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Research Articles

Collection of Research Articles
Verification of systems biology research in the age of collaborative competition
Nature Biotechnology 29, 811–815 (2011)
OpenFreezer: a reagent information management software system
Nature Methods 8, 612–613 (2011)
Response to Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”
Science 20 May 2011: Vol. 332 no. 6032 p. 917
Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling.
Cell. 2015 Sep 16. pii: S0092-8674(15)01108-3. doi: 10.1016/j.cell.2015.08.056.
Unmasking Determinants of Specificity in the Human Kinome.
Cell. 2015 Sep 16. pii: S0092-8674(15)01109-5. doi: 10.1016/j.cell.2015.08.057.
Pathway and network analysis of cancer genomes.
Nature Methods. 2015 Jun 30;12(7):615-21.
The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase
Nature. 2015 Jun 4;522(7554):106-10.
Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy
Science Signaling, 7 April 2015 Vol. 8, Issue 371, p. rs3
Bowhead: Bayesian modelling of cell velocity during concerted cell migration.
PLoS Comput Biol. 2018 Jan 8;14(1):e1005900. doi: 10.1371/journal.pcbi.1005900.
Farnesylated heat shock protein 40 is a component of membrane-bound RISC in Arabidopsis.
J Biol Chem. 2018 Oct 26;293(43):16608-16622. doi: 10.1074/jbc.RA118.003887.
Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output.
PLoS Biology 2019 Mar 21;17(3):e2006540. doi: 10.1371/journal.pbio.2006540.
Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs.
Elife. 2019 May 24;8. pii: e44635. doi: 10.7554/eLife.44635.
Global view of the RAF-MEK-ERK module and its immediate downstream effectors.
Sci Rep. 2019 Jul 26;9(1):10865. doi: 10.1038/s41598-019-47245-x.
Probability-based detection of phosphoproteomic uncertainty reveals rare signaling events driven by oncogenic kinase gene fusion
PREPRINT
High-dose oncogenic PIK3CA drives constitutive cellular stemness through self-sustained TGFβ pathway activation
PREPRINT
Deep Neural Networks Identify Signaling Mechanisms of ErbB-Family Drug Resistance From a Continuous Cell Morphology State Space
PREPRINT
PhD thesis (Rune Linding)
EMBL April 2004.
Cell-Specific Information Processing in Segregating Cell Populations
In this Research Article published in Science, we provide the first systems- and cell-specific network models of contact-initiated signaling between two distinct cell types.
Systematic discovery of in vivo phosphorylation networks.
Cell. 2007 Jun 29;129(7):1415-26. Epub 2007 Jun 14.
NetworKIN: a resource for exploring cellular phosphorylation networks.
Nucleic Acids Res. 2008 Jan;36(Database issue):D695-9. Epub 2007 Nov 2.