There is always a way up ...

Matthias E. Futschik (PhD) - Principal Investigator

Centre of Marine Sciences (CCMAR)

Center of Biomedical Research (CBMR)

Faculty of Sciences and Technology (building 8)

University of Algarve

Phone: + 351 289 244 403 (extn. 7403)



Academic Degrees


Positions


Links


Publications

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, RK 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)

Richard Hill, Ravi Kiran Reddy Kalathur, Sergio Callejas, Laura Colaço, Ricardo Brandão, Beatriz Serelde, Antonio Cebriá, Carmen Blanco-Aparicio, Joaquín Pastor, Matthias Futschik, Ana Dopazo and Wolfgang 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 (pdf + html)

Julian Kamhieh-Milz, Reham Moftah, Gürkan Bal, Matthias Futschik, Viktor Sterzer, Omid Khorramshahi, Martin Burow, Gundula Thiel, Annegret Stuke-Sontheimer, Rabih Chaoui, Sundrela Kamhieh-Milz, and Abdulgabar 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 (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, Chapter 24, 399-418, , Springer Handbook of Bio- and Neuroinformatics, ed. Nik Kasabov, Springer (preprint-pdf, Book's web-page)

Ravi K. Kalathur, José P. Pinto, Miguel Hernandez, Rui 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. (html, pdf)

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 (html, pdf)

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 (html, pdf)

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 (Manuscript Html/Pdf)

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 (abstract)

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 (PubMed, pdf)

C. 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 (PubMed, 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 (pdf,html)

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 (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)

Claudia Steglich, Matthias E. Futschik, Debbie Lindell, Bjoern Voss, Sallie W. Chisholm and Wolfgang R. Hess (2008) The challenge of regulation in a minimal photoautotroph: Non-coding RNAs in Prochlorococcus, Plos Genetics 4(8): e1000173 (pdf)

Matthias E. Futschik and Hanspeter Herzel (2008) Are we overestimating the number of cell-cycling genes? The impact of background models on time series analysis, Bioinformatics, 24(8):1063-1069 (pdf)

Matthias E. Futschik, Gautam Chaurasia, Anna Tschaut, Jenny Russ, M. Madan Babu and Hanspeter Herzel (2007) Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network, Journal of Integrative Bioinformatics, 4(3):76 (pdf)

Matthias Futschik, Anna Tschaut, Gautam Chaurasia, and Hanspeter Herzel (2007) Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks, Genome Informatics, 18, 141-15 (pdf)

D. Lindell, J. Jaffe, M. Coleman, M. Futschik, I. Axmann, T. Rector, G. Kettler, M. Sullivan, R. Steen, W. Hess, G. Church and S. Chisholm (2007) Genome-Wide Expression Dynamics of a Marine Virus and its Host Reveal Features of Co-evolution, Nature, 449, 83 - 86 (pdf)

P. Umbach, M. Futschik, U.Stelzl and E.Wanker (2007) Funktion durch Netzwerke von Proteinen und ihren Wechselwirkungen, Laborwelt, 8(2):9-11 (ps)

L. Kumar and M.E. Futschik (2007) Mfuzz: a software package for soft clustering of microarray data, Bioinformation, 2(1) 5-7 (pdf)

Matthias Futschik, Gautam Chaurasia, and Hanspeter Herzel (2007) Comparison of human protein-protein interaction maps, Bioinformatics, 23(5):605-611 (pdf)

G. Chaurasia, C. Hänig, Y. Iqbal, H. Herzel, E.Wanker and M. E. Futschik (2007) Flexible web-based integration of distributed large-scale interaction data sets, Journal of Integrative Bioinformatics, 4(1) (pdf)

G. Chaurasia, Y. Iqbal, C. Hänig, H. Herzel, E. E. Wanker and M. E. Futschik (2007) UniHI: An Entry Gate to the Human Protein Interactome, Nucleic Acids Research Database issue, 35, D590-4 (pdf)

C. Steglich, M. Futschik, T. Rector and S.W. Chisholm (2006) Genome-wide analysis of light sensing in Prochlorococcus, Journal of Bacteriology, 188(22):7796-806 (pdf)

Gautam Chaurasia, Hanspeter Herzel, Erich Wanker and Matthias E. Futschik (2006) Systematic functional assessment of human protein interaction maps, Genome Informatics, 17(1), 36-45. (pdf)

L. Kumar, M. Futschik and H. Herzel (2006) DNA motifs and sequence periodicities, In Silico Biology, 6, 0008 (html)

M.E. Futschik and B. Charlisle (2005) Noise robust soft clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 4, 965-98 (pdf)

M.E. Futschik and T. Crompton (2005) OLIN: optimized normalization, visualization and quality testing of two-channel microarray data, Bioinformatics, 21(8):1724-6 (pdf)

M. Futschik and T. Crompton (2004) Model selection and efficiency testing for normalization of cDNA microarray, Genome Biology, 5(8):R60 (pdf)

M.E. Futschik, M. Sullivan, A. Reeve, N. Kasabov (2003) Prediction of clinical behaviour and treatment for cancers, Applied Bioinformatics, 3(2): S53-58 (pdf)

M.E. Futschik, A. Reeve and N. Kasabov (2003) Evolving connectionist systems for knowledge discovery from gene expression data of gene expression data of cancer tissue, Artificial Intelligence in Medicine, 28: 165-189, 2003 (pdf)

M.E. Futschik and N.K. Kasabov (2002). Fuzzy clustering of gene expression data, Proceedings of World Congress of Computational Intelligence WCCI 2002, IEEE Press.(pdf)

B. Humar, F. Graziano, S. Cascinu, V. Catalano, A.M. Ruzzo, M. Magnani, T. Turo, M.E. Futschik, T.Merriman and P. Guilford, (2002) Association of CDH1 haplotypes with susceptibility to sporadic diffuse gastric cancer, Oncogene, 21(53): 8192-8195 (pdf)

M. Futschik, A. Jeffs, S. Pattison, N. Kasabov, M. Sullivan, A. Merrie and A. Reeve (2002) Gene expression profiling of metastatic and non-metastatic colorectal cancer cell-lines, Genome Letters, vol.1, No.1, 26-34 (pdf)

C. Brown, G. Jacobs, M. Schreiber, J. Magnum, J. McNaughton, M. Cambray, M. Futschik, Major, O. Rackham, W. Tate, P. Stockwell, C. Thompson and N. Kasabov, (2000) Using bioinformatics to investigate post-transcriptional control of gene expression, NZ Bio Science, 7(4), 11-12


Presentations

José Pedro Pinto, Ravi Kalathur, Daniel V. Oliveira, Tânia Barata, Rui Machado, Susana Machado, Ivette Pacheco-Leyva, Joana M. Xavier, Bragança José, Isabel Duarte and Matthias Futschik (2016) SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology, INFORUM 2016, Lisbon, Portugal

M Futschik, J Giner-Lamia, M Hernandez-Prieto (2016) CyanoEXpress: An interactive web-tool for exploration and visualization of gene expression data from cyanobacteria, NorPlantBio 2016, Trondheim, Norway (abstract)

M Hernandez-Prieto, T Semeniuk, J Giner-Lamia, M Futschik (2016) Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis, NorPlantBio 2016, Trondheim, Norway (abstract)

Isabel Duarte, D.Oliveira, T. Justo, J. Bragança and M. Futschik (2015) Predicting Cardiac Novel Splice Variantes from RNAseq data, Bioinformatics for the Life Sciences, Universidade do Minho, Braga, Portugal

DV Oliveira, I Duarte, RS Machado, I Pacheco-Leyva, T Justo, JP Pinto, S Machado, JA Belo, J Bragança & ME Futschik (2015) From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

RS Machado, JP Pinto, DV Oliveira, I. Duarte, S Machado, J Bragança & M Futschik (2015) A meta-analysis study of stem cell differentiation in the context of cardiogenesis.9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

S Machado, R Kalathur, DV Oliveira, T Barata, R Machado, I Pacheco-Leyva, I Duarte, M Futschik, J Pinto (2015) StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

JP Pinto, R Kalathur, RS Machado, J Xavier, J Bragança & ME Futschik (2015) StemCellNet: an interactive platform for network -oriented investigations in stem cell biology. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

Matthias Futschik, Joaquín Giner-Lamia and Miguel Hernández-Prieto(2015) Transcriptional regulation and coordination of photosynthetic genes in Synechocystis: a comprehensive study based on CyanoEXpress, ISPP 2015, Tübingen, Germany (abstract)

Joaquin Giner-Lamia, Miquel Bovea-Marco, Miguel A. Hernández-Prieto and Matthias E. Futschik (2015) CyanoEXpress: An enhanced tool for on-line analysis and visualization of gene expression data from cyanobacteria, ISPP 2015, Tübingen, Germany (abstract)

Isabel Duarte, D.Oliveira, T. Justo, J. Bragança, J Belo and M. Futschik (2015) From Stem Cells 2 Heart: Estudo do Impacto do Splice Alternativo durante o Desenvolvimento Cardiaco, Molecular Genetics Anual Seminar Series, Universidade do Algarve, Faro, Portugal

J. Pinto, R. Kalathur, R. Machado , J. Xavier, J. Bragança, and Matthias E. Futschik (2014) StemCellNet: an interactive platform for network-oriented investigations in stem cell biology, Heart without Boarders, International Conference, Porto, Portugal (abstract)

I. Duarte, T. Justo, J. Pinto, D.Oliveira, J. Bragança, J. Belo and Matthias Futschik (2014) From Stem Cells 2 heart: Elucidating the role of alternative splicing in cardiomyogenesis, Heart without Boarders, International Conference, Porto, Portugal (abstract)

D Oliveira, R. Machado, I. Pacheco-Leyva, I. Duarte, T. Justo , J. Pinto, J. Belo, J. Bragança and Matthias Futschik (2014) From Stem Cells 2 heart: Finding novel candidate genes for cardiomyogenesis, Heart without Boarders, International Conference, Porto, Portugal (abstract)

Matthias E. Futschik (2014) Systems Biology: Can it help in the study of neurodegeneration? 1st Neuroimmunology Workshop, ICM, Paris, France.

Matthias E. Futschik (2013) How Synechocystis adapts to changes in environment: A meta-analysis of its transcriptional responses, Invited Lecture, CyanoFactory Meeting, Porto, Portugal

Rui S.R. Machado, José Pedro B. G. P. Pinto, José Bragança and Matthias E. Futschik (2013) What a heart makes or breaks: A meta-analysis of gene expression profiles , 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal

José Pedro B. G. P. Pinto, Rui S.R. Machado, Ravi K.R. Kalathur, and Matthias E. Futschik (2013) StemCellNet: A web-based Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells, 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal

Miguel A. Hernández-Prieto and Matthias E. Futschik (2013) Combined analysis under iron limiting conditions of microarray and RNA-seq data reveals novel transcriptional units and facilitates the prediction of a Fur-box in Synechocystis, ESF-EMBO Symposium, Pultusk, Poland

Matthias E. Futschik (2013) How the internal world of Synechocystis adapts to the ever-changing world outside: A comprehensive meta-analysis of its transcriptional responses, ESF-EMBO Symposium, Pultusk, Poland

Miguel A. Hernández-Prieto and Matthias E. Futschik (2012) CyanoExpress: A Comprehensive Database for Evaluating the Transcriptional Response in Synechocystis, ISPP 2012, Porto, Portugal (pdf)

Miguel A. Hernández-Prieto, Verena Schön, Claudia Steglich, Wolfgang Hess and Matthias E. Futschik (2012) Simultaneous profiling of coding and non-coding RNAs from Synechocystis under iron-limiting conditions, ISPP 2012, Porto, Portugal

Matthias Futschik (2012) UniHI: Network biology goes to the bench, Contributed Talk, 3nd Meeting of the Institute for Biotechnology and Bioengineering, Lisboa, Portugal

Ravi Kalathur, Kameshwar Ayasolla and Matthias Futschik (2012) The Unfolded Protein Response and its potential role in Huntington's disease; Nature Precedings, dx.doi.org/10.1038/npre.2012.7145.1 (html)

Ravi K Kalathur and Matthias.E. Futschik (2011) The UniHI Database: A Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells, STEM 2011, Lisbon, Portugal

Matthias E. Futschik and Miguel A. Hernández-Prietoa (2011) The Transcriptional Landscape of the Cyanobacterium Synechocystis, 8th European Workshop on Molecular Biology of Cyanobacteria, Naantali, Finland

Matthias.E. Futschik (2011) Network biology, a key to understand the complexity of molecular systems, University of Otago, NZ

Matthias.E. Futschik (2011) Concepts and applications of network biology, Auckland University of Technology, NZ

Matthias Futschik (2010) Chorea Huntington: A thousand changes due to a single mutation, Contributed Talk, 2nd Meeting of the Institute for Biotechnology and Bioengineering, Universidade do Minho, Braga, Portugal (pdf)

Ravi K Kalathur and Matthias.E. Futschik (2010) Network-based analyses of Huntington's disease; Nature Precedings; dx.doi.org/10.1038/npre.2012.7078.1 (html)

Kameshwar Ayasolla, Ravi Kalathur and Matthias Futschik (2010) A systems biology approach towards deciphering the unfolded protein response in Huntington's disease; Nature Precedings; dx.doi.org/10.1038/npre.2012.7078.1 (html)

Kameshwar Ayasolla, Ravi Kalathurand Matthias Futschik (2010) ER stress: an initiator of neuroinflammation in Huntington's disease? J Neurol Neurosurg Psychiatry 81:A5 doi:10.1136/jnnp.2010.222570.16 (abstract)

Matthias Futschik (2010) A Network Perspective on Signalling, 4th National Meeting on Signal Transduction, SINAL 2010, Invited Talk, Faro, Portugal

Miguel A. Hernández-Prietoa, Luisa Barreirab, João Varelab & Matthias E. Futschik (2010) Concerted responses to iron availability in cyanobacteria, SINAL 2010, Faro, Portugal

M. Futschik (2009) Disentangling molecular interaction networks for Huntington´s Disease, Weizmann Institute, Rehovot, Israel

Matthias Futschik (2009) Disentangling molecular interaction networks for Chorea Huntington, Invited Talk, Institute for Systems Biology, Seattle, US.

ME Futschik (2009) Revealing the molecular Complexity of Human Diseases, 15th Annual German-American Kavli Frontiers of Science Symposium, Alexander von Humboldt-Stiftung - U.S. National Academy of Sciences- Irvine, California, US

Matthias Futschik, Gautam Chaurasia and Erich Wanker, Disentangling molecular intaction networks for Chorea Huntington, European Huntington's Diesease Network Meeting, Lisbon, Portugal, 2008 (html)

M. Futschik, Large-scale human protein-protein interacton maps: A tool for finding the magical bullets against complex diseases, Invited Talk, Protein-Protein Interactions as Drug Targets Symposium , Berlin, Germany, 2008

M. Futschik, Network biology, a key to understand the complexity of molecular systems, Invited Talk, University of Algarve, Faro, Portugal, 2007

M. Futschik and Hanspeter Herzel, Are we overestimating the number of cell-cycling genes? The impact of background models, Contributed Talk, German Conference on Bioinformatics, Potsdam, Germany, 2007 (pdf)

M.E. Futschik, Gautam Chaurasia, Anna Tschaut, Jenny Russ, M. Madan Babu and Hanspeter Herzel (2007) Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Networks, Contributed Talk, International workshop in Integrative Bioinformatics, Ghent, Belgim

M.E. Futschik, Anna Tschaut, Gautam Chaurasia, and Hanspeter Herzel (2007) Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks, Contributed Talk, International Workshop on Bioinformatics and Systems Biology, Tokyo, Japan

M.E. Futschik (2007) Concurrency between and coherency within human PPI maps HUPO PSI, Spring Meeting, Lyon, France

M.E. Futschik, G. Chaurasia, E. Wanker and H. Herzel, Comparison of Human Protein-Protein Interaction Maps (2006) German Conference on Bioinformatics, Contributed Talk, Tübingen, Germany

M.E. Futschik, G. Chaurasia, E. Wanker and H. Herzel (2006) Comparison and integration of human protein interaction maps, Comparison of Human Protein-Protein Interaction Maps, Contributed Talk, Interactome Networks, Wellcome Trust/Cold Spring Harbour Laboratory Conference, Hinxton, Cambridge

M.E. Futschik, C. Hänig, G. Chaurasia, E. Wanker and H. Herzel, UniHI: Unifying Large-Scale Maps of the Human Protein Interactome, Poster, ISMB 2006, Fortaleza, Brasil

M. Futschik, S. Legewie and H. Herzel (2005) Prometheus under the microscope: Modelling the complex dynamics of liver regeneration, Contributed Talk, European Conference on Mathematical and Theoretical Biology, Dresden, Germany

C. Steglich, M. Futschik, D. Lindell, W.R. Hess and S. W. Chisholm (2005) Whole genome screening for non-coding RNAs in Prochlorococcus MED4 using a high-density oligonucleotide probe microarray, International Symposium on the Genomics of Marine Phytoplankton, Roscoff, France

M. Futschik S. Legewie and H.Herzel (2005), Dynamics of Liver Regeneration- Microarrays, Arrays and Modelling, BMBF-Initiative "Systembiologie", Platform Meeting "Modeling & Bioinformatics"

M. Futschik and S. Legewie (2004), Prometheus under the microscope, Systems-Biological approaches to liver regeneration , Invited Talk, Freiburger Zentrum für Datenanalyse und Modellbildung

M.E. Futschik (2004) Microarray data analysis - Gold-mining in a minefield, Invited Talk, Mathematical Interdisciplinary Research Day: Genetic Networks, Warwick Mathematical Instituts (pdf)

M.E. Futschik (2004) Microarrays & Expression Profiling, Bioinformatics summer school in Sile-Istanbul/Turkey (Link)

M.E. Futschik (2004),Microarray data analysis I-V, Summer school on cell biology and mathematical modelling in Hvar/Croatia (Link)

M.E. Futschik, M. Sullivan, A. Reeve and N. Kasabov (2003) Modular Decision System and Information Integration for Improved Disease Outcome prediction, ECCB 2003, Oral presentation, Proceedings of the ECCB, pp.13-15, Paris, France (ps,pdf).

M.E. Futschik, M. Sullivan, A. Reeve and N. Kasabov (2003) Modular decision system and information integration for cancer outcome prediction. Currents in Computational Molecular Biology 2003, R. Sprang, P. Bézat and M. Vingron (eds.), RECOMB 2003, Berlin, Germany.

M.E. Futschik, M. Sullivan, A. Reeve and N. Kasabov (2003) Prediction of clinical behaviours and treatment for cancers. New Zealand Bioinformatics Conference, Wellington, NZ

M.E. Futschik and N.K. Kasabov (2002). Fuzzy clustering of gene expression data, Proceedings of World Congress of Computational Intelligence WCCI 2002, Hawaii, IEEE Press (pdf)

M.E. Futschik and N.K. Kasabov (2001). Revealing the Fine-Structures: Wavelet-based fuzzy clustering of gene expression data, ISMB 2001 - Programme and Abstracts, Copenhagen, p.47 (html)

N. Kasabov and M. Futschik (2001) Evolving Fuzzy Neural Networks for Knowledge Discovery from Gene Expression Data - A Case Study, RECOMB'2001 Proceedings - Currents in Computational Molecular Biology 2001, T. Lengauer and D. Sankoff (eds), Montreal, Canada, pp. 175-177

N. Kasabov and M.J. Middlemiss and M.E. Futschik (2001). Knowledge Based Neural Networks for On-Line and Off-Line Modeling and Rule Extraction in Bioinformatics, CGBI'2001 Atlantic Symposium on Computational Biology, Genome Information Systems and Technology, Durham, North Carolina, USA

M.E. Futschik, C. Brown and N. Kasabov (2000). Clustering of gene expression data by evolving self-organising maps, The 10th annual Queenstown Molecular Biology Meeting, Queenstown, New Zealand

M.E. Futschik, M. Schreiber, C. Brown and N. Kasabov (1999) Comparative studies of neural network models for ribosome binding site recognition, Proceedings of the ICONIP/ANZIIS/ANNES'99 Workshop , Dunedin, New Zealand, pp. 141-146

M. Futschik, M.Schreiber, C.M. Brown, and N. Kasabov (1999). Comparative Studies of Neural Network Models for mRNA Analysis, Poster and Software Demonstrations , ISMB 1999, Heidelberg, p. 43 (ps)


Patents

N.K. Kasabov, M.E. Futschik and A.E. Reeve (2003). Medical decision support system utilising gene expression and clinical information and method for use, International Patent, PCT/US03/025563 (WO 04/016218)

A.E. Reeve, M.E. Futschik and N.K. Kasabov (2005). Medical decision support system utilising gene expression and clinical information and method for use, European Patent, EP03788512.6-2108

A.E. Reeve, M.E. Futschik, M.J. Sullivan, N.K. Kasabov and P.J. Guilford (2002). Medical applications of adaptive learning systems using gene expression data,New Zealand Patent, No. 547894