My inaugural lecture is on youtube

Last Wednesday was my inaugural lecture. Thank you to all my family, friends and colleagues who came and made it such a special day; it was a real celebration. Thanks also for the people who helped organize it: Emma Hooley and Diane Levine, and also Steve Wang for use of a video camera.

The video of the lecture is now on Youtube. I am often out of frame – the camera was mounted on a tripod but nobody was operating it (except for one moment when one friend turned it slightly).

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PostDoc Opportunity: Research Associate/Fellow in Machine Learning (fixed term)

Here is another great opportunity to work with Tania Dottorini and me in an exciting AMR project

FARM WATCH: Fight AbR with Machine learning and a Wide Array of sensing TeCHnologies

Applications are invited from research scientists for the above post in the School of Veterinary Medicine and Science to join an exciting project dealing with antimicrobial/antibacterial resistance (ABR).

The successful candidate will work closely with an interdisciplinary and international team of academics and industrial partners. The project offers a unique combination of expertise in machine learning, statistical and mathematical modelling, bioinformatics, sequencing, cloud computing, microbiology, infection control, food safety, surveillance, epidemiology.

Applicants must have, or be very close to completing, a PhD in statistics, mathematics, computer science, computational biology, engineering, physics or relevant computational fields. Candidates must have knowledge and experience in statistical modeling, machine learning and data mining methods and algorithms for processing heterogeneous, complex large-data, including sequencing, sensor and biological data.

The School of Veterinary Medicine and Science is committed to diversity and equality of opportunity.  The School holds a Bronze Athena SWAN award in recognition of its commitment to equality and diversity and advance the representation of women in veterinary medicine.

This is a full time, fixed-term from 1 May 2019 to 31 December 2021. Job share arrangements may be considered.

Informal enquiries may be addressed to Dr Tania Dottorini, email: tania.dottorini@nottingham.ac.uk.Please note that applications sent directly to this Email address will not be accepted

Our University has always been a supportive, inclusive, caring and positive community. We warmly welcome those of different cultures, ethnicities and beliefs – indeed this very diversity is vital to our success, it is fundamental to our values and enriches life on campus. We welcome applications from UK, Europe and from across the globe. For more information on the support we offer our international colleagues, visit; https://www.nottingham.ac.uk/jobs/applyingfromoverseas/index2.aspx

Job Opportunity: Research Associate/Fellow in Bioinformatics (fixed term)

A great opportunity to work on a project led by my colleague Tania Dottorini, in collaboration with Richard Emes and Matt Loose.

FARM WATCH: Fight AbR with Machine learning and a Wide Array of sensing TeCHnologies

Applications are invited from research scientists for the above post in the School of Veterinary Medicine and Science to join an exciting project dealing with antimicrobial/antibacterial resistance (ABR).

The successful candidate will work closely with an interdisciplinary and international team of academics and industrial partners. The project offers a unique combination of expertise in machine learning, statistical and mathematical modelling, bioinformatics, sequencing, cloud computing, microbiology, infection control, food safety, surveillance, epidemiology.

Applicants must have, or be very close to completing, a PhD in computational biology, computer science, mathematics, statistics, engineering, physics, or relevant fields. The candidate must have knowledge and experience in bioinformatics techniques and approaches, particularly related to genome biology and sequence analysis e.g. (genome assembly, sequence mapping, metagenomics, transcriptomics, and annotation).

The School of Veterinary Medicine and Science is committed to diversity and equality of opportunity.  The School holds a Bronze Athena SWAN award in recognition of its commitment to equality and diversity and advance the representation of women in veterinary medicine.

This is a full time, fixed-term post from 1 May 2019 to 30 June 2021. Job share arrangements may be considered.

Informal enquiries may be addressed to Dr Tania Dottorini, email tania.dottorini@nottingham.ac.uk. Please note that applications sent directly to this email address will not be accepted.

Our University has always been a supportive, inclusive, caring and positive community. We warmly welcome those of different cultures, ethnicities and beliefs – indeed this very diversity is vital to our success, it is fundamental to our values and enriches life on campus. We welcome applications from UK, Europe and from across the globe. For more information on the support we offer our international colleagues, visit; https://www.nottingham.ac.uk/jobs/applyingfromoverseas/index2.aspx

Further thoughts on REF review: writing great papers: make the significance of the results clear

Following on from my previous post, the exercise of reading papers outside of my main discipline, and trying to rate them for originality, significance and rigour, has led me to think deeply about how to write great papers. There is now one thing I will do differently in the papers I (or rather, my group) write, which is to state clearly what the significance of the results are. I will come back to that later in the post.

More generally,  the obvious part of writing great papers is to do great research. But whether the research is truly great, or merely very good, you still need to write a great (or very good paper): great research badly written risks not being recognized.

What I have noticed is that we (the academic community) are can be very good at presenting our rigour, can be a bit mixed at presenting the novelty, but are often less good at explaining the significance – we rather tend to leave that to our readers. Underlying this is the presumption that we are writing for experts in our field. But the REF means that we need to write for a broader audience – yes, we need to write for experts, but some parts of the paper (especially in the Abstract and Conclusions, but also, as I will argue, how the Results and Discussion are structured), can really help non-experts understand what your paper is about, along with its originality and significance, without compromising its rigour.

The way I encourage my group members to write papers is to identify the key results – key messages – as simple bullet points that can be easily understood. These become the main subheadings of the Results section: clear and informative. So, for example, instead of a subheading “Results of Analysis X”, a better subheading might be “Protein A interacts with Protein B” (or whatever the result happens to be). I then ask my students/postdocs to provide the evidence in support of the messages – these become the figures/tables; next I ask what scientific questions are answered by these results – these become the questions in the Introduction, and motivate the literature review in the introduction.

Here is what I will now do differently (and encourage others to do the same): for each of the main results, I will ask the question: what is the significance/importance of this result – expressed as a single sentence. The resulting sentences can then be used to structure the Discussion and Conclusions, as well as form the final sentence(s) of  the Abstract. The important point is you tell the non-expert reader what the significance of the results are – this is essential for REF panels, who might then score the paper better for significance – but also improves the paper, without compromising its integrity. After all, for example, not many people might care that “Protein A interacts with Protein B” but if “therefore we could use Protein A as a drug target for disease Z” (or whatever the significance of the result happens to be) the importance is explained, and a wider community might benefit from your result.

 

REF readiness review activity: the good, the bad and the plain silly

One of the ‘perks’ of my professorial promotion is that I get to partake in our school’s REF (Research Excellence Framework) readiness review – that is, I get to read a stack of papers from my colleagues, and decide whether they deserve 1, 2, 3 or 4 stars (or even no stars at all) according to a scale that takes into account novelty, significance, rigour, and ‘other’ (that sprinkling of magic fairy dust that makes a 4* paper).  In doing this I realized that the process can be broken into two separate activities:

1. Reading research papers written by my colleagues, that are outside of my normal discipline. Actually, that is a really positive thing – something we should all do more often. I now know more about the research of some of my colleagues, know more about the world (some of the papers were genuinely interesting, even if outside my area of research), and have even learned some things that might be useful for my own group (an R package I wasn’t previously aware of). Verdict: let’s all make an effort to read our colleagues’ papers some more, perhaps especially those colleagues whose work we are not familiar with.

2. Grading my colleagues’ papers for REF starriness. This is plain silly, but no more silly than the real REF: I have some expertise in some of what my colleagues have written, but, in truth, I was not truly expert in any of the papers I scored – which is probably true of most of what happens on real REF panels too. Well, I completed the process, filled in the numbers, and seemed to be quite harsh in my judgment (~ a 1:2:3  ratio if 4*:3*:2* papers). How good can my scores really be? Was I really too harsh? Or is that about the right proportion? It is difficult to tell. One thing that was frustrating was realizing that I was doing this at the wrong time. When I read a paper, and, let’s say, at no point is written why the results of the paper might be important, surely it would be better to let my colleagues know before they publish it that they might want to explain why their results are important in their Conclusions section, rather than just have non-experts pass judgment after publication?

In the end, the whole exercise reminded me of a conversation I had a couple of years ago with our older daughter – who was 5 at the time – in which I explained the REF to her. “Every time we do some work, we get given some stars for it. If the work is not very good, we get one star; if it is quite good, we get two stars; if it is very good, we get three stars; if it is totally excellent, we get four stars.” Five-year-old completely understands the system, and says to me “Daddy, I will always give you four stars.” From this I learn two lessons: first, in the REF, we are treated like 5-year-olds; and second, that there are far more important things in life, so it is important not to get too emotional about the REF and its peculiarities.

New publication: DNA traffic in the environment and antimicrobial resistance

Our book chapter on DNA traffic in the environment and antimicrobial resistance is now published, with particular thanks to Steve Hooton who has taken the lead on this. The book is more generally about DNA traffic in the environment, co-edited by our amazing Japanese collaborator Taku Oshima. This is a really great review, bringing together the importance of the environment to gene transfer of ARGs into medically or veterinarily relevant organisms..

Hooton SP, Millard AD, Baker M, Stekel DJ and Hobman JL 2019. DNA Traffic in the Environment and Antimicrobial Resistance. In: Nishida H., Oshima T. (eds) DNA Traffic in the Environment. Springer, Singapore.

Abstract

The seemingly insurmountable problem of antimicrobial resistance (AMR) in clinical, food, and agricultural environments requires considerable efforts to be made in order to mitigate associated risks. Understanding the dynamics of the multitude of processes contributing towards AMR development, spread, and persistence in microbial populations will prove paramount in resolving these problems. Mobile genetic elements (MGEs) such as plasmids, transposons/insertion sequences, and bacteriophages contribute towards horizontal gene transfer of antimicrobial resistance genes (ARGs) in the environment. ARGs can be transferred from naturally resistant, ubiquitously distributed microbial populations acting as reservoirs for these genes. When ARGs are introduced into pathogens or opportunistic pathogens, these microorganisms subsequently become problematic when introduced into human/animal populations.

The role of MGEs in the evolution and emergence of pathogens of significant clinical and veterinary importance is well-documented. From a microbiological perspective, improving our knowledge of MGE-mediated AMR transmission by the application of traditional microbial culture techniques, molecular biology methods, and genomic/metagenomic/transcriptomic approaches will enhance our understanding of the flow of genetic information in bacteria. Mathematical modelling will prove to be integral to developing testable hypotheses regarding gene transfer rates, the consequences of positive selection, persistence in the absence of selection, and the fitness cost of gaining/losing resistance.

Horizontal gene transfer of AMR genes has led to the emergence of significant globally distributed enterobacterial pathogens such as Escherichia coli, Salmonella spp., and Klebsiella spp. The consequences of the emergence of these pathogens pose significant risks for humans and veterinary medicine, in what is a highly convoluted and at present, a seemingly intractable problem.

PhD Opportunity: Modelling the Risks of Antimicrobial Resistance from Agricultural Waste to Animal and Human Health

We are advertising for a PhD in my laboratory – Modelling the Risks of Antimicrobial Resistance from Agricultural Waste to Animal and Human Health – jointly supervised with colleagues from the School of Mathematics and School of Veterinary Medicine, and jointly funded by the Medical Research Foundation and the University of Nottingham. This studentship is fully funded (fees and stipend) for four years for students from the UK or EU.

Project description

This project will use mathematical modelling to evaluate the risks to human and animal health of antibiotics and antimicrobials given to farm animals. In particular, we are concerned about the risks associated with application to land of slurry or manure, which contain antibiotics and antimicrobial resistant bacteria because of that use. You will look at two systems: the risk of antibiotic resistant bacteria in crops grown for human food; and the risk associated with sheep transferring resistance around fields that have received slurry.

Two different modelling paradigms will be compared: Bayesian Network models, that allow for probabilistic description of impact of different factors on outcomes; and Dynamical Systems models, that consider changes in populations over time. The project will benefit from extensive data we have generated both on characterising dairy slurry and its impact upon soil, and on resistance in sheep hooves, as well as data from other laboratories.

Supervisors

  • Prof Dov Stekel, School of Biosciences
  • Dr Sabine Tötemeyer, School of Veterinary Medicine and Science
  • Dr Theodore Kypraios, School of Mathematical Sciences

Benefits of joining the Medical Research Foundation National PhD Training Programme in AMR Research.

  • All PhD projects will be based within interdisciplinary research consortia funded by the UKRI Cross-Council AMR Initiative.
  • All students will have access to enhanced training opportunities including residential skills and training courses, cohort-building activities, and annual conferences. All are designed to expose students to a range of discipline-specific languages and interdisciplinary research skills, which are essential for enabling them to thrive as multidisciplinary AMR researchers.
  • PhD students will undertake a fully-funded 3-month interdisciplinary AMR project allowing them to work outside of their primary research area or an elective placement in industry, publishing, media, policy development or in AMR-relevant charities and organisations.
  • All Medical Research Foundation-funded PhD students will also be part of a wider cohort of 150 PhD students from across the UK who are also studying AMR. The cohort will have access to a bespoke, innovative online learning environment, which will facilitate peer-to-peer networking, question setting and mentoring.

Further information can be found on the programme’s website: https://www.bristol.ac.uk/cellmolmed/study/postgraduate/amr/

To apply

Apply here: http://www.nottingham.ac.uk/pgstudy/how-to-apply/apply-online.aspx

You should have a BSc and/or MSc degree in a quantitative subject, such as mathematics, statistics, physics or computer science, and a strong interest in applying your quantitative skills to a biomedical problem of huge public importance. Potential applicants interested in further information are encouraged to contact me at Dov.stekel@nottingham.ac.uk

Please give the project title and name Professor Dov Stekel as the main supervisor. You do not need to provide a research proposal as requested on the form; instead indicate that you are applying for a Medical Research Foundation National PhD Training Programme in AMR Research funded project. Please contact me at dov.stekel@nottingham.ac.uk if you are intending to make an application so that your application can be processed quickly. You can also contact me with informal enquiries or help with the application.