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Early Neolithic genomes from the eastern Fertile Crescent

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UGI's Dr Garrett Hellenthal, Professor Mark Thomas and colleagues published in Science on the origins of the worlds first farmers. By sequencing early Neolithic genomes from the Zagros region of Iran where the earliest evidence for farming is found, they were able to identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed significantly to the ancestry of modern Europeans. They estimated that these people separated from Early Neolithic farmers in Anatolia around 46-77,000 years ago and show close genetic affinities to modern day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. This work suggests that it was not just a single group of hunter-gatherers that adopted farming but that multiple genetically differentiated people developed farming, with the Zagros region representing a cradle of eastward expansion.

PhD available: Dissecting the role of RNA processing and long gene regulation in the aetiology of ALS

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Supervisor: Dr Vincent Plagnol

Project Description

ALS is a rapidly progressive, incurable and fatal disease that causes the degeneration of motor neurons (MNs) and consequent generalized paralysis. While the causes of the disease remain unknown, several studies have highlighted the role of genes implicated in RNA metabolism, and the potential for impaired RNA processing to play a key role in disease initiation. The UCL Institute of Neurology, a leading clinical center in the UK, leads a comprehensive research program to test this hypothesis. 

New technologies, such as RNA-sequencing, can now be used to provide a genome-wide assessment of the transcriptome in human cells as well as other model organisms. Our expectation is that the combination of quantitative data from multiple sources can provide novel clues into disease aetiology. However, this integrative analysis is a challenging computational and statistical task. During this PhD, the student will work on computational biology questions and large scale transcriptome sequencing datasets in the research group of Dr Plagnol, in collaboration with the clinical and cell biology teams led by Drs Fratta and Isaacs. 

The ideal student would have a background in computer science, statistics, or potentially biology with a strong interest in computational work. Prior experience in programming (in particular R) and/or high throughput DNA sequencing analysis is welcome but not necessary. This 3 year fully funded PhD, including consumables, can start from October 1st 2016. 

WT collaborative award for Garrett Hellenthal

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Building a platform for genetic inference from the Genomics England data

Collaborators: Jonathan Marchini, Simon Myers (University of Oxford)

AMR grant awarded to Francois Balloux and collaborators

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Title: An integrated approach to understand the emergence and spread of extensively resistant Gram-negative bacteria in China

Prof Richard Mott publishes in Nature Genetics

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Two linked papers by Richard Mott and colleagues, published online on 4th July 2016 in Nature Genetics (Nicod et al and Davies et al)  describe a study in which 1887 outbred mice were phenotyped for multiple traits and sequenced at low coverage. 156 loci associated with 92 traits were identified, including  pleiotropic  loci affecting multiple phenotypes. These findings have implications for diverse areas of mammalian biology and demonstrate how genome-wide association studies can be extended via low-coverage sequencing to species with highly recombinant outbred populations. The analysis used a novel algorithm, STITCH, for imputing genotypes from ultra-low sequence coverage. 

Genetic Complexity of Crohn’s Disease in 2 Large Ashkenazi Jewish Families

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Adam P. Levine, Nikolas Pontikos, Elena R. Schiff, Luke Jostins, Doug Speed, NIDDK Inflammatory Bowel Disease Genetics Consortium, Laurence B. Lovat, Jeffrey C. Barrett, Helmut Grasberger, Vincent Plagnol, Anthony W. Sega

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