University College London (UCL), London, United Kingdom
University College London is ranked fourth in the world and second in the UK in the 2009 QS World Rankings, with competitively won research grants and contracts accounting for a third of UCL's income. UCL's defined research strategy includes building on this expertise to tackle four initial Grand Challenges by actively facilitating cross-disciplinary interaction, within and beyond UCL, and applying collective strengths, insights and creativity to overcome problems of global significance. The first of these is Grand Challenge for Global health.
Centre for Computational Statistics and Machine Learning (UCL CSML)
The centre for Computational Statistics and Machine Learning (CSML) is a grouping of researchers spanning the departments of Computer Science, Statistics and Gatsby Computational Neuroscience at University College London. CSML brings together researchers studying next generation data analysis techniques particularly with a view to addressing the challenges that large scale data analysis brings. CSML members address these challenges by developing novel methodologies and exploiting computational developments and apply these to a variety of data analysis problems across the sciences.
Previous experience
CSML has for the last 8 years organised the PASCAL European network of excellence in machine learning, coordinating the activity of over 50 sites in Europe and beyond. This represents the largest network of machine learning researchers in Europe. CSML is well known for its plurality of approaches, being a world leading centre for excellence in Bayesian Statistics and probabilistic modelling. CSML is involved in several FP7 projects, including COMPLACS, PASCAL, LeSTRUM and holds a platform grant from the UK EPSRC, in addition to numerous individual grants.
Profile of staff members
David Barber is director of the CSML machine learning group and is well known for his expertise in large scale probabilistic inference with a recent international textbook on this topic. Profs John Shawe Taylor, Mark Girolami and Peter Dayan lead the respective departments constituting the CSML research group, each internationally recognised experts in data analysis, methodological development and applications in the biological sciences. Members of CSML also include experts in large scale bioinformatics, including Prof Benny Chain (UCL Infection and Immunity) who is co chair of the Weizmann UK Scientific Advisory Group.
Five recent publications relevant to the project
D. Barber. Bayesian Reasoning and Machine Learning. Cambridge University Press 2012.
E. Challis and D. Barber Affine Independent Variational Inference. Neural Information Processing Systems (NIPS) 2012.
T. Furmston and D. Barber A Unifying Perspective of Parametric Policy Search Methods for Markov Decision Processes. Neural Information Processing Systems (NIPS) 2012.
D. Barber, A. T. Cemgil and S. Chiappa. Bayesian Time Series Models. Cambridge University Press 2012.
E. Challis, D. Barber, Concave Gaussian Variational Approximations for Inference in Large Scale Bayesian Linear Models. Proceedings of The Fourteenth International Conference on Artificial Intelligence and Statistics (AISTATS) 2011
Centre for Computational Science (UCL CCS)
The Centre for Computational Science (CCS) at University College London (UCL) is concerned with many aspects of theoretical and computational science, from chemistry and physics to materials, life and medical sciences. The UCL Computational Life and Medical Sciences (CLMS) Network aims to encourage and support collaboration, communication and co operation between the various domains that promote the development of computational life and medical (basic and clinical) science at UCL. UCL works with UCL Partners, a UK Academic Health Science Centre that brings together world‐class medical researchers and clinicians from UCL and sixteen NHS Trusts, and is one of Europe's largest and strongest academic health science partnerships. UCL Partners works to advance medical research, quality patient care and education. UCL is one of eight universities that have been recognised by the EPSRC and the UK Government Communications Headquarters (GCHQ) as an Academic Centre of Excellence in Cyber Security Research CCS researchers are leading innovative users of the XSEDE, PRACE and EUDAT, and UK NES e infrastructures and work in partnership with them to develop novel access policies appropriate to biomedical computing
Previous experience
CCS is leading the VPH Network of Excellence and is a partner in several FP7 projects (p medicine, VPH SHARE, EUDAT, INBIOMEDVISION, DIGITAL PATIENT). CCS has a strong expertise in federated security infrastructure development and data warehousing, integration with existing EU infrastructures (PRACE, EUDAT), computational simulation of molecular and arterial systems, patient specific medical simulation, and high performance computing.
Profile of staff members
Peter Coveney is the director of CCS and he is active in a broad area of interdisciplinary theoretical research including life and medical sciences and collaborations with clinicians. Coveney is PI of the Virtual Physiological Human (VPH) Network of Excellence and partner in several FP7 projects. Ali Nasrat Haidar is an information security and assurance specialist and will be involved in ITFoM federated data warehousing and security infrastructure design and implementation. Stefan Zasada is a software engineer at CCS, developing lightweight grid middleware and enabling tools for e Science. He will be leading the work on HPC middleware (AHE) that enables running ITFoM simulation on EU infrastructure (PRACE, EUDAT). David Wright is a research associate and he is interested in integrating molecular modelling approaches within the wider context of systems biology and medical research
Five recent publications relevant to the project
A. N. Haidar et. al. "Audited Credential Delegation: A Usable Security Solution for the Virtual Physiological Human Toolkit". Interface Focus, March 30, 2011.
S. J. Zasada et. al, "IMENSE: An e Infrastructure Environment for Patient Specific Multiscale Modelling and Treatment", Journal of Computational Science, (2011).
S. J. Zasada, et al, "On the Usability of Grid Middleware and Security Mechanisms". Phil. Trans. R. Soc. A August 28, 2011 369 (1949) 3413 3428.
A. N. Haidar et. al. "Managing Security and Privacy on Patient Data Sharing Platforms". VPH book, Oxford University Press, to appear 2013.
D. W. Wright et. al. "From base pair to bedside: molecular simulation and the translation of genomics to personalised medicine", Wiley Interdisciplinary Reviews: Systems Biology and Medicine, (2012), 4(6), pp 585 598.
UCL Cancer Institute
UCL is one of UK's premier teaching and research institutions (ranked 4 th in the QS and THES world rankings for 2009 and 2010). The UCL Cancer Institute (where the PI is located) has strengths in systems biology and systems medicine of cancer and other common diseases. The Institute has state-of-the-art facilities for microarrays, NGS sequencing, genotyping, mass spectrometry, FACS, imaging and high- performance computing. Using these facilities, the Beck lab has pioneered methods for methylome analysis
and is recognised for its expertise in experimental and computational approaches to generate and interpret epigenome maps in health and disease.
Previous experience
Stephan Beck is Professor of Medical Genomics at the UCL Cancer Institute. He has over 25 years experience in high-throughput genomics and has (co)authored over 200 publications that have attracted over 11,000 citations to date. He was ranked 7 th in the 2009 THES world-ranking for genetics and molecular biology. During his tenure as Head of Human Sequencing (1996-2007) at the Wellcome Trust Sanger Institute, he played a leading role in the sequencing of the human, mouse and zebrafish genomes and is a founding member of the Human Epigenome Project (HEP). His lab has pioneered array- and sequencing- based DNA methylation reference maps and was among the first to conduct epigenome-wide disease association studies. He was/is a partner in numerous EU projects, including the Human Epigenome Project (HEP) under FP5, High throughput Epigenetic Regulatory Organisation In Chromatin (HEROIC) under FP6 and two EU Networks of Excellence under FP7, EpiGenetics towards Systems Biology (EpiGeneSys) and Integrated research on DEvelopmental determinants of Aging and Longevity (IDEAL). Moreover, he is a member of the US Epigenome Taskforce and an advisor to the NIH Epigenome Roadmap program, the Swiss Initiative in Systems Biology, the British Columbia Cancer Agency and the EU READNA project. He is a Fellow of the Academy of Medical Sciences and holder of a Royal Society Wolfson Research Merit Award.
Profile of staff members
Stephan Beck (PhD, FMedSci) is Professor of Medical Genomics at the UCL Cancer Institute. He is a recognised expert in epigenome analysis and will direct the UCL contribution of this application. Christopher Bell (PhD) is a research associate with expertise in epigenome-wide association studies (EWAS). Lee Butcher (PhD) is a research associate with expertise in metyhylome analysis using AutoMeDIP-seq. Andrew Feber (PhD) is a research associate with expertise in metyhylome analysis using the 27k Infinium assay. Andrew Teschendorff (PhD) is a principal research associate with expertise in biomedical statistics. Christina Thirlwell (PhD) is a clinical principal research associate with expertise in clinical epigenetics. Gareth Wilson (PhD) is a research associate with expertise in pipeline development and methylome analysis.
Webpage
Recent publications relevant to the project
1. Li Y Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J, Zhang H, Chen Q, Luo R, Chen M, He Y, Jin X, Zhang Q, Yu C, Zhou G, Sun J, Huang Y, Zheng H, Cao H, Zou X, Hu X, Li X, Kristiansen K, Bolund L, Xu J, Wang W, Yang H, Wang J, Li R, Beck S, Wang J, Zhang X. The DNA Methylome of Human Peripheral Blood Mononuclear Cells. PLoS Biol. 2010 Nov 9;8(11):e1000533.
2. Beck S. Taking the measure of the methylome. Nat Biotechnol. 2010 Oct;28(10):1026-8.
3. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJP, Durbin R, Tavaré S, Beck S. "A Bayesian Deconvolution Strategy for Immunoprecipitation-Based DNA Methylome Analysis." Nat Biotechnol 2008 26:779- 85.
4. Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJP, Carter NP, Tavaré S, Beck S. "An Integrated Resource for Genome-Wide Identification and Analysis of Human Tissue-Specific Differentially Methylated Regions." Genome Res 2008 18: 1518-29.
5. Eckhardt F, Lewin J, Cortese C, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, David Niblett, Thomas Otto, Roger Pettett, Stefanie Seemann, Christian Thompson, Tony West, Jane Rogers, Alex Olek, Berlin K, Beck S. "DNA Methylation Profiling of Human Chromosomes 6, 20 and 22." Nat Genet 2006 38:1378-85.