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

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.

New Student- Jonna

NewsPosted by ISB Group Thu, September 06, 2018 11:56:14


My name is Jonna and I am a Dutch student doing my internship at the ISB group. I will be staying in Sweden to work on this project for 3 months. Back home I am a master student in the Medical Engineering program of Eindhoven Universtity of Technology. This externship is the final part of my master studies.

Previously I have done most of my projects on bioinformatics/data analysis so I am very excited to learn more about the systems biology modeling techniques. This project is a great opportunity to gain more modeling experience. During my time here I will be working on modeling the liver.

In my free time I like to swim and explore the city/area a bit since I am new in town. I’ve spent many of my holidays in Scandinavia (mostly Sweden) so I am very happy to be living here for a few months. I have had a part-time job in a swimming pool where I received my first aid certificate, which I used my first morning in Linköping during helping a patient in the street after a traffic accident in the city center. So my time in Sweden started out quit hectic, hopefully that is not a precursor to how the coming months will be.

I am looking forward to meeting all group members and working on the project within the ISB group.

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