Royal Society Summer Science Exhibition Stall July 2-8

Next week researchers from the Modernising Medical Microbiology consortium, collaborating groups and I will exhibit the Resistance is Futile stall at the Royal Society Summer Science Exhibition. The exhibition is a free event in central London open to all visitors. Our stall is an opportunity to tell visitors about our research, and how advances in genetics are influencing day-to-day life. On show at the Resistance is Futile stall:

Oxford Nanopore Technology Demos

DNA sequencing in the NHS is shortening the time to diagnose antibiotic resistance in serious infections

Evolution Dance Mat

Resistance mutants arise spontaneously through chance copying errors during DNA replication

Antibiotic Resistance Coconut Shy

Antibiotic use gives resistance mutants a strong advantage so they rapidly increase in frequency.

The exhibition runs from Monday 2 July - Sunday 8 July at Carlton House Terrace, London, SW1Y 5AG. For more information about our stall click here and for general visitor information about the exhibition click here. Please spread the word!

During the exhibition we will be tweeting from @ResistanceIF

Our stall is generously supported by Oxford Nanopore Technology, the Nuffield Department of Medicine, and through public engagement research funding awarded to our research groups by the Wellcome Trust, the Royal Society, the National Institute for Health Research, the Oxford Biomedical Research Centre, the Natural Environment Research Council, the Medical Research Council, the Newton Fund and the Bill & Melinda Gates Foundation.

Postdoc positions in Data Science and Molecular Microbiology

These positions are now closed
As part of the move to the Big Data Institute, two new postdoctoral positions funded by the Robertson Foundation are available in Data Science and Molecular Microbiology.

The BDI is a new interdisciplinary research centre aiming to develop, evaluate and deploy efficient methods for acquiring and analysing biomedical data at scale and for exploiting the opportunities arising from such studies. The BDI is a joint venture between the renowned Nuffield Department of Population Health (NDPH) and NDM.

The Data Scientist role, split between the BDI and London, will be part of a team developing systems for continuous record linkage between Public Health England and other population health records. The aims are to design record linkage algorithms, manage front ends for viewing the data source, and analyse and interpret results. We're looking for a graduate or equivalent experience in computer science, data science, statistics, or any other relevant subject with a strong quantitative component. Knowledge of databases like SQL and computer programming are needed.

The Molecular Microbiology role, based mainly at the John Radcliffe Hospital Microbiology Department, will be part of a team researching Staphylococcus aureus infection using RNA sequencing, genome wide association studies, and biochemical and immunological assays of bacterial behaviour. The aims include designing microbiological protocols, researching bacterial molecular genetics and data analysis. We're looking for a PhD or equivalent experience in a relevant subject such as microbiology, immunology, genetics or biochemistry. Experience designing protocols and basic microbiological and immunological skills are required.

The deadline for the posts is Noon on 6 June 2018. Both are one year positions. For more details or to apply click here for the Data Scientist role and here for the Molecular Microbiologist role.

Prize PhD Studentships available

I am offering two PhD projects as part of the annual Nuffield Department of Medicine Prize Studentship competition:

• Real-time detection of multidrug resistant tuberculosis and transmission in England
  Joint with David Wyllie, molecular microbiologist, this project is focused on developing statistical methods for recognizing transmission clusters, integrating genomics approaches with molecular typing schemes and developing future-proof taxonomy for strain identification.
  
  
• Tracking future infection threats using genomic data and electronic health records
  Joint with David Clifton, biomedical engineer, this project aims to develop new machine learning and statistical methods to identify genomic markers of antibiotic resistance and susceptibility within various pathogens, to help track future infection threats.

These are fully-funded, four-year awards open to outstanding students of any nationality. Applicants nominate three projects, in order of preference, from the available pool. For how to apply, click here. Only applications submitted through the online system will be considered, but interested applicants are welcome to contact me informally. The deadline for applications is noon, 6th January 2017.

In addition to my projects, the Modernising Medical Microbiology project has announced the following PhD projects as part of the competition:

• Antimicrobial resistance gene/vector transmission across human, animal and environmental reservoirs
  Supervised by Nicole Stoesser, Nicola De Maio and Derrick Crook
  
  
• Healthcare big data and genomics for infectious disease threat detection
  Supervised by David Clifton, David Eyre and Tim Peto
  
  
• Prediction of Mycobacterium tuberculosis drug resistance through genome sequencing clinical samples
  Supervised by Tim Walker and Tim Peto
  
  
• Antibiotic resistance in Tuberculosis: Predicting de novo the effect of individual genetic mutations
  Supervised by Phil Fowler and Sarah Walker

Cheltenham Science Festival

Earlier this week members of the group represented the Nuffield Department of Medicine at the Cheltenham Science Festival with our Modernising Medical Microbiology stall, featuring the Antibiotic Resistance Coconut Shy and the Genome Evolution Dance Mat.

Antibiotic Resistance Coconut Shy

Antibiotic Resistance Coconut Shy: The children (and adults) visiting the stall were given five bean bags (antibiotics) to throw at the coconuts (bacterial pathogens) to try to knock them off. The front row of coconuts, representing bacteria more susceptible to antibiotics, were easier to knock off than the back row, which represented more resistant bacteria. The aim was to show the children that an unwanted side effect of using antibiotics is to increase the frequency of resistant bacteria, because they were usually the ones left standing.

The game was more difficult than it looks, and just one visitor knocked off all five coconuts. We gave out NDM pens to the sixty visitors who managed to knock off three or more.

Microscope and Top Trumps

Digital Microscope: We brought along a light microscope to show the children what bacteria really look like, which helps emphasize how small they are since they are difficult to see even under the highest magnification. We prepared slides for several Gram positive and Gram negative species, and provided a key to help identify them. We also brought along a number of games that have been used in previous departmental outreach activities, including Pathogen Top Trumps and Fact or Fiction.

Genome Evolution Dance Mat

Genome Evolution Dance Mat: In this game, the children had to copy a bacterial DNA sequence by replicating a sequence of dance moves (up=A, left=C, right=G, down=T) without introducing new errors (mutations). Any mutations that were introduced were passed on to the next template sequence. In this way we aimed to show how mutations occur by errors in DNA replication, and that they are inherited. This generates unique DNA fingerprints for bacteria, which we can use to track the spread of outbreaks.

Outbreak Map

The game, which was kindly programmed by Gareth Jenkin-Jones, included a form of natural selection, so that if too many errors were introduced at once, the sequence was considered inviable and did not survive to be passed on. There was also a speed control, which was handy since some people appear to have spent a lot more of their youth playing dance mats than others.

Outbreak Map: We made an Outbreak Map to show the reach of our stall over the day, with visitors that scored highly on the coconut shy pushing in pins to show where they had travelled from. Had we been handing out germs instead of pens, we could have started outbreaks as far afield as Edinburgh, France and Spain, as well as a large cluster in Cheltenham and the surrounding counties.

Other research groups are representing the department throughout the week.

NDM Microbiology Stall at the Cheltenham Science Festival (L-R): Sarah Earle, Louise Pankhurst, Danny Wilson, Liz Batty, Dilrini De Silva, Jess Hedge, Catrin Moore. Amy Mason, Gareth Jenkin-Jones and Jane Charlesworth also helped with the preparations, and Jen Bardsley co-ordinated all the NDM Stalls.

Postdoctoral Position in Statistical Genomics

The position of Postdoctoral Scientist is available in my group to lead research on the Wellcome Trust and Royal Society funded project Statistical Methods for Whole Genome Phenotype Mapping in Bacterial Populations.

Bacteria cause disease throughout the world. Different strains vary in disease severity, but the genetic variants responsible remain largely undiscovered. Recent breakthroughs in whole genome sequencing provide new opportunities for discovery, but the lack of statistical analysis tools tailored to the special structure of bacterial populations presents a roadblock. The goal of the project is to develop an analysis framework for mapping genes underlying naturally variable traits in bacterial populations. Focusing on the hospital-associated pathogens Staphylococcus aureus and Clostridium difficile, we will investigate the role of bacterial variants on disease severity.

The role of the Postdoctoral Scientist is to develop novel statistical methods for analysing genotype-phenotype associations in bacteria at the whole genome level. The successful candidate will write software implementing the statistical methods and apply them to design and carry out investigations into the genetic basis of virulence in natural populations of bacterial pathogens. The ideal candidate would be a recently graduating PhD student with experience of statistical genetics and computer programming, with evidence of publicly released software. Experience of population genetics or microbiology would be advantageous but is not essential.

The post is available immediately, and is available for up to 3 years in the first instance. For more details on this position, including salary, job description, selection criteria and how to apply, please see the University of Oxford recruitment page.

Applications for this vacancy are to be made online. The closing date is 12.00 noon on Monday 4 November 2013. Applicants will be asked to upload a CV and a supporting statement as part of the online application. For informal enquiries, please email me. More information about the group's research is available here.

James Martin Fellowship

This position is now closed. A prestigious James Martin Fellowship funded by the Oxford Martin School is available in my research group for a highly motivated and creative population geneticist interested in developing cutting edge methods for the analysis of high-throughput whole genome sequencing data to better understand the evolution and epidemiology of the major pathogens HIV and Hepatitis C Virus.

The position, which is part of the Curing Chronic Viral Infections project, is fully funded for three years and is affiliated with the Institute for Emerging Infections, the Modernising Medical Microbiology consortium, the Peter Medawar Building for Pathogen Research and the Nuffield Department of Medicine. The ideal candidate will have a track record in statistical or computational genetics and experience of programming in a language such as C++ or Java.

Full details can be found on the University of Oxford Recruitment website. Please send informal enquiries, with a CV, to me by email. The deadline for applications is 12 noon on 27th November 2012.