 2014 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The Medical Research Conference on Biostatistics, was international event in celebration of the MRC Biostatistics Unit's Centenary Year. It took place at Queens' College Cambridge, UK, on 24th - 26th March 2014.
230 delegates from different parts of the world converged in Cambridge last week for three days of Biostatistics' training, knowledge transfer partnerships, networking and fun. This was the first year that the MRC Biostatistics Unit organised an event of this type, leading to a great interest from those who attended to start new collaborations and strengthen the existing ones.

BSU strengthened its reputation as a major centre for knowledge transfer.
Delegates' reactions to the BSU centenary conference were overwhelmingly positive with many singling out the "great research", "excellent speakers", "sparkling conference", and the work of the organising team as "great" and "smooth".
This event facilitated communication, interaction and collaboration between member statisticians.
This event contributed to raise the profile of Biostatistics in medical research.
This event contributed to enhance the methodological quality of medical research developed by BSU staff.
This event contributed to enable Best Research for Best Health.
Year(s) Of Engagement Activity 2014
URL http://www.mrc-bsu.cam.ac.uk/news-and-events/mrc-biostatistics-conference/
 
Description Chair of the Institute of Mathematical Statistics Committee on Special Lectures 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Appointed Chair of the Institute of Mathematical Statistics Committee on Special Lectures.
The Committee on Special Lectures invites eight individuals to deliver Medallion Lectures annually. Medallion Lectures are distinct from
Invited Papers, which are chosen by the various Program Committees for specific meetings. Each Medallion Lecturer will receive a Medallion in
a brief ceremony preceding the lecture. For more information, see here: http://imstat.org/handbook/committees.html

The Committee on Special Lectures arranges for papers of unusual interest to be given at regular meetings by distinguished scientists. It also selects the lecturers for the IMS Named Lectures. The names of the selected lecturers are usually announced at the IMS Annual Meeting at least one year in advance. See http://imstat.org/handbook/committees.html
Year(s) Of Engagement Activity 2011,2012,2013,2014
URL http://imstat.org/officials/current_committees.html
 
Description Computational Medicine Research Skills Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Workshop for Cambridge University medical students, organised under the auspices of the Cambridge University Student Clinical Research Society. Paul Kirk, Senior Statistician, organised and delivered the workshop (jointly with Dr Caroline Morton, education fellow at Imperial College London).
Year(s) Of Engagement Activity 2018
URL https://www.facebook.com/events/146342029489401/
 
Description Conseil Scientifique de l'ANSES (France) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Appointed member of the Scientific Council at ANSES (French Agency for Food, Environmental and Work Safety)
The ANSES missions is to ensure expertise, research and reference covering a wide range of human health, health and animal welfare and plant health. It provides a cross research of health issues. The Agency thus comprehensively covers all exposures (particles, waves, inhalation, ingestion...) to which a person may be subject, voluntarily or not, at all ages and stages of his/her life (whether at work, transportation, recreation, or via the food).
The ANSES assesses transverse risks and health benefits by including the contribution of human and social sciences, and provides advice and recommendations to governments and routinely makes public its work.
The Agency relies on a network of 11 reference laboratories and research in 16 geographical locations in the country and it is internationally recognized in several fields or disciplines. It has nearly 1,350 agents and involves approximately 800 external experts through its group of experts.

The ANSES assesses transverse risks and health benefits by including the contribution of human and social sciences, and provides advice and recommendations to governments and routinely makes public its work.
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014
URL https://www.anses.fr/fr/content/pr%C3%A9sentation-de-lanses
 
Description International Advisory Board of the programme "Statistics for Innovation, SFI", University of Oslo 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Member of the International Advisory Board of the programme "Statistics for Innovation, SFI", University of Oslo (2009-2014)
SFI is one of the fourteen Norwegian Centres for Research-based Innovation. (sfi)² develops core statistical methodologies, strategically necessary to achieve innovation goals in four key sectors: petroleum, finance, marine and health. See: http://sfi.nr.no/

PL invited to give a seminar. Title: Approximate Bayesian Computation under model uncertainty, with application to protein network evolution.
Date: Tuesday August 25, 2009
Place: University of Oslo, Mathematics building (Niels Henrik Abels hus), 12th floor, seminar room
Event: Tuesday statistics seminar (Joint (sfi)² and Dept Mathematics)
Speaker: Sylvia Richardson (Imperial College London, UK)
14.15-15.00: Lecture

http://sfi.nr.no/sfi/images/e/ee/Oslo_abstract.pdf
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013
URL http://sfi.nr.no/sfi/index.php/Passed_events_2009
 
Description MRC BSU Armitage Lecture and Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact More than 120 participants attended this annual event during which an eminent medical statistician visits for a week and works with members of the Unit. The highlight is the delivery of the Armitage Lecture which is free and open to other health related professionals.

Raised the profile of the Unit and strenghted its links with international institutions.
BSU strengthened its reputation as a major centre for knowledge transfer.
Attendees' reactions to the lectureships and worshops have been overwhelmingly positive.
Year(s) Of Engagement Activity 2012,2013,2014,2015
URL http://www.mrc-bsu.cam.ac.uk/training/workshops/armitage-lectureships-and-workshops/
 
Description MRC Centenary & International Year of Statistics 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact More than 600 people attended a series of Free Public Lectures co-hosted by the MRC BSU and the Cambridge Statistical Laboratory :
- Professor Sir Michael Rawlins, of NICE, "Failings in hierarchies of evidence for controversial health-policy decisions" (29 April 2013)
- Tim Harford, of More or Less, "Numbers are weapons: a self defence guide" (22nd May 2013)
- Professor Sir John Beddington FRS FRSE, "What's happening to the world?" (28th May 2013)
- Professor David J. Spiegelhalter OBE FRS, "Putting life into numbers - how statistical science has transformed health care" (20th June 2013)

Raising the profile of the Unit in the local region
Year(s) Of Engagement Activity 2013
URL http://www.mrc-bsu.cam.ac.uk/NewsandEvents/mrccentenary.html
 
Description MRC Centenary Open Week (BSU Open Day) 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 50 + people attended an exhibition about the history, pioneers and discoveries of the MRC Biostatistics Unit, and a series of talks/discussions series of talks and lectures as part of the BSU contribution to MRC Centenary Open Days

Raising the profile of the Unit in the local region.
This event facilitated communication, interaction and collaboration between member statisticians.
This event contributed to enhance the methodological quality of medical research developed by BSU staff.
This event contributed to enable Best Research for Best Health.
Year(s) Of Engagement Activity 2013
URL http://www.mrc-bsu.cam.ac.uk/NewsandEvents/mrccentenary.html
 
Description MRC Cognition and Brain Sciences Unit Methods Day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Staff and students of the MRC CBU attended a seminar and subsequent discussion of work by Paul Kirk, Senior Statistician, leading to ideas for future work and potential collaborations.
Year(s) Of Engagement Activity 2016
 
Description Media enquiry - Cambridge TV 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Media (as a channel to the public)
Results and Impact Paul Kirk, Senior Investigator Statistician, gave interview for Cambridge TV about the BSU open day, discussing what the open day is about, the activities involved, and who it is for. Promoting the MRC Festival of Medical Research.
Year(s) Of Engagement Activity 2016
 
Description Newcastle University Mathematics and Statistics Seminar Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Staff and students of the University of Newcastle attended a seminar and subsequent discussion of work by Paul Kirk, Senior Statistician, leading to ideas for future work and potential collaborations.
Year(s) Of Engagement Activity 2016
 
Description Panel discussant and organising committee (`Recent and future trends in biostatistics` workshop) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Early career statisticians from the UK and EU attended a workshop on "Recent and future trends in biostatistics", hosted at the MRC Biostatistics Unit in Cambridge. Paul Kirk, Senior Statistician, took part in a panel discussion and helped to organise the event.
Year(s) Of Engagement Activity 2017
URL https://www.mrc-bsu.cam.ac.uk/blog/workshop-inspires-early-career-biostatisticians/
 
Description Science Showoff 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Paul Kirk, Senior Investigator Statistician, took part in Cambridge and London Science Showoff events, combining statistical research and comedy in a 10 minute talk, demonstrating that science can be accessible to wide variety of audiences.

Paul has since been asked to take part in similar future events.
Year(s) Of Engagement Activity 2016
 
Description Scientific Steering Committee - Isaac Newton Institute for Mathematical Science 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The PL contributed to considering proposals for research programmes.

Contributing to the strengthening of the Institute's reputation as a leadins institute attracting leading mathematical scientists from the UK and overseas to interact in research over an extended period.
Year(s) Of Engagement Activity 2012,2013,2014
URL https://www.newton.ac.uk/about/governance/scientific-steering-committee
 
Description Statistical Methods for (post-) Genomics Data (SMPGD) Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact More than 100 people attended this annual workshop/meeting, which aims at gathering statisticians, bioinformaticians and biologists to discuss new statistical methodology for the analysis of genomics data and challenging, new types of genomics data requiring further development of such methodology. This is a 2-day workshop, with invited and contributed sessions.

Raising the profile of the Unit in the European region
Year(s) Of Engagement Activity 2013
URL http://www.smpgd2013.nl/smpgd/
 
Description Statistics and public health talk at Emmanuel College - 'Mapping Health' 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Talk at Emmanuel College on 'Mapping Health' as part of the 'Statistics Meets the Public's Health' seminar series. A non-technical talk illustrating how statistics helps to find answers to a range of public health related questions.

50+ audience members - ranging from academics, students and members of the general public.

Due to the success of the seminar series, future upcoming talks have been organised.
Year(s) Of Engagement Activity 2016
 
Description Talk for Statistics Meets Public Health seminar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Talk on "Mapping Health" for new seminar series established by Sylvia Richardson - aiming to illustrate how statistics helps to find answers to a range of public health related questions.
Year(s) Of Engagement Activity 2016
 
Description University of Birmingham Centre for Computational Biology Seminar Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Staff and students of the University of Birmingham attended a seminar and subsequent discussion of work by Paul Kirk, Senior Statistician, leading to ideas for future work and potential collaborations.
Year(s) Of Engagement Activity 2018
URL https://www.birmingham.ac.uk/research/activity/mds/centres/computational-biology/news/2017/CCB-Semin...
 
Description University of South Wales Mathematics and Statistics Seminar Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Staff and students of the University of South Wales attended a seminar and subsequent discussion of work by Paul Kirk, Senior Statistician, leading to ideas for future work and potential collaborations.
Year(s) Of Engagement Activity 2016
 
Description University of Warwick Statistics Seminar Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Staff and students of the University of Warwick attended a seminar and subsequent discussion of work by Paul Kirk, Senior Statistician, leading to ideas for future work and potential collaborations.
Year(s) Of Engagement Activity 2017
URL https://warwick.ac.uk/fac/sci/news/filtered/?calendarItem=8a17841a5c872aca015cd045dbfa7ad0
 
Description Workshop on Network Science and its Applications at Isaac Newton Institute for Mathematical Sciences (Cambridge, UK) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Internationally recognized researchers attended the Workshop, which sparked interesting questions and discussions afterwards.
Year(s) Of Engagement Activity 2016
URL https://www.newton.ac.uk/event/snaw02
 
Description Workshop on Statistical Methods for Post Genomic Data (SMPGD) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Internationally recognized researchers attended the Workshop, which sparked questions and discussion afterwards.
Year(s) Of Engagement Activity 2017
URL https://smpgd2017.wordpress.com/
 
Description Workshop talk at Berkley 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Sylvia Richardson gave talk on "Statistical approaches for Precision Medicine"
Year(s) Of Engagement Activity 2016
 
Description Workshop talk at Brunel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Sylvia Richardson gave talk on " Analysis of complex phenotypes in genomics"
Year(s) Of Engagement Activity 2016
 
Description Workshop talk at Lancaster University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Sylvia Richardson gave talk to students at Lancaster University on "Using random matrix projections to facilitate analyses of very large data sets in genomics"
Year(s) Of Engagement Activity 2016