SMIDDY Newsletter (29.11.2013)

1. New SMIDDY email:
2. Postdoc: HIV Modelling – Institute for Disease Modelling, Intellectual Ventures Lab
3. Postdoc: Modeling HIV treatment as prevention, University Medical Centre Utrecht, The Netherlands
4. Conference: VPH Annual Conference 2013, Bern, Switzerland
5. Conference: From emerging to pandemic viruses: Interplay between host ecology and viral evolution, 2-6 April, 2014, Roscoff, France
6. Postdoc and PhD positions: Quantifying population dynamics of viruses, ETH Zurich, Switzerland
7. PhD position: Mathematical Immunology, Heidelberg, Germany
8. Infectious disease modeller position at Public Health England Centre, London, UK
9. PhD position: Modeling the dynamics of plant-insect interactions, Wageningen, The Netherlands

1. New SMIDDY email:

We are restructuring our online presence and change the official email address of the Swiss Meeting for Infectious Disease Dynamics (SMIDDY) to

The old email address will no longer be active from 1 December, 2013.

2. Postdoc: HIV Modelling – Institute for Disease Modelling, Intellectual Ventures Lab

The Institute for Disease Modeling (IDM) creates disease modeling and data analysis tools for understanding diseases, their causes, the way they spread, and the planning and optimization of global health interventions. IDM is composed of research scientists and software professionals, and collaborates with universities, NGOs, government ministries, and other research and public health institutions.

IDM seek a postdoctoral researcher to join the IDM HIV modelling team for a three-year term. The researcher will collaborate on the development, refinement, and utilization of a sophisticated epidemiological model of HIV transmission; analyze epidemiologically- and policy-relevant data sets; and help to identify critical knowledge gaps. The researcher will configure, calibrate, and exercise disease models to answer questions aimed at refining the HIV research agenda, improving understanding of disease dynamics, informing effective public health campaigns, and guiding rational development of new interventions. The research, models, and results will be presented to collaborators and stakeholders, presented at conferences, and published in academic journals.


– Builds and improves models of HIV transmission
– Writes software code (in C/C++) to implement model features
– Works closely with the modelers, programmers, and statisticians on the team to refine the models and use them to conduct sensitivity analyses, and explore tradeoffs among possible interventions
– Finds, organizes, and interprets sources for the necessary input data to the models
– Collects, analyzes, and presents data on model results and performance
– Prepares research articles and conference presentations
– Communicates the project and its results to the scientific community

Key Qualifications and Required Skills:

– Ph.D. in a quantitative field (e.g. Applied Mathematics, Statistics, Epidemiology, Quantitative Biology, Experimental Physics, Computer Science)
– At least 2 years’ experience in C/C++ software development
– Proficiency in at least one data-analysis or scripting language (e.g. MATLAB, python, R)
– Principles, techniques, and tools of computational epidemiology
– Passion for improving public health in developing world settings
– Multiple published articles in peer-reviewed scientific journals (to be submitted with application)

Joining our group provides unique opportunities to interact with global-health policymakers, to collaborate with world-class research laboratories and non-profit organizations, and to contribute to global and national disease control strategies.
Interested candidates should apply with a CV and list of publications by emailing Anna Bershteyn at

3. Postdoc: Modeling HIV treatment as prevention, University Medical Centre Utrecht, The Netherlands

Project: Prospects of elimination of HIV by treatment as prevention in MSM in the Netherlands

The Post-doc researcher will work as part of a multidisciplinary team that has long-standing experience in collaboration on the interface between mathematical modeling and statistics, epidemiology and public health. The project will be conducted within the Utrecht Centre for Infection Dynamics, which is a centre of collaboration between the University Medical Centre Utrecht, Utrecht University and the RIVM. The UCID seeks to bring together expertise in epidemiology, microbiology, immunology, mathematics, biostatistics, and public health. The successful candidate will be based at the University Medical Centre Utrechtand will have close collaboration with the virology department. The project involves close collaboration with the infectious diseases research team of the Public Health Service Amsterdam (GGD Amsterdam) and the HIV Monitoring Foundation (Stichting HIV Monitoring). Furthermore, we are collaborating with biostatisticians at the MRC Biostatistics Unit in Cambridge, UK, with the research team of Prof. Dr. Jim Koopman at the School of Public Health of the University of Michigan, USA, and with the team of Prof. Dr. Nicola Low at the University of Bern, Switzerland.

Conditions The project is funded by the AIDS Fonds Netherlands. The duration of this project is three years. Part-time employment is optional.

The Post-doc researcher should have successfully completed PhD in theoretical biology, mathematics, biostatistics or a similar discipline. Experience with mathematical modelling of infectious diseases (or a related research field) is required, experience with statistical analysis of observational data and/or the analysis of genetic sequence data and coalescent analysis is an advantage. The candidate should have a broad interest in the application of mathematical methods to epidemiological and public health questions. He/she should be able to communicate well with researchers from other disciplines and should be able to build up and organize a research network. With support of the research team, the applicant is expected to write scientific papers on the results of the project and give presentations at national and international meetings. The applicant is also expected to organize meetings of the research team and to facilitate smooth communication between the various groups involved in the project. We also encourage the applicant to spend some time at other institutions to learn some of the techniques needed for the analysis of genetic sequence data.

Contact For further information please contact Dr. Mirjam Kretzschmar at Letters of application can be sent to the same address. Deadline for application is 22 November, 2013.

4. Conference: VPH Annual Conference 2013, Bern, Switzerland

On behalf of the organizing committee we hereby invite you to the 2013 VPH Conference that will be held on:

Wednesday December 4, 2013, at the Vetsuisse Faculty, University of Bern

Further details about the scientific program can be found on our website

Please use the registration link located there to indicate your attendance so that we can plan for the sponsored coffee and lunch break.

Again we do have 2 key note speakers:

1. Fernanda Dorea, DVM, PhD from the National Veterinary Institute (SVA) in Uppsala, Sweden: “Veterinary epidemiology in the era of big data: value, volume and velocity of information extraction”

2. Matthias Greiner. Prof. Dr. from the Bundesinstitut für Risikobewertung (BfR) in Berlin, Germany: “Veterinary Public Health in practice: lessons learnt after the dioxin and EHEC events in Germany”

Immediately after the closure of the scientific program the EpiForum ( will hold its Annual Meeting – all EpiForum members and guests are welcome to attend.

5. Conference: From emerging to pandemic viruses: Interplay between host ecology and viral evolution, 2-6 April, 2014, Roscoff, France

Emerging viruses are recognized to be a threat not only to human health but also to activities, such as crop or cattle farming, and even to endangered species. This conference will study virus evolution and emergence through an original perspective by focusing on where viruses thrive. A first series of lectures will present virus outbreaks in the wild, ranging from ‘classical’ topics (ebola in humans) to more unusual viruses (viruses infecting Archae or viruses infecting… viruses). A second series of lectures will present experimental results on outbreaks, with a particular focus on bacteriophages, which are particularly amenable to experimental evolution approaches. Finally, the third series of lectures will focus on deciphering the dynamical processes that can lead to outbreaks of new viruses. Overall, this conference stands out as one of the few that gathers researchers, who use different approaches (molecular biology, experimental evolution, mathematical modeling) and work on viruses infecting a wide variety of hosts (animals, plants, bacteria, Archae, viruses) but who are all interested in virus emergence.

Deadline for registration: Jan 10, 2014

Deadline for support grants: Dec 10, 2013

6. Postdoc and PhD positions: Quantifying population dynamics of viruses, ETH Zurich, Switzerland

Positions are available in the group of Roland Regoes at the ETH Zurich (see In our group we study quantitative aspects of infectious diseases within their hosts.

We are looking for a PhD student and a postdoc interested in studying the within host dynamics of viruses and their interaction with the immune system. Applicants for the positions should have strong quantitative skills. We therefore encourage people with a background in mathematics, biostatistics, bioinformatics or physics to apply. The starting date can be as soon as possible, but we are fairly flexible what that is concerned.

The specific questions, which we would like to address over the next years, revolve around infering the population dynamics of the virus from high-throughput genetic data. We would like to find out what the viral sequence data, collected in infected hosts over time, tells us about the replication and spread of the virus within its host. We also plan to investigate the population dynamics of B-cells using detailed genetic data on antibody responses.

Experience of phylogenetic and phylogeographic methods would be advantageous, especially if you apply for the postdoc position. The research in our group is conducted in close collaboration with experimental groups in Switzerland and oversees.

Our group is strongly linked with the theoretical biology group of Sebastian Bonhoeffer ( who works on the emergence and dynamics of drug resistance. This means that we have common group meetings, and the PhD student and the postdoc will be exposed to a wide range of interesting research on infectious disease dynamics.

Zurich is a great place to live and to do research. It is the home of two big universties (the University of Zurich and the ETH), and is an attractive city in beautiful surroundings with a multinational population and many educational and recreational opportunities.

To apply please send a letter describing your interest in this position, a CV and the names and contact addresses of two referees to me by email: Please apply until December 20, 2013. Informal enquires are also welcome.

7. PhD position: Mathematical Immunology, Heidelberg, Germany

We are looking for a highly motivated PhD student on projects in the field of mathematical immunology and virology. The aim is to combine experimental data with mathematical models and computational simulations in order to understand the dynamics and the mechanisms of infectious diseases and immune responses. The student will work on a specified project in the area of Malaria infection, but is also highly encouraged to develop and pursue own projects in the proposed area of research.

The applicant should hold a Masters degree in a discipline relevant to the project (e.g. Mathematics, Statistics, Computational Biology, Biomedical Sciences, Immunology, Computer Sciences, (Bio-)Physics). The willingness for interdisciplinary work and a strong quantitative background are required. Good programming skills (e.g. C/C++) and a good working knowledge of one or more mathematical packages (R, Mathematica, MatLab, …) are desirable.

The research will be conducted in the newly established research group Mathematical Immunology at the Center for Modeling and Simulation in the Biosciences (BIOMS). The group is part of the Interdisciplinary Center for Scientific Computing (IWR) of the University of Heidelberg and located at the BioQuant-Center. The BioQuant-Center in Heidelberg provides a stimulating interdisciplinary working environment hosting various groups that work on quantitative aspects in biology and the life sciences. The PhD student will participate in a team that has close collaborations to experimental scientists.

The position will be paid according to the German salary system with TV-L 13/2 , the start is expected to be in early 2014. Applicants should send a cover letter stating their interest of research and their previous work, a detailed CV and contact information for two or three academic references to

For more information please contact or go to

8. Infectious disease modeller position at Public Health England Centre, London, UK

Job reference J84-HP-MK-11608090

Application deadline 10 November 2013

Salary range 37,175-45,769 pa

Duration: available immediately, until 31 August 2014

We have a post available until 31 August 2014, working on a project to develop a user-friendly modelling tool for chlamydia, based at the Public Health England (PHE) Centre for Infectious Disease Surveillance and Control (CIDSC) in north-west London, in the HIV and Sexually Transmitted Infections Department and the Modelling and Economics Unit.

The project is funded by the Technology Strategy Board and is led by Public Health England (PHE), with a strong group of inter-disciplinary collaborators (including Johns Hopkins University, University of Oxford, St George’s University of London, University College London, and industrial partners).

This project will improve our understanding of fundamental chlamydia epidemiology as well as developing an important tool. The post-holder will gain valuable experience working closely with epidemiologists, statisticians, modellers and health economists at PHE and experts in collaborating institutions to analyse the extensive data-sets that PHE holds (National Chlamydia Screening Programme; Genito-Urinary Medicine Clinic Activity Dataset; and Chlamydia Testing Activity Dataset) and help develop the model at the heart of the decision-makers’ tool. Other data that will inform the work come from the recently-completed MSTIC (Maximising STI Control) study, and new data collected from clinic patients as part of this study.

The post-holder will contribute to the development of the transmission-dynamic model required for this project and will be based in the Modelling and Economics Unit. /Whilst experience in health economics is desirable it is not essential/.

Further details are attached, and there is more information on the NHS jobs website – search using the job reference J84-HP-MK-11608090 or use the link

Applicants are _very strongly_ advised to use the criteria in the person specification (available online) as sub-headings in their application to make it clear how they meet each of the selection criteria. Interviews are expected to be approximately 2 weeks after the application deadline. Applicants who are invited for interview will be asked to give a 5-minute presentation explaining how they meet the selection criteria.

Further information is also available from Dr Peter White ( ) or Dr Kathy Lowndes( ).

9. PhD position: Modeling the dynamics of plant-insect interactions, Wageningen, The Netherlands

This PhD project focuses on the modelling of plant-insect interactions. Although a lot is known about specific aspects of plant responses to attacks by herbivores (see below), a model that describesthe complex dynamical behaviour of the full system of plants, plant volatiles, herbivores, and predators is still missing. These
components together form a network evolving in time. Knowledge of its behavior in time may be of great help in the agricultural practice. In this project we want to unravel the structure of this network and find
expressions for the interactions between the components. The dynamics could be described in terms of matrix models as common in the population dynamics literature, but also an approach in terms of differential equations could be followed. We start from available data, but in the course of the project also new experiments may be proposed to calibrate and validate the model.

Description of the specific system: Plants are well-known for their tremendous variation in secondary metabolites. The expression of the plant metabolome is an important determinant of a plant’s phenotype in terms of its resistance to attack. The level and composition of chemical defences of a plant is determined by a combination of (a) the plant genotype and (b) the interaction of the plant with its environment (induced changes, phenotypic plasticity). A major component of a plant’s defensive phenotype, is how plants shift their metabolic profile in response to insect attack, in terms of volatiles. The combination of constitutive and herbivore-specific responses in induced chemical defences have been identified as key components of resistance in pair-wise interactions with a specific attacker. However, individual chemical compounds may differ in effectiveness to or have contrasting effects on different herbivore species. Therefore, an intriguing question is how is insect community dynamics influenced by a plant’s (dynamic) chemical profile.

The three research questions of this project are:

(1) Which insect species are most affected by chemical perturbations of the plant chemical profile and how?
(2) Which insect species of the community have the strongest effect on plant chemistry and subsequently on insect community dynamics?
(3) Which chemicals have the strongest effects on insect community dynamics?

There are initial datasets available, but there is also opportunity to do further well-chosen experiments.
The project is a collaborative effort of modellers, ecologists, and physiologists.

The candidate should be motivated and experienced to model the dynamical behaviour of a complex ecological system. This requires a solid background in mathematical modelling, in combination with knowledge of or interest in ecology. You have an MSc degree in Biology with ample experience with modeling, or an MSc in Bioinformatics, Mathematics, or Physics with a strong drive to specialize in the modelling of biological systems. You are a team player with demonstrable experience in collaboration with system biologists, modelers, ecologists and physiologists. You have excellent communication skills. Conditions of employment

A full-time position (38 hours), initially for 1 year after which a go/no go decision will be taken on extension with another three years. Gross salary per month euro 2042,- in the first year rising to euro 2612,- per month in the fourth year, for a fulltime appointment. Hay-profile: Promovendus

Information on the research: Prof. dr. Jaap Molenaar, Prof dr Marcel Dicke, dr Maarten de Gee or dr Erik Poelman.

Information on the selection procedure: Mrs. D. Wissink (