PUBLICATIONS

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

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

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

M. Futschik, Anna Tschaut, Gautam Chaurasia, and Hanspeter Herzel (2007) Graph-Theoretical Comparison Reveals Structural Divergence of Human Protein Interaction Networks, Genome Informatics, 18, 141-151, 2007 (pdf, Supplementary Materials)

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

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

M. Futschik and Hanspeter Herzel, Are we overestimating the number of cell-cycling genes? The impact of background models for time series data, Lecture Notes in Informatics, 115, 2-14, 2007 (pdf, Supplementary Materials)

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

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

M.E. Futschik, G. Chaurasia and H. Herzel, Comparison of Human Protein-Protein Interaction Maps, Bioinformatics, 23(5):605-611, 2007 (PubMed, pdf, Supplementary Materials)

G. Chaurasia, Y. Iqbal, C. Hänig, H. Herzel, E.E. Wanker and M.E. Futschik, Flexible web-based integration of distributed large-scale human protein interaction maps, Journal of Integrative Bioinformatics, 4 (1):51, 2007 (Abstract, pdf)

G. Chaurasia, Y. Iqbal, C. Hänig, H. Herzel, E.E. Wanker and M.E. Futschik, UniHI: an entry gate to the human protein interactome, Nucleic Acids Research, Database issue, D590-4, 2007 (pdf, PubMed,Supplementary Materials)

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

M.E. Futschik, G. Chaurasia, E. Wanker and H. Herzel, Comparison of Human Protein-Protein Interaction Maps, Lecture Notes in Informatics, P-83, 21-32, 2006 (preprint-pdf)

G. Chaurasia, H. Herzel, E.E. Wanker and M.E. Futschik, Systematic functional assessment of human proteins-protein interaction maps, Genome Informatics, 17(1), 36-45, 2006 (pdf)

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

M.E. Futschik and B. Charlisle, Noise robust clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, Vol. 3, No. 4, 965-988, 2005 (pdf , PubMed)

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

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

M.E. Futschik, M. Sullivan, A. Reeve, N. Kasabov, Prediction of clinical behaviour and treatment for cancers, Applied Bioinformatics, Vol.2(3) S53-S58, 2003 (Abstract , pre-print pdf, PubMed)

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

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

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

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

PRESENTATIONS AND ABSTRACTS

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

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, Dynamics of Liver Regeneration- Microarrays, Arrays and Modelling, BMBF-Initiative "Systembiologie", Platform Meeting "Modeling & Bioinformatics" (Link), January 2005

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

M.E. Futschik, Microarray data analysis - Gold-mining in a minefield, Invited Talk, Mathematical Interdisciplinary Research Day: Genetic Networks, Warwick Mathematical Instituts, 15 November 2004 (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, p. 8

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, Programme and Abstracts: The 10th annual Queenstown Molecular Biology Meeting, Queenstown, New Zealand, p.76

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

M.E. Futschik, N.K. Kasabov, M.J. Sullivan and A.E. Reeve (2002). Combining clinical and microarray-based prognostic models for improved DLBCL outcome prediction, U.S. Provisional Patent Application, No. 60/403808

N.K. Kasabov, M.E. Futschik, M.J. Sullivan and A.E. Reeve (2002). Method and a medical decision support system utilising gene expression and clinical information, U.S. Provisional Patent Application , No. 60/403756

N.K. Kasabov, M.E. Futschik, M.J. Sullivan and A.E. Reeve (2002). Modular decision systems for disease outcome prediction, U.S. Provisional Patent Application , No. 60/403754

A.E. Reeve, M.E. Futschik, M.J. Sullivan, N.K. Kasabov and P.J. Guilford (2002), Medical applications of adaptive learning systems, New Zealand patent application, No. 517817