Research Topics
| Matthias E FutschikSummaryAffiliation: Humboldt University Country: Germany Publications
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Detail Information
Publications
Comparison of human protein-protein interaction mapsMatthias E Futschik
Institute for Theoretical Biology, Charite, Humboldt Universitat, 10115 Berlin, Germany
Bioinformatics 23:605-11. 2007..To tackle this enormous challenge, different approaches have been proposed and pursued. While several large-scale human protein interaction maps have recently been published, their quality remains to be critically assessed...- Model selection and efficiency testing for normalization of cDNA microarray dataMatthias Futschik
Institute for Theoretical Biology, Humboldt Universitat, Invalidenstrasse 43, 10115 Berlin, Germany
Genome Biol 5:R60. 2004..The analysis also reveals that without parameter optimization local regression is frequently insufficient to remove systematic errors in microarray data... - OLIN: optimized normalization, visualization and quality testing of two-channel microarray dataMatthias E Futschik
Institute for Theoretical Biology, Humboldt Universitat, Invalidenstrasse 43, 10115 Berlin, Germany
Bioinformatics 21:1724-6. 2005..CONTACT: m.futschik@biologie.hu-berlin.de SUPPLEMENTARY INFORMATION: Further information about the methods used in the OLIN software package can be found at http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN... - Noise-robust soft clustering of gene expression time-course dataMatthias E Futschik
Institute of Theoretical Biology, Humboldt University, Invalidenstr 43, 10115 Berlin, Germany
J Bioinform Comput Biol 3:965-88. 2005..Procedures to find optimal clustering parameters were developed. A software package for soft clustering has been developed based on the open-source statistical language R. The package called Mfuzz is freely available... - UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactomeGautam Chaurasia
Institute for Theoretical Biology, Charite, Humboldt University, Berlin, Germany
Nucleic Acids Res 37:D657-60. 2009..This will enable researchers to target their analysis and to prioritize candidate proteins for follow-up studies... - UniHI: an entry gate to the human protein interactomeGautam Chaurasia
Institute for Theoretical Biology, Charite, Humboldt Universitat, Berlin, Germany
Nucleic Acids Res 35:D590-4. 2007..It includes more than 150,000 distinct interactions between more than 17 000 unique human proteins. UniHI provides researchers with a flexible integrated tool for finding and using comprehensive information about the human interactome... - Systematic functional assessment of human protein-protein interaction mapsGautam Chaurasia
Institute for Theoretical Biology, Humboldt Universitat, Berlin, Germany
Genome Inform 17:36-45. 2006..The analysis shows that these maps include a large number of common proteins, but only a small number of common interactions. We detected several types of biases that need to be considered in the future utilization of these maps... - Graph-theoretical comparison reveals structural divergence of human protein interaction networksMatthias E Futschik
Institute for Theoretical Biology, Charite, Humboldt Universitat, Berlin, Germany
Genome Inform 18:141-51. 2007..Our study strongly indicates that graph-theoretical analysis can be severely compromised by the observed structural divergence and reassessment of earlier results might be warranted... - Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysisMatthias E Futschik
Institute for Theoretical Biology, Charite, Humboldt Universitat, Invalidenstrasse 43, 10115 Berlin, Germany
Bioinformatics 24:1063-9. 2008..Frequently, quite large numbers of genes have been detected as periodically expressed. However, the small overlap between genes identified in different studies has cast some doubts on the reliability of the periodic expression detected... - Comparison and consolidation of microarray data sets of human tissue expressionJenny Russ
Institute for Theoretical Biology, Charite, Humboldt University, Berlin, Germany
BMC Genomics 11:305. 2010..Critical comparison of different data sets can help to reveal such errors and to avoid pitfalls in their application... - Prediction of clinical behaviour and treatment for cancersMatthias E Futschik
Departments of Information Science and Biochemistry, University of Otago, Dunedin, New Zealand
Appl Bioinformatics 2:S53-8. 2003..6%. The model introduced here may be generally applicable to the combination of various types of molecular and clinical data for improving medical decision support systems and individualising patient care... - Evolving connectionist systems for knowledge discovery from gene expression data of cancer tissueMatthias E Futschik
Department of Information Science, University of Otago, P O Box 56, Dunedin, New Zealand
Artif Intell Med 28:165-89. 2003..These rules point to genes that are strongly associated with specific types of cancer and may be used for the development of new tests and treatment discoveries... - Genome-wide expression dynamics of a marine virus and host reveal features of co-evolutionDebbie Lindell
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nature 449:83-6. 2007..Thus activation of host genes during infection may be directing the co-evolution of gene content in both host and phage genomes...