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VISITING FELLOW AT THE DEPARTMENT OF BIOLOGICAL STATISTICS AND COMPUTATIONAL BIOLOGY, CORNELL UNIVERSITY, NEW YORK, USA

20. August, 2018

By: Anna-Simone Josefine Frank

I’m currently a PhD student at the School of Pharmacy (UiO) with a background in mathematics. A travel grant from NORBIS, for which I’m grateful, enabled me to spend six months (January to June 2018) as Visiting Fellow at Cornell University in New York, USA. My main affiliation at Cornell was with the Department of Biological Statistics and Computational Biology (BSCB).

Picture: On campus in early 2018 (Winter at Cornell was harsh)

My PHD project and purpose of my stay
My PhD research focuses on the use of thyroid hormone replacement therapy (THRT) during pregnancy. The goal is to investigate whether THRT has effect on immediate birth outcomes. The project relies on the use of statistical methodologies and analysis tools. Hence the goal of my visit at Cornell was to spend time in a quantitative research environment renowned for the development of novel statistical methodologies.

The Department and Collaboration
I joined the research group of Professor Matteson early January, and felt very welcome by him, students, faculty members and administrative staff. I was immediately offered office space and the necessary research facilities. Professor Matteson and I agreed on regular meetings. These meetings created a forum for discussion, where I have had to answer questions that have contributed to deepen my own understanding of the project. Most challenging however, was explaining to a statistician with no background in pharmacoepidemiology what my research is about.

Outcomes of Visit
Our first collaborative project aimed to classify women according to similar patterns of medication use, and to compare these patterns across different data sources. We applied Group-based  trajectory models (GBTM) to the data and identified four disjoint groups of adherence patterns of medication use. The results were summarized in a manuscript, entitled ‘Group-based trajectory models to determine patterns from different data sources on maternal use of thyroid hormone replacement therapy’. This manuscript, submitted whiles at Cornell, is currently under review.
As an extension of this project, we have started work on quantifying the effect of THRT use on immediate pregnancy outcomes. Collaboration on this project will continue beyond my research visit.

Picture: Cornell Tower (left) and Flower Garden on campus in summer (right)

Academic Seminars and Workshops
In addition to research, I attended weekly seminars at the department of statistics as well as took part in workshops on statistical methods, which was organized by the Cornell Statistical Consulting Unit (CSCU). Graduate students at the department usually present their latest research results during a bi-weekly seminar. I had the opportunity of presenting my research project during one of the seminar meetings in March.

Community engagement
Besides academia, I supported the Cornell University hockey team (the Big Red), during their their Ivy league hockey tournament. In April, I also participated as a panelist to share my career path experience with undergraduate students at Cornell University. In May, I got accepted to participate in a “Julie Tumbles Leadership retreat” workshop tailored specifically to young, female researchers and organized by CORNELL’S GRADUATE & PROFESSIONAL WOMEN’S NETWORK (GPWOMEN). The workshop discussed the obstacles women face during their career and how to deal with them.

Picture: Hockey trophies, tickets (up) and Lynah Rink (down)

In total, my six months stay abroad at the department of BSCB was very stimulating experience both personally and academically. So far it was the best and most rewarding experience during my PhD, and I’m grateful to NORBIS for making this possible. I can strongly recommend every PhD student to spend some time abroad.

MedBioInfo course in ‘Machine Learning in Medical Bioinformatics’ June 11-15

24. April, 2018

We are happy to announce that NORBIS will have a number of seats available for our members at the course in ‘Machine Learning in Medical Bioinformatics’, organised by our Swedish collaborators MedBioInfo.se in Linköping, Sweden, June 11-15. NORBIS members may apply for a seat and a travel grant to attend the course, please read more here.

Cancer genomics at Stanford

13. April, 2018

by Chloe Steen, University of Oslo
 
I have always wanted to go abroad for research. I did not know where, or when, I just knew that I wanted to experience a lab in another country, see how they worked, organized their projects, and their everyday life in the lab. Even though I have international experiences in my education, all of my research experience was from labs in Oslo. 
 
When NORBIS posted that they would award travel grants for research stays abroad to its PhD-students, I immediately jumped on the occasion. One of my co-supervisors, June Myklebust, had previously mentioned Stanford as a possibility, as she had been there as a postdoc herself. We reached out to Ash Alizadeh, an assistant professor who is famous for the seminal paper that first showed how whole-transcriptome analysis can reveal new cancer subtypes, which revolutionized cancer research. This paper was from his PhD, and very strong research has also come from the research group that he leads, with particular emphasis on circulating tumor DNA. He was very positive to have me as a visiting PhD-student, and this was the start of a great collaboration. 
 
Before starting, many logistical details needed to be settled. I applied for funding from NORBIS on the February 15th, 2017 deadline and I was notified that it was granted mid-march. My supervisor Knut Liestøl strongly suggested that I made a pre-visit to Stanford before starting a six-month-long stay. I went there in the end of June, and was there just in time to receive the paperwork I needed from Stanford to apply for a visa interview at the American embassy (the DS-2019). I was also given a Stanford account, and could do all the training required before starting in the lab, so that I could hit the ground running as soon as I got there on September 1st. 
 
When I arrived at Stanford, I was immediately involved in a project studying deconvolution of gene expression profiles in cancer samples. This project was in collaboration with Aaron Newman, a previous postdoc in Ash Alizadeh’s lab, who had recently been made faculty, and co-mentored me during my stay. My first task was to write code for a new bioinformatics tool they were developing. This turned out to be one of my main projects while at Stanford, and I learned a lot from it.
 
The main challenge was to keep touch with my supervisors in Norway. We managed to have regular Skype meetings, but the time difference with Norway (nine hours) made communication a bit challenging. But as long as you have agreed on a clear plan with your supervisors before leaving Norway, this should not be too much of an issue. 
 
On the other hand, I received very close supervision from my mentors at Stanford. As a full member of the lab at Stanford, I had weekly progress meetings with my mentors, and I participated in the weekly lab meetings, journal clubs, and social events. Two weeks before the end of my stay, I gave a presentation to the research group summarizing my accomplishments during my six months at Stanford. 
 
I was worried going abroad would delay my research, that I would spend time waiting for things, and that settling in a new lab would take some time. It was not the case at all, and it is due to three main reasons. 
  1. The pre-visit a couple of months before helped a lot to get practical matters out of the way. In addition to take care of paper work, I also took advantage of that week to look for housing for September. 
  2. The US is known to have longer work days than Norway. Indeed, my colleagues would rarely leave the lab before 6pm. 
  3. People are very efficient, and won’t keep you waiting. Projects move forward at incredible speed. They have to if you want to do top science.
Overall, I couldn’t be more happy about my experience at Stanford, and I am extremely grateful for the financial support from NORBIS. I recommend anyone who is doing a PhD to consider a stay abroad, and being a member of NORBIS is a great way to make it happen. 

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Five international travel grants awarded!

4. April, 2018

We are happy to announce that the NORBIS board has awarded a total of 275 000 NOK, to support the research exchange of five NORBIS PhD students during 2018. Each student will receive funding corresponding to the NORBIS international travel grant guidelines, which may be found here.

 

The five successful students are as follows:

Name Institution Destination Department Duration
Asan Mohideen Nord University St.John’s, Canada Memorial University of Newfoundland  4 months, Sept 2018 – Jan 2019
José Cerca UiO Edinburgh, UK Edinburgh Genomics, University of Edinburgh 3 months, Nov 2018 -Jan 2019
Martin Wohlwend NTNU Lausanne, Switzerland École polytechnique fédérale de Lausanne (EPFL) 6 months, June – Nov  2018
Zhi Zhao UiO London, UK London School of Hygiene & Tropical Medicine, 4 months, July – Oct 2018
Yaxin Xue UiB Berkeley, USA Lawrence Berkeley National Laboratory 6 months, July 2018-Jan 2019

 

We wish you all good luck, and look forward to reading your reports when you return!

Integration of knowledge and logical modeling at Institut Curie and ENS in Paris

12. March, 2018

by Vasundra Touré, NTNU

I had the chance to do my international exchange in Paris for 6months where I visited two research groups: Pr. Emmanuel Barillot’s group at Institut Curie and Pr. Denis Thieffry’s group at ENS Paris. Both have common domains of interest with my group. With the approval of my supervisor, I did this research stay in the first year of my PhD to help me comfort the structure of my research project. Plus, while still be at the beginning of my PhD, I was flexible to add new insights or new areas to explore in my project.

For me, it has been a good experience. You get to see how the different groups work and you benefit from the richness of skills of each group. I learned a lot about certain topics that I didn’t know anything about (e.g, computation of trap spaces to find stable states for boolean models) and also got feedbacks regarding my own project from an external point of view (e.g, representation of causality statements and ways to extract them from existing repositories). I also had the opportunity to help people in the groups with certain topics that I was familiar with. So, I was happy to return the favor! I attended the groups meetings where I got to know about projects of the teams and, lab seminars that involved more people from the department with topics that were sometimes completely different to what I am doing, but still interesting to listen to.

During this research stay, I have been able to attend several meetings and workshops relevant for my project (e.g, GREEKC, Curation Workshop on Molecular and Causal Interaction, COMBINE) which helped me to put on track one part of my PhD project and for which I am currently writing a paper.

 

 

Besides work, I enjoyed my time in Paris. Most of my family and friends are there, so it was refreshing to spend some time with them. And Paris is a beautiful city.

 

 

Thank you NORBIS for funding this research stay. I would also like to thank both groups that hosted me. This has been resourceful for my PhD, which is definitely on tracks now! A couple of ideas emerged from this research stay, some work done, some work still in progress. One month after my stay, I am still working on some of the tasks started during my stay abroad and this gave to my group new perspectives to study as well!

Developing new ideas at the Institute of Genetic Medicine in Newcastle

22. January, 2018


Newcastle International Centre for Life, Newcastle University

by Miriam Gjerdevik, University of Bergen

 

I visited Heather J. Cordell, Professor of Statistical Genetics, and her research group at Newcastle University, Institute of Genetic Medicine, from September 2017 to December 2017.

Heather Cordell is a world-leading researcher within the development and application of statistical methodology to genetic studies of complex diseases. We have several research interests in common, in particular statistical analyses involving case-parent trios. The purpose of my research exchange was to expand my international network and establish a connection and collaboration with Cordell and her group.

I started working on my third PhD paper in the beginning of my research stay. With excellent supervising from both my main supervisor, Håkon Gjessing, and Cordell, I managed to write a decent first draft of the paper during my three-month stay. The input from Cordell has improved the quality of my paper, and the collaboration has been very fruitful. During my exchange, I had regular phone meetings with my supervisor. This was an excellent way of keeping in touch and discussing my ongoing research.

I was warmly welcomed by Cordell and her group. Within the office, the group organized fortnightly informal seminars where we could share new thoughts and ideas for research. Moreover, the group met for dinner and institution drinks after work, which made it easy to get to know everyone and to socialise in the evenings. I also joined the group for a one-day conference in Edinburgh, which further expanded my international network.

My stay in Newcastle has been very successful! I have developed new ideas for research and increased my knowledge of complex trait research. Moreover, I have met several new colleagues and friends, with whom I hope to cooperate throughout my career.

I truly enjoyed each and every day at the Institute of Genetic Medicine in Newcastle!  I am very grateful for receiving this opportunity, and I would like to thank Gjessing and Cordell for all their help in making this international exchange possible, as well as the National research school in bioinformatics, biostatistics and systems biology (NORBIS) and the University of Bergen for the necessary funding.

 

Future advice:

Prior to my research stay, there was quite a lot of paperwork to complete (applications for funding, occasional student application, NAV, insurances, etc.). In addition, there were practical concerns such as finding an apartment. I recommend starting the paperwork as early as possible, as it took longer than expected. Moreover, I regret not going for a longer period of time. I would encourage others to apply for a six-month exchange if possible.

Learning advanced analysis of gene regulation in Zaragoza

12. January, 2018


CSIC – Estación Experimental de Aula Dei (EEAD), Zaragoza, Spain

by Teshome Mulugeta, NMBU

 

I am so grateful to NORBIS that I was given the opportunity to travel to EEAD-CSIC, Zaragoza, Spain as a visiting PhD student. It was a useful experience to me to work and talk with several outstanding people. My visit to EEAD-CSIC was arranged and supervised by Dr. Bruno Contreras-Moreira. The primary goal of my visit was to spend time doing research related to my PhD with relevant professionals.

 

Research achievement

Upon arrival at EEAD-CSIC, I presented my PhD projects. We had a very productive discussion and I got useful feedback from relevant EEAD-CSIC research groups. We started by outlining the activities to perform during my stay at EEAD-CSIC. During my stay at EEAD-CSIC, I learned new proven approaches and methods to annotate transcription factors and their binding sites, to analyse expression based cis-regulatory motifs and to develop comparative database for orthology to be used for phylogenetic de novo regulatory motif discovery. The knowledge and experience i gained from EEAD-CSIC visit helped me to move my PhD projects forward.

 

Professional training

My presence at EEAD-CSIC provided me an opportunity to be invited to participate in one of the European Cooperation in Science and Technology (COST) action in Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) which was held in Lisbon, Portugal. The main goal of the workshop was to get a first hand hack-a-thon training from GREEKC resources and experts in gene regulation. The workshop helped me to assess the state of the art in gene regulatory process and its subsequent use in computational biology. I got the opportunity to discuss my PhD projects with trainers and trainee. I was active in the discussions and I believe my participation had a significant contribution in defining action points and future improvements at the end.

 

Professional network

My visit to EEAD-CSIC helped me to expand my professional network both in Spain and internationally especially at the GREEKC event that i participated in Lisbon. I met extraordinary professionals and experts in my PhD study area and had established a strong network with them. I am now active member of Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC http://greekc.org/) and will participate their annual workshops and trainings in the future.

 

Adventures and holidays

Zaragoza is located in northeastern Spain, Aragon region. I was fortunate to be in Zaragoza where the Pilar Festival (Las Fiestas del Pilar) is celebrated on the 12th of October. During the official celebration week, there comes wide variety of events like concerts, parades, flowers and theatre. It was amazing festival that brought people from every corner of Spain.

 


People show devotion to the Virgin del Pilar by leaving flowers

 

I had also the opportunity to revel in the incredible mountain scenery of the Pyrenees Spain arranged by EEAD-CSIC work colleagues. The experience was a truly engaging and  captivating which has left me awestruck.

 


Hiking to the Pyrenees

 

Conclusion

In general, my visit was a very fruitful and enriching experience. I am grateful to NORBIS for providing this opportunity. I would also like to thank Dr. Bruno for the hospitality and assistance during my stay in Spain. I also would like to thank my supervisors Prof. Dag Inge Våge, Associate Prof. Simen Rød Sandve, Dr. Torfinn Nome and Prof. Torgeir R. Hvidsten. Thanks for EEAD-CSIC colleagues and staff for their kindness and warm welcome.

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An autumn with Bayesian approaches in Vienna

14. December, 2017

 

Hi, my name is Aliaksandr Hubin and I am a PhD student at the department of Mathematics of the University of Oslo. In this report I would like to share my international exchange experience, which took place in Autumn 2017 and was funded by the NORBIS travel grant.

 

During my exchange I was staying in Vienna, Austria for a period of 3 months (from September to November 2017). There I was visiting Dr. Florian Frommlet, an assistant professor in statistics at the Center for Medical Statistics, Informatics and Intelligent Systems of Medical University of  Vienna.

 

During the stay we have been working jointly on several projects. First of all we continued the collaboration and applied previously developed MJMCMC and GMJMCMC algorithms to GWAS studies. Performance of the algorithms was compared to other popular Bayesian approaches to GWAS such as MOSGWA and PiMass. The comparison was made on several simulation scenarios. Now the real data analysis is to be performed to finalize the paper. The results are to be published in the article entitled “A comprehensive study of Bayesian approaches to Genome-Wide Association Studies” written in collaboration with Michael Hagmann, Bernhard Bodenstorfer, Artur Gola, Małgorzata Bogdan, and Florian Frommlet.

 

Additionally we were finalizing the paper entitled “Deep nonlinear regression models in a Bayesian framework”, written together with Geir Storvik and Florian Frommlet. In this paper we have introduced the concept of a Deep Bayesian Regression model, which generalizes logic regressions, neural networks, fractional polynomials, and tree based regressions (and some other statistical learning approaches) into a flexible and general Bayesian framework. We then have suggested several algorithms for fitting DBR models. Several inference and prediction based examples were studied. In particular we have shown that the approach allows to recover highly nonlinear physical laws (like for example the 3rd Keppler’s law) in a closed form with a large power and low proportion of false positives. Additionally it showed good performance in asteroid and breast cancer classification problems. Finally some epigenetic study was performed with a goal to find optimal structure of dependence between the epigenetic observations and genetic factors in Arabidopsis thaliana.

 

Within the exchange duration I have given a talk entitled “Deep nonlinear regression models in a Bayesian framework” within Wiener Biometrische Sektion series of seminars. I have also had a chance to attend several other talks within Wiener Biometrische Sektion seminars and the as​ ​ autumn seminar “Young​ ​ Statisticians”, held at the Medical University of Vienna. Apart from that I attended the doctoral thesis defence of one of the fellow PhD students. This was an extremely interesting experience too, since the defense procedure was quite different from what I had seen in Norway.

 

The last but not least I met extremely interesting people carrying out advanced research in medical statistics ranging from clinical trials to survival analysis.

 

To conclude, I would like to thank NORBIS for an opportunity to spend these fantastic three months in beautiful Vienna, where not only I carried out some interesting research, but also had a chance to enjoy the imperial architecture and see numerous performances at the Opera House and Volksoper.

 

 

 

 

 

 

 

 

 

A report from the Center of Systems Biology in Reykjavik, Iceland

27. November, 2017

by Kjersti Rise, NTNU

 

I hadn’t really given a research stay abroad much thought when I started my PhD, it seemed like fun, but too much extra work in order to make it happen, and there were so many other things I already had to do. Then suddenly one day well into my second year everything changed, and I was writing applications and talking to scientists abroad, and about two months later I was on my way to the Center of Systems Biology in Reykjavik, Iceland!

 

 

Thanks to the travel grant from NORBIS, I ended up having the time of my life. I got to work in an exciting group, learning how to create and use genome scale models of cells, further develop code for these analyses, meet new people, and I got to discover Iceland! Working on a (for me) new topic was challenging, it required a lot of work, but I also learned way beyond what I had expected. It helped me learn a new programming language, a new way of thinking, getting a new perspective on possibilities in analysing biological data, and develop me as a scientist. Working together with brand new people with different backgrounds than myself was also very interesting, and I learned a lot from working with them. I made both new friends and new connections, and hopefully some of these new connections will become collaborators in the future.

 

 

Although the Icelandic climate is not all that different from the Norwegian one, and most of the people living in Iceland speak fairly understandable English, it was still a both strange and wonderful experience living in a foreign country for a while. Iceland is absolutely stunning, and learning Icelandic is really not for the faint at heart. I fell in love with the country, the science, the language, pretty much everything, and that’s all thanks to NORBIS who supported me financially, and made it possible. Travelling alone and figuring things out by yourself in a foreign country is always a good way of learning a lot about yourself, and the world around you. It changes perspective, not only in regards to science and work, but also in the way one sees the world. Yes, there was a bit of work required to make it happen (most of it when I came home, actually!), but not as much as I initially thought, and it was all so worth it. I’m so grateful I got to have this experience, and I can highly recommend some time abroad to anyone!

Kjersti Rise, September, 2017

 

 

 

 

 

 

 

 

Funding available for international exchange!

27. November, 2017

Once more, we encourage you as a NORBIS member to spend part of your PhD period (at least 3-6 months) at an institution abroad, to benefit from international expertise and to expand your international network. We have funding available for such an exchange, and we now invite you to apply for financial support for your stay. Read more and apply here by 1st March!

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