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Systems Biology and Bioinformatics Laboratory

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Systems Biology and Bioinformatics Laboratory


About the SysBioLab

The Systems Biology and Bioinformatics Laboratory (SysBioLab) is active in the development of novel computational methodologies, and the implementation of software and databases such as Unified Human InteractomeHDNetDBStemChecker, StemCellNet, StemMapper, HeartMiR StemCellNet and HeartEXpress. The lab is also involved in the study of various complex processes with strong relevance to medicine including stem cell differentiation, oncogenesis and neurodegeneration.


Publications (2008-2018)

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) (pdf+html)

Davood Sabour, , 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 (pdf+html)

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 (pdf+html)

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 (pdf+html)

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 (pdf+html)

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 (pdf+html)

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 (pdf+html)

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 (pdf+html)

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 (pdf+html)

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 (pdf+html)

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

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 (pdf + html)

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. (pdf + html)

Ravi Kiran Reddy Kalathur, Joaquin 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 (pdf + html)

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. (pdf + html)

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 (pdf + html)

M. Stroedicke, 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 (pdf + html)

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 (pdf + html)

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 (pdf + html)

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. (pdf+html)

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

Miguel Hernandez-Prieto, Ravi Kalathur and Matthias E. Futschik (2014) Molecular networks, their analysis and representation, Springer Handbook of Bio- and Neuroinformatics, ed. Nik Kasabov, Springer (preprint-pdfBook’s web-page)

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 (htmlpdf)

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 (htmlpdf)

Miguel A. Hernández-Prieto, Verena Schön, Jens Georg,Luísa Barreira, João Varela, Wolfgang R. Hess and Matthias E. Futschik (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 (htmlpdf)

Miguel Hernandez-Prieto and Matthias E. Futschik (2012) CyanoEXpress: a web database for interactive exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803, Bioinformation, 8 (13),634-638 (Abstract, Pdf, Website of Database)

Ravi Kalathur, Miguel Hernandez-Prieto and Matthias E. Futschik (2012) Huntington´s Disease and its target genes: A global functional profile based on the HD Research Crossroads database, BMC Neurology, 12:47 (html, PdfSupplementary Material)

Gürkan Bal, Julian Kamhieh-Milz, Tayseer Zaid, Matthias Futschik, Thomas Häupl, Abdulgabar Salama and Anja Moldenhauer (2012) Molecular profiling of the haematopoietic support of interleukin-stimulated human umbilical vein endothelial cells (HUVEC), Cell Transplantation 21(1):251-67(pdf)

Gautam Chaurasia and Matthias E. Futschik (2012) The Integration and Annotation of the Human Interactome in the UniHI Database Methods in Molecular Biology 812: 175-188 (PubMedpdf)

T. Duong, L. Strack, M. Futschik, Y. Katou, Y. Nakao, T. Fujimura, K. Shirahige, Y. Kodama, E. Nevoigt (2011) Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers’ yeast, Metabolic Engineering, 13(6):638-47 (PubMedpdf)

Miguel A. Hernandez-Prieto, Tania Tibiletti, Leyla Abasova, Diana Kirilovsky, Imre Vass and Christiane Funk (2011) The small CAB-like proteins of the cyanobacterium Synechocystis sp. PCC 6803: Their involvement in chlorophyll biogenesis for Photosystem II, Biochimica et Biophysica Acta, 1807:1143-1151 (pdf)

Anja Moldenhauer, Matthias Futschik, Huili Lu, Melanie Helmig, Patricc Götze, Gürkan Bal, Martin Zenke,Wei Han an Abdulgabar Salama (2011) Interleukin 32 promotes hematopoietic progenitor expansion and attenuates bone marrow cytotoxicity, European Journal of Immunology, 41(6):1774-86 (pdf)

Elisabetta Marras, Antonella Travaglione, Gautam Chaurasia, Matthias Futschik and Enrico Capobianco (2010) Inferring modules from human protein interactome classes, BMC Systems Biology, 4:102 (pdf,html)

Jenny Russ and Matthias E. Futschik (2010) Comparison and consolidation of microarray data sets of human tissue expression, BMC Genomics 11:305 (pdf,htmlSupplementary Materials)

Claudia Steglich, Debbie Lindell,Matthias Futschik, Trent Rector, Robert Steen and Sallie W. Chisholm (2010) Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus, Genome Biology 11:R54 (pdf html)

Gautam Chaurasia and Matthias E. Futschik (2009) Interactomics and Cancer, An Omics Perspective of Cancer, eds. W. Cho, Springer, Chapter 5: 167- 182 (pdf)

Michael J. Allen, Bela Tiwari, Matthias E. Futschik and Debbie Lindell (2009) Methods in aquatic virus ecology: Construction of microarrays and their application to virus analysis, Manual of Aquatic Viral Ecology, American Society of Limnology and Oceanography, Chapter 5: 34–56 (pdf)

E.R. Zinser, D. Lindell, Z.I.Johnson, M.E. Futschik, C. Steglich, M.L. Coleman, M.A. Wright, T. Rector, R. Steen, N, McNulty, L.R. Thompson and S.W. Chisholm (2009) Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus, PlosONE, 4(4): e5135. doi:10.1371/journal.pone.0005135 (pdf)

Matthias Futschik, Wolfgang Kemmner, Reinhold Schäfer and Christine Sers (2009) The Human Transcriptome: Implications for the Understanding of Human Diseases, Molecular Pathology, eds. W.B. Coleman and G. Tsongalis, Academic Press, Elsevier, Chapter 7 :123-150 (pdf)

Gautam Chaurasia, Soniya Malhotra, Jenny Russ, Sigrid Schnoegl, Christian. Hänig, Erich. E. Wanker and Matthias. E. Futschik. (2009) UniHI 4: New tools for query, analysis and visualization of the human protein-protein interactome, Nucleic Acids Research, 37, Database issue: D657-D660 (pdf)

Jörg Gsponer, Matthias E. Futschik, Sarah A. Teichmann and M. Madan Babu (2008) Tight regulation of intrinsically unstructured proteins: from transcript synthesis to protein degradation, Science, 322, 1365-1368 (pdf)



Project Leader

PTDC/BIA-GEN/116519/2010 – Alternative splicing and its impact on molecular interaction networks. 2012-2015.

PTDC/BIA-MIC/101036/2008 – Regulation of iron homeostasis in cyanobacteria. 2010-2013.

CHDI – Visualization and Analysis of HD-Related Molecular Interaction Networks – 2010-2011.

DEUTSCHE FORSCHUNGSGESELLSCHAFT: SFB 618 (A5) – Robustness, modularity and dynamics of protein-protein interaction networks, 2005-2009.


PTDC/BIA-BCM/117975/2010 – The role and regulation of alpha-synuclein phosphorylation in both pathological and physiological conditions. 2012-2015.


Representative Images