Walter Kolch

Summary

Affiliation: University College Dublin
Country: Ireland

Publications

  1. pmc Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise
    Marc R Birtwistle
    Dept of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    BMC Syst Biol 6:109. 2012
  2. pmc Addressing the challenge of defining valid proteomic biomarkers and classifiers
    Mohammed Dakna
    Mosaiques Diagnostics and Therapeutics, Hannover, Germany
    BMC Bioinformatics 11:594. 2010
  3. doi request reprint The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier
    Oliver E Sturm
    Department of Computing Science, University of Glasgow, Glasgow G12 8QQ, UK
    Sci Signal 3:ra90. 2010
  4. doi request reprint Functional proteomics to dissect tyrosine kinase signalling pathways in cancer
    Walter Kolch
    Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
    Nat Rev Cancer 10:618-29. 2010
  5. pmc Eukaryotic translation initiation factor 3, subunit a, regulates the extracellular signal-regulated kinase pathway
    Tian Rui Xu
    Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
    Mol Cell Biol 32:88-95. 2012
  6. pmc The differential effects of wild-type and mutated K-Ras on MST2 signaling are determined by K-Ras activation kinetics
    David Romano
    Systems Biology Ireland, University College Dublin, Dublin, Ireland
    Mol Cell Biol 33:1859-68. 2013
  7. doi request reprint Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species
    Tian Rui Xu
    Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G128QQ, UK
    Sci Signal 3:ra20. 2010
  8. doi request reprint An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells
    Tapesh Santra
    Systems Biology Ireland, Conway Institute, University College Dublin UCD, Belfield, Dublin 4, Ireland
    Adv Exp Med Biol 736:59-80. 2012
  9. pmc Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway
    Richard J Orton
    Institute of Comparative Medicine, Faculty of Veterinary Medicine, University of Glasgow, Glasgow, UK
    BMC Syst Biol 3:100. 2009
  10. pmc Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology
    Tapesh Santra
    Systems Biology Ireland, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    BMC Syst Biol 7:57. 2013

Collaborators

Detail Information

Publications34

  1. pmc Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise
    Marc R Birtwistle
    Dept of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
    BMC Syst Biol 6:109. 2012
    ..Here, we apply deterministic and probabilistic models and biochemical measurements to study how network topologies and cell-to-cell protein abundance variations interact to shape signaling responses...
  2. pmc Addressing the challenge of defining valid proteomic biomarkers and classifiers
    Mohammed Dakna
    Mosaiques Diagnostics and Therapeutics, Hannover, Germany
    BMC Bioinformatics 11:594. 2010
    ..The second urine of the morning was collected from apparently healthy male and female volunteers (aged 21-40) in the course of the routine medical check-up before recruitment at the Hannover Medical School...
  3. doi request reprint The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier
    Oliver E Sturm
    Department of Computing Science, University of Glasgow, Glasgow G12 8QQ, UK
    Sci Signal 3:ra90. 2010
    ..These properties determine biological behavior, including activation kinetics and the response to drugs...
  4. doi request reprint Functional proteomics to dissect tyrosine kinase signalling pathways in cancer
    Walter Kolch
    Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
    Nat Rev Cancer 10:618-29. 2010
    ..Cancerous genetic mutations derange these protein networks in complex ways that are tractable by proteomics...
  5. pmc Eukaryotic translation initiation factor 3, subunit a, regulates the extracellular signal-regulated kinase pathway
    Tian Rui Xu
    Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
    Mol Cell Biol 32:88-95. 2012
    ..Thus, eIF3a is a negative modulator of ERK pathway activation and its biological effects...
  6. pmc The differential effects of wild-type and mutated K-Ras on MST2 signaling are determined by K-Ras activation kinetics
    David Romano
    Systems Biology Ireland, University College Dublin, Dublin, Ireland
    Mol Cell Biol 33:1859-68. 2013
    ..Our data suggest that the close relationship between Ras prosurvival and proapoptotic signaling is coordinated via the differential regulation of the MST2-LATS1 interaction by transient and chronic stimuli...
  7. doi request reprint Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species
    Tian Rui Xu
    Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G128QQ, UK
    Sci Signal 3:ra20. 2010
    ..Thus, our formal methodology rationally infers evidentially supported pathway topologies even when a limited number of biochemical and kinetic measurements are available...
  8. doi request reprint An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells
    Tapesh Santra
    Systems Biology Ireland, Conway Institute, University College Dublin UCD, Belfield, Dublin 4, Ireland
    Adv Exp Med Biol 736:59-80. 2012
    ..We compared our results with data available from public databases and report a high level of prediction accuracy...
  9. pmc Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway
    Richard J Orton
    Institute of Comparative Medicine, Faculty of Veterinary Medicine, University of Glasgow, Glasgow, UK
    BMC Syst Biol 3:100. 2009
    ..In this study, we have used computational modelling techniques to investigate what effects various cancerous alterations have on the signalling flow through the ERK pathway...
  10. pmc Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology
    Tapesh Santra
    Systems Biology Ireland, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    BMC Syst Biol 7:57. 2013
    ..Here, we focus on unraveling network topologies from steady state responses of biochemical networks to successive experimental perturbations...
  11. doi request reprint Computational approaches for analyzing information flow in biological networks
    BORIS KHOLODENKO
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Sci Signal 5:re1. 2012
    ....
  12. doi request reprint It takes two to tango--signalling by dimeric Raf kinases
    Angela Baljuls
    Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
    Mol Biosyst 9:551-8. 2013
    ....
  13. pmc Phosphodiesterase-8A binds to and regulates Raf-1 kinase
    Kim M Brown
    Institute of Cardiovascular and Medical Science, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
    Proc Natl Acad Sci U S A 110:E1533-42. 2013
    ..Similarly, PDE8 deletion in Drosophila melanogaster reduced basal ERK activation and sensitized flies to stress-induced death. We propose that PDE8A is a physiological regulator of Raf-1 signaling in some cells...
  14. pmc c-Myc regulates RNA splicing of the A-Raf kinase and its activation of the ERK pathway
    Jens Rauch
    Systems Biology Ireland, University College Dublin, Dublin, Ireland
    Cancer Res 71:4664-74. 2011
    ..Our findings offered a new paradigm to understand how c-Myc coordinates diverse cell functions by directly affecting alternate splicing of key signaling components...
  15. pmc Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway
    Richard J Orton
    Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
    Biochem J 392:249-61. 2005
    ..Focusing on the MAPK pathway, we introduce the features and functions of the pathway itself before comparing the available models and describing what new biological insights they have led to...
  16. pmc Signalling ballet in space and time
    Boris N Kholodenko
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Nat Rev Mol Cell Biol 11:414-26. 2010
    ..They reveal design principles of spatiotemporal organization that are crucial for network function and cell fate decisions...
  17. doi request reprint Systems medicine: opportunities and challenges for systems biology approaches
    Walter Kolch
    Systems Biology Ireland, Conway Institute of Biomolecular and Biomedical Research and School of Medicine and Medical Science, University College Dublin, Ireland
    FEBS J 280:5937. 2013
    ....
  18. doi request reprint Mutations of beta-arrestin 2 that limit self-association also interfere with interactions with the beta2-adrenoceptor and the ERK1/2 MAPKs: implications for beta2-adrenoceptor signalling via the ERK1/2 MAPKs
    Tian Rui Xu
    Sir Henry Welcome Functional Genomics Facility, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
    Biochem J 413:51-60. 2008
    ..Regulation of beta-arrestin 2 self-association may therefore control beta-arrestin 2-mediated beta2-adrenoceptor-ERK1/2 MAPK signalling...
  19. pmc Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modeling
    Marc R Birtwistle
    Systems Biology Ireland, University College Dublin, Belfield, Republic of Ireland
    PLoS ONE 6:e27823. 2011
    ..Thus, our results suggest that either FLIM or ratiometric methods based on R(alt) are the preferred techniques for obtaining quantitative data from FRET probe experiments for mathematical modeling purposes...
  20. doi request reprint On-chip immunoprecipitation for protein purification
    Mairi E Sandison
    Integrative and Systems Biology, FBLS, University of Glasgow, Glasgow, G12 8QQ, UK
    Lab Chip 10:2805-13. 2010
    ..The optimised µIP method was used to obtain purified fractions of affinity-tagged protein from a bacterial lysate...
  21. pmc When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling
    Lan K Nguyen
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Cell Commun Signal 11:52. 2013
    ..We argue that given the overwhelming complexity arising from inter-connected PTMs, a quantitative framework based on systems biology and mathematical modelling is needed to efficiently understand their roles in cell signalling. ..
  22. pmc Cell type-specific activation of AKT and ERK signaling pathways by small negatively-charged magnetic nanoparticles
    Jens Rauch
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Sci Rep 2:868. 2012
    ..Importantly, snSPIONs stimulated the proliferation of Ras transformed breast epithelial cells as efficiently as EGF suggesting that NPs can mimic physiological growth factors...
  23. ncbi request reprint When kinases meet mathematics: the systems biology of MAPK signalling
    Walter Kolch
    Sir Henry Wellcome Functional Genomics Facility, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    FEBS Lett 579:1891-5. 2005
    ..Systems biology tries to decode this complexity through mathematical modelling and prediction in order to gain a deeper insight into the inner works of signalling networks...
  24. pmc The secret life of kinases: functions beyond catalysis
    Jens Rauch
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Cell Commun Signal 9:23. 2011
    ..Here, we discuss such kinase independent functions of protein and lipid kinases focussing on kinases that play a role in the regulation of cell proliferation, differentiation, apoptosis, and motility...
  25. doi request reprint Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
    Simon Rogers
    Department of Computing Science, University of Glasgow, Glasgow G128QQ, UK
    Bioinformatics 24:2894-900. 2008
    ..A major open question is whether transcriptome and proteome expression is linked and how it is coordinated...
  26. ncbi request reprint The molecular make-up of a tumour: proteomics in cancer research
    Walter Kolch
    Sir Henry Wellcome Functional Genomics Facility, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
    Clin Sci (Lond) 108:369-83. 2005
    ..A major challenge will be the integration of proteomics with genomics and metabolomics data and their functional interpretation in conjunction with clinical results and epidemiology...
  27. doi request reprint Control of the G-protein cascade dynamics by GDP dissociation inhibitors
    Elena Nikonova
    Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
    Mol Biosyst 9:2454-62. 2013
    ..These RhoGDI1-controlled dynamic modes of RhoA and Rac1 activities form the basis of cell migration behaviors, including protrusion-retraction cycles at the leading edge of migrating cells. ..
  28. pmc Raf family kinases: old dogs have learned new tricks
    David Matallanas
    Systems Biology Ireland, University College Dublin, Dublin, Ireland
    Genes Cancer 2:232-60. 2011
    ..Finally, we also argue for the necessity of more systemic approaches to obtain a better understanding of how the Ras-Raf signaling network generates biological specificity...
  29. pmc Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system
    Lan K Nguyen
    Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
    PLoS Comput Biol 7:e1002317. 2011
    ....
  30. pmc Biology using engineering tools: the negative feedback amplifier
    Marc R Birtwistle
    Systems Biology Ireland, University College Dublin, Belfield, Dublin, Republic of Ireland
    Cell Cycle 10:2069-76. 2011
    ..Such behavior has important implications for how to attack deregulated signaling networks containing negative feedback in diseases such as cancer...
  31. pmc The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells
    Meesbah Jiwaji
    Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
    BMC Mol Biol 11:103. 2010
    ..We have developed and validated a normalization method for qPCR using a co-transfected plasmid...
  32. doi request reprint Mutant K-Ras activation of the proapoptotic MST2 pathway is antagonized by wild-type K-Ras
    David Matallanas
    Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
    Mol Cell 44:893-906. 2011
    ..The small number of tumors with co-expression of mutant K-Ras and MST2 has elevated apoptosis rates. Thus, in CRC, mutant K-Ras transformation is supported by the wild-type allele...
  33. doi request reprint Chip-based dynamic real-time quantification of drug-induced cytotoxicity in human tumor cells
    Donald Wlodkowic
    The Bioelectronics Research Center, Department of Electronics and Electrical Engineering, University of Glasgow, G12 8LT Glasgow, UK
    Anal Chem 81:6952-9. 2009
    ....
  34. ncbi request reprint The role of Raf kinases in malignant transformation
    Walter Kolch
    Institute for Biomedical and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
    Expert Rev Mol Med 4:1-18. 2002
    ..The molecular mechanisms underlying the role of Raf kinase in tumourigenesis and the opportunities for therapeutic intervention are reviewed in this article...