Swedish research groups in Systems Biology
The list is not claiming to be complete, if you want to be listed here please contact us. It is intended primarily as an overview and for more detailed information go to the respective homepages. The groups are classified according to their systems level, however this classification may be a bit oversimplified: intracellular level, cellular networks, organism level, clinical systems biology
Intracellular level
Uppsala University:
PI Måns Ehrenberg
Research: We focus on the global and specific regulation of protein synthesis and its relation to bacterial growth and evolution. Our group in Uppsala has had a pioneering role in developing the theoretical and computational methods for analysis of stochastic aspects of intracellular kinetics, including noise in gene expression and spatial aspects of cell signaling.
Website: http://www.icm.uu.se/molbio/ehrenberg/index.shtml
PI Johan Elf
Research: To understand transcription factor mediated regulation in bacteria we are using novel single molecule in vivo imaging techniques in combination with biophysical modeling. Together with the Ehrenberg group our modeling efforts have been focused on global regulation and stress response in E. coli.
Website: http://www.icm.uu.se/molbio/elflab/index.html
Karolinska Institutet:
PI: Björn Öbrink
Research: Systems Biology of the Eukaryotic Plasma Membrane.
Our interest is to achieve a better understanding of the role of the eukaryotic plasma membrane in its role as a transducer and integrator of information obtained from the extracellular environment using the CEACAM proteins as models for signal transduction and signal regulation.
Website: http://ki.se/ki/jsp/polopoly.jsp?l=sv&d=6154
Stockholm University/Royal Institute of Technology:
PI: Erik Sonnhammer
Research: At Stockholm Bioinformatics Centre (SBC), which is shared between SU and KTH, several projects related to systems biology are ongoing. For instance, methods have been developed to integrate heterogeneous large-scale data from genomics, proteomics, and transcriptomics to reconstruct global networks of functional coupling between genes and proteins. These networks are available and queryable at http://FunCoup.sbc.su.se/ and represent the most complete networks for many higher eukaryotes. FunCoup has been used e.g. to find new candidate disease genes in cancer and neurodegeneration.
Website: http://sonnhammer.sbc.su.se/
Royal Institute of Technology:
PI: Elling Jacobssen
Research: With a basis in systems and control theory, our research aims at developing theory and tools for modeling, analysis and control of the dynamic behavior of biochemical networks. The focus is on facilitating the understanding of how dynamic interactions at the molecular level give rise to system level functions and properties such as robustness.
Website: http://www.s3.kth.se/~jacobsen/Sysbio.shtml
Chalmers University of Technology:
PI: Jens Nielsen
Research: Our research focus is on systems biology of metabolism utilizing Saccharomyces cerevisiae as our key model organism, but also Aspergilli (experimental and theoretical) and mammalian cells (theoretical). We are studying regulatory pathways conserved in the eukaryal kingdom such as Snf1/AMPK, Tor1, protein folding, secretion and apoptosis. We are also developing metabolic models for eukaryal cells with the aim of understanding responses to nutrients and disease. Thirdly, we are developing efficient cell factories for sustainable production of chemicals.
Website: www.sysbio.se
Göteborg University:
PI: Stefan Hohmann
Research: We are studying how the dynamic operation of signalling pathways is controlled and how the control of metabolism, signalling and cell growth and proliferation are controlled. In particular, the group focuses on the AMPK/Snf1 pathways, which control cellular energy homeostasis, as well as MAPK pathways, which control stress, hormone and nutrient responses and coordinate cell morphology and proliferation. The group has contributed to an understanding of pathway operation and feedback control mechanisms.
Website: http://www.gmm.gu.se/groups/hohmann/
Royal Institute of Technology:
PI: Anders Lansner
Research: Our group has a focus on modeling of neuronal networks and neurocomputing which we have developed since the 1980’s in close collaboration with experimentalists at the Karolinska Institute (KI) neuroscience division. Our current main focus is the study of dynamical processes related to memory storage and recall in cortical neuronal circuits using large-scale neuronal network simulations on supercomputers.
Website: http://www.nada.kth.se/~ala/
PI: Jeanette Hellgren-Kotaleski
Research: Our group is focused on modeling of the basal ganglia at levels ranging from intracellular biochemical pathways involved in synaptic plasticity to neuronal network models of the striatum, driven by input from neocortex.
Website: http://researchprojects.kth.se/index.php/kb_1/pb_850/pb.html
Swedish University in Agricultural Sciences:
PI Hans Liljenström
Research: My research is in the fields of theoretical biology and biophysics. It involves modeling biological (biochemical, genetic, neural, and ecological) networks, with an aim to relate structure, dynamics and functions of such networks. It also includes investigating the efficiency of biological processes, in the presence of internal and external fluctuations. Specifically, I have been modeling the olfactory systems of mammals and insects, with a focus on perception, learning and associative memory of odorous signals. I have also modeled and analyzed EEG signals, with relation to attention and mental disorders. Other scientific interests concern computation with complex dynamics, interactions between different organizational levels of biological systems and processes, and relations between brain and mind.
Website: www.et.slu.se/hanslil
Lund University:
PI: Carsten Peterson
Research: Our main focuses are on stem cell regulation in plants and animals as well as organ and cancer initiation and development. Both transcriptional regulation and spatial modeling techniques are employed and developed. Furthermore, bioinformatic efforts for network reconstruction are pursued.
Website: http://home.thep.lu.se/~carsten/
PI: Henrik Jönsson
Research: My main interest is to develop models for multicellular developmental systems in collaboration with experimental biologists. Included in this are models for gene regulation, molecular reactions and transport, as well as models for cellular growth and proliferation and mechanical interactions.
Website: http://home.thep.lu.se/~henrik/
References:
Developmental patterning by mechanical signals in Arabidopsis O. Hamant*, M. Heisler*, H. Jönsson*, P. Krupinski, M. Uyttewaal, P.
Bokov, F. Corson, P. Sahlin, A. Boudaoud, E. M. Meyerowitz, Y. Couder, and J. Traas Science 322, 1650-1655 (2008)
Self-organization in high density bacterial colonies: Efficient crowd control H. J. Cho*, H. Jönsson*, J. K. Cambell, P. Melke, J. W. Williams, B.
Jedynak, A. M. Stevens, A. Groisman, and A. Levchenko PLoS Biology 5, e302 (2007)
An auxin-driven polarized transport model for phyllotaxis H. Jönsson*, M. Heisler*, B.E. Shapiro, E.M. Meyerowitz, and E. Mjolsness Proceedings of the National Academy of Sciences USA 103, 1633-1638 (2006)
Umeå University:
PI Johan Trygg.
Research: Within Systems biology, we work alongside UPSC and FuncFiber Excellence centres at Umeå University, to unravel the function of genes in transgenic poplar trees. We are developing data driven tools and strategies on how to combine, model and predict biological information based on transgenic trees generated from multiple profiling platforms (e.g. NIR, FTIR-imaging, PyMS, metabolomics, enzymology and transcriptomics).
Website: http://www.chemistry.umu.se/index.php?option=com_content&task=view&id=66&Itemid=51#p_4
Institute of Technology (Linköping University)/Karolinska Institutet:
PI: Jesper Tegnér
Research: Our work focuses on feature selection, network identification, modeling and simulation of dynamical processes trying to better understand clinical problems in cardiovascular inflammatory diseases, Parkinson’s disease, memory networks in ADHD/schizophrenia, cancer (cell cycle regulation) etc. The goal is predictive biomedical informatics enabling personalized medicine. - Editorial Boards: BMC Systems Biology, IET Systems Biology. Published 48 papers and 13 reviews since 2002. These include Nature Genetics (1), Science (1), PNAS (5), Circulation (1), PLoS Genetics (1), PLoS Computational Biology (1),PLoS one (1), IET Systems Biology (2), Journal of Machine Learning Research (2), BMC Bioinformatics (3), Trends in Genetics (1).
Website: http://www.karlavagen90.se/index.php
Göteborg University/Sahlgrenska University Hospital:
PI: Mikael Benson
Research: The Unit for Clinical Systems Biology (UCSB) aims to apply systems biology to clinical research. It is an integrated laboratory for clinical and experimental high-throughput analyses, which is linked to the Sahlgrenska University Hospital.
It is led by a clinician and specifically aims to develop methods for personalized medication. Network-based analysis of genomic high-throughput data is used to identify disease pathways and key regulatory genes. The corresponding proteins are tried as diagnostic markers for personalized medicine in clinical studies. The project is based on a multi-disciplinary collaboration supported by two EU grants, both of which are led by the UCSB.
Website: http://www.complexdis.org.gu.se/
