Research Topics
| Rune LindingSummaryAffiliation: Samuel Lunenfeld Research Institute Country: Canada Publications
| Collaborators
|
Detail Information
Publications
NetworKIN: a resource for exploring cellular phosphorylation networksRune 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...- Systematic discovery of in vivo phosphorylation networksRune 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... 
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseasesChris 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...- Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cellsClaus 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... - Positive selection of tyrosine loss in metazoan evolutionChris 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... 
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...- Eukaryotic protein domains as functional units of cellular evolutionJing 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... - WW domains provide a platform for the assembly of multiprotein networksRobert 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... - Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networksChris Soon Heng Tan
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
Proteomics 9:5233-42. 2009.... - Dynamic modularity in protein interaction networks predicts breast cancer outcomeIan 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... - Network medicineTony Pawson
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Canada
FEBS Lett 582:1266-70. 2008..We term this approach, network medicine... - Synthetic modular systems--reverse engineering of signal transductionTony 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... - Phosphorylation networks regulating JNK activity in diverse genetic backgroundsChris Bakal
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02215, USA
Science 322:453-6. 2008.... - Linear motif atlas for phosphorylation-dependent signalingMartin 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)... - Directional and quantitative phosphorylation networksClaus 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... - Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteinsFrancesca 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... - BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databasesKonstantinos 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... - GlobPlot: Exploring protein sequences for globularity and disorderRune 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... - ELM server: A new resource for investigating short functional sites in modular eukaryotic proteinsPål 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... - Systematic discovery of new recognition peptides mediating protein interaction networksVictor 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... - Normalization of nomenclature for peptide motifs as ligands of modular protein domainsRein 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...