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Linding Lab, BRIC & DTU [2011-2018]

Publications from our group at the Biotech Research & Innovation Center (BRIC), University of Copenhagen (UCPH) and DTU.
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.
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.
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.
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.
Cancer systems biology: Harnessing off-target effects.
Nature Chemical Biology 2017 Nov 21;13(12):1204-1205. doi: 10.1038/nchembio.2519.
Dynamic Rearrangement of Cell States Detected by Systematic Screening of Sequential Anticancer Treatments
Cell Reports 2017 Sep 19;20(12):2784-2791. doi: 10.1016/j.celrep.2017.08.095.
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.
The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase
Nature. 2015 Jun 4;522(7554):106-10.
Pathway and network analysis of cancer genomes.
Nature Methods. 2015 Jun 30;12(7):615-21.
Modulation of the chromatin phosphoproteome by the haspin protein kinase.
Mol Cell Proteomics. 2014 Jul;13(7):1724-40.
KinomeXplorer: an integrated platform for kinome biology studies.
Nat Methods. 2014 Jun;11(6):603-4.
Identification of Hypoxia-Regulated Proteins Using MALDI-Mass Spectrometry Imaging Combined with Quantitative Proteomics.
J Proteome Res. 2014 Apr 24.
CoreFlow: a computational platform for integration, analysis and modeling of complex biological data.
J Proteomics. 2014 Apr 4;100:167-73.
Experimental and computational tools for analysis of signaling networks in primary cells.
Curr Protoc Immunol. 2014 Feb 4;104:Unit 11.11.
Personalized network-based treatments in oncology.
Clin Pharmacol Ther. 2013 Dec;94(6):646-50.
Computational approaches to identify functional genetic variants in cancer genomes.
Nature Methods 2013 Jul 30;10(8):723-9.
Global characterization of signalling networks associated with tamoxifen resistance in breast cancer.
FEBS Journal 2013 Jul 22.
PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development
J Proteomics. 2012 Dec 7. pii: S1874-3919(12)00755-5.
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
In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis
Cell Reports. 2013 Jan 30. pii: S2211-1247(13)00010-7.
Navigating cancer network attractors for tumor-specific therapy
Nature Biotechnology 30, 842–848 (2012)
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).
Proteomics Clin Appl. 2011 Dec;5(11-12):580-9.
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).
Proteomics. 2012 Jan;12(1):11-20.
Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam principles).
Mol Cell Proteomics. 2011 Dec;10(12):O111.015446.
Mutational Properties of Amino Acid Residues - Implications for Evolvability of Phosphorylatable Residues
Phil. Trans. R. Soc. B 19 September 2012 vol. 367 no. 1602 2584-2593
Cells, shared memory and breaking the PTM code
Molecular Systems Biology 8 Article number: 598 doi:10.1038/msb.2012.33
Network Medicine Strikes a Blow against Breast Cancer
Cell. 2012 May 11;149(4):731-3.
Recommendations for mass spectrometry data quality metrics for open access data (Corollary to the Amsterdam principles).
J Proteome Res. 2012 Feb 3;11(2):1412-9.
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