Introducing the Information Dynamics Lab
A new spin-off group of CompMed, The Information Dynamics Lab (Info Dyn Lab), led by Dr. Narsis Kiani and Dr. Hector Zenil, seeks to combine the power of the theories of dynamic systems and algorithmic information with applications to algebraic graph theory, network genetics, structural and molecular biology.
The main aim of the Info Dyn lab is to mine and exploit results drawn from mathematics, to undertake research in fundamental science and to bring mature concepts and methods from the theoretical realm to systems applications, specifically (though not limited) to network science and computational biology, using these concepts to devise novel techniques with which to effectively reprogram cells as well as to better understand evolving artificial and biological systems.
A recent publication by our group (see link) shows that long-term endurance training in a stable way alters the epigenetic pattern in the human skeletal muscle. The research team behind the study, which is being published in the journal Epigenetics, also found strong links between these altered epigenetic patterns and the activity in genes controlling improved metabolism and inflammation. The results may have future implications for prevention and treatment of heart disease, diabetes, and obesity.
We are proud to say that this paper caught the attention of different international media from US to all over the Europe.
The German Television has also recorded a movie about this work and you can see it here:
And the link to the whole program (the whole 45 minutes) is here:
Unfortunately it is all in german - and the voices are overdubbed - but we hope, it is still interesting and fun to watch for you.
- The International Solvay Institute will host the Event "Bridging the gaps at the PCB interface" Multiscale Modelling in Physics, Chemistry and Biology. Prof. Jesper Tegnér has been invited to give a talk at this interesting Symposium.
Omics and Data Integration
- Omics and Data Integration: STATegra is a FP7 funded project that aims to develop statistical methods and software for the integration of NGS and omics data. The goal is to provide bioinformatics resources that the genomics community can easily use to integrate and to understand their experiments involving a variety of omics measurements. Within the project, Dr. Gomez-Cabrero coordinated the Summer School in Omics and Data Integration (September 2015). During the event, him and his collaborators provided training to experimentalists and bioinformaticians in the analysis of multi-omics experiments. Useful links below:
Introduction to the summer school
NGS introduction: https://www.youtube.com/watch?v=R3eCTh1VYto
RNA-seq introduction: https://www.youtube.com/watch?v=VqYLG2tp_YI
DNA Methylation introduction: https://www.youtube.com/watch?v=wUFnYIXEOpISingle-Cell Through Time: https://www.youtube.com/watch?v=j8T3nbFD_Q4
- Systems Medicine: Under the auspices of CaSYM, with support of FEBS, Raffaella Giugliano (Scientific Coordinator in the CompMed team) has coordinated the organization of the First European Summer School on Systems Medicine in Stockholm (June 2015) where the best examples of how to use advanced computational tools in translational clinical research were presented and discussed. Useful link below:
- Introduction to the summer school
- Topics available
- Systems Biology of the Mammalian Circadian Clock: https://youtu.be/2EY_iL9fD10
- Computational Tissue Engineering: https://youtu.be/LZlJ8NGPaXM
- Solving the puzzle of Multiple Sclerosis: https://youtu.be/s8ZCnv4y5RM
- From Systems to Personalized Medicine: https://youtu.be/IX-9iwDOtkM
- Understanding of necrotizing soft tissue infections: https://youtu.be/UXWQGDuuAIU
CASyM is funded by the European Union, Seventh Framework Programme under the Health Cooperation Theme and Grant Agreement # 305033.
- Translational Medicine: In a joint international effort, Dr. Gomez-Cabrero has been leading the contributions from the team w.r.t systems understanding of COPD and translating the results into the clinic, & 11 papers were published during 2014.
- Theory: Spearheaded by Dr. Zenil, we have developed a novel conceptual framework to understand key elements in complex networks from the standpoint of information, structure and dynamics. See for example this paper published in the journal of Seminars in Cell and Developmental Biology (and more in Publications).
- Wellness and Exercise: The team (shared first and last author) discovered coordinated epigenetic and transcriptomics changes in response to physical training. Dr Marabita's work caught the interest of the media and New York Times highlighted this in one column. (for more info see http://compmed.se/blog/training-dna-methylation/)
- One Clinical Publication from our team (Dr. Gomez-Cabrero) on epigenetic effect on cesarean delivery was awarded with the Regnell Prize in Medicine 2014 from the Swedish Medical Science http://www.mynewsdesk.com/se/svenska-laekaresaellskapet/pressreleases/epigenetikens-betydelse-foer-haelsan-svenska-laekaresaellskapet-stoedjer-och-beloenar-medicinsk-forskning-1011104
- The PhD courses on bioinformatics organized by the team (Drs Gomez-Cabrero, Marabita, Ball) received the highest scores from the students (see the latest courses here: http://kiwas.ki.se/katalog/katalog/kurs/1927 and http://kiwas.ki.se/katalog/katalog/kurs/1928)