RelEx—Relation extraction using dependency parse trees von Fundel, Katrin, Küffner, Robert, Zimmer, Ralf

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Wisdom of crowds for robust gene network inference von Marbach, Daniel, Costello, James C, Küffner, Robert, Vega, Nicole M, Prill, Robert J, Camacho, Diogo M, Allison, Kyle R, Kellis, Manolis, Collins, James J, Stolovitzky, Gustavo

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Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression von Küffner, Robert, Zach, Neta, Norel, Raquel, Hawe, Johann, Schoenfeld, David, Wang, Liuxia, Li, Guang, Fang, Lilly, Mackey, Lester, Hardiman, Orla, Cudkowicz, Merit, Sherman, Alexander, Ertaylan, Gokhan, Grosse-Wentrup, Moritz, Hothorn, Torsten, van Ligtenberg, Jules, Macke, Jakob H, Meyer, Timm, Schölkopf, Bernhard, Tran, Linh, Vaughan, Rubio, Stolovitzky, Gustavo, Leitner, Melanie L

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Inferring gene regulatory networks by ANOVA von KUFFNER, Robert, PETRI, Tobias, TAVAKKOLKHAH, Pegah, WINDHAGER, Lukas, ZIMMER, Ralf

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On protocols and measures for the validation of supervised methods for the inference of biological networks von Schrynemackers, Marie, Küffner, Robert, Geurts, Pierre

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Detection of network motifs using three-way ANOVA von Tavakkolkhah, Pegah, Zimmer, Ralf, Küffner, Robert

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miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature von Naeem, Haroon, Küffner, Robert, Csaba, Gergely, Zimmer, Ralf

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Rigorous assessment of gene set enrichment tests von NAEEM, Haroon, ZIMMER, Ralf, TAVAKKOLKHAH, Pegah, KUFFNER, Robert

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Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets von Windhager, Lukas, Zierer, Jonas, Küffner, Robert

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Pathway analysis in metabolic databases via differential metabolic display (DMD) von Küffner, Robert, Zimmer, Ralf, Lengauer, Thomas

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MIRTFnet: analysis of miRNA regulated transcription factors von Naeem, Haroon, Küffner, Robert, Zimmer, Ralf

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Petri Nets with Fuzzy Logic (PNFL): reverse engineering and parametrization von Küffner, Robert, Petri, Tobias, Windhager, Lukas, Zimmer, Ralf

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Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts von Küffner, Robert, Fundel, Katrin, Zimmer, Ralf

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Experiment specific expression patterns von Petri, Tobias, Küfner, Robert, Zimmer, Ralf

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Reliable gene signatures for microarray classification: assessment of stability and performance von Davis, Chad A., Gerick, Fabian, Hintermair, Volker, Friedel, Caroline C., Fundel, Katrin, Küffner, Robert, Zimmer, Ralf

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DREAMTools: a Python package for scoring collaborative challenges [version 2; peer review: 1 approved, 2 approved with reservations] von Cokelaer, Thomas, Bansal, Mukesh, Bare, Christopher, Bilal, Erhan, Bot, Brian M, Chaibub Neto, Elias, Eduati, Federica, de la Fuente, Alberto, Gönen, Mehmet, Hill, Steven M, Hoff, Bruce, Karr, Jonathan R, Küffner, Robert, Menden, Michael P, Meyer, Pablo, Norel, Raquel, Pratap, Abhishek, Prill, Robert J, Weirauch, Matthew T, Costello, James C, Stolovitzky, Gustavo, Saez-Rodriguez, Julio

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A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae von Geistlinger, Ludwig, Csaba, Gergely, Dirmeier, Simon, Küffner, Robert, Zimmer, Ralf

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From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems von Geistlinger, Ludwig, Csaba, Gergely, Küffner, Robert, Mulder, Nicola, Zimmer, Ralf

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Addressing false discoveries in network inference von Petri, Tobias, Altmann, Stefan, Geistlinger, Ludwig, Zimmer, Ralf, Küffner, Robert

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A Turing test for artificial expression data von Maier, Robert, Zimmer, Ralf, Küffner, Robert

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