Past Events

OCTOBER-SEPTEMBER 2010

• September 13, 15.30-17, Martin Adiels, Gothenburg University, "Whole-body models for fatty acid homeostasis", Hälsans hus, lärosal 1, (map)

• September 17, 10.15-12, Jan Hasenauer, University of Stuttgart,  Tutorial in the set-identification matlab toolbox, HUB8, (in the HU library).

• September 20, 15.30-17, Jan Hasenauer, University of Stuttgart, "Guaranteed predictions in spite of limited knowledge and uncertainties? - A case study for the NF-kB signaling pathway", Glashuset, B-house, Campus Valla

  Abstract:
  The main goal of system biology is a quantitative description of cellular processes and the understanding of those. Unfortunately, achieving this aim is rather difficult, as models of biological systems are subject to a significant degree of uncertainty. This uncertainty arise from limited knowledge about the system, mostly due to limitations in the experimental technology, and/or large variations in environmental and internal boundary conditions. The uncertainties become manifest in a only partially known interactome as well as unknown parameter values. 
   
  Despite of these uncertainties, in particular the revealing of key signaling mechanism is often possible. In this presentation an approach is introduced which allows the analysis of key properties of biological networks subject to uncertainties. Furthermore, the approach allows us to make guaranteed predictions. The methods are illustrated by studying a model of the NF-kB signal transduction pathway, involved in anti-apoptotic signaling.
• October 10-15, 2010, International Conference of Systems Biology, Edinborough, UK, (link)

June 2010

• June 3-5, 2010, Systems Biology of Mammalian Cells, Freiburg, Germany (link). Elin Nyman and Gunnar Cedersund will give the oral presentation: "Combined top-down and bottom-up modelling provides internally consistent explanations of whole-body glucose homeostasis through the identification and elimination of data inconsistencies and missing regulations" Rikard Johansson will present the poster "A two-dimensional boostrap method for model discrimination", Gunnar Cedersund will present the poster "Mass and information feedbacks through receptor endocytosis govern insulin signaling as revealed using a parameter-free modeling framework", and Eva-Maria Hansson will present the poster "Towards a mechanistic explanation of the causes of insulin resistance in type 2 diabetes, which incorporates mTOR, autophagy, and mitochondrial dysfunction".

• June 26-July 1, 2010, 35th FEBS Conference, Gothenburg, Sweden (link) (special focus on systems biology this year). Gunnar Cedersund and Marcus Krantz will present the short talk: "Mapping cellular signal transduction", in Section B3 - Global networks, June 29 at 13:00.

• June 7, 15.30-17 Maria Bartholome Rodriguez, Freiburg University, Germany, "Towards mathematical modelliing of insulin induced signalling in hepatocytes: The point of view of an experimentalist." Conradsalen (HU, main house, A-elevators, floor 11, right in the corridor) (map)
  Abstract: 

  The enormous regenerative capacity of the liver is unique among mammals. Strikingly, during this intensive phase of proliferation, hepatocytes continue to ensure their essential metabolic functions such as glucose regulation, degradation of toxic compounds, and synthesis of proteins. The hormone insulin is an essential factor in all these processes. The complexity and the unique effects of insulin in the liver are the particular concerns in which our group has been involved over the last years. Thus, the peculiarities of the insulin signaling in the liver will be focal point of my talk.  I will give you first a short overview of our efforts concerning the detailed recovery of dynamic, spatially resolved and reproducible high quality experimental data on insulin-induced signal transduction in primary murine hepatocytes, involving several experimental techniques. Second, I will concentrate my talk to the experimental steps involved in constructing a mathematical model for the complex dynamics regulating the activation of the insulin receptor - a key molecule for insulin signalling in the liver.

• June 8, 10.15-12 Cecilia Brännmark, isbgroup/IKE, will defend her mid-term Ph.D. thesis "An integrative systems biology approach to insulin signaling" Hälsans hus, Lärosal 1, (map) Paper 1, Paper 2. Opponents: Roland Nilsson (KI, Stockholm, Sweden; Harvard, Boston, US), Maria Bartholome Rodriguez (Freiburg Klinikum - Freiburg, Germany)

  • June 9, 13.15-14 Amanda Jonsson, isbgroup/IKE, will defend her M.Sc. thesis "Modelling frameworks for cellular signalling". Conradsalen (HU, main house, A-elevators, floor 11, right in the corridor) (map)

    Abstract:
    Type II diabetes is one of many diseases that are coupled to dysfunctional information processing on the cellular level. Such cellular information processing is carried out by highly complex protein networks, and this complexity is the main reason why mathematical models are becoming increasingly useful in the area of cell biology and drug discovery. The most widely used modeling framework is ordinary differential equations (ODEs). However, to be able to formulate ODE models, a detailed knowledge of the system is needed. As data are often sparse, and as high confidence prior knowledge is in general missing, alternative modeling frameworks are in many cases advantageous, and can serve as a useful complements to ODEs.
        We here present an evaluation of different modeling frameworks, with focus on Boolean Networks and Bayesian Networks. A survey of the properties of the frameworks as well as a re-analysis of models previously built using ODEs is performed. Boolean Networks, which constitute a rough and less detailed modeling framework than ODEs, have been used to create middle-sized networks of the early insulin signaling events involving a few down-stream mediators in the insulin signaling pathway. Bayesian Networks, which are fundamentally different from both ODEs and Boolean Networks, have been thoroughly investigated. An attempt has been made to re-create predictions from a formerly created ODE-model in a Bayesian Network framework. Our experience is that Bayesian Networks may not be able to give as specified predictions as ODEs, but that they are useful in situations where Boolean Networks and ODEs both fail.
        In summary, all modeling frameworks have their strengths and weaknesses, and depending on the question, available data, and prior knowledge, different frameworks should be chosen. As a final step, the insights gained through the evaluation of modeling frameworks have been used to create a recommendation on how different types of information can be put together into a meaningful modeloriented database, and how to link this database to the creation of a multi-physics adipose tissue module, in which different modeling frameworks can be combined.

May 2010

• May 7, 9.30-16, Presentation day with ISB-group (open for all), see www.isbgroup.eu, Hälsans hus, Lärosal 1, map
• May 11, 16.30-17.15, Gunnar Cedersund gives a lecture at the Ph.D. course SIMON, "What can you do with your relaxation data. A systems biology approach." Conradsalen (map)
• May 17, 15.30-17, Roland Nilsson, Harvard/Karolinska Institutet, "Discovering regulators of metabolic pathways through large-scale integration of gene expression data" Almen, HU, (map, map2 entrance 65, directly up to the right))

Abstract:
As whole-genome expression profiling has become increasingly affordable, publicly available repositories of microarray data are expanding rapidly. Still, a large fraction of the enormous information content in these databases remains unexplored. In this talk, I will discuss data integration techniques allowing us to take advantage of this data to discover new components of metabolic pathways. Specifically, we have developed a technique that systematically searches data repositories for genes that are consistently and specifically co-expressed with a pathway of interest. Using this method, we have successfully identified five proteins as required for functional heme biosynthesis, and a novel regulator of oxidative phosphorylation acting on mitochondrial mRNA.

• May 19, 14-14.45 Mikael Benson (Gothenburg University, leader of 2 systems biology FP7-networks) will present his research, "Kan nätverksbaserad analys av genomik data användas för att skräddarsy mediciner?" (might be in Swedish), Library of Children's clinic, level 15, Campus-US, Hospital main building
• May 20, 15.15-17, Student presentations from the project course TSRT17, 3x10 min presentations from projects related to systems biology of type 2 diabetes and insulin signalling, and 2x10 minute presentations from projects related to image analysis using MRI to diagnos liver and brain. The last hour contains a poster session. C3, C-house, Campus Valla (map)

Earlier than may 2010
 

Mika Gustafsson will defend his dissertation

“Gene networks from high-throughput data – Reverse engineering and analysis” two weeks from now. The thesis can be found at DIVA.

Time: Friday 26 March 2010 at 13.15

Place: Kåkenhus, Campus Norrköping, lecture hall K3 (Önnesjösalen)

Opponent: Prof. Reinhard Guthke, Jena

You are all most welcome.

Michael Hörnquist, itn