It is my pleasure to announce that two projects which has modellers from the systems biology core facility involved has been chosen as this years flagship projects for CMIV (Center for Medical Image science and Visualisation). One is the SAND:MAN project, in which we are modelling the neurovascular coupling that is the link between the neuronal activity of the brain and the signal measured in an MRI scanner when we study the activity of the brain. This will give us a deeper understanding of how the brain works and how the neuronal signalling changes in different diseases and disorders of the brain.
The other project is the non-invasive liver biopsy (NILB) project in which we models how contrast fluid travels through the liver and how that differs between healthy persons and patients who have liver disease. This model is being developed into a tool that will help medical doctors make better diagnosis for their patients.
The flagship projects were presented at a seminar on the 29th of February at CMIV. The third flagship project is the Seeing Organ Function project, which is also connected to the SAND:MAN project.
All the new flagship projects will soon be featured with a more in depth presentation on the front page of the CMIV webpage.
I’m Tim
Beishuizen, a Dutch student at Eindhoven, University of Technology. Currently I
am doing a dual master’s program Biomedical Engineering and Computer Science
and Engineering. At the ending of my Bachelor Biomedical Engineering I was
wondering what to do in my Master phase. My interests were broad and so I
finally chose to study three more years in a combination of two masters.
After searching
a good place to have an internship, I came in contact with Gunnar Cedersund and
the ISB group. Soon after we agreed on a project for my internship I came to
Linköping and started the project. The project is a continuation of the Markus
Karlsson’s Master’s Thesis. It is about creating simplified models of more
complex models to reduce complexity and computation time, also known as
metamodeling. I particularly focus on partial least squares regression in
combination with non-linear mixed effects to retrieve the best results.
Aside from
the project I am in Linköping to see something from Sweden as well. I haven’t
been in Sweden before and would like to experience what it has to offer. Taking
a break from life in The Netherlands, I can meet new people and find out the
Swedish living style.
After taking almost 1.5 year Biomedical Engineering Master program here in Linkoping University, it is a new journey for me to join the ISBgroup to do my Master Thesis work. Differing from the daily courses I took before, working with people in ISBgroup is a brand new experience, the whole atmosphere is relaxing while they have a very precise attitude on academy.
Now I am working on the Multi-level modeling project which has very little in common with the knowledge I had before. However, it doesn’t become a problem due to the help from a two-week pre-course where some background information and basic skills were taught. Gunnar is the lecturer of that course and after taking it, I know it will be a very interesting period of time for me to work with this project and the people in ISBgroup.
My Master thesis started around the middle of the February and I’ll work on it for 4 to 5 months, with the help and cooperation with all ISBgroup members, the following time will be full of challenge and fun!
For the
last couple of years the students in Engineering Biology (TB) have done their bachelor’s
projects under our supervision. This year is no different! Right now the
students are finishing phase 1, where they are learning about systems biology
and how to implement, optimize, and analyze models. They are also right now
meeting their customers for the projects they will start on later this spring.
This year
we have four exciting projects. In the first project, the students will attempt
to unravel new insights of intracellular signaling in different tissues. They
will at the same time attempt to bridge the understandings of insulin signaling
with adrenergic signaling. The end-goal is to gain new knowledge of metabolic
and cardiovascular diseases.
In the
second project, the insulin-glucose dynamics at the whole-body level is the
focus. Three subgroups will work with variating glucose levels in the Intensive
Care Unit (ICU), the interplay between insulin, glucose and NEFA, and the long term
effects of antioxidants respectively.
In the third project, five students will work together to understand
important aspects of the immune system. By modeling both the transcription of
genes within T-cells, and by bench marking the algorithms to do so, important
aspects of diseases, e.g. allergy, can be explained. This work is
potentially important in a wide variety of applications, both for drug
development, diagnosis, and for understanding of the pathology involved in a
wide variety of diseases.
In final
project, five students will work in a combined effort to further improve the
current understanding of the fMRI-BOLD response and its underlying neurovascular coupling.
They will contribute towards explaining current research questions such as
blood flow regulation in ischemia patients, neural metabolism and potential
bio-markers for brain function. By this, we aim towards bridging the gap
between our modelling efforts and future clinical applications.
These projects
have been started already now but will take on full speed during the second
half of the spring. Three times the students will present their ongoing
findings, and during the final presentation this spring one group might find
themselves the winner of the yearly logo-competition.
Last years winners of the prestigeous trophy: “Improvement of a Mathematical Liver Model for Diagnosis and Surgical Planning”
2015 was the most expansive and important year so far, since we started, and there were many important things that happened.
The perhaps most important thing was that Gunnar Cedersund, the leader of the group, got a permanent position, a senior lecturer position (Swedish: Universitetslektor). This ensures that the group will live on for many years to come: Gunnar is bound to retire only in 2046, and the plan is to stay in Linköping and help lead this group at least until then! Apart from this, the new position also implied that Gunnar was elected into the board of our department. During 2015, we also recruited 3 new Ph.D. students: Markus Karlsson, Sebastian Sten, and Natasha Morales Drissi (see picture above). Markus will continue our work on MRI-based modelling of the liver, together with Peter Lundberg (who will act as main supervisor) and the other guys at CMIV. Sebastian and Natasha will focus on fMRI and how this can be combined with EEG data using mathematical modelling. Both of them will do both modelling and data collection, but Sebastian will focus mostly on modelling, and Natasha mostly on experiments. The main supervisor of both Sebastian and Natasha is Maria Engström.
In May of 2015, Elin Nyman was awarded a prize: “the best pre-clinical Ph.D. thesis published during 2014“. This prize is awarded by the Swedish association for diabetes research, and it is especially encouraging to notice that they think that our work om multi-level modelling of diabetes now is mature enough to really make a difference in the diabetes field.
Picture of Gunnar Cedersund giving a lecture at the award ceremony for Nytänkaren (photo by Anette Persson)
In December 2015, Gunnar Cedersund was awarded another prize: “Nytänkaren”. This prize is awarded by the “Swedish Fund for Research Without Animal Experiments“, who made a study visit in our group earlier in the year. During this visit, they became so enthusiastic over our results, and the general results of the field, that they decided to create a brand new award. Nytänkaren is a Swedish word, which means “The Innovator”, or “The Thinker of New Ideas”. This prize has also been reported in several news outlets, including the daily newspaper ETC, and Swedish television (see video below for English translation).
During the year, we also expanded and deepened our collaboration with AstraZeneca. This included the launching of several new projects, the publication of some first papers, and we also planned for the hiring of a new postdoc, to start in the Summer of 2016. Apart from this, Gunnar also gave a 3 day intensive course on systems biology.
In the summer of 2015, we had many internship students, and several of those have remained with us for the following year as well. A picture of our group during the summer is given below.
In the autumn of 2015, we spent 2 days in an internal workshop on the country side, to talk about joint decisions, ongoing work, and to create new visions for the coming years. Below you can see a few pictures from this event.
Finally, and perhaps most importantly, 2015 was also the year when we broke our own record in terms of number of publications: 4 published journal articles, 2 accepted journal articles, and 2 published book chapters. The full list is given below.
In summary, 2015 has been our most productive and expansive year: we have published the most number of publications, hired the most number of Ph.D. students, and received the most number of awards.
PUBLICATIONS (all were accepted during 2015):
Nyman E,
Lindgren I, Lövfors W, Lundengård K, Cervin I, Arbring Sjöström T, Altimiras J,
Cedersund G, Mathematical modeling
improves EC50 estimations from classical dose-response curves, FEBS J, 2015, 282(5):951-62.
Jullesson D, Johansson R, Rohini Rajan M,
Strålfors P, Cedersund G, Dominant
negative inhibition data should be analyzed using mathematical modeling:
re-interpreting data from insulin signaling, FEBS J, 2015, 282(4):788-802.
Karlsson M, Janzén DL, Durrieu L, Colman-Lerner
A, Kjellsson MC, Cedersund G, Nonlinear
mixed-effects modelling for single cell estimation: when, why, and how to use
it, BMC Syst Biol, 2015, 9:52.
Sips FL, Nyman E, Adiels M, Hilbers PA,
Strålfors P, van Riel NA, Cedersund G,
Model-Based Quantification of the Systemic Interplay between Glucose and Fatty
Acids in the Postprandial State, PLoS One, 2015,10(9):e0135665.
Schleicher J, Conrad T, Gustafsson M, Cedersund G, Guthke R, Linde J, Facing
the challenges of multiscale modelling of bacterial and fungal pathogen-host
interactions, Briefings in Functional Genomics 2016; doi: 10.1093/bfgp/elv064 (accepted during 2015)
Nyman
E, Rozendaal YJW, Helmlinger G, Hamrén B, Kjellsson MC, Strålfors P, van Riel
NAW, Gennemark P, Cedersund G, Requirements
for multi-level systems pharmacology models to reach end-usage: the case of
type 2 diabetes, J Royal Society Interface Focus, 2016, (accepted during 2015)
Cedersund G,
Prediction uncertainty: a comparison of recent method developments, in
Uncertainty in Biology, from Uncertainty in Biology, Edited by Gomez D and Tegnér
J, Springer-Verlag, 2016
Cedersund G, Samuelsson O, Ball G, Tegnér J, Gomez-Cabrero D, Optimization in
Biology: Parameter Estimation and the Associated Optimization Problem, from
Uncertainty in Biology, Edited by Gomez D and Tegnér J, Springer-Verlag, 2016
Our research is spreading and more people are becoming aware of the possibilities of systems biology!
A few weeks ago, we had a visit from the local TV news station, Östnytt. They had become interested in our work after reading about Gunnar’s award as “Årets Nytänkare” (Innovator of the Year) from the Swedish Found for Research Without Animal Experiments. More information about the award can be found here (only in Swedish).
I already joined the
ISB group last summer, but left in late August to travel some of the countries in Southeast Asia. A couple of months have now passed and I have now returned to
the office for another 5 months.
I first got
into contact with the group during my Bachelor’s thesis last year, where I was
part of a two-man team of Engineering Biology students who did a project
regarding adiponectin release in fat cells. I then applied for an internship at
ISB-group, got accepted and started in June 2015.
Since then I have been working with the minimization of a previously created mathematical
model aimed at describing the desensitization of G protein-coupled β2 adrenergic
receptors which are crucial
for heart muscle contraction.
As I
already stated, I took a break from science and my studies for 4 months to travel
in Southeast Asia. There, my days were spent with things like hiking through
the rice fields in the mountain regions of northern Vietnam, joining a Muay-Thai
training camp in Thailand, scuba diving and of course relaxing by various
beaches throughout the region. Although last year was an amazing experience I
could not be more thrilled to be back at ISB group to continue with my project and
hopefully reach more satisfying results than I did last summer.
If you like
to know more about me, meet me, poke me, see me or speak with me about anything you want – then come
find me during working hours at Gunnar’s office at floor 13.
As a Medical Informatics student from the Netherlands, I will do an internship project for 4,5 month at ISB Group. I arrived just three weeks ago and I already feel at home both at ISB Group and Sweden in general (as you can see in the photo).
My background consists of three years of Medicine bachelor (in Rotterdam, NL) and three years of Medical Informatics bachelor (Amsterdam, NL). I switched from my first to my second bachelor, because I missed the technical challenge a lot. This internship will lead to a thesis that will conclude the last-mentioned bachelor.
The project I am doing at ISB Group consists of the making of an advanced model for the prediction of cardiovascular disease in diabetes patients. Hopefully this predictive model will become more accurate and adaptive to the individual patient than existing models. In order to achieve this, a Bayesian network will be used, instead of the more common regression analysis.
I’m really looking forward to the rest of the months here in Sweden! Luckily there are lots of activities for internationals in Linköping, which you can also visit if you’re not in an official exchange program like me.
I’m Tim
Last years winners of the prestigeous trophy: “Improvement of a Mathematical Liver Model for Diagnosis and Surgical Planning”
Picture of Gunnar Cedersund giving a lecture at the award ceremony for Nytänkaren (photo by Anette Persson)
