Public viva: 17th August - Computational identification of regulatory features affecting splicing in the human brain
Newsletter January 2016
A message from UGI’s outgoing director, Professor Steve Humphries, who has done excellent work leading the Institute over the past 6 years
I am pleased to announce that the new Director of UGI is Professor Francois Balloux. I have thoroughly enjoyed being the Director of UGI and recognise the astounding achievements of all the investigators and their teams over the years. UGI was established in 2009 and has come on in leaps and bounds since its establishment. Our first appointments were Professor David Balding and Dr Vincent Plagnol – since then we have grown a lot with the appointments of Professors Balloux and Luscombe joining the team in 2011 and 2012 respectively. Additionally, the independently funded Research Fellows, Julie Bertrand, Garrett Hellenthal, Matteo Fumagalli and Doug Speed have contributed immensely and have very promising careers ahead of them. Our most recent recruit, Professor Richard Mott, will I’m sure be a valued member of UGI. Of course there have also been a great number of postdocs and researchers who have gone on to great positions following their time in UGI!
I look forward to seeing the next phase of development of the Institute in the coming years.
Our new Director is a familiar face in UGI, Professor Francois Balloux
Prof Balloux studied at the University of Lausanne in Switzerland and obtained a Masters and PhD from the same institution in 1996, and 2000, respectively. He then moved to Edinburgh, which was at the time the Mecca of population genetics, as a postdoctoral research associate and then as a postdoctoral fellow. He was offered a lectureship in the Department of Genetics in Cambridge in 2002, where he stayed for five years. In 2007, he moved to the newly formed MRC Centre for Outbreak Analysis at Imperial College London as a Reader and joined UGI as professor of Computational Systems Biology in 2012.
New members of UGI
Richard Mott - Weldon Professor of Computational and Statistical Genetics
Richard read Mathematics at Cambridge, followed by an MSc in Biometry at Reading University. He gained his PhD in 1989 on the Statistics of DNA Sequence Homologies, which was supervised by Tom Kirkwood (MRC NIMR London) and Robert Curnow (Reading). This was followed by post-doc at NIMR on protein sequence alignment.
In 1991, Richard moved fields to work on physical genome mapping with Hans Lehrach, ICRF London (now CRUK) where he developed software for constructing some of the first physical maps (Mott et al, 1993), including those of S. pombe (Maier at al, 1992, Hoheisel et al 1993), and helped build the human physical map used to clone Huntingtin (Baxendale et al, 1993). He moved to the Sanger Centre in 1995 to create the CAFtools sequence assembly software (Dear et al, 1998) for the Human Genome Project, used extensively to automate the production of finished sequence. Richard also devised one of the first algorithms for spliced alignment of ESTs to genomic DNA (Mott 1997). In 1997 he moved to SmithKline Beecham Pharmaceuticals; with Roger Tribe (Warwick), he devised a novel approach to the statistics of gapped protein sequence alignments (Mott and Tribe 1999, Mott 2000) and generalised it to non-affine gap penalties (Mott 1999).
In 1999 Richard joined the Wellcome Trust Centre for Human Genetics, Oxford, eventually becoming Professor by Research. There he made various contributions to the computational analysis of biological data, e.g. protein sequence similarities (Mott 2000), protein subcellular localisation (Mott et al, 2002), DNA- protein binding (Udalova et al, 2002), SNP tagging (Ackerman et al, 2004), genetic mapping (Mott and Flint 2002, Valdar et al, 2003), replication timing (Wodefine et al, 2004) and mouse genome assembly (Waterston et al, 2003). However, most of his research work was in analysis of complex traits in rodent models (Valdar et al, 2006, Baud et al, 2013); he developed the HAPPY software (Mott et al 2000, Yalcin et al 2005), characterised the haplotype structure of the mouse genome (Yalcin et al, 2004) and helped identify one of the first quantitative trait genes for behaviour (Yalcin et al, 2004)
Richard also co-led the effort to breed the mouse collaborative cross (Durrant et al, 2011) and collaborated in the sequencing of inbred mouse strains (Keane et al, 2011, Agam et al, 2011). He developed similar programs in the plant Arabidopsis thaliana (Kover et al, 2009, Gan et al, 2011). Richard’s most recent major work has been an analysis of parent of origin effects in mice (Mott et al, 2014). He is also a member of the CONVERGE consortium which identified the first replicated genetic loci associated with major depression (Na et al 2015).
Leilei is in the second year of his PhD in the State Key Laboratory for Pig Genetic Improvement and Production Technology, China. He came to UCL to research "the genetic basis of heterosis in pig and mouse/rat HS population “and "Systematic comparative study on the GWAS results from mouse, rat, pig and human" as a Joint PhD student of Prof. Richard Mott. He had been to the Animal Breeding and genomics Centre of Wageningen University for a short visit to analysis the population structure and introgression of global pigs using 60K SNP genotype data from 120+ indigenous pig breeds worldwide. He had also worked on an analysis on sexual dimorphism of complex traits using data of a large scale pig F2 intercoss.
Ponkgsakorn is a PhD student in Garrett Hellental’s Group. Prior to joining UCL he received a BSc in Mathematics from Mahidol University and a MSc in Bioinformatics from KMUTT, Thailand. After completing his studies, Ponkgsakorn worked as a research assistant at the Biostatistics and Informatics Lab at BIOTECH,
Thailand’s national research agency for 6 years. His research was focused on the study of genetic diversity among Thai and the Mainland Southeast Asian populations in both human and bovine groups. In Hellental’s Group, he will be involved in the development of an improved version of existing statistical methods for genetic admixture history inference, GLOBETROTTER, which will be able to handle whole-genome sequencing data of up to ten thousand subjects in forthcoming and existing studies (e.g. Genomics England). This approach will provide novel insights into the ancestral histories of world-wide human groups.
We would like to say goodbye to the following members of staff:
Adrian Rieux, Florent Lassalle, Kitty Lo and Alethea Wang. Goodbye and good luck in your new posts!
UGI MSc courses
Term 1 passed by swiftly and all our Masters students settled down well into their studies here at UCL. It was great to hear from the students’ representatives at the Staff-Student Consultative Committee meeting that all students are enjoying their course modules despite some of them being challenging. Several social events organised by the program tutors brought the MSc students and teaching staff together in a relaxed and informal environment.
Over the past month our MSc students were not only busy with their studies but also had to select a research project which they will embark on from Term 2. Each year we offer a wide range of lab and computer-based projects supervised by world-class researchers from across UCL.
Here at UCL Genetics Institute, we ensure our students are fully aware of the wide range of networking and learning opportunities available to the students in the form of lectures, seminars and other activities which are not included in the MSc syllabus both around the campus and external to UCL. During the first term, all students were invited to attend various events including Infectious Disease Genomics Symposium Beer & Pizza Science Evening hosted by Professor Francois Balloux, UCL Genetics Institute, Research Department of Genetics Evolution and Environment, and a lecture on “Human Phenotype Ontology-Driven Prioritisation of Coding and Noncoding Variants in Exome and Genome Sequencing” by Professor Peter Robinson, Professor of Medical Genomics & Professor of Bioinformatics, Freie Universität, Berlin. In January, students are invited to attend the lecture of Prof Richard Martin, University of Bristol, titled “Mendelian randomization: maximising the impact of genetic data for causal inference, disease prevention & translation”.
The admissions for 2016-17 academic year are now open. For further information and to apply for our MSc courses visit:
Please contact Dr Elvira Mambetisaeva (email@example.com) if you have any question related to our MSc courses.
The Centre will run two short courses in September 2016.
Course 1: Introduction to Genetic Epidemiology in the GWAS era
(6 – 9 September 2016)
Genetic epidemiology holds great potential for personalised medicine and improved biological knowledge of disease processes. This course provides an introduction to the design, analysis and interpretation of genetic studies of disease, with a focus on state of the art analysis of genomewide association scans. Throughout the course participants will gain practical experience of analysing genetic data in population and family studies. By the end of the course participants will have an understanding of the fundamental concepts of genetic epidemiology, will have a working knowledge of the terminology and current status of the field, and will be able to perform many basic analyses of genetic data.
Course 2: High throughput sequencing in disease studies
(12 – 15 September 2016)
Rapidly developing technologies now allow genomes to be sequenced more quickly and cheaply than ever before. This course will cover state of the art methods and applications of next generation sequencing. The course runs over 4 days and participants will be introduced to tools for analysing high throughput sequence data, including methods for measuring copy number variants and allele-specific expression, and conducting disease association analysis with sequence data. There will be considerable opportunities to gain practical experience with new data types such as whole genome sequence, RNA- and ChIP-seq data. By the end of the course participants will have a broad knowledge of the state of the art and will be well equipped to analyse their own data.
Booking for both courses will be available at the end of January 2016.
To stay informed about the centre’s activities such as seminars & conferences join our mailing list - contact Simona Wade (firstname.lastname@example.org)
PhD Student Symposium
The 2016 symposium was held on Monday 18th January 2016. The event was wonderful opportunity for PhD students to present their work to a diverse audience and to find out about other research taking place at departments and institutions in the Bloomsbury area.
Friday 12 February 2016, 1-2pm, Room LG81, LSHTM Speaker: Dr Stephen Burgess, Department of Public Health and Primary Care, University of Cambridge Title: Towards more reliable Mendelian randomization investigations
Date for your diary - BCGES Annual Conference
The conference will take place on Tuesday 21 June 2016 in Darwin LT, Darwin Building, UCL. The programme will be announced in Spring 2016.
Travel Grants now available
These grants are designed to support attendance at scientific meetings and conferences that relate directly to the applicant’s research interests, and where they will be presenting original work. Support will not normally be given where the applicant is supported by a Fellowship or grant funding that already provides travel costs; nor for research visits that form part of an ongoing grant-supported collaboration.
Further details and the application form can be obtained from our website
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Page last modified on 25 jan 16 11:02