UiB Blogg            

International exchange report from Xiaokang Zhang

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

Report from exchange to École Polytechnique Fédérale de Lausanne (EPFL)

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.

Martin

Zhi Zhao’ research stay at the London School of Hygiene & Tropical Medicine

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

 

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. 

LagreLagre

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.

LagreLagreLagreLagre

Next Page »