- Petri Nets with Fuzzy Logic (PNFL): reverse engineering and parametrizationRobert Küffner
Institut fur Informatik, Ludwig Maximilians Universitat, Munchen, Germany
PLoS ONE 5:. 2010..The in silico part of DREAM4 solicited the inference of cycle-rich gene regulatory networks from heterogeneous, noisy expression data including time courses as well as knockout, knockdown and multifactorial perturbations...
- 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...
- A Turing test for artificial expression dataRobert 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...
- Reliable gene signatures for microarray classification: assessment of stability and performanceChad 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...
- 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...
- 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...
- Addressing false discoveries in network inferenceTobias Petri
Ludwig Maximilians Universitat Munchen, Institut fur Informatik, Munich, Germany and
Bioinformatics 31:2836-43. 2015..Recently, published methods report improved predictions by exploiting the a priori known targets of a regulator (its local topology) in addition to expression profiles...
- 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...
- A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiaeLudwig 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. ..
- Refining ensembles of predicted gene regulatory networks based on characteristic interaction setsLukas 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. ..
- 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...