Inferences from tip-calibrated phylogenies: a review and a practical guide

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UGI's Adrien Rieux and Francois Balloux publish in Molecular Ecology

Molecular dating of phylogenetic trees is a growing discipline using sequence data to co-estimate the timing of evolutionary events and rates of molecular evolution. All molecular-dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast-evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip-based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip-dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a ‘how to’ guide to thoroughly perform such analyses.

Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out

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UGI's Vegard Eldhom and Francois Balloux publish in Trends in Microbiology

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Strongest single gene conclusively implicated in schizophrenia

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An international consortium of researchers, including Prof Dave Curtis from UCL Genetics Institute, has discovered conclusive evidence for the involvement of a gene called SETD1A in schizophrenia. Damaging changes to this gene, which occur rarely, increase the risk of schizophrenia 35-fold and also increase risk for a wide range of neurodevelopmental disorders.

The UCL-Birkbeck MRC Doctoral Training Programme - deadline 25 January 2016

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The first fine-scale genetic map of the British Isles - Garrett Hellenthal 

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The regions of ancient British, Irish and Saxon control in the 7th Century

Many people in the UK feel a strong sense of regional identity, and it now appears that there may be a scientific basis to this feeling, according to a landmark new study into the genetic makeup of the British Isles.

Job: Weldon Chair/Readership in Computational and Statistical Genetics

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Deadline: 13 Feb 2015

University College London is expanding research into computational and statistical genetics as a central component of its scientific strategy. We seek to appoint a scientist to the Weldon Chair/Readership in Computational and Statistical Genetics to be held in the UCL Genetics Institute. The successful candidate will have an international reputation in their field and will provide leadership in exploiting the continued expansion of human “-omic” data across UCL. The postholder’s research is expected to involve computational methods development and may also focus on disease areas in which UCL has exceptional research strength including neurology, cancer, rare childhood diseases and cardiovascular diseases among others. The successful applicant will demonstrate capability for teaching in order to contribute to UCL's portfolios of graduate and undergraduate teaching.

Same genes drive maths and reading ability - Oliver Davis publishes in Nature Communications

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Around half of the genes that influence how well a child can read also play a role in their mathematics ability, say scientists from UCL, the University of Oxford and King’s College London who led a study into the genetic basis of cognitive traits.

Nick Luscombe receives MRC Grant as part of the Medical Bioinformatics Initiative

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Medical informatics is about to come of age. What has been an emerging trickle of funding is starting to amount to a substantial flow. In the UK alone, the Medical Research Council (MRC) along with other research councils, charities, and health departments are investing in big data to the tune of £90 million over a 5-year period.

UCL Genetics Institute outreach activities

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UCL Academy

Professor Steve Jones with UCL Academy students



UGI's Oliver Davis featured in current edition of the MRC Network magazine

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Oliver Davis features in the current edition of the MRC Network Magazine as part of the MRC Centenary Awards update. 

NEW MSc Computational and Genomic Medicine 2014-15

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Course organisers: Professor Steve Humphries, Professor Nick Luscombe and Francois Balloux 

This new MSc provides students with general knowledge of Bioinformatics as well as equipping them with the specialised knowledge and skills required to use post-genomic data for predicting and defining the genetic basis of various human diseases. It will provide an integrated view of computational and genomic science research and in-depth knowledge and skills of different research techniques in these fields.

Genomics—from the lab to clinical practice - BMJ Editor's Choice 30 Nov 2013

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There are about 20 000 genes in the human genome. Until recently, clinicians seeking to diagnose a genetic condition have had to select single genes to be sequenced. The process is slow, expensive, and often unsuccessful. Now that the cost of DNA sequencing has fallen so dramatically, it’s cheaper and easier to sequence the entire genome, with huge potential benefit to our understanding of disease. But this bounty brings with it clinical and ethical questions, as Caroline Wright and colleagues explain (full article). Who should be tested? How much of the genome should be sequenced? What should patients be told? What do we do about incidental findings? And how should an individual’s genomic data be stored?  Uppermost in clinicians’ minds may be the question of how best to interpret the information that is now so abundantly available. It may be easy enough to identify a gene that explains a patient’s clinical presentation, such as the genetic variant for Charcot- Marie-Tooth disease. But because of incomplete or age dependent penetrance, finding a genetic variant that is known to cause a disease doesn’t mean the person has or will develop that disease. Because we still have limited understanding of many genetic variants, we should beware of overinterpreting the data, say Wright and colleagues. “Our ability to generate data now far outstrips our ability to interpret them.” Sequencing the entire genome will inevitably reveal unexpected findings, some of which will cause confusion and distress. In a linked commentary, Alastair Kent discusses the impact on patients (full article). The new ease of genomic testing is mainly good news, he says. But the potential for unexpected findings makes it hard for patients to specify in advance how they would like these to be dealt with. “Do I want to know if my genome reveals that I am likely to develop a serious condition which may or may not be related to the one for which I had DNA analysis in the first place? Is there a difference between diseases that have treatments and those that do not?” He would like his doctor to discuss these things before proceeding. But what levels of consent need to be obtained ahead of time? Wright and colleagues warn that genomic sequencing too easily becomes screening by another name. As with all screening, we will need to avoid overstating the benefits and underestimating the harms. And each combination of genetic variant and associated disease will need to beevaluated separately in terms of whether the disease is treatable and at what risk and cost. To stop us straying into untargeted and unmanageable genomic screening, the authors suggest a clinically targeted approach. This would mean partitioning the data and only interrogating those parts that relate to the presenting clinical problem.

Research Associate - Parkinson's Biocurator position available

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We are seeking a full-time or part-time Biocurator for the Parkinson’s Gene Ontology Annotation Project. 

For further details visit UCL vacancies page

UCL's Prof Hugh Gurling dies aged 63

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It is with great sadness that I want to inform you of the sudden death of Prof Hugh Gurling. Hugh has been a personal friend and colleague for many years, and has been an Associate Member of UGI and served on its Advisory Board since its inception. Prof Dave Curtis has written an obituary for Hugh which can be accessed here. He will be sorely missed.

Cellular resolution models for even skipped regulation in the entire Drosophila embryo - Nick Luscombe publishes in eLIFE

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Full Article: e-LIFE

Congratulations to Doug Speed for being named the best FMT-BIR Young Biometrician of the year!

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Doug Speed Reward

Photo L-R: Professor David Spiegelhalter,  Professor Stephen Senn, Doug Speed and Professor Simon Thompson

Doug has been named the best young biometrician in the UK by the Fisher Memorial Trust and Biometric Society. Stephen Senn, the Secretary of the Fisher Memorial Trust, presented the award to Doug Speed on 3rd July 2013 before David Spiegelhalter gave the keynote talk. 

Mapping the effects of nature and nurture, Oliver Davis features in Wellcome Trust blog

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Link to full article: Wellcome Trust blog

BHF Grant awarded to Dr Ruth Lovering

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Dr Ruth Lovering, Professor Philippa Talmud, Professor Steve Humphries, Professor Manuel Mayr (King's College) and Dr Rolf Apweiler (EBI) have been awarded over £500,000 funding from the British Heart Foundation to improve the annotation of genes associated with cardiovascular diseases and processes. The funding will support two post-doctoral research associates for 5 years in the Institute of Cardiovascular Science. The team will create protein and microRNA annotations using Gene Ontology as well as capture protein-protein interactions. The project is dependent on established and new collaborations with the European Bioinformatics Institute and the Sanger Institute (Hinxton).

Nick Luscombe elected to EMBO

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 Nick Luscombe has been elected as a member of EMBO - congratulations to Nick!

Please find further details here:

Study questions effectiveness of genetic testing strategy for inherited high cholesterol, Steve Humphries publishes in The Lancet

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Prof Steve Humphries

A substantial proportion of individuals with a clinical diagnosis of Familial Hypercholesterolaemia (FH) inherit a combination of small-effect changes in several genes (polygenic) rather than a large-effect mutation in a single gene (monogenic), according to a new paper in The Lancet.

Blood screening that is preventing heart attacks–but not in England, Prof Humphries is mentioned in a Guardian article

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Suzanne Sheppard is painfully aware of the devastation heart disease can wreak. Her father, Christopher Rogers, died of a massive heart attack in 1988 when he was 41 and she was 15. His father had also died unusually young – at 54 – and, again, of what doctors call a myocardial infarction.

Nick Luscombe publishes in Cell

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Direct competition between hnRNP C and U2AF65 protects the transcriptome from the uncontrolled exonization of Alu elements.

Vacancy: Research Associate in Statistical Genetics

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Salary: £32,055 - £38,744 per annum
Closing Date: 5pm on 14 Dec 2012
Further information: main UCL vacancy page

UGI's Prof Francois Balloux co-authors paper on genetics and climate reconstructions to track the global spread of modern humans out of Africa

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Research indicates the out-of-Africa spread of humans was dictated by the appearance of favourable climatic windows. By integrating genetics with high resolution historical climate reconstructions, scientists have been able to predict the timing and routes taken by modern humans during their expansion out of Africa. Their research reveals that the spread of humans out of Africa was dictated by climate, with their entry into Europe possibly delayed by competition with Neanderthals.  

UGI's Prof Andres Ruiz-Linares reports in Nature Native Americans descend from three key migrations

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Scientists have found that Native American populations — from Canada to the southern tip of Chile — arose from at least three migrations, with the majority descended entirely from a single group of First American migrants that crossed over through Beringia, a land bridge between Asia and America that existed during the ice ages, more than 15,000 years ago.

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