Seminar 26 Sept: Modelling rate of decline (slope) of a biomarker as a quantitative genetic trait using mixed effects models: application to loss of renal function (GFR) in type 1 diabetes
UGI Newsletter January 2014
New members of UGI
Stephen has recently finished his PhD at Queen Mary and the Institute of Zoology. His research combined trips to collect frog carcasses from pensioners' garden ponds, lots of hours in the lab, computational models of spread as well as genomics, and implicated human activities heavily in the emergence and spread of some virulent amphibian viruses. He joins Francois Balloux's group to focus in on spatial genetic patterns and genome evolution of these viruses.
Kitty has recently joined Vincent Plagnol's group in UGI. She holds degrees in BSc Physics (BSc) and Computing (BEng) from the University of New South Wales. After her undergraduate studies, she spent a few years working as a management consultant with the Boston Consulting Group before returning to the University of Sydney to complete a PhD in Astrophysics. Her PhD work was on using machine learning techniques to analyse data from all-sky time domain surveys. In her new role, she will be applying statistical and computational methods to the analysis of next-generation sequencing data.
Lucy van Dorp
Prior to coming to UGI, Lucy received a first class honours degree in Zoology from Royal Holloway and an MRes in UCL’s Centre of Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX).Her PhD, supervised by Professor David Balding and Dr Garrett Hellenthal, will investigate the processes, which drive genetic diversity among human populations. We aim to describe genetic patterns among a wide range of human groups and characterize the primary historical, anthropological and sociological factors that contribute to observed levels of genetic diversity among these groups. This will be achieved through development and application of a novel statistical methodology to genome-wide data across world-wide populations. This data includes detailed sociological and genetic information from the world's largest DNA collection of individuals from Ethiopia, an important country for studying the origins of anatomically modern humans and their subsequent dispersal from Africa throughout the rest of the world.
Marcus has just started a PhD at UGI working under Dr Oliver Davis. He has a BSc in Microbiology and Virology from the University of Warwick, and a Masters in Bioinformatics from Cranfield University, where his thesis involved the creation of statistical classification models for metabolomics fingerprint data in meat production. He is now getting involved in the TEDS longitudinal twin study. The aim of his PhD, will be to look for novel ways to exploit the vast amounts of data collected by the TEDS project, with a focus on visualisation, to further elucidate the roles of genetics and environment in cognitive development.
Florent studied Biology at the Ecole Normale Supérieure de Lyon (France) followed by a PhD at the Université Claude Bernard (Lyon 1) in interaction between the departments of Microbial Ecology and Biometry & Evolutionary Biology. He studied how the history of homologous recombination and horizontal gene transfer along bacterial cladogenesis have shaped bacterial genomes through adaptive and non-adaptive processes. He notably used phylogenetic approaches to unravel past ecological adaptation of clade ancestors of the model taxon Agrobacterium tumefaciens, a rhizospheric bacterium.
Florent’s current work in the team of Francois Balloux will consist of studying the evolution of human pathogenic microbes from a population genomic perspective, with a particular focus on the role of recombination and gene transfer in shaping the genomic diversity of microbial genomes. New methods will be developed to model the processes of gene flow within microbial populations together with their demographic history. Characterization of such processes and their contribution to the emergence of new genotypes is the key to the identification of relevant selective pressures experienced by microbes, that would ultimately help us better prevent and manage epidemics.
We would like congratulate to Sonia Shah on the award of her PhD!
On September 3rd the MSc teaching staff met with the 2011-12 cohort of MSc students to celebrate their academic achievement at the 2013 Graduation Ceremony. Not all of our students could make it but we were very excited to have a chance to catch up with a few of them who came back to UCL for this special occasion. It was great to find out that Anna Sanniti (MSc Pharmacogenetics and Stratified Medicine) will be starting her PhD in Oxford.
The 2012-13 cohort of students sat their modular exams in the summer term. They all submitted their projects in August. As usual, we were able to offer our students a wide and diverse range of laboratory and computer-based projects supervised by the researchers from a number of UCL Institutes including the Institute of Child Health, Cancer Institute and the School of Pharmacy. All students’ presented their projectsin September 2013.
New MSc programme in Computational and Genomic Medicine
UGI is pleased to announce that an exciting new MSc programme in Computational and Genomic Medicine will be launched September 2014.
The new MSc in Computational and Genomic Medicine aims not only to provide students with general knowledge in Bioinformatics but also to equip them with the specialised skills and knowledge required to use post-genomic data for predicting and defining the genetic basis of various human diseases, and to allow students to be able to analyse human genomic data to develop innovative diagnostic tools and therapeutic approaches. It will provide an integrated view of Computational and Genomic scientific research, with modules in Biocomputing offered by Birkbeck College, Gene Ontology, Statistical Computing, Genomic Analysis, Bioinformatics and Translational Medicine, as well as providing technical, in-depth knowledge and skills of different research techniques in these fields. Through choice of optional modules, students will be able to focus on Molecular Evolution, Computational and Systems biology and Statistics for Interpreting Genetic data. We believe that this will be a popular and important addition to the Masters’ portfolio of the UCL Faculty of Life Sciences.
Admission starts from January 2014 (please go to http://www.ucl.ac.uk/prospective-students/graduate-study/taught and http://www.ucl.ac.uk/ugi/education for further details). Please contact Dr Elvira Mambetisaeva (email@example.com) for any academic enquiries.
News from our former students
We are always delighted to hear from our former students and learn about their achievements. Marilena Mela, a graduate of the MSc in Genetics of Human Disease, sent us her greetings from the University of Southern California where she was offered a job as a research laboratory specialist with the further opportunities to do a PhD there.
Mark Bartlett who completed the MSc in Pharmacogenetics and Stratified Medicine programme last year has set up Geneix, a London-based health-tech startup. Mark and the cofounder Adam Harman-Clarke have developed InterAct, an app to screen new medications against a patient’s current prescriptions and, for the first time in the UK, against a patient’s genetic profile as well. You can find more about Geneix and InterAct by visiting www.geneix.co.uk.
The other Mark’s big achievement is that the results of his MSc project were published recently in the Lancet (Vol.381; Number 988, Jun 01, 2013). The paper discusses the results of the a quantitative online survey which was design to assess whether physicians' opinion is acting as a barrier to the adoption of genetic testing in drug prescription processes in the UK. Mark was supervised by Professor Elizabeth Shephard from the UCL Institute of Structural and Molecular Biology, Division of Biosciences. You can access the article via the following link - Article
MSc Genetics of Human Disease
In the 2012-13 academic year 22 students enrolled. Among them were 17 overseas students from 9 different countries, 2 students from EU region and 3 UK students. The good quality of students’ performance is reflected in the final grades with 10 students awarded Distinctions and 5 Merits. Jaime Stafford was awarded the UGI Masters Prize of £100 for the best project and Aara Patel – for excellence in her studies. The external examiner, Professor Charalambos Kyriacou, met with the students after their vivas and was pleased to report to the Exam Board committee that students were very pleased with the course syllabus and teaching standards. The majority of graduates from this course pursue careers as research scientists but also go to work in pharmaceutical and clinical organisations.
Currently we have 16 students enrolled onto the course. Among this years’ intake there are 6 UK students, 2 EU students and 8 overseas students.
MSc Pharmacogenetics and Stratified Medicine
In 2012-13 we had a cohort of 11 students of which 8 were overseas students, 2 EU students and 1 home student. The external examiner, Professor Anne Daly, was pleased by improvements made to the course programme including more projects related to pharmacogenetics that were offered to students. One student completed the course with Distinction and 4 students with Merit. Two students were awarded a UGI Masters Prize of £100: Man Yuan - for the best project and Ornicha Prapapan – for excellence in studies.
This academic year 7 students enrolled from 27 applications made. Among them there are 3 UK students, 2 overseas students and 2 EU students.
Admission to the Masters courses for the 2013-14 academic year
If you are still looking for an exciting postgraduate programme in Biomedical Sciences then why not to look for our interdisciplinary MSc in Genetics of Human Disease and the MSc in Pharmacogenetics and Stratified Medicine programmes at our website.
We welcome students to apply and the on-line admissions start from January 2014
We believe that you will find the Division of Biosciences at UCL to be a stimulating and invigorating environment in which to carry out your postgraduate studies. We also believe that that these programmes will improve your career prospects.
Bloomsbury Centre for Genetics Epidemiology and Statistics (BCGES)
The Centre will run two short courses in September 2014.
Course 1: Introduction to Genetic Epidemiology in the GWAS era
(2 – 5 September 2014)
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
(8 – 12 September 2014)
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.
Early bird booking will be available from February 2014.
Tuesday 11 February, 5 – 7:30pm - Population Genetics Methods and Findings Beer & Pizza Science Evening
The event is free to attend however places are limited so please register via Eventbrite.
Tuesday 4 February 2014, 4:30pm, Manson LT (LSHTM)
Dr David Conti, Zilkha Neurogenetic Institute, University of Southern California Title: “Incorporating Prior Biological Knowledge into Genetic Association Studies”
Tuesday 11 March 2014, 1-2pm, Chadwick 2.18, UCL
Dr Trevor Graham, Lecturer in Tumour Biology, Barts Cancer Institute
Tuesday 8 April 2014, 1-2pm, venue TBC
Dr Nic Timpson, Reader in Genetic Epidemiology, Bristol Heart Institute, University of Bristol
Tuesday 6 May 2014, 1-2pm, John Snow LT, LSHTM
Prof Anthony Edwards, University of Cambridge
BCGES annual meeting will be held in June 2014
Recent papers and publications
Identification of a rare coding variant in complement 3 associated with age-related macular degeneration - Valentina Cipriani co-authors publication in Nature Genetics
Cellular resolution models for even skipped regulation in the entire Drosophila embryo - Nick Luscombe publishes paper on fly modelling in eLife
Improving the efficiency of genomic selection – Marco Scutari and David Balding publish in Statistical Applications in Genetics and Molecular Biology
On the Prior and Posterior Distributions Used in Graphical Modelling – Marco Scutari publishes in Bayesian Analysis
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