Robert Küffner

Summary

Country: Germany

Publications

  1. ncbi request reprint Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts
    Robert Küffner
    Department of Informatics, Ludwig Maximilians Universitat Munchen, Munchen, Germany
    Bioinformatics 21:ii259-67. 2005
  2. doi request reprint Rigorous assessment of gene set enrichment tests
    Haroon Naeem
    Department of Informatics, Ludwig Maximilians Universitat, Amalienstrasse 17, Munich, Germany
    Bioinformatics 28:1480-6. 2012
  3. pmc MIRTFnet: analysis of miRNA regulated transcription factors
    Haroon Naeem
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Germany
    PLoS ONE 6:e22519. 2011
  4. ncbi request reprint RelEx--relation extraction using dependency parse trees
    Katrin Fundel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    Bioinformatics 23:365-71. 2007
  5. doi request reprint Inferring gene regulatory networks by ANOVA
    Robert Küffner
    Department of Informatics, Ludwig Maximilians University, Amalienstr 17, 80333 Munich, Germany
    Bioinformatics 28:1376-82. 2012
  6. pmc miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature
    Haroon Naeem
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstr, 17 80333 München, Germany
    BMC Bioinformatics 11:135. 2010
  7. pmc ProSAS: a database for analyzing alternative splicing in the context of protein structures
    Fabian Birzele
    Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig Maximilians University, Amalienstrasse 17, D 80333 Munich, Germany
    Nucleic Acids Res 36:D63-8. 2008

Collaborators

Detail Information

Publications7

  1. ncbi request reprint Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts
    Robert Küffner
    Department of Informatics, Ludwig Maximilians Universitat Munchen, Munchen, Germany
    Bioinformatics 21:ii259-67. 2005
    ..However, comparing experimental results against manually compiled knowledge resources might limit or bias the perspective on the data. Thus, manual analysis by experts is required to obtain confident predictions about involved processes...
  2. doi request reprint Rigorous assessment of gene set enrichment tests
    Haroon Naeem
    Department of Informatics, Ludwig Maximilians Universitat, Amalienstrasse 17, Munich, Germany
    Bioinformatics 28:1480-6. 2012
    ..The objective evaluation of tests on real measurements has not been possible as it is difficult to decide a priori, which processes will be affected in given experiments...
  3. pmc MIRTFnet: analysis of miRNA regulated transcription factors
    Haroon Naeem
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Germany
    PLoS ONE 6:e22519. 2011
    ..The miRNA induced regulatory effects can be propagated via transcription factors (TFs). We propose the method MIRTFnet to identify miRNA controlled TFs as active regulators if their downstream target genes are differentially expressed...
  4. ncbi request reprint RelEx--relation extraction using dependency parse trees
    Katrin Fundel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    Bioinformatics 23:365-71. 2007
    ..g. physical or regulatory interactions between genes and proteins. Most interactions mentioned in the free text of biomedical publications are not yet contained in structured databases...
  5. doi request reprint Inferring gene regulatory networks by ANOVA
    Robert Küffner
    Department of Informatics, Ludwig Maximilians University, Amalienstr 17, 80333 Munich, Germany
    Bioinformatics 28:1376-82. 2012
    ..To improve the understanding of molecular regulation events, various approaches have been developed for deducing gene regulatory networks from mRNA expression data...
  6. pmc miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature
    Haroon Naeem
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstr, 17 80333 München, Germany
    BMC Bioinformatics 11:135. 2010
    ..We propose to use text mining of publication abstracts for extracting microRNA-gene associations including microRNA-target relations to complement current repositories...
  7. pmc ProSAS: a database for analyzing alternative splicing in the context of protein structures
    Fabian Birzele
    Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig Maximilians University, Amalienstrasse 17, D 80333 Munich, Germany
    Nucleic Acids Res 36:D63-8. 2008
    ..The ProSAS database is freely accessible at http://www.bio.ifi.lmu.de/ProSAS...