Research Topics
Genomes and Genes | Walter KolchSummaryAffiliation: University College Dublin Country: Ireland Publications
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Publications
Addressing the challenge of defining valid proteomic biomarkers and classifiersMohammed 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...
The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifierOliver 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...- Functional proteomics to dissect tyrosine kinase signalling pathways in cancerWalter 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... - Eukaryotic translation initiation factor 3, subunit a, regulates the extracellular signal-regulated kinase pathwayTian 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... - Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical speciesTian 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... - An integrated Bayesian framework for identifying phosphorylation networks in stimulated cellsTapesh 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... - Computational modelling of cancerous mutations in the EGFR/ERK signalling pathwayRichard 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... - Computational approaches for analyzing information flow in biological networksBORIS KHOLODENKO
Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
Sci Signal 5:re1. 2012.... - c-Myc regulates RNA splicing of the A-Raf kinase and its activation of the ERK pathwayJens 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... - Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathwayRichard 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... - Signalling ballet in space and timeBoris 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... - 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 MAPKsTian 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... - Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noiseMarc 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... - Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modelingMarc 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... - On-chip immunoprecipitation for protein purificationMairi 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... 
When kinases meet mathematics: the systems biology of MAPK signallingWalter 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...- The secret life of kinases: functions beyond catalysisJens 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... - Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster modelsSimon 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... - The molecular make-up of a tumour: proteomics in cancer researchWalter 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... - It takes two to tango--signalling by dimeric Raf kinasesAngela Baljuls
Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
Mol Biosyst 9:551-8. 2013.... - Raf family kinases: old dogs have learned new tricksDavid 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... - Cell type-specific activation of AKT and ERK signaling pathways by small negatively-charged magnetic nanoparticlesJens 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... - Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination systemLan K Nguyen
Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
PLoS Comput Biol 7:e1002317. 2011.... - Biology using engineering tools: the negative feedback amplifierMarc 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... - The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cellsMeesbah 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... - Mutant K-Ras activation of the proapoptotic MST2 pathway is antagonized by wild-type K-RasDavid 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... - Chip-based dynamic real-time quantification of drug-induced cytotoxicity in human tumor cellsDonald Wlodkowic
The Bioelectronics Research Center, Department of Electronics and Electrical Engineering, University of Glasgow, G12 8LT Glasgow, UK
Anal Chem 81:6952-9. 2009.... - The role of Raf kinases in malignant transformationWalter 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...