28. October, 2020
Friday 30th at 10:15, NORBIS PhD member Xiaokang Zhang is defending his PhD thesis entitled “Biomarker Discovery Using Statistical and Machine Learning Approaches on Gene Expression Data”.
To follow his defense, see who have defended their thesis lately and who will be next, please see our Dissertation site.
28. October, 2020
The 6th NROBIS Annual Conference will due to the Covid-19 situation be different than normal years. This year we will organize the conference as a hybrid meeting over one and a half days. We plan for the meeting to be streamed online and the different partner institutions that can, arrange a local gathering for those who will/can meet in person. This depends on local restrictions.
We also want to encourage supervisors and other researchers to join our meeting, both to facilitate discussion across several levels of experience, to inspire our students, and to increase your own national network.
We have student talks, poster sessions and keynote speakers. See program HERE.
22. October, 2020
Last winter I was able to spend 6 months at the Daniel Segrè lab at Boston University thanks to financial support from NORBIS and SINTEF. I arrived on October 1st 2019, in time to enjoy the fall season with beautiful colors, nice weather and good opportunities to explore Boston.
Because I found it difficult to decide on a long-term housing option prior to my arrival I spent the first 10 days in an AirBnB that was a bit too far from the city center. Due to the extreme number of Universities in Boston housing is very expensive, and it was difficult to find something that was acceptable with respect to price and standard. After nearly being scammed twice in my effort to find an apartment on craigslist, I finally found a reasonable long-term flat through https://junehomes.com/ that I shared with 5 other. This worked surprisingly well.
Figure 1: Watching Boston Bruins beat Vancouver Canucks at TD garden.
Daniel Segrè hosts a moderately sized group (8 PhDs and 2 researchers) that works both experimental and computational aspects of microbes and microbial interactions. The quality of their work was impressive and it was very motivating to collaborate closely with these people. I learnt a lot of microbiology and ecology from the group meetings and journal clubs. Another cool aspect of working at Boston University is the proximity to other top-notch research institutions and therefore easy access a lot of relevant conferences, meetings or other research groups. To get the most out of my research stay I wanted engage in their ongoing projects and I ended up studying the fascinating phototrophic marine bacteria Prochlorococcus (preprint on BioRxiv) using an updated genome-scale metabolic model. To understand how the metabolism of Prochlorococcus is affected by nutrient limitations and diel cycles we simulated growth using COMETS. To facilitate these simulations we developed light absorption and time-dependent light availability as new features in COMETS (read about the recent COMETS release on arXiv).
My research stay ended abruptly with the arrival of covid-19, but I was satisfied with my stay. I can highly recommend a research exchange to Boston. I addition to great science, Boston also offers an active running community and reasonable access to (disappointing) skiing in winter. The public transport is average, the traffic is one of the worst in US, but the city is small enough that you can easily bike anywhere. By a refurbished race bike at https://bikesnotbombs.org/ if you want to get the most out of your stay.
Figure 2: There is also good skiing in North America, but not close to Boston.
16. October, 2020
NORBIS has gotten a new director!
On October 1st, professor Susanna Röblitz took over the position as director of NORBIS. Susanna is a group leader at Computational Biology Unit (CBU) at University of Bergen (UiB). Her research group focuses on the construction, simulation, analysis and optimization of dynamic, mathematical models for biological and biochemical processes on different levels of organization. You can read more about Susanna and her research at CBU and UiB.
We would like to thank our former NORBIS director, professor Inge Jonassen, and we are happy that he will continue to be a part of the NORBIS family as a member of our scientific advisory board (SAB).
22. May, 2020
To present some of the work done related to the novel disease Covid_19, NORBIS is arranging a webinar mini-series.
First lecture is May 27th at 12.30. The lecturer is Kyrre Lekve from Simula Research Laboratories and topic is “Smittestopp”. Kyrre Lekve is Deputy Managing Director at Simula Research Laboratories and also member of the NORBIS scientific advisory board.
Second lecture will be June 17th at 11:00 by Inge Jonassen, professor at CBU/UiB and director at NORBIS and head of ELIXIR Norway. Topic for this lecture is “ELIXIR – sharing of biological data – and efforts linked with the Covid-19 pandemic”.
Registration for the webinar miniseries can be found HERE.
6. April, 2020
With the support of NORBIS, I visited Professor Bernhard Palsson’s group, Systems Biology Research Group, in University of California, San Diego, USA, from September 2019 to February 2020.
The original plan was actually from May to November 2020, but my application of the US visa was pending in the so-called “administrative process” for four months. But this delay took me to UCSD right at the beginning of the new semester. There are good and bad of that: good thing is that there were lots of welcoming activities on campus; bad thing is that accommodation is in short, especially the flights and (temporary) accommodation were almost booked at the last minute because I couldn’t make any travelling plan before I got the Visa, and the long-term accommodation was booked after I arrived there when most of the resources had already been reserved by the freshmen. So advice from me will be: plan ahead and start the paperwork early.
Bear at Jacobs School of Engineering, UCSD. Photo: Xiaokang Zhang
The campus of UCSD is in La Jolla, 20 minutes’ drive to the north of San Diego downtown. Everything in La Jolla is far away from each other. Even though it’s a good opportunity for walking since it’s very sunny almost the whole time (and for Bergen, it’s rainy or cloudy almost the whole time 😉 but walking from my apartment to the campus is 40 minutes, and another 40 minutes to the nearest supermarket. Public transportation is sort of useless. But that’s a common problem for the people who don’t have a car, so carpooling is very popular. So that problem can be naturally solved after you make enough friends.
My main job there is to continue our collaboration which already started one year before I went there. Carrying particular questions in mind, my work started immediately after I arrived. The first problem solved was visualization of our draft reconstruction model. With the help of Zachary A. King, the main developer of Escher (https://escher.github.io/#/), and the others in the Escher group, our ugly and messy metabolic map was replaced with an elegant and informative Escher map. From there, I worked closely with Daniel Zielinski to explore the draft model. Our work was later presented in the conference Winter Q-Bio 2020 (https://w-qbio.org/), and will also be included in the manuscript currently in preparation from dCod project (https://www.uib.no/en/dcod).
Besides the project mentioned above, a paper from our previous work (An Ensemble Feature Selection Framework Integrating Stability, DOI: https://doi.org/10.1109/BIBM47256.2019.8983310) was accepted as conference proceedings paper in BIBM 2019 which happened to take place in San Diego two months after I went there. Another manuscript was also finished and submitted to BMC Bioinformatics during my stay there, and it was accepted just before I came back to Bergen (RASflow: an RNA-Seq analysis workflow with Snakemake, DOI: https://doi.org/10.1186/s12859-020-3433-x).
NCAA football match UCLA vs. CAL. Photo: Xiaokang Zhang
By attending the group meeting every two weeks and the group’s winter retreat day, I got to learn the many interesting research topics going on in the group and was also shocked by the large publication number shown in the annual summary on the group retreat day.
Overall, it was an excellent research visit with lots of research input and output, and also lots of cool friends, good food, beautiful beaches, sunshine.
Laguna Beach. Photo Xiaokang Zhang
18. March, 2019
The workshop Towards in Silico-Guided Clinical Trials in Cancer
to be held in Oslo, 15-16 May 2019 at Scandic Holmenkollen Hotel.
We bring together experts in systems medicine, mathematical oncology and bioinformatics to discuss novel concepts for personalise cancer medicine. Check the workshop website for more details and for registration: https://osloinsilico2019.weebly.com/
- Robert A. Gatenby, Moffitt Cancer Center, USA
- Ivo Gut, Centre for Genomic Regulation, Spain
- Francesca Buffa, University of Oxford, UK
- Gyan Bhanot, Rutgers University, USA
- Peter Van Loo, The Francis Crick Institute, UK
- Sampsa Hautaniemi, University of Helsinki, Finland
- Wenyi Wang, MD Anderson Cancer Center, USA
- Haralampos Hatzikirou, Helmholtz Center, Germany
- Dominique Barbolosi, Aix Marseille University, France
- Rebecka Jörnsten, University of Gothenburg, Sweden
- Mark Robertson-Tessi, Moffit Cancer Center, USA
- Julia Casado, University of Helsinki, Finland
- Kevin Leder, University of Minnesota, USA
- Shridar Ganesan Rutgers Cancer Institute, USA
- Peter A. Fasching Erlangen University Hospital, Germany
- Jasmine Foo University of Minnesota, USA
- Alvaro Köhn-Luque, University of Oslo, Norway
Registration is free but mandatory in a first come first serve bases for up to 75 participants. It includes two full days of lectures, lunches and coffee breaks with refreshments (thanks to funding from BigInsight, UiO: Life Science, NORBIS, Norwegian Biochemical Society and Digital Life Norway).
We hope many of you will join. If so, you should register as soon as possible. Also, we would be very grateful if you may share this information among potentially interested students and colleagues.
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.