Professor Matthias Futschik
Professor in Bioinformatics
School of Biomedical & Healthcare Sciences (Plymouth University Peninsula Schools of Medicine and Dentistry)
- Professor in Bioinformatics at Plymouth University Peninsula Schools of Medicine and Dentistry
I studied physics at the Eberhard Karls University (Tübingen, Germany), the Brown University (Rhode Island, USA) and the Humboldt University (Berlin, Germany), and carried out research work in the field of photobiophysics for my Master degree. In 1999, I went to Dunedin, New Zealand, where I pursued a PhD in Information Science at the University of Otago. My focus was the development of new computational methods for microarray data analysis and their application in cancer research. After working for some time in a spin-off company (Pacific Edge Biotech. Ltd) as senior bioinformatician, I returned to Berlin to take up a position as Assistant Professor at the Charité, Humboldt-University, where I became interested in the structure, function and regulation of molecular networks. In 2008, I moved to Faro,Portugal, to establish my own independent lab in the field of systems biology (SysBioLab, http://www.sysbiolab.eu ) at the University of Algarve, where we combine experimental and computational methods to elucidate complex processes in living organisms ranging from gene regulation in cyanobacteria to differentation of stem cells. I aim to continue and expend these lines of investigations in my position as Professor in Bioinformatics at the Plymouth University.
Roles on external bodies
- Honorary senior researcher at the Centre of Marine Science, University of Algarve, Faro, Portugal (webpage)
- Acting head of the SysBioLab at the University of Algarve, Portugal
My teaching interests comprise different areas of bioinformatics and systems biology and include genomics, transcriptomics, and network biology. I also give introductory courses in applied bioinformatics and statistics using R/Bioconductor.
My area of research comprises bioinformatics and systems biology with the aim to connect molecular mechanisms with their phenotypic manifestations in living organisms. I aminterested in a wide range of biological processes ranging from gene regulation in bacteria to the determination of cell fate in organ development. To facilitate gaining knowledge from biological data, I have also led the development of databases and software tools, that have been publicly available. Current topics of my research include:MOLECULAR NETWORKS IN HUMAN HEALTH AND DISEASE
Most functions within cells are carried out not by single molecules, but result from the collaborative interaction of numerous molecules such as proteins, nucleic acids or metabolites, which form miraculously complex networks. Understanding the functions of a molecular single component, thus, requires the knowledge of its various interactions to components in the organism and its environment. Toset the groundwork for holistic studies of physiological and pathological processes in human, we have integrated various molecular interaction maps and established several publicly accessible resources for network-oriented investigations such as the Unified Human Interactome (UniHI) and HDNetDB. Incooperation with other research groups, we utilize these resources, for instance, to detect changes of network structures during disease development and to identify novel molecular targets for therapies.SYSTEMS BIOLOGY OF STEM CELLS
Stem cells hold a great potential for medicine. They could provide a source for tissue and organ regeneration. . For safe clinical application,however, we need fully understand how stem cells maintain the identity and which factors controls their differentiation towards other cell types. To achieve this, we have collected and integrated numerous molecular interactiondata for stem cells in StemCellNet - a web-server for network-oriented investigations in stem cell biology. Additionally,we curated a large number of genetic signatures for stemness - the defining characteristic of stem cells - and included them in our StemChecker web-tool. Using these resources, we seek to reveal the complex mechanisms underlying stemcell maintenance differentiation using a systems biology approach to address the question how a pluripotent cell determines its specific fate based on its internal state and external cues.GENE REGULATION IN CYANOBACTERIA
As cyanobacteria have the distinct capability to utilize solar energy as power supply for their metabolic processes, they emerged as ideal cellular production systems, combining plant-like photosynthesis with fast growth, small genome size and ease in genetic modification. To efficiently utilize and modify cyanobacteria in green biotechnology, a detailed knowledge of their gene regulatory networks is necessary. At present, however, such knowledge exists only in rudimentary form. To derive and validate detailed models of gene regulatory networks in cyanobacteria, we are combining experimental and computational approachesincluding transcriptome profiling and in silico reverse engineering.As basis for modelling the regulation of processes on systems-level, we have developed the CyanoEXpress database comprising the largest integrated gene expression dataset for the model cyanobacterium Synechocystis to date.
Grants & contracts
· FCT/DAADTransnational cooperation: From Petri Dish to the living heart: Asystems biology approach to identify and validate key genes and processesdriving cardiogenesis. 2016-2017
· FCT-SFRH/BPD/96890/2013: Development of software tools for theprediction of cellular fate in stem cell differentiation 2014-2016
· FCT-PTDC/BIA-MIC/4418/2012: The regulation of photosynthesis in cyanobacteria: A systems biology approach. 2013-2015
· FCT-PTDC/BIA-GEN/116519/2010: Alternative splicing and its impact on molecular interaction networks during stem cell differentiation. 2012-2015
· FCT-PTDC/BIA-BCM/117975/2010 (Collaborator): The role and regulation of alpha-synuclein phosphorylation in both pathological and physiological conditions. 2012-2015
· FCT- SFRH/BPD/70718/2010: Systems Biology approach to unravel the molecular mechanisms involved in T-Cell Acute Lymphoblastic Leukaemia. 2011-2014
· FCT-PTDC/BIA-MIC/101036/2008: Regulation of iron homeostasis in cyanobacteria. 2010-2013
· CHDI Foundation: Visualization and Analysis ofHD-Related Molecular Interaction Networks. 2010-2011.
· DEUTSCHE FORSCHUNGSGESELLSCHAFT SFB 618: Robustness,modularity and dynamics of protein-protein interaction networks 2005-2009.
Key publications are highlightedJournals
- My PhD thesis (a classic!)
· OLIN webpage: Bioconductor package for optimised normalisation of microarray data and detection of hybridisation artifacts
· Mfuzz webpage: Bioconductor package for clustering and visualisation of time series gene expression data
· Cycle webpage: Bioconductor package for detection of periodically expressed genes in time series expression data