The ISBGroup Blog

There is a now a first postdoc position open in the new X-HiDE project, of which we are a central part. X-HiDE is a new major systems biology center that is about to launch in Sweden, which recently got a major grant of 12 MEuro, over an 8 year period. The topic will be systems biology of immunology. The over-arching goal is to build up a comprehensive and re-usable model, to be useful as a module in other models for a wide variety of diseases associated with dysfunctional inflammation: cardiovascular disease, auto-immune diseases, NASH, COPD, diabetes, cancer, etc. There are more than 10 experimental and clinical partners on board, which all will contribute with data and biological/medical expertise. Apart from this, a number of large and small companies are on board as co-funders, including e.g. AstraZeneca, and Wolfram MathCore. This particular postdoc is focused on modelling, and the main expertise sought after is data-driven mechanistic modelling (typically done using ODEs).

Because of the existence of the long-term substantial funding, there will be more similar modelling positions opened up later, including a soon to be announced more senior tenure-track position. These early positions will be excellent opportunities for junior researchers, who want to be a part of building up a new systems biology center.

NOTE: Deadline for this first postdoc position is midnight September 1 CEST!

/Gunnar Cedersund, leader of X-HiDE’s workpackage on modelling

We have several master-thesis and internship students working in our group this spring. Here is a small introduction!

Gustav Magnusson
I’m a master student in Physics with a hope to contribute something to the world of Systems Biology. The aim of my master thesis is to work with the Digital Twin, to put together the various models produced here at ISB to form an interface for users such as patient and researchers to test various situations and hypothesis. The goal is also to work on my own model which could be a part of the Digital Twin, perhaps with focus towards phyisical training, atherosclerosis or the immune system.

Lucas Raihle
Hi! I’m Lucas and I will be interning at ISB group during March-September. My project will revolve around making a model that can describe how diet affects the progression of NAFLD (non-alcoholic fatty liver disease). NAFLD is the most common liver disease in the world and is heavily correlated with the metabolic syndrome. Understanding the progression of NAFLD could lead to more effective forms of treatment and diagnosing. I’m happy to join this group and excited to start my project.

Johanna Hansson
Hi, my name is Johanna Hansson and I have just started an internship at ISB group. I will be working on a project to describe the disease progression of atherosclerosis to stroke and how the consequential oxygen loss affects the brain function. First, I will develop a mechanistic atherosclerosis model and later connect it with existing models of e.g. blood flow and stroke. Understanding atherosclerosis and its relationship with stroke could help predict who is at risk of having one. With that knowledge, we may be able to prevent the stroke from happening and save lives. I will work on my project for 6 months and I am excited to see the result!

Jonatan Baggman
Hi! My name is Jonatan and I’m doing my master thesis here at ISB group this spring. For my master thesis I’m looking into imputations for the Digital Twin, how to estimate the input values which are not measured directly from the patient. I will look into different methods of imputation and will compare these. Hopefully, I will be able to present how to make the Digital Twin personalized without measuring all values from the patient!

Elin has received two substantial grants, from the Swedish Research Council (VR) and from the Center for Industrial Information Technology (CENIIT). Both grants are given to young and promising researchers.

VR-NT From omics to patient specific simulations (950 000 SEK per year for 4 years)
CENIIT Executable models for drug development (450 000 SEK per year for up to 6 years)

Today, Therese Alenvret presented here master thesis on how health information from the clinic and/or different mobile devices can be retrieved and modeled to be used by our digital twin. So now we now more about the posibilities and challanges with accessing personal data to the digital twin. Good job Therese!

With the summer long gone, and a new term in full swing, it is time for a very late and past-due update post! The autumn of 2019 was hectic, exciting and rewarding! The year started off with the addition of three new group members, two PhDs and a post-doc (more about this further down). We also started our to date most collaborative effort, which was to connect (almost) all of our existing models. The first phase of this project culminated in a fully packed event at the Almedalen week in the beginning of the summer, but more about this in a later blog post.

The group has grown. We have had several new (but old) additions. Both me (Christian Simonsson) and Nicolas Sundqvist, both previous master-thesis students in systems biology, started PhD-positions in the group. Here’s a short update from us. I’m finishing up my projects concerning the metabolic syndrome and I have just started new projects concerning disease progression in the liver (ASH/NASH).  Adding to this, I will spend half of my PhD working at the Division of Radiological Sciences (RAD) in the group of Peter Lundberg, doing clinical research. Right now, I am analyzing MRE data for patients with suspected liver fibrosis. Nicolas is continuing his work with metabolic flux modelling, but he has also branched out, and is now doing modelling of fMRI data and brain metabolism in the group of Maria Engstrom. Also, Belen Casas is doing her post-doc in our group. Her post-doc project concerns mechanistic modeling of MPS-systems.

Three talented internship-students have just ended their one year stay with us. Kajsa Tunedal has worked with several projects, including modelling of NEFA circulation and uptake in the liver, and modelling of cortisol levels in relation to stress. Henrik Podéus has worked with connecting several models describing the different aspects of the neurovascular coupling in collaboration with Sebastian Sten (PhD in Maria Engstroms group). Anton Tornerefelt has with collaborators from Örebro’s University created a model of Macrophages activation. You all have done great work and we wish you the best of luck in all your future endeavors!

Here is two of our latest group photos! The latter is from our latest group retreat, which took place at the beautiful Omberg eco-park.

Two exciting days of biomedical engineering just ended after our division hosted the annual MTD conference. The purpose of MTD is to be the most important meeting place for medical technology in Sweden. Where all key stakeholders; researchers, company representatives and medical experts can meet and discuss important questions. Our presence was at the digitalization of healthcare track where our PI, Gunnar, held the opening talk. He presented our group vision of personalized medicine: digital twins – physiologically based, personalized, simulation models to be used in healthcare. Also, Elin and Tilda each had poster presentations representing modelling research. All in all, two good days where we could showcase our research vision to the Swedish biomedical community.

Hello, my name is Antonia and I’m the new intern in the ISB group. My research project is about the dietary effects on acute and chronic inflammation in the human liver, and also how exercise and muscle growth is affected by switching diets. The state of the liver is strongly associated with both physical activity and your dietary habits, therefore it’s quite relevant to look at these two factors and how they could affect the liver. My focus will be on the switching from an omnivore to a strict plant-based diet. Since I’m vegan myself, I thought it would be interesting to do a project that is connected to my lifestyle. I’m planning on working on this project throughout the whole year and I’m excited to see how it goes!

This week we are going to Medicinteknikdagarna – a conference for medical engineering here in Linköping (at Konsert & kongress). We have a presentation on Wednesday 13:30 and we have two posters. We will also be present in the LiU monter. The poster session and LiU monter is open for the public. Hope to see you there!

Info about the conference: https://www.mtf.nu/event/medicinteknikdagarna-2019/