3. January, 2019
Report from exchange to École Polytechnique Fédérale de Lausanne (EPFL)
Thanks to NORBIS I got the unique opportunity to experience a different laboratory in Switzerland for 6 months. First, upon arrival in Switzerland it took some time to organize everything before being able to start experiments. However, as soon as everything was in place the pace at which my host laboratory worked was overwhelming and allowed me to finish many important experiments in a rather short time.
I learned different new techniques such as QTL mapping and usage of big datasets. In particular, the usage of a genetic reference population allowed me to identify new potential mechanisms driven by my gene of interest. In summary, both my research project and me personally benefited tremendously from this research stay.
Most importantly, I was very lucky to meet outstanding colleagues with whom I spent long nights in the laboratory learning various things, but additionally we also shared beautiful moments in the swiss mountains.
In general, I would recommend planning more time than anticipated as settling in a new laboratory takes time. However, once the first hurdle is overcome it is an unforgettable time that everyone should experience at some point.
17. December, 2018
Developing new Bayesian models in London
I am a PhD student at the Department of Biostatistics of the University of Oslo. I had stayed in London for four months funded by the NORBIS, as a visiting PhD student with the group of Dr. Alex Lewin, who is Associate Professor in Biostatistics at the Department of Medical Statistics at the London School of Hygiene & Tropical Medicine.
London School of Hygiene & Tropical Medicine, London, UK
I was collaborating with Dr. Alex Lewin and Dr. Marco Banterle on new Bayesian models for drug sensitivity prediction and integration of multi-omics data. The developed computational tools for the analysis of these data can consider the intrinsic relationships between the various omics data sources and also between different anti-cancer drugs, and generate new biological knowledge by helping us to identify which omics data sources and which individual features are most predictive for the sensitivity of which (classes of) drugs.
We have adapted a promising modelling approach, that was previously developed in Dr. Lewin’s group, to our situation. We have established a new Bayesian model framework for drug sensitivity prediction and drug targets identification. The new Bayesian model uses Seemly Unrelated Regressions for estimating a large covariance matrix efficiently, a spike-and-slab prior for selecting sparsely relevant molecular features, and a Markov random field prior for capturing the drug-drug similarity and related targeted genes/pathways. During my stay in the UK, I also had a good opportunity to visit the MRC Biostatistics Unit at the University of Cambridge and have nice discussions with some researchers there. Although I am now back in Oslo, our collaboration on this project is continuing and will result in a joint publication.
This year London had a very good summer, a lot of sunny days rather than mostly rainy days. The best relaxing ways for me were taking a stroll along the Thames and enjoying the Hampstead Heath walking. But it was extremely hot some days in July, especially in many buildings and on the underground trains (the “Tube”) without air conditioners. In General, I had an enjoyable summer visit in London. However, I don’t highly recommend others for such short international exchange during summer. It might be better to avoid the holiday season,
so that you could have more opportunities to discuss with your collaborators.
In addition, since London is a super-rich city and one of the world’s largest trading centres, it is difficult to find a not so expensive accommodation for a short stay. I regret not to spend more time on looking for one fixed accommodation rather than living in three places during four months.
Finally, I would like to thank NORBIS for the travel grant, and the collaborators in London very much.
Tower Bridge, London, UK
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.
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.
29. June, 2018
We are excited to invite you to join this year’s annual conference of NORBIS, the national research school in bioinformatics, biostatistics and systems biology. Our fourth conference takes place in alpine surroundings at Voss, along the train track between Oslo and Bergen, on October 17-19. Join us there for great talks by international experts and PhD candidates, poster sessions, team building activities and an opportunity to build your network and hang out with a great gang of people sharing many of your interests.
The conference is open for everyone. We cover travel and accommodation costs for all PhD students, and master students and post docs can apply for support. We also want to encourage supervisors and other researchers to join our conference, both to facilitate discussion across several levels of experience, to inspire our students, and to increase your own national network.
Read more and register here by September 10!
18. June, 2018
Do you carry an idea for a course or a workshop within the fields of bioinformatics, biostatistics or systems biology? Want to invite international experts to give lectures at this event? Once again it is time for NORBIS to ask you to propose a course or a workshop to be organised with financial and administrative support from us. We welcome brand new ideas, as well as adaptations of already existing courses and workshops.
Our financial support will cover travel related expenses for invited and internal lecturers as well as participating student members, for both courses and workshops. For courses, we will in addition give a flat sum of 60 000 NOK per course to the responsible department, to compensate time spent preparing and teaching the course. Our administrative support may help during both planning and execution of the course or the workshop, and will ease the process of making a course available across institutions.
Please visit this page to get an overview of the activities that we already offer, and to read our guidelines.
Our members currently have the following topics on their wish list (among many other!):
– proteomics analysis (statistics and bioinformatics)
– basic and advanced statistics on molecular data (in high demand!)
– high dimensional data analysis
– evolutionary genomics
– network biology
– machine learning
– clinical NGS analysis
– open source data
You are of course free to propose other topics within the scope of NORBIS.
We aim for our courses to be organized in a biannual fashion. We therefore encourage organisers of previous NORBIS courses to apply with an updated proposal, and to kindly add a summary of the participation and evaluation from the last round, as well as a note describing any updates and changes.
Please read more and register your proposal here: by September 28 2018.
12. June, 2018
We are happy to again offer you the opportunity to attend a Nature Masterclass workshop on scientific writing, in Fredrikstad September 6-7. The training is delivered by two senior editors from the Nature Publishing Group (Nature Biotechnology and Nature Communications), who will teach you how to get the most out of the writing process, to understand the editorial processes and how to work with them, and to know what it takes to get published in top-ranked journals.
This workshop is organised as a collaboration with the national research schools ForBio, IBA, NFIF and DEEP. NORBIS has a limited number of places at this workshop, and will prioritise senior PhD students already in the process of preparing a manuscript. In the submission form, you will be asked to upload an abstract for the paper you plan to work on during the workshop. We will select those of you whom are most likely to benefit from this workshop.
Read more and register here by August 1.
7. May, 2018
We are happy to announce that registration now is open for this year’s NORBIS summer school, ‘Robust and reproducible practices in bioinformatics programming‘, which takes place in Oslo, August 6-10. Please read more and register here, by June 20.
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.
11. April, 2018
Post-docs working in fields related to those of NORBIS may now sign up as post-doc members and enjoy the benefits of prioritised access to, and the possibility to apply for funding to join, NORBIS courses and workshops. In return, NORBIS expects post-docs to agree to list your project and areas of expertise in a database at the NORBIS web page, and to thereby pose as potential mentors and advisors for our PhD student members.
Read more and apply for membership here!
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:
||Memorial University of Newfoundland
|| 4 months, Sept 2018 – Jan 2019
||Edinburgh Genomics, University of Edinburgh
||3 months, Nov 2018 -Jan 2019
||École polytechnique fédérale de Lausanne (EPFL)
||6 months, June – Nov 2018
||London School of Hygiene & Tropical Medicine,
||4 months, July – Oct 2018
||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!
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