The Systems Biology and Bioinformatics Laboratory

MAtthius_01

Location

Building 8, Laboratory 2.22

Department of Biomedical Sciences and Medicine.

University of Algarve

Phone: +351 289 244 403

mfutschik@ualg.pt

Team Members

Matthias Futschik (Principal Investigator)

Miguel Hernández (Post Doctoral Researcher)

Ravi Kalathur (Post Doctoral Researcher)

José Pinto (Post Doctoral Researcher)

Isabel Duarte (Research Student)

Daniel Oliveira  (Research Student)

About the SBBL

The Systems Biology and Bioinformatics laboratory (SBBL) is active in the development of novel methodologies, and the implementation of software and databases in the area of systems biology. Examples of web-based tools developed within the SBBL include the Unified Human Interactome (UniHI), which is one of the most comprehensive resources of human molecular interaction and used by researchers world-wide, and the HeartEXpress database, that merges expression data associated with cardiogenesis and cardiac linage reprogramming. Additionally, the SBBL unit has extensive expertise in processing and analysis of high-throughput data, and has contributed several popular R packages to the community-based Bioconductor project. Besides developing computational resources, the research is focused on the deciphering and in silico reconstruction of molecular networks underlying several physiological and pathophysiological processes. The lab is actively involved in the study of various biological systems with strong relevance to medicine. Ongoing projects include network-based investigations into stem cell differentiation, oncogenesis and neurodegeneration in close collaboration with local experimentally working groups including international partners.

Publications (2008-2014)

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 Research42: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-PrietoRavi 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 (AbstractPdfWebsite of Database)

Ravi KalathurMiguel 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 (htmlPdfSupplementary 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)

Example Networks

Matthius_Network_02
Mathius_Network_01

Projects

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.

Colaborator

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

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