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Newsletter Autumn 2012
Welcome to the UGI Autumn 2012 Newsletter. Please contact Simona Wade (firstname.lastname@example.org) if you have any comments or information to be included in the next edition.
Welcome to the new members of UGI
Warren Emmet - member of UGI Core Team
Warren has been working in bioinformatics (both commercial and core academic service) for the past four years focusing on the analysis of next generation sequencing data. This included development of software pipelines to automate the processing of large data volumes produced by this technology as well as the interpretation and exploration of the data. Warren holds a bachelors degree in Human physiology and Genetics as well as an Honors and Masters degree in Bioinformatics.
Garratt Hellenthal - Sir Henry Dale Fellow
Garrett joined UGI in September 2012. He acquired a PhD in Statistics at the University of Washington in 2006 under the supervision of Matthew Stephens, with his thesis on inferring features of recombination via statistical modelling. He subsequently worked at the University of Oxford as a post-doctoral research assistant. Most recently this has involved working in Peter Donnelly's group at the Wellcome Trust Centre for Human Genetics (WTCHG), conducting genome-wide association studies as part of the Case Control Consortium 2 (CCC2) and exploring the colonisation history of the United Kingdom as part of the People of the British Isles (POBI) project. He recently received a Sir Henry Dale Fellowship, funded jointly by the Wellcome Trust and Royal Society, for the next five years at UCL, where he will continue developing and applying techniques to capture relatedness among populations and infer colonisation history using DNA.
Margarida Cabrita Lopes - Research Associate
Margarida is currently undertaking her postdoctoral training in human population genetics at UCL Genetics Institute (UGI). Her work mainly focuses on human demographic history and selection in human genome. Margarida graduated from Lisbon University in 2006 with a BSc degree (Licenciatura) in Biology and completed an MSc in population genetics in 2007 at the same university. In 2010 she earned her PhD in Genetic Epidemiology of astigmatism from King’s College London under the supervision of Professor Chris Hammond and subsequently took a postdoctoral position at the Wellcome Trust Sanger Institute where she specialised in the analysis of large-scale association studies with focus on the genetics of metabolic diseases.
Ferran Palero - Visiting Research Associate
Ferran is a Postdoctoral Researcher at University of Valencia, Spain (Instituto Cavanilles de Biodiversidad y Biología Evolutiva) and Genomics and Health Area, CSISP. His main interests are Evolutionary Biology, Population Genetics and Conservation Genetics. Ferran is currently visiting François Balloux to apply spatial genetics and phylogeography methods on genetic data from Legionella pneumophila populations.
Adrien Rieux - Research Associate
Adrien started his first Postdoctoral position in François Balloux‘s group in June 2012. In his PhD and previous academic path, based in Montpellier (south of France), he gained experience in population genetics and spatial statistics analyses of infectious diseases. His PhD was dealing with the estimation of dispersal and the management of fungicide resistance in an African plant pathogen fungus. One of Adrien's main scientific interests is to describe spatial distribution of genetic diversity in natural populations of infectious diseases with the objective to reconstruct their evolutionary and demographic history (such as their dispersal abilities, population sizes, phylogenetic relationships, routes of expansion, substitution rates, etc…). He likes to think that the research he contributes to is situated at the interface between fundamental and applied science. Studying infectious disease is thus fascinating as fundamental work can directly help to better predict patterns of i) disease spread both at local and global scale and ii) pathogen’s evolutionary potential. A better understanding of both processes is useful to improve our abilities to control disease propagation and to define new efficient management strategies. Adrien's mission statement at UCL is to generate and analyse genomic datasets, mainly (but not only) in human pathogens, to address relevant questions in evolution, epidemiology and public health.
Ben Sobkowiak - PhD student
Ben has recently started a PhD in the Balloux group focusing on the effects of population dynamics on the rate of evolution at neutral genes. He obtained his BSc in Biology at Bristol University (2005-2008) and an MRes in Biosystematics jointly at Imperial College and the Natural Histopry Museum (2009-2010) where he completed three small independent research projects including a study on the macroecological correlates determining global monocot plant species diversity, the first such analysis of plants on this scale. Between finishing his masters degree and now, he worked in various jobs including medical research at UCLH and on a conservation project in central Tanzania.
Matteo Spagnelotti - Research Associate
Matteo studied Biology at the University of Rome Sapienza, Italy, where he obtained a PhD in Cellular and Developmental Biology in the laboratory of Prof Mauro Colombo. During his PhD studies he has progressively dealt with a computational approach to biology, working mainly in the fields of comparative genomics and molecular evolution of the bacterial pathogen Vibrio cholerae. For his post-doc Matteo won a fellowship from the Institute Pasteur Cenci Boglognetti Foundation to study abroad . He is now interested in bacterial population genetics, and how evolutionary processes drive patterns of genetic diversity and differentiation in human oral bacteria.
Chris Steele - PhD student
Chris has already been at UCL for a year, having just finished MSc in Genetics of Human Disease. Prior to this he completed an undergraduate degree in Biology at the University of Bristol. This autumn he started a BBSRC CASE PhD studenstship with David Balding in conjunction with the Cellmark Forensic Services. Initially, the work will entail tweaking likeLTD; a programme that David has already developed that provides a likelihood ratio for the prosecution/defense case related to who is assumed to contribute to a DNA sample. Following this phase of the PhD his options are fairly open in the realm of forensic genetics, however, he is leaning towards investigating the utility of DNA methylation profiles in providing extra information regarding the originator of the DNA. The most useful example in relation to forensics would be predicting the contributors age through their methylation profile.
Kaustubh Adhikari - Research Associate
Kaustubh joined David Balding's group in May this year.
UGI MSc courses
We were delighted to see some of our graduates from the class of 2011, return to UCL for their graduation ceremony this summer. This was a wonderful occasion for the academic staff to celebrate and catch up with the students and meet their families and friends.
In September, last year’s students presented their research projects in front of their peers and teaching staff. The external examiners were impressed by the quality of students’ projects and their presentations. We are proud that all of our 18 students successfully completed their courses, with fantastic results: eight distinctions and five merits. Congratulations to Lydia Leon for the overall Best Student prize and Emily Armstrong for the prize for Excellence. Emily reflected later in her testimonial: “I chose to study the MSc in the Genetics of Human Disease because I have a very strong interest in this subject and I wanted to improve my career prospects in this field. The highlight of my experience was the laboratory project. During my project I had the opportunity to work with Professor Hugh Gurling in the Molecular Psychiatry laboratory screening for rare variants in the PCM1 gene that may cause Schizophrenia. Following identification of novel SNPs using both bioinformatic and laboratory-based techniques, I assessed their frequency in Schizophrenia cases and control subjects using KASPar genotyping and statistical analysis.
I am extremely happy to receive the ‘Prize for Excellence’ because I invested a great amount of time and energy into my project and I strongly believe that my experience at UCL will be very beneficial to my future career.”
Our first cohort of Pharmacogenetics and Stratified Medicine programme students have successfully completed their courses, with one distinction, three merits and the rest passing. Congratulations to Anna Sanniti in obtaining a Distinction and being awarded the overall Best Student prize and Rouba Hoteit for having the Best Project prize.
The new academic year is in full swing! We’d like to extend a warm but belated welcome to 22 students from 13 countries who joined the MSc in Genetics of Human disease programme and 11 students from 8 countries that started the MSc in Pharmacogenetics and Stratified Medicine. The UGI management team wish to all our new students a good year full of excitement, friendship and of course SUCCESS in their studies
Bloomsbury Centre for Genetic Epidemiology and Statistics (BCGES)
The centre held its second Annual Scientific Meeting in June. This year’s theme was infectious and non-communicable genetic epidemiology, epigenetics, high-throughput sequence analysis and other topics at the leading edge of genomics research. The event was attended by colleagues from UCL / LSHTM and other UK research centre, with keynote talk from Dr Stephen Bentley (Wellcome Trust Sanger Institute) with a range of further speakers from UCL and LSHTM.
Thursday 29th November, 1-2pm, Biochemistry LT, Darwin Building
Dr David Curtis - "25 years searching for the gene for schizophrenia"
Tuesday 4th December, 12 -1 pm, Gordon House 106 (UCL)
Dr Zamin Iqbal, Wellcome Trust Centre for Human Genetics, University of Oxford,
Title: “Building better maps of genetic variation using de novo assembly: examples from human and microbial genomics”
Upcoming Beer and Pizza event on Pharmacogenetics in January
Watch this space!!!
Upcoming deadlines for Funding Opportunities:
7th December 2012
SLMS Excellence Fellowships
9th January 2013
New investigator scheme
Responsive research grants
Industrial partnership awards
5th December 2012
Ecology and evolution of infectious diseases, National Science Foundation, US and other funders
8th January 2013
- Research grants - Infections and Immunity, Medical Research Council, GB, recurring opportunity
- Research grants - Molecular and cellular medicine, Medical Research Council, GB, recurring opportunity
15th January 2013
Clinical research training fellowships
24th January 2013
Methodology research programme - investigator-led research
29 January 2013
Research grants - neurosciences and mental health
New/Senior Investigator Awards - 26th November
Senior Research Fellowships Basic/Clinical - 10th December
International Senior Research Fellowships - 10th December
Four-year PhD programmes - 10th December
New Phd programmes for clinicians - 10th December
Wellcome Trust/MIT postdoctoral fellowships - 18th January ‘13
UGI email distribution list
If you would like to subscribe to the list to receive information about events organised by UGI please go here (insert linkhttps://www.mailinglists.ucl.ac.uk/mailman/listinfo/ugi-events)
UGI is on Facebook
UGI have a Facebook page where you can find all the latest information and events taking place. Visit us at www.facebook.com/uclgeneticsinstitute
Currently, the UGI has 14 affiliate members. Being an affiliate brings the following benefits:
1. Access to the core team for research support, for example, to provide data analysis or to provide assistance with grant applications. The core team consist of: the Bioinformaticians (Sonia Shah, Warren Emmett), Statistical Geneticist (Delilah Zabaneh, Jon White), UGI Manager (Susmita Datta) and Executive Officer (Elvira Mambetisaeva). Affiliates have access to the core team by submitting a short request form to the UGI Manager. The costs of the core team used in the generation of research data (Bioinformatican and Statistical Geneticist) should be recovered from any grant obtained, their time and therefore cost should be included in any future grant application.
3. The UGI organises a series of workshops and seminars with the aim of facilitating interaction and fostering collaboration in genetics research. Affiliates have the opportunity to co-organise and suggest such events.
2. Affiliates will have the opportunity to identify strong candidates for postgraduate study through interaction and engagement with MSc students from the MSc in the Genetics of Human Disease, MSc in Statistical Genetics and MSC in Pharmacogenetics. Affiliates will be asked to consider providing an MSc student project for these courses (bench fees provided) and other masters courses as they become available.
If you are interested in becoming a UGI Affiliate please contact Sushmita Datta
Introducing a UGI affiliate – Dr Hynek Pikhart
Dr Hynek Pikhart is a senior lecturer at the Department of Epidemiology and Public Health. His current research is focused on determinants of health in countries of Central and Eastern Europe. In particular, he works on The Health, Alcohol and Psychosocial factors In Eastern Europe (HAPIEE) Study, the Wellcome Trust and NIA funded project concentrating on determinants of poor health status in samples of general population in Russia, Poland, Lithuania and the Czech Republic. His work includes research on the measurement of socioeconomic position in relation to various health outcomes, analysing and explaining the role of psychosocial factors in health, and explaining social variations in health in several countries undergoing social and economic transformation.
Page last modified on 12 jul 13 15:56