Call for researchers interested in a MSCA Individual Fellowship

Research groups at Haukeland University Hospital (HUH) are looking for researchers interested in a MSCA Individual Fellowship with HUH as a host institution within the following fields: 

 

1. Neurology/ Neuroepidemiology

We search for talented, young researchers within the field of Neurology/ Neuroepidemiology as presented by Associated Professor Marte H. Bjørk and Professor Nils Erik Gilhus:

Bergen Epilepsy Research Group (BERG) has a major focus on the effects of antiepileptic drugs taken by female patients with epilepsy from conception until giving birth on the developing child. We are especially interested in variation between different types of antiepileptic drugs as well as the interactions between antiepileptic drugs and genetic and environmental risk factors.  We are examining a large Norwegian cohort with more than 100 000 individuals (MoBa; The Norwegian Mother and Child study), and combining this with data from the compulsory Norwegian Birth Registry and the MoBa biobank.

BERG is based at Department of Neurology, Haukeland University Hospital and Department of Clinical Medicine, University of Bergen. The research group has around 15 active members, including researchers from neurology, obstetrics, epidemiology, pharmacology, neurophysiology, and pediatrics. We have recently received major funding for a joint Nordic project (SCAN-AED; The Scandinavian Antiepileptic Drug Teratogenicity Study). The SCAN-AED links 17 population registries from four Nordic countries. The database will yield individual level data from around 4 million births in 2019. The goal is to study rare outcomes of in utero antiepileptic drug exposure, as well as interactions between environmental and pharmacological factors.
Furthermore, Department of Neurology has recently received major funding for the first national research center for clinical treatment (Neuro-Sysmed), to perform research on severe brain disorders. BERG has annually published 5-15 original papers in high-impact journals, includes 7 PhD-candidates and several postdocs. The research takes place in a clinical context, near to and associated with ongoing treatment and diagnostic work.  

We seek a candidate with interest in working with large epidemiological datasets using STATA programming, or a candidate with interests in genetic epidemiology.

Examples of potential projects for the candidate:

The interaction between antiepileptic drug exposure in pregnancy and maternal psychiatric disease for the risk of childhood autism based on Nordic population data.

The impact of maternal genetic risk factors and low folate levels on risk of developmental delay in children of mothers using antiepileptic drugs.

Does high dose folic acid in women using antiepileptic drugs in pregnancy increase long-term cancer risk in mother and child in the Nordic population?

2. Medical neuroimaging/biological psychiatry 

We are looking for ambitious, creative and scientifically curious early career researchers within the field of medical neuroimaging/biological psychiatry as presented by senior consultant and associated professor Leif Oltedal:

The research group explores brain changes induced by electroconvulsive therapy (ECT) with the aim to understand treatment mechanisms and predictors of clinical response (see protocol here).

ECT is a treatment administered under general anesthesia and muscle relaxation. A transient seizure is induced by electrical current transferred through scalp electrodes. Although (ECT) has remained the most effective acute treatment for major depressive episodes for about 80 years, it is not known why it is effective or how it works. Only a small proportion of patients with treatment resistant depression are offered ECT, and typically 60-80% experience a good response (> 50% symptom reduction). Several neuroimaging studies of ECT have demonstrated volume increases of brain areas after treatment. The most consistent finding has been volume increase of the hippocampus. However, a link between the treatment induced brain changes and clinical improvement has not been established.

An important reason for our knowledge gap is that single studies have limited samples and lack statistical power to reach firm conclusions. The Global ECT-MRI Research Collaboration (GEMRIC) is led from our group in Bergen and was founded with a belief that collaboration and mega-analysis of combined data will lead to new knowledge that can be generalized across individual research sites. Within GEMRIC we have the world’s largest data sample with clinical and MRI neuroimaging data before and after ECT – our initial study includes up to 550 subjects (including controls). In our next study we aim at increasing the sample size to 2000 subjects. GEMRIC uses state-of-the-art imaging tools to study structural and functional changes that are associated with the treatment.

We seek a candidate who is motivated to work within a multidisciplinary international team and investigate mechanisms of action of ECT. Prior experience in with neuroimaging methods is important.

3. Bioinformatic strategies in marker gene analyses of low-biomass samples 

We search for talented, young researchers within the field of bioinformatics as presented by doctor and associated professor Rune Nielsen and professor Tomas Eagan:

The pathogenesis of inflammatory mediated lung and airways diseases such as sarcoidosis, asthma and COPD remain elusive for a large number of patients. The microbiome revolution has led to significant insights in other fields of medicine, but in respiratory research we still struggle with analytic strategies for hard-to-get, low-biomass airway samples.

The Bergen Respiratory Research Cluster have sampled airways and lungs of patients with sarcoidosis, asthma and COPD in two of the largest single-site lung microbiome studies in the world (MicroCOPD and MicroILD). These studies carry with them an unprecedented amount of metadata, including lung function measurements, blood samples, CT coronary angiography, HRCT of the lungs and more. Currently, six PhD students, one post-doc and two professors are involved in ongoing analyses of these projects. The applicant will work autonomously with his/her own project in addition to rich opportunities for collaboration and student supervision within the group.

Requirements:
Bioinformatics: PhD or equivalent
Experience with marker gene analyses of the microbiome.

4. Intestinal pathogens microbiology and host immune responses 

We search for talented, young researchers within the field of intestinal pathogens microbiology and host immune responses as presented by Associate Professor Kurt Hanevik and Professor Nina Langeland:

In our research group, we are examining several large cohorts of infants with diarrhea and controls from Tanzania and Ethiopia, as well as stool and blood samples from experimental human infections.

We are interested in the issue of interactions between pathogens, and between pathogens and the intestinal microbiota and host responses, as well as antimicrobial resistance in pathogens and commensals. Main pathogens of interest are Giardia lamblia, Cryptosporidium and Enterotoxic E. coli. We have many years of experience in conducting epidemiological studies, diagnostic studies, and regularly employ qPCR, ELISA, flow and mass cytometry in our research.

The research group has 13 active members including infectious disease specialists and microbiologists. We have considerable international collaboration with groups in Sweden, UK, Germany, USA, Tanzania and Ethiopia. The group is based at the Medical Department, Haukeland University Hospital and Department of Clinical Science, University of Bergen. Over the last years the group has secured funding from national and local research grants as well as from Bill & Melinda Gates Foundation. Our group annually publishes 10-15 papers in international scientific journals, including major epidemiological and infectious diseases journals.

We seek a candidate who has experience and interest in multifactorial analysis of diarrheal diseases, examining both intestinal pathogens and host defence mechanisms.

Examples of potential projects for the candidate:
Longitudinal profiling of inflammatory markers, and protective luminal factors in ETEC infection.

Mapping of markers for metronidazole resistance in Giardia infection using clinical samples and data.


5. Brain-gut interaction and medical image analysis 

We search for talented, young researchers within the field of brain-gut interaction and medical image analysis as presented by Dr. Birgitte Berentsen:

Bergen Brain-gut research group has a major focus on Brain-Gut Microbiota Interaction in Irritable Bowel Syndrome. There is increasing awareness that the brain and the gut are intimately linked, and that massive and diverse community of bacteria in the digestive tract aid digestion, regulates immune homeostasis and interacts with the central nervous system. In a clinical setting there has been great research interest in perturbations and dysfunction of the brain-gut-microbiota axis in functional gastrointestinal disorders. These new insights have been especially relevant to our understanding and treatment strategies of the widespread condition labelled irritable bowel syndrome (IBS). We address research challenges in the following five key areas: (i) Brain structure and function and gastrointestinal motility in IBS, (ii) Cognition and emotion in IBS, (iii) Microbiota profiles in IBS, (iv) The importance of diet in driving IBS, (v) Patient phenotypes and identification of clinically useful molecular and imaging-derived biomarkers.

For image analysis, we apply next-generation techniques behind an ongoing revolution in both clinical and preclinical imaging: the machine learning methods deep neural networks (DNN) and convolutional neural networks (CNN). With top international collaborators (UCLA, Heidelberg, Nottingham, Adelaide) and being a multidisciplinary team of gastroenterologists, neuroscientists, nutritionist, clinical neuropsychologist, imaging specialists, geneticists, microbiologist, and data analysts, including three early career researchers, and access to an outstanding imaging infrastructure, we are in a very good position to advance the clinical science of IBS.

The research group is situated at The Norwegian National Center for Functional Gastrointestinal Disorders, Medical Department  and the newly established Mohn Medical Imaging and Visualization Center , Department of Radiology, both at Haukeland University Hospital.

6. Multi-omics of aging and neurodegeneration 

The candidate will work in the Neuromics lab and the newly-found Neuro-SysMed Center of Excellence for research in brain diseases, which is officially opening in October 2019 (website under construction). 
The Group Leader, Professor Charalampos Tzoulis, is the Director of the Neuromics Group and Vice Director of the Neuro-SysMed Center of Excellence. He has an extensive track record in the field of neurodegeneration and an excellent record in promoting the career of young scientists.  

The Neuromics lab comprises 18 members, including clinical scientists, experimentalists, computational scientists and epidemiologists devoted to the study of human aging and neurodegenerative disorders. Available facilities include well-equipped biomedical and computational laboratories with state-of-the-art equipment and analysis tools. In addition, the group has full access to a wide range of university platforms that cover microscopy, metabolomics, transcriptomic and proteomics. The candidate will work closely with experienced senior researchers, postdoctoral fellows and PhD students with broad skillset and expertise covering all aspects of the planned experimental work.

We are seeking talented and highly ambitious scientist holding a relevant PhD degree in bioinformatics or molecular biology and/or similar disciplines meet the eligibility criteria for the MSCA IF program.


About the Projects

Neurodegenerative disorders (ND) such as Parkinson and Alzheimer’s disease are a major cause of death and disability and have a devastating worldwide socioeconomic impact. Having no understanding of the pathogenic processes involved, we are unable to develop disease-modifying therapies. Therefore, patients confront a future of progressive disability and premature death with treatments that are at best symptomatic. Since demographic studies show that patient numbers will continue to grow, our failure to make any significant impact means that ND are now the major challenge to health care provision in the 21st century. 

The overarching aim of our work is to decipher the molecular pathogenesis of ND and pave the way for precision medicine and patient-tailored therapies. Our Center integrates cutting-edge molecular, computational and clinical neuroscience in order to subclassify the highly heterogeneous spectrum of ND into molecularly homogeneous clusters. Emerging molecular fingerprints will be exploited as biomarkers for patient stratification and therapeutic targets for drug development. The projects are highly transdisciplinary, seamlessly combining leading research environments with industrial partners capable of supporting commercialization of project deliverables.

A constantly expanding data-bank of comprehensive phenotypical (clinical, neuroimaging, pathology) and environmental data is available. Brain tissue and other biological material are used to map and digitalize the molecular landscape of each individual. State-of-the-art multi-omics analyses produce high-resolution maps of the genome, epigenome, transcriptome, proteome and metabolome at the tissue (e.g. brain) and single-cell (e.g. neuron, astrocyte) level. All molecular, phenotypical and environmental data are collected in a single, unique database at our Center.

Projects generally fall into two categories:

  1. Wet lab genomics & epigenomics. The candidates will process human whole-tissue (e.g. brain, muscle, blood) and single-cells (e.g. 10X Genomics platform) and perform the appropriate extractions and library preparations for downstream ChIP-sequencing of selected targets, ATAC-sequencing, RNA-Sequencing and similar techniques. 
  2. Bioinformatics & computational modelling. The candidates will analyse genomic and epigenomic data from patient whole-tissue (e.g. brain, muscle, blood) and single-cells (e.g. 10X Genomics platform), in order to elucidate novel molecular signatures and networks underlying aging and disease initiation and progression. Typical datasets include: whole exome sequencing, whole genome sequencing, whole genome bisulfite sequencing, ChIP-sequencing, RNA sequencing and proteomics. Key-tasks include: data quality control, multi-omic integration and statistical analyses, advanced network analyses and machine learning. We are looking in particular for expertise in supervised and unsupervised learning approaches to stratify and subclassify disease.  

The following qualifications are important for a fellowship in wet lab genomics & epigenomics: 

  • Extensive knowledge of neurobiology, genomics and epigenomics
  • Substantial experience working with brain tissue and other human tissues
  • Experience with single cell isolation from tissue and downstream analyses 
  • Extensive experience in genetics/epigenetics including DNA/RNA sequencing, methylation analyses, chromatin state and modification analyses
  • Extensive experience in ChiP-Seq and ATAC-Seq
  • Experience with FACS will be an advantage
  • Fluency in spoken and written English at a very high level

The following qualifications are important for a fellowship in Bioinformatics & computational modelling: 

  • Substantial formal training in bioinformatics
  • Fluency in Unix-based environments
  • Background in programming, preferably including use of R and python
  • Relevant training in machine learning and modelling algorithms and in statistics
  • Expertise in integrative omics data analyses at post-PhD level documented by relevant publications
  • First, second or last authorship in relevant publications
  • Experience with analysis of chromatin-modification data including: ChIPseq, ATACseq and Hi-C.
  • Knowledge of basic molecular biology and genomics
  • Fluency in spoken and written English at a very high level




Application support program:


  1. Prospective research fellows will be selected by HUH supervisors and invited to Bergen for a MSCA-IF application writing workshop on June 3-5, 2019, free of charge.
  2. HUH will reimburse all travel and accommodation costs for the participants.
  3. After the workshop, the candidates will get further support in the application process by experienced advisors until the submission deadline on 12 September 2019.

How can a MSCA IF at HUH enhance your research career?

Haukeland University Hospital has a high international profile with close collaboration and shared infrastructure with the University of Bergen. With an MSCA fellowship at HUH, you will develop research experience and autonomy, hone your professional skills and grow your international profile and network. You will also live in a charming, vibrant and international city and benefit from the advantageous working conditions enjoyed in Norway.

HUH offers: 

  • An excellent research environment with dedicated top researchers
  • An excellent assemblage of state-of-the-art research infrastructure
  • An attractive remuneration package including top-up funding to ensure Norwegian standard salary for postdocs (> the EC contribution). (Yearly salary from 520 000 kr before taxes).
  • Free courses in transferable skills
  • Free assistance from the Bergen Technology Transfer office (BTO)
  • Flexible working time
  • Attractive welfare schemes
  • Norway provides attractive conditions for families including affordable kindergartens, free school for children from 6 years and above (in State or Communal schools) and the facilitation of social integration of foreigners from early childhood.

MSCA IF eligibility criteria:

  • The program is open for all academic disciplines.
  • A researcher can move to a country that is a member of the European Union or an associated country to conduct research for up to 24 months.
  • Before applying, the researcher should have a PhD-degree or 4 years of research experience after attained master's degree and there is no upper age limit after achieving the PhD-degree.
  • The researcher cannot have been living or have had his main occupation in the country of the host institution (Norway) for more than 12 months within the last 3 years counting from the time of application. The researcher can come from anywhere in the world.
  • The 2019th call is not open yet, but it will be very similar to the last call

How to apply?

Applications should include the following:

  • Cover letter outlining your eligibility and motivation for applying (max 1 side A4)
  • Short summary of the proposed project (max 1 page)
  • CV (max 2 pages plus a list of publications and full contact details)
Please send the application documents to forskning@helse-bergen.no

Application deadline: 16th March 2019.

The supervisors will conduct skype interviews and notify selected candidates by mid-april 2019.

For more information, please contact: forskning@helse-bergen.no








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