Matthias E. Futschik
  • Faculty, University of Plymouth
  • Systems biology


My lab is active in the areas of bioinformatics and systems biology with the aim to connect molecular mechanisms with their phenotypic manifestations in living organisms. We are interested 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, we have also led the development of databases and software tools, that are publicly available.


Bioinformatics, Genomics, Transcriptomics, Proteomics, Cyanobacteria, Stem cell biology, Cancer, Neurodegenerative diseases

Marinella N Ghezzo, Mónica T Fernandes, Ivette Pacheco-Leyva, Pedro M Rodrigues, Rui S Machado, Marta A S Araújo, Ravi K Kalathur, Matthias E Futschik, Nuno L Alves and Nuno R dos Santos; FoxN1-dependent thymic epithelial cells promote T-cell leukemia development, Carcinogenesis (in print)

Davood Sabour, Rui S.R. Machado, José P. Pinto, Susan Rohani, Raja G.A. Sahito, Jürgen Hescheler, Matthias E. Futschik and Agapios Sachinidis (2018) Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart, Molecular Therapy - Nucleic Acids, 12, 158-173

Joaquín Giner-Lamia, Miguel A. Hernández-Prieto, and Matthias E. Futschik (2018) ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803. Bio-protocol 8(12): e2895

Ping-Wei Ho, Mathias Klein, Matthias Futschik & Elke Nevoigt (2018) Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae. FEMS Yeast Research, 18, 3 foy019

José Pinto, Rui Machado, Ramiro Magno, Daniel Oliveira, Susana Machado, Raquel Andrade, José Bragança, Isabel Duarte & Matthias Futschik (2018) StemMapper: A Curated Gene Expression Database for Stem Cell Lineage Analysis, Nucleic Acids Research D1: D788-D793

Joaquín Giner-Lamia, Rocio Robles-Rengel, Miguel A. Hernández-Prieto, M. Isabel Muro-Pastor, Francisco J. Florencio, and Matthias E. Futschik (2017) Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803, Nucleic Acids Research 45: 11800 - 11820

Matthias Futschik, Markus Morkel, Reinhold Schäfer and Christine Sers (2017) The Human Transcriptome: Implications for the Understanding, Diagnosing and Treating of Human Disease. In: Molecular Pathology, 2nd edition. W.B. Coleman and G. Tsongalis, Academic Press, Elsevier, Chapter 7 :136-164

Ravi Kiran Reddy Kalathur, José Pedro Pinto, Biswanath Sahoo, Gautam Chaurasia & Matthias E. Futschik (2017) HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease, Scientific Reports 7: 5216

Jens Georg, Gergana Kostova , Linda Vuorijoki, Verena Schön, Taro Kadowaki, Tuomas Huokko, Desirée Baumgartner, Maximilian Müller, Stephan Klähn, Yagut Allahverdiyeva , Yukako Hihara, Matthias E. Futschik, Eva-Mari Aro, Wolfgang R. Hess (2017) Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1, Current Biology 27(10): 1425-1436

JA Macedo, D Schrama, I Duarte, E Tavares, J Renaut, ME Futschik, PM Rodrigues , EP Melo (2017) Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells BMC Genomics 18: 319

Joaquín Giner-Lamia, Sara B. Pereira, Miquel Bovea-Marco, Matthias E. Futschik, Paula Tamagnini, and Paulo Oliveira (2016) Extracellular proteins: Novel key components of metal homeostasis in cyanobacteria? Frontiers in Microbiology 7:878

Miguel Hernández-Prieto , Trudi Semeniuk , Joaquín Giner-Lamia and Matthias Futschik (2016) The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803, Scientific Reports 6:22168

Shany Doron, Ayalla Fedida, Miguel A Hernández-Prieto, Gazalah Sabehi, Iris Karunker, Damir Stazic, Roi Feingersch, Claudia Steglich, Matthias Futschik, Debbie Lindell and Rotem Sorek (2016) Transcriptome dynamics of a broad host-range cyanophage and its hosts. The ISME Journal 10, 1437-1455

Gürkan Bal, Matthias E. Futschik, Daniela Hartl, Frauke Ringel, Julian Kamhieh-Milz, Viktor Sterzer, Jörg D. Hoheisel, Mohamed S. S. Alhamdani, and Abdulgabar Salama (2016) Identification of novel biomarkers in chronic immune thrombocytopenia (ITP) by microarray-based serum protein profiling, British Journal of Haematology, 172(4):602-15.

Ravi Kiran Reddy Kalathur, Joaquín Giner-Lamia, Susana Machado, Tânia Barata, Kameshwar R S Ayasolla, and Matthias E. Futschik (2015) The unfolded protein response and its potential role in Huntington's disease elucidated by a systems biology approach, F1000Research 4:103

Stephen Pells, Eirini Koutsouraki, Sofia Morfopoulou, Sara Valencia-Cadavid, Simon Tomlinson, Ravi Kalathur, Matthias Futschik and Paul De Sousa (2015) Novel human embryonic stem cell regulators identified by conserved and distinct CpG island methylation state, PLoS ONE 10(7): e0131102.

José P. Pinto, Ravi K. Kalathur, Daniel V. Oliveira, Tânia Barata, Rui S. R. Machado, Susana Machado, Ivette Pacheco-Leyva, Isabel Duarte and Matthias E. Futschik (2015) StemChecker: a web-based tool to discover and explore stemness signatures in gene sets, Nucleic Acids Research, 43 (W1): W72-W77

M. Strödicke, Y. Bounab, N. Strempel, K. Klockmeier, S. Yigit, RP Friedrich, G. Chaurasia, S. Li, F. Hesse, SP Riechers, J. Russ, C. Nicoletti, A. Boeddrich, T. Wiglenda, C. Haenig, S. Schnoegl, D. Fournier, RK Graham, MR Hayden, S. Sigrist, GP Bates, J. Priller, Ma Andrade-Navarro, Matthias E. Futschik and EE Wanker (2015) Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity. Genome Research 25: 701-713

R. Hill, Ravi K. Kalathur, L. Colaço, R. Brandão, S. Ugurel, Matthias Futschik and W. Link (2015) TRIB2 as a biomarker for diagnosis and progression of melanoma. Carcinogenesis 36(4):469-77

R. Hill, Ravi Kalathur, S. Callejas, L. Colaço, R. Brandão, Beatriz Serelde, A. Cebriá, C. Blanco-Aparicio, J. Pastor, Matthias Futschik, A. Dopazo and W. Link (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):482

J. Kamhieh-Milz, R. Moftah, G. Bal, Matthias Futschik, V. Sterzer, O. Khorramshahi, M. Burow, G. Thiel, A. Stuke-Sontheimer, R. Chaoui, S. Kamhieh-Milz, and A. Salama (2014) Differentially Expressed MicroRNAs in Maternal Plasma for the Noninvasive Prenatal Diagnosis of Down Syndrome (Trisomy 21), BioMed Research International, Volume 2014, Article ID 402475

Miguel A. Hernández-Prieto, Trudi A. Semeniuk and Matthias E. Futschik (2014) Towards a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. Frontiers in Genetics 5:191

José P. Pinto, Ravi K.R. Kalathur, Rui S. R. Machado, Joana M. Xavier, José Bragança, and Matthias E. Futschik (2014) StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. Nucleic Acids Research 42:W154-W160.

José P. Pinto, Rui Machado, Joana Xavier and Matthias E. Futschik (2014) Targeting molecular networks for drug research. Frontiers in Genetics 5:160

Miguel Hernandez-Prieto, Ravi Kalathur and Matthias E. Futschik (2014) Molecular networks, their analysis and representation, Chapter 24, 399-418, Springer Handbook of Bio- and Neuroinformatics, ed. Nik Kasabov, Springer

Ravi K. Kalathur, José P. Pinto,Miguel A. Hernández-Prieto, Rui S.R. Machado, Dulce Almeida, Gautam Chaurasia and Matthias Futschik (2014) UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks, Nucleic Acids Research, Database issue, 42 (D1): D408-D414

Thomas Wallach, Katja Schellenberg, Bert Maier, Ravi Kalathur , Pablo Porras, Erich E. Wanker, Matthias E. Futschik and Achim Kramer (2013) Dynamic Circadian Protein-Protein Interaction Networks Predict Temporal Organization of Cellular Functions, PloS Genetics , 9(3): e1003398. doi:10.1371/journal.pgen.1003398