The ISBGroup Blog

The ISBGroup Blog

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Here you can read about everything that's happening in the ISB Group.

Ellen’s master thesis defence

EventsPosted by ISB Group Wed, January 23, 2019 14:53:04

Today, Ellen Lesshammar defended her master thesis project: ‘Mathematical modelling of TLR4-activated macrophages in inflammation’. The project aimed to use a model-based approach to investigate the synthesis and release of cytokines from macrophages during inflammation and also when inflammatory response is suppressed by anti-inflammatory drugs. The models Ellen constructed have the potential of being further refined and extended to include other aspects of inflammation and might thus hold the possibility to contribute to the further understanding of inflammation and how it can be the root cause to several common diseases.

The work was done here in the ISB-group but also at the Linköping based company Wolfram MathCore. We would like to congratulate Ellen on a job well done, and we wish her luck with all future endeavours!

Nicolas’s master thesis defence

EventsPosted by ISB Group Mon, December 03, 2018 14:56:21

Nicolas’s master thesis defence

Last week a member of our group held his master thesis defence. The member in question was Nicolas who has been doing in his master thesis in our group, as well as some work prior to that.

Nicolas hold a well-structured and informative presentation of his work and defended his thesis in a great way.

Nicolas project aimed to characterize the metabolic fluxes of carbon-13 labelled metabolites throughout parts of the metabolic system. The fluxes were determined from the structure of the metabolites in the end of the metabolic system. By knowing the reactions in the system and the number of intermediate products from the inserted labelled metabolites, one can determent the fluxes between the reactions. This method is called metabolic flux analysis. Although this is to hard math to do by hand, one can use mathematical modelling.

The second part of Nicolas project was to validate that his model could accurately predict the quantities of the metabolic fluxes. However, today, there is no established method for this kind of validation. Nicolas validated his model by the model’s ability to predict a validation dataset, data that the model have not seen before. By using this approach, one wish to see how the model react to new data and judge the model quality by how true the model’s prediction of this data is.

Additionally, the uncertainty of the predictions was analysed with a profile likelihood analysis. With such predictions, one can place more trust in fluxes determined by the model. Consequently, this allows for more challenging issues to be tackled in the development process of new treatments.

With this we want to congratulate Nicolas on his completed master thesis and wish good luck in the future.

New PhD student

NewsPosted by ISB Group Wed, November 21, 2018 13:20:01


My name is Tilda and I have been in the isb group before, but this November I started my phd here. I am financed by an EU project called precise4Q. The project aims at personalising treatment of stroke by developing model-based decision support systems. I will be working with combining mechanistic multi-level models and machine learning models.

3th national diabetes summit

EventsPosted by ISB Group Wed, November 21, 2018 12:16:27

On November 16th and 17th Gunnar, Elin, William, Tilda, Christian, Kajsa and Jonna attended the 3th national diabetes summit in Stockholm. During this conference the Karolinska institute was the scene of many interesting conversations, posters and presentations.

The program consisted of many interesting presentations covering various aspects of diabetes research. Our group was represented with, apart from a poster, a very nice talk by Elin. We have had many interesting conversations with other researchers that may lead to some very nice collaborations. For me personally the conference was a unique chance to see what kind of diabetes research is performed in Sweden.

Since the end of November is approaching rapidly my time in Sweden is almost coming to an end. I look back at a very nice time in Sweden were I’ve learned a lot about modeling and applications of modeling to the liver. And of course my new knowledge about things like Fika and warm meals during lunch ;)

Regards, Jonna

Ph.D defence of Belén Casas

EventsPosted by ISB Group Fri, November 16, 2018 13:19:11

Last week we attended the Ph.D defence of Belén Casas, who has worked with our group during her research.

It was a pleasure to listen to the great presentation of her work and her defence. A short description about her work follows below.

Belén’s work aimed at improving the current diagnostic tools in the field of heart diseases. By analysing data gathered from using 4D flow-MRI (a technique with 3D time resolution and phase contrast magnetic resonance imaging) with mathematical models, Belén has developed tools that can be of help to improve a subject specific assessment of a patient’s cardiovascular function.

After a successful defence, there was a celebratory afterwork in Belén’s honour. We want to take our time to congratulate Belén to her well-deserved Ph.D title and wish her good luck in her future work.

Links to published articles
Briding the gap between measurment and modelling: a cardiovascular functional avatar

Non-invasive Assessment of Systolic and Diastolic Cardiac Function During Rest and Stress Conditions Using an Integrated Image-Modelling Approach

New money, from VR, SSF, H2020, and AstraZeneca

NewsPosted by Gunnar Cedersund Sun, October 28, 2018 16:57:59

We have gotten money - and lot's of it!

While on a 6h train ride between Malmö and Stockholm, I at last have time to share some of the good news that have come to us, one after the other, but that I haven't had the time to share with you here until now. The good news is that we have had a series of successful grant applications, which mean that we now have reached a whole new level, in terms of money flows, and that our group will significantly grow in the next 2-3 months.

This new money flow actually started about a year ago, when I got money for a new 2 year postdoc position from AstraZeneca, i.e. approx 3 MSEK (300 000 USD). In this postdoc, we will create models for a new type of animal-free experiments, called organ-on-a-chip. In this technique, you build a system of realistic 3D organs made up of human cells, which are interconnected by an artificial blood flow. This is a supercool possibility, which is ideal for both modelling, for replacing animal experiments, and for understanding diseases.

This grant was then followed by a new EU project, called PRECISE4Q, which was approved in January this year. In this project, we will make use of our multi-level mathematical models for diabetes and cardiovascular disease, to create a new clinically useful tool. The basis of this tool will be quite general, and applicable to a wide range of diseases, but the focus will be on helping patients who have or who are at risk of suffering a stroke. The total budget of this project is 60 MSEK (approx 6 million USD), and of that approx 4 MSEK goes to my group (400 000 USD).

After that, during the spring, I used these already approved projects to write applications about other projects, which could build upon my already approved projects. And this too has now started to bear fruit.

First off was an application to SSF, the Swedish Foundation for Strategic Research. They have awarded me and a researcher from Karolinska Institutet in Stockholm (Roland Nilsson) a grant of 7.5 MSEK in total, out of which I will receive 3.5 MSEK (~350 000 USD). The topic of this project is to use my modelling to extract quantitative fluxes for all of the metabolic reactions in a cell; this is possible because of Roland's unique experimental skills, where he tags metabolites outside of the cell with C13 carbon molecules, and then uses mass spectrometry to measure where these tagged carbon molecules ends up in all in metabolites inside the cell. We will use these money to both transform this tool from a big potential to something that is useful in practice, and then also to apply the technique to understanding both metabolic diseases and cancer on a new level - useful for both research, drug development, and diagnosis.

The last major grant we got, and just a few days ago, this Thursday, was from VR, the Swedish Research Council. This high-prestige grant builds upon my previous collaboration with AstraZeneca, and will allow us to spend 4.2 MSEK (420 000 USD) to further strengthen our collaboration with AstraZeneca. More specifically, we will make use of the new and more complete models developed within the PRECISE4Q EU network (mentioned above) to understand how a brand new diabetes drug, dapagliflozin, works, and if, how, and when it can be used to also treat cardiovascular diseases like stroke, heart attack, and heart failure. This project will also allow us to understand more about which patients that should have which treatments, and more about the different mechanisms at play in the newly sub-divided grouping of diabetes into 5 sub-types.

One very good aspect of this new situation is that we are really well-prepared for it. This is due, in part, to some very useful grants we have gotten from the Swedish Foundation for Research without Animal Experiments. Using this money, we have been able to train talented undergraduate students in real research projects, which they have done in parallel to their M.Sc. studies, by awarding them scholarships (several of the recent blog posts have been devoted to presenting new such students). These new, and previous old, such quite unique students are now ready and eager to start as Ph.D. students, and they are much more well-trained than normal applicants would be, which we could find in normal open announcements. For this reason, we already now know that we will be able to fill all of the new positions with really great people, and are therefore looking much forward to working with for, at least, the next 4-5 years. However, all of the new positions will be announced in open competition, so if you are a great candidate, who wants to join our group, don't hesitate to apply, or to contact me for discussions on joint collaborations or positions.

All in all, it is also a very great feeling to suddenly have such much money now at our disposal. And also quite humbling. Now we need to really demonstrate to our funders that we can convert these great money into the equally great research we have described in our visionary applications. Into research that will be useful for both other researchers and for those who want to develop and use new and improved treatments - both treatments such as drugs, and treatments such as yoga and meditation. It will be great fun to enter this next step in our group's development!

This is a picture of our group during a recent group meeting. Not all were there, but most of them were. Some of the people in the picture are excellent M.Sc. students in the end of their studies, who we now can offer 2 Ph.D. positions. Apart from that, we will hire two new people, one new Ph.D. student, and one postdoc, but also those will probably be recruits building on previous collaborations and projects. To help as manage all of these new people, we are also very fortunate that Gunnar's second-in-command in the group, Associate Professor Elin Nyman, now is due to come back after an almost 2.5 year long leave in Harvard, Portland, and an almost 1 year maternity leave. For all of these reasons, made possible thanks to the new money described in the post above, our group will now take a step up to functioning on a new level - one with more senior people, more people financed fully by the group itself, and with long-term funding secured. Now we will be able to fully focus on all of the great research projects we are working on, without worrying if the money will ebb out in the middle of the project!

Retreat Liu Circ-M

EventsPosted by ISB Group Fri, October 12, 2018 14:59:02
At the time of writing some members of the ISB-group (Henrik, Kajsa and Gunnar) just returned from attending the retreat of the research network CircM. Here they took part of presentations born from the network, one of which Gunnar took part in. Discussions of how the network can move forward with new ideas and challanges were also a part of the agenda.

We enjoyed the retreat, which took place outside Norrköping, and we are glad that we could take part of the presentations and discussions during the retreat.

Down below we leave you a link if you want to check out CircM and get into contact with the network.

Regarding the picture down below, the wheater was unaccounted for, and an idea of a picture with Bråviken as background, turned out to be one with a nice forrest background instead.

New student - Kajsa

NewsPosted by ISB Group Tue, September 11, 2018 11:28:30


My name is Kajsa and I just finished my bachelor at the engineering biology program. This autumn, and maybe the spring, I’m joining the research preparatory course. I´m also teaching in a beginners programming course at campus Valla, so I will spend some time there as well. In my spare time I like to stay active, which includes everything from movie nights to climbing Sweden’s highest mountain Kebnekaise.

Here in the ISB group I will get the chance to continue with the project I was involved in during the bachelor. In the bachelor project we created a new liver model describing fatty acid conversion. Now, I will continue the work of the previous students Valentin Kindesjö, Thirza Poot and Johanna Fridberger to put together a model that describes fatty acid and glucose fluxes during the day and how it’s affected by different factors such as insulin and cortisol. My main focus will be at the fatty acid part and I will continue to work on my liver model as well as Valentin’s adipose- and cortisol module, which all will be parts of the bigger model.

I will also look at newly published data on body fat distribution in connection to diseases such as type 2 diabetes and coronary heart disease. A future goal is to connect the data to our models and being able to describe how the fatty acid homeostasis is affected by stress factors such as disturbed cortisol levels and why this in some cases cause diseases. By doing this, we are getting closer to simulating clinical studies and predicting diseases.

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