Rune Linding

Summary

Affiliation: Samuel Lunenfeld Research Institute
Country: Canada

Publications

  1. pmc NetworKIN: a resource for exploring cellular phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Nucleic Acids Res 36:D695-9. 2008
  2. pmc Systematic discovery of in vivo phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Cell 129:1415-26. 2007
  3. ncbi Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
    Sci Signal 2:ra39. 2009
  4. ncbi Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells
    Claus Jørgensen
    Samuel Lunenfeld Research Institute SLRI, Mount Sinai Hospital, Toronto M5G 1X5, Canada
    Science 326:1502-9. 2009
  5. pmc Positive selection of tyrosine loss in metazoan evolution
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada
    Science 325:1686-8. 2009
  6. ncbi Roles of “junk phosphorylation” in modulating biomolecular association of phosphorylated proteins?
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Cell Cycle 9:1276-80. 2010
  7. ncbi Eukaryotic protein domains as functional units of cellular evolution
    Jing Jin
    Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Ontario, Canada
    Sci Signal 2:ra76. 2009
  8. doi Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Proteomics 9:5233-42. 2009
  9. pmc WW domains provide a platform for the assembly of multiprotein networks
    Robert J Ingham
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Mol Cell Biol 25:7092-106. 2005
  10. ncbi CoreFlow: a computational platform for integration, analysis and modeling of complex biological data
    Adrian Pasculescu
    Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    J Proteomics 100:167-73. 2014

Collaborators

Detail Information

Publications22

  1. pmc NetworKIN: a resource for exploring cellular phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Nucleic Acids Res 36:D695-9. 2008
    ..The database currently contains a predicted phosphorylation network with 20,224 site-specific interactions involving 3978 phosphoproteins and 73 human kinases from 20 families...
  2. pmc Systematic discovery of in vivo phosphorylation networks
    Rune Linding
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Cell 129:1415-26. 2007
    ..Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate...
  3. ncbi Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
    Sci Signal 2:ra39. 2009
    ..We reveal that multiple complex diseases seem to converge within the conserved networks, suggesting that disease development might rely on common molecular networks...
  4. ncbi Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells
    Claus Jørgensen
    Samuel Lunenfeld Research Institute SLRI, Mount Sinai Hospital, Toronto M5G 1X5, Canada
    Science 326:1502-9. 2009
    ..We provide systems- and cell-specific network models of contact-initiated signaling between two distinct cell types...
  5. pmc Positive selection of tyrosine loss in metazoan evolution
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada
    Science 325:1686-8. 2009
    ..We propose that this phenomenon illustrates genome-wide adaptive evolution to accommodate beneficial genetic perturbation...
  6. ncbi Roles of “junk phosphorylation” in modulating biomolecular association of phosphorylated proteins?
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Cell Cycle 9:1276-80. 2010
    ..We, therefore, advocate the development of complementary evolutionary approaches to interpret physiological important sites...
  7. ncbi Eukaryotic protein domains as functional units of cellular evolution
    Jing Jin
    Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Ontario, Canada
    Sci Signal 2:ra76. 2009
    ..Based on this scheme, we propose a mechanism by which Tudor domains may have evolved to support different modes of epigenetic regulation and suggest a role for the germline group of mammalian Tudor domains in Piwi-regulated RNA biology...
  8. doi Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks
    Chris Soon Heng Tan
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
    Proteomics 9:5233-42. 2009
    ....
  9. pmc WW domains provide a platform for the assembly of multiprotein networks
    Robert J Ingham
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Mol Cell Biol 25:7092-106. 2005
    ..These data suggest that WW domains provide a versatile platform to link individual proteins into physiologically important networks...
  10. ncbi CoreFlow: a computational platform for integration, analysis and modeling of complex biological data
    Adrian Pasculescu
    Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    J Proteomics 100:167-73. 2014
    ....
  11. doi Dynamic modularity in protein interaction networks predicts breast cancer outcome
    Ian W Taylor
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, Ontario M5G 1X5, Canada
    Nat Biotechnol 27:199-204. 2009
    ..Analysis of two breast cancer patient cohorts revealed that altered modularity of the human interactome may be useful as an indicator of breast cancer prognosis...
  12. doi Network medicine
    Tony Pawson
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Canada
    FEBS Lett 582:1266-70. 2008
    ..We term this approach, network medicine...
  13. ncbi Synthetic modular systems--reverse engineering of signal transduction
    Tony Pawson
    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5
    FEBS Lett 579:1808-14. 2005
    ..Designing and successfully introducing synthetic proteins into cellular pathways would provide us with a powerful research tool with many applications, such as development of biosensors, protein drugs and rewiring of biological pathways...
  14. ncbi Linear motif atlas for phosphorylation-dependent signaling
    Martin Lee Miller
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    Sci Signal 1:ra2. 2008
    ..The atlas is available as a community resource (http://netphorest.info)...
  15. pmc ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
    Pål Puntervoll
    Department of Molecular Biology, University of Bergen, Norway
    Nucleic Acids Res 31:3625-30. 2003
    ..Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more...
  16. pmc GlobPlot: Exploring protein sequences for globularity and disorder
    Rune Linding
    European Molecular Biology Laboratory, Biocomputing Unit, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3701-8. 2003
    ..GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity...
  17. pmc BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
    Konstantinos Bimpikis
    European Molecular Biology Laboratory, Postfach 10 2209, 69012 Heidelberg, Germany
    Nucleic Acids Res 31:3792-4. 2003
    ..By allowing the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword...
  18. pmc Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Francesca Diella
    Cellzome AG, Heidelberg, Germany
    BMC Bioinformatics 5:79. 2004
    ..The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins...
  19. doi Directional and quantitative phosphorylation networks
    Claus Jørgensen
    Brief Funct Genomic Proteomic 7:17-26. 2008
    ..By combining quantitative measurements of phosphorylation events with computational approaches, we argue that systems level models will help to decipher complex diseases through the ability to predict cellular systems trajectories...
  20. pmc Phosphorylation networks regulating JNK activity in diverse genetic backgrounds
    Chris Bakal
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02215, USA
    Science 322:453-6. 2008
    ....
  21. pmc Systematic discovery of new recognition peptides mediating protein interaction networks
    Victor Neduva
    European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Biol 3:e405. 2005
    ..We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes...
  22. ncbi Normalization of nomenclature for peptide motifs as ligands of modular protein domains
    Rein Aasland
    Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
    FEBS Lett 513:141-4. 2002
    ..This proposal will be reviewed in the future and will therefore be open for the inclusion of new rules, modifications and changes...