Robert Küffner

Summary

Country: Germany

Publications

  1. pmc MIRTFnet: analysis of miRNA regulated transcription factors
    Haroon Naeem
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Germany
    PLoS ONE 6:e22519. 2011
  2. 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
  3. 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
  4. doi request reprint A Turing test for artificial expression data
    Robert Maier
    Department of Informatics, Ludwig Maximilians Universitat, 80333 München, Germany
    Bioinformatics 29:2603-9. 2013
  5. ncbi request reprint Reliable gene signatures for microarray classification: assessment of stability and performance
    Chad A Davis
    Institute of Informatics, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17 80333 Munich, Germany
    Bioinformatics 22:2356-63. 2006
  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. 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
  8. pmc A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae
    Ludwig Geistlinger
    Practical Informatics and Bioinformatics, Institute for Informatics, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 Munich, Germany
    Nucleic Acids Res 41:8452-63. 2013
  9. 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
  10. pmc Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets
    Lukas Windhager
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich, Germany
    PLoS ONE 9:e84596. 2014

Collaborators

Detail Information

Publications12

  1. 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...
  2. 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...
  3. 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...
  4. doi request reprint A Turing test for artificial expression data
    Robert Maier
    Department of Informatics, Ludwig Maximilians Universitat, 80333 München, Germany
    Bioinformatics 29:2603-9. 2013
    ..However, this just defers the problem, as it is difficult to assess how closely simulators emulate the properties of real data...
  5. ncbi request reprint Reliable gene signatures for microarray classification: assessment of stability and performance
    Chad A Davis
    Institute of Informatics, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17 80333 Munich, Germany
    Bioinformatics 22:2356-63. 2006
    ..Both unstable gene signatures and overestimated classification accuracy can impair biological conclusions...
  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. 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...
  8. pmc A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae
    Ludwig Geistlinger
    Practical Informatics and Bioinformatics, Institute for Informatics, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 Munich, Germany
    Nucleic Acids Res 41:8452-63. 2013
    ..Additionally, we developed a browsable system organizing the network into pathway maps, which allows to inspect and trace the evidence for each annotated regulation in the model. ..
  9. 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...
  10. pmc Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets
    Lukas Windhager
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich, Germany
    PLoS ONE 9:e84596. 2014
    ..g. due to probabilistic optimization or a cross-validation procedure. ..
  11. 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...