Professor Matthias Futschik
Profiles

Professor Matthias Futschik

Professor in Bioinformatics

School of Biomedical & Healthcare Sciences (Plymouth University Peninsula Schools of Medicine and Dentistry)

Role

  • Professor in Bioinformatics at Plymouth University Peninsula Schools of Medicine and Dentistry

Qualifications

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

Teaching interests

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.

Research interests

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 highlighted

Journals
Articles
Georg J, Kostova G, Vuorijoki L, Schön V, Kadowaki T, Huokko T, Baumgartner D, Müller M, Klähn S & Allahverdiyeva Y 2017 'Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1' Current Biology , DOI PEARL
Kalathur RKR, Pedro Pinto J, Sahoo B, Chaurasia G & Futschik ME 2017 'HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington’s Disease' Scientific Reports 7, (1) , DOI PEARL
Macedo JA, Schrama D, Duarte I, Tavares E, Renaut J, Futschik ME, Rodrigues PM & Melo EP 2017 'Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells' BMC Genomics 18, (1) , DOI PEARL
Giner-Lamia J, Pereira SB, Bovea-Marco M, Futschik ME, Tamagnini P & Oliveira P 2016 'Extracellular Proteins: Novel Key Components of Metal Resistance in Cyanobacteria?' Frontiers in Microbiology 7, , DOI PEARL
Bal G, Futschik ME, Hartl D, Ringel F, Kamhieh-Milz J, Sterzer V, Hoheisel JD, Alhamdani MSS & Salama A 2016 'Identification of novel biomarkers in chronic immune thrombocytopenia (ITP) by microarray-based serum protein profiling' British Journal of Haematology 172, (4) 602-615 , DOI
Hernández-Prieto MA, Semeniuk TA, Giner-Lamia J & Futschik ME 2016 'The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803' Scientific Reports 6, (1) , DOI PEARL
Doron S, Fedida A, Hernández-Prieto MA, Sabehi G, Karunker I, Stazic D, Feingersch R, Steglich C, Futschik M & Lindell D 2016 'Transcriptome dynamics of a broad host-range cyanophage and its hosts' The ISME Journal 10, (6) 1437-1455 , DOI
Pells S, Koutsouraki E, Morfopoulou S, Valencia-Cadavid S, Tomlinson SR, Kalathur R, Futschik ME & De Sousa PA 2015 'Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State' PLOS ONE 10, (7) e0131102-e0131102 , DOI PEARL
Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RSR, Machado S, Pacheco-Leyva I, Duarte I & Futschik ME 2015 'StemChecker: a web-based tool to discover and explore stemness signatures in gene sets' Nucleic Acids Research 43, (W1) W72-W77 , DOI PEARL
Stroedicke M, Bounab Y, Strempel N, Klockmeier K, Yigit S, Friedrich RP, Chaurasia G, Li S, Hesse F & Riechers S-P 2015 'Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity' Genome Research 25, (5) 701-713 , DOI
Kalathur RKR, Giner-Lamia J, Machado S, Barata T, Ayasolla KRS & Futschik ME 2015 'The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach' F1000Research 4, 103-103 , DOI PEARL
Hill R, Kalathur RKR, Colaço L, Brandão R, Ugurel S, Futschik M & Link W 2015 'TRIB2 as a biomarker for diagnosis and progression of melanoma' Carcinogenesis 36, (4) 469-477 , DOI
Hill R, Kalathur RKR, Callejas S, Colaço L, Brandão R, Serelde B, Cebriá A, Blanco-Aparicio C, Pastor J & Futschik M 2014 'A novel phosphatidylinositol 3-kinase (PI3K) inhibitor directs a potent FOXO-dependent, p53-independent cell cycle arrest phenotype characterized by the differential induction of a subset of FOXO-regulated genes' Breast Cancer Research 16, (6) , DOI PEARL
Kamhieh-Milz J, Moftah RFH, Bal G, Futschik M, Sterzer V, Khorramshahi O, Burow M, Thiel G, Stuke-Sontheimer A & Chaoui R 2014 'Differentially Expressed MicroRNAs in Maternal Plasma for the Noninvasive Prenatal Diagnosis of Down Syndrome (Trisomy 21)' BioMed Research International 2014, 1-9 , DOI PEARL
Pinto JP, Reddy Kalathur RK, Machado RSR, Xavier JM, Braganca J & Futschik ME 2014 'StemCellNet: an interactive platform for network-oriented investigations in stem cell biology' Nucleic Acids Research 42, (W1) W154-W160 , DOI PEARL
Pinto JP, Machado RSR, Xavier JM & Futschik ME 2014 'Targeting molecular networks for drug research' Frontiers in Genetics 5, , DOI PEARL
Hernández-Prieto MA, Semeniuk TA & Futschik ME 2014 'Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria' Frontiers in Genetics 5, , DOI PEARL
Kalathur RKR, Pinto JP, Hernández-Prieto MA, Machado RSR, Almeida D, Chaurasia G & Futschik ME 2014 'UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks' Nucleic Acids Research 42, (D1) D408-D414 , DOI PEARL
Wallach T, Schellenberg K, Maier B, Kalathur RKR, Porras P, Wanker EE, Futschik ME & Kramer A 2013 'Dynamic Circadian Protein–Protein Interaction Networks Predict Temporal Organization of Cellular Functions' PLoS Genetics 9, (3) e1003398-e1003398 , DOI PEARL
Hernandez-Prieto MA 2012 'CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803' Bioinformation 8, (13) 634-638 , DOI PEARL
Kalathur RKR, Hernández-Prieto MA & Futschik ME 2012 'Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database' BMC Neurology 12, (1) , DOI PEARL
Hernández-Prieto MA, Schön V, Georg J, Barreira L, Varela J, Hess WR & Futschik ME 2012 'Iron Deprivation in Synechocystis : Inference of Pathways, Non-coding RNAs, and Regulatory Elements from Comprehensive Expression Profiling ' G3: Genes|Genomes|Genetics 2, (12) 1475-1495 , DOI PEARL
Chaurasia G & Futschik M 2012 'The integration and annotation of the human interactome in the UniHI Database' Methods Mol Biol 812, 175-188 Author Site , DOI
Bal G, Kamhieh-Milz J, Futschik M, Häupl T, Salama A & Moldenhauer A 2012 'Transcriptional Profiling of the Hematopoietic Support of Interleukin-Stimulated Human Umbilical Vein Endothelial Cells (HUVECs)' Cell Transplantation 21, (1) 251-267 , DOI
Duong CT, Strack L, Futschik M, Katou Y, Nakao Y, Fujimura T, Shirahige K, Kodama Y & Nevoigt E 2011 'Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers' yeast' Metabolic Engineering 13, (6) 638-647 , DOI
Moldenhauer A, Futschik M, Lu H, Helmig M, Götze P, Bal G, Zenke M, Han W & Salama A 2011 'Interleukin 32 promotes hematopoietic progenitor expansion and attenuates bone marrow cytotoxicity' European Journal of Immunology 41, (6) 1774-1786 , DOI
Russ J & Futschik ME 2010 'Comparison and consolidation of microarray data sets of human tissue expression' BMC Genomics 11, (1) 305-305 , DOI PEARL
Marras E, Travaglione A, Chaurasia G, Futschik M & Capobianco E 2010 'Inferring modules from human protein interactome classes' BMC Systems Biology 4, (1) 102-102 , DOI PEARL
Steglich C, Lindell D, Futschik M, Rector T, Steen R & Chisholm SW 2010 'Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus' Genome Biology 11, (5) R54-R54 , DOI PEARL
Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, Rector T, Steen R & McNulty N 2009 'Choreography of the Transcriptome, Photophysiology, and Cell Cycle of a Minimal Photoautotroph, Prochlorococcus' PLoS ONE 4, (4) e5135-e5135 , DOI PEARL
Chaurasia G, Malhotra S, Russ J, Schnoegl S, Hänig C, Wanker EE & Futschik ME 2009 'UniHI 4: new tools for query, analysis and visualization of the human protein–protein interactome' Nucleic Acids Research 37, (suppl_1) D657-D660 , DOI PEARL
Futschik ME & Herzel H 2008 'Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis' Bioinformatics 24, (8) 1063-1069 , DOI
Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW & Hess WR 2008 'The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus' PLoS Genetics 4, (8) e1000173-e1000173 , DOI PEARL
Gsponer J, Futschik ME, Teichmann SA & Babu MM 2008 'Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation' Science 322, (5906) 1365-1368 , DOI
Futschik ME, Chaurasia G & Herzel H 2007 'Comparison of human protein–protein interaction maps' Bioinformatics 23, (5) 605-611 , DOI
Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R & Hess WR 2007 'Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution' Nature 449, (7158) 83-86 , DOI
Futschik ME, Tschaut A, Chaurasia G & Herzel H 2007 'Graph-theoretical comparison reveals structural divergence of human protein interaction networks' GENOME INFORMATICS 2007, VOL 18 18, 141-+ Author Site
Chaurasia G, Iqbal Y, Hänig C, Herzel H, Wanker EE & Futschik ME 2007 'UniHI: an entry gate to the human protein interactome' Nucleic Acids Research 35, (suppl_1) D590-D594 , DOI PEARL
Kumar L, Futschik M & Herzel H 2006 'DNA motifs and sequence periodicities' In Silico Biol 6, (1-2) 71-78 Author Site
Steglich C, Futschik M, Rector T, Steen R & Chisholm SW 2006 'Genome-Wide Analysis of Light Sensing in Prochlorococcus' Journal of Bacteriology 188, (22) 7796-7806 , DOI
Chaurasia G, Herzel H, Wanker EE & Futschik ME 2006 'Systematic functional assessment of human protein-protein interaction maps' Genome Inform 17, (1) 36-45 Author Site
FUTSCHIK MATTHIASE & CARLISLE BRONWYN 2005 'NOISE-ROBUST SOFT CLUSTERING OF GENE EXPRESSION TIME-COURSE DATA' Journal of Bioinformatics and Computational Biology 03, (04) 965-988 , DOI
Futschik ME & Crompton T 2005 'OLIN: optimized normalization, visualization and quality testing of two-channel microarray data' Bioinformatics 21, (8) 1724-1726 , DOI
Futschik M & Crompton T 2004 'Model selection and efficiency testing for normalization of cDNA microarray data' GENOME BIOLOGY 5, (8) Author Site , DOI PEARL
Futschik ME, Reeve A & Kasabov N 2003 'Evolving connectionist systems for knowledge discovery from gene expression data of cancer tissue' Artificial Intelligence in Medicine 28, (2) 165-189 , DOI
Futschik ME, Sullivan M, Reeve A & Kasabov N 2003 'Prediction of clinical behaviour and treatment for cancers' Appl Bioinformatics 2, (3 Suppl) S53-S58 Author Site
Humar B, Graziano F, Cascinu S, Catalano V, Ruzzo AM, Magnani M, Toro T, Burchill T, Futschik ME & Merriman T 2002 'Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer' Oncogene 21, (53) 8192-8195 , DOI
Chapters
Chaurasia G & Futschik ME 2010 'Interactomics and cancer' An Omics Perspective on Cancer Research 167-182 , DOI
Futschik ME, Kemmner W, Schäfer R & Sers C 2009 'The Human Transcriptome: Implications for the Understanding of Human Disease' Molecular Pathology: The Molecular Basis of Human Disease 123-149 , DOI
Conference Papers
Wallach T, Futschik M, Millan PP, Wendt S, Wanker EE & Kramer A 2009 'A mammalian circadian interactome' 8-8
Futschik ME, Chaurasia G & Wanker E 2008 'Disentangling molecular interaction networks for chorea Huntington' A1-A1
Futschik ME & Herzel H 2007 'Are we overestimating the number of cell-cycling genes? The impact of background models for time series data' 2-14
Chaurasia G, Herzel H & Futschik ME 2007 'Comparison and integration of large-scale human protein-protein interaction maps' 300-300
Futschik ME, Chaurasia G, Wanker E & Herzel H 2006 'Comparison of human protein-protein interaction maps' 21-32
Moldenhauer A, Selders L, Genter G, Hieronymus T, Ruau D, Lun A, Futschik M, Kiesewetter H, Zenke M & Salama A 2005 'Cocultures of umbilical cord blood hematopoietic progenitor cells and umbilical cord endothelium' 131B-132B
Futschik ME, Kasabov NK, IEEE & IEEE 2002 'Fuzzy clustering of gene expression data' 414-419
Kasabov N, Middlemiss M & Futschik M 2001 'Knowledge based neural networks for on-line and off-line modeling and rule extraction' 240-244

Additional information

Links

Some R/Bioconductor packages that I have developed:

·        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