- Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contextsRobert 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...
- Rigorous assessment of gene set enrichment testsHaroon 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...
- MIRTFnet: analysis of miRNA regulated transcription factorsHaroon 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...
- RelEx--relation extraction using dependency parse treesKatrin 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...
- Inferring gene regulatory networks by ANOVARobert 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...
- miRSel: automated extraction of associations between microRNAs and genes from the biomedical literatureHaroon 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...
- ProSAS: a database for analyzing alternative splicing in the context of protein structuresFabian 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...