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Researchers at UCD

Norman Davey

Research Fellow

School Of Medicine

Tel:
Email: norman.davey@ucd.ie

Biography

Norman received his Ph.D. degree (2009) from the Conway Institute of Biomolecular & Biomedical Research at University College Dublin, Dublin, Ireland, working on short, linear motif discovery methods. He subsequently moved to the European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, as an EIPOD postdoctoral fellow to work on various aspects of motif biology including the prominent role of SLiMs in regulatory decision making, splice isoform-specific functionality, and viral pathogenesis. In 2013, he joined the Department of Physiology at the University of California, San Francisco (UCSF) as a postdoctoral fellow with Professor David O. Morgan characterizing novel motifs in the cell cycle. His research focuses on the role of SLiM within intrinsically disordered regions in directing cell regulation. In September 2014, he returned to University College Dublin to start his own group studying motif function. He has authored over 20 papers on various aspects of SLiM biology. He continues to utilize evolutionary, proteomic, and genomic data to examine two major open questions about intrinsically disordered regions: (i) what are the modules that are responsible for their functionality and (ii) how do perturbations in the cell modulate the functionality of these modules.

Publications

 

Book Chapters

Mooney, Catherine and Davey, Norman and Martin, Alberto JM and Walsh, Ian and Shields, Denis C and Pollastri, Gianluca (2011) 'In Silico Protein Motif Discovery and Structural Analysis' In: Humana Press. , pp.341-353 [Details]
Mooney, C. and Davey, N. and Martin, AJ and Walsh, I. and Shields, D.C. and Pollastri, G.; (2011) 'In Silico Protein Motif Discovery and Structural Analysis' In: Bing Yu and Marcus Hinchcliffe (eds). In Silico Tools in Gene Discovery. Humana Press. , pp.341-353 Available Online [DOI] [Details]
 

Peer Reviewed Journals

Jehl P, Manguy J;Shields DC;Higgins DG;Davey NE (2016) 'ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences'. Nucleic Acids Research, . [DOI] [Details]
Van Roey, Kim and Uyar, Bora and Weatheritt, Robert J and Dinkel, Holger and Seiler, Markus and Budd, Aidan and Gibson, Toby J and Davey, Norman E (2014) 'Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation'. Chemical Reviews, 114 (13):6733-6778. [Details]
Tompa, Peter and Davey, Norman E and Gibson, Toby J and Babu, M Madan (2014) 'A Million Peptide Motifs for the Molecular Biologist'. Molecular Cell, 55 (2):161-169. [Details]
Uyar, Bora and Weatheritt, Robert J and Dinkel, Holger and Davey, Norman E and Gibson, Toby J (2014) 'Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?'. Molecular BioSystems, 10 (10):2626-2642. [Details]
Perfetto, Livia and Gherardini, Pier Federico and Davey, Norman E and Diella, Francesca and Helmer-Citterich, Manuela and Cesareni, Gianni (2013) 'Exploring the diversity of SPRY/B30. 2-mediated interactions'. Trends in Biochemical Sciences, 38 (1):38-46. [Details]
Pushker, Ravindra and Mooney, Catherine and Davey, Norman E and Jacqu\'e (2013) 'Marked Variability in the Extent of Protein Disorder within and between Viral Families'. PLoS ONE, 8 (4):e60724. [Details]
Van Roey, Kim and Dinkel, Holger and Weatheritt, Robert J and Gibson, Toby J and Davey, Norman E (2013) 'The switches. ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces'. Science signaling, 6 (269):rs7. [Details]
Jiang, Kai and Toedt, Grischa and Montenegro Gouveia, Susana and Davey, Norman E and Hua, Shasha and van der Vaart, Babet and Grigoriev, Ilya and Larsen, Jesper and Pedersen, Lotte B and Bezstarosti, Karel and others (2012) 'A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins'. Current Biology, 22 (19):1800-1807. [Details]
Vijayakumar V, Guerrero AN, Davey N, Lebrilla CB, Shields DC, Khaldi N (2012) 'EnzymePredictor: A Tool for Predicting and Visualizing Enzymatic Cleavages of Digested Proteins'. Journal of Proteome Research, . [DOI] [Details]
Bharat, Tanmay AM and Davey, Norman E and Ulbrich, Pavel and Riches, James D and De Marco, Alex and Rumlova, Michaela and Sachse, Carsten and Ruml, Tomas and Briggs, John AG (2012) 'Structure of the immature retroviral capsid at 8 [thinsp] A resolution by cryo-electron microscopy'. Nature, 487 (7407):385-389. [Details]
Castello, Alfredo and Fischer, Bernd and Eichelbaum, Katrin and Horos, Rastislav and Beckmann, Benedikt M and Strein, Claudia and Davey, Norman E and Humphreys, David T and Preiss, Thomas and Steinmetz, Lars M and others (2012) 'Insights into RNA biology from an atlas of mammalian mRNA-binding proteins'. Cell, 149 (6):1393-1406. [Details]
Weatheritt, Robert J and Davey, Norman E and Gibson, Toby J (2012) 'Linear motifs confer functional diversity onto splice variants'. Nucleic Acids Research, 40 (15):7123-7131. [Details]
Van Roey, Kim and Gibson, Toby J and Davey, Norman E (2012) 'Motif switches: decision-making in cell regulation'. Current Opinion in Structural Biology, 22 (3):378-385. [Details]
Weatheritt, Robert J and Luck, Katja and Petsalaki, E and Davey, Norman E and Gibson, Toby J (2012) 'The identification of short linear motif-mediated interfaces within the human interactome'. Bioinformatics, 28 (7):976-982. [Details]
Stavropoulos, Ilias and Khaldi, Nora and Davey, Norman E and Oâ¿¿Brien, Kevin and Martin, Finian and Shields, Denis C (2012) 'Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins'. PLoS ONE, 7 (9):e44389. [Details]
Davey, Norman E and Cowan, Joanne L and Shields, Denis C and Gibson, Toby J and Coldwell, Mark J and Edwards, Richard J (2012) 'SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions'. Nucleic Acids Research, 40 (21):10628-10641. [Details]
Naumer, Matthias and Sonntag, Florian and Schmidt, Kristin and Nieto, Karen and Panke, Christian and Davey, Norman E and Popa-Wagner, Ruth and Kleinschmidt, J\"urgen A (2012) 'Properties of the adeno-associated virus assembly-activating protein'. Journal of Virology, 86 (23):13038-13048. [Details]
Davey, Norman E and Haslam, Niall J and Shields, Denis C and Edwards, Richard J (2011) 'SLiMSearch 2.0: biological context for short linear motifs in proteins'. Nucleic acids research, 39 (suppl 2):W56. [Details]
Mooney C, Davey N, Martin AJ, Walsh I, Shields DC, Pollastri G; (2011) 'In silico protein motif discovery and structural analysis'. Methods, 760 :341-353. [DOI] [Details]
Bharat, Tanmay AM and Riches, James D and Kolesnikova, Larissa and Welsch, Sonja and Kr\"ahling, Verena and Davey, Norman and Parsy, Marie-Laure and Becker, Stephan and Briggs, John AG (2011) 'Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells'. PLoS biology, 9 (11):e1001196. [Details]
Edwards, Richard J and Davey, Norman E and O'Brien, Kevin and Shields, Denis C (2011) 'Interactome-wide prediction of short, disordered protein interaction motifs in humans'. Mol. BioSyst, . [Details]
Davey, Norman E and Van Roey, Kim and Weatheritt, Robert J and Toedt, Grischa and Uyar, Bora and Altenberg, Brigitte and Budd, Aidan and Diella, Francesca and Dinkel, Holger and Gibson, Toby J (2011) 'Attributes of short linear motifs'. Mol. BioSyst, . [Details]
Davey, Norman E and Trave, Gilles and Gibson, Toby J (2010) 'How viruses hijack cell regulation'. Trends in biochemical sciences, . [Details]
de Marco, Alex and Davey, Norman E and Ulbrich, Pavel and Phillips, Judith M and Lux, Vanda and Riches, James D and Fuzik, Tibor and Ruml, Tomas and Kr\"ausslich, Hans-Georg and Vogt, Volker M and others (2010) 'Conserved and variable features of Gag structure and arrangement in immature retrovirus particles'. Journal of virology, 84 (22):11729-11736. [Details]
Davey, Norman and Haslam, Niall and Shields, Denis and Edwards, Richard (2010) 'SLiMSearch: a webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context'. Pattern Recognition in Bioinformatics, :50-61. [Details]
Davey, Norman E and Edwards, Richard J and Shields, Denis C (2010) 'Computational identification and analysis of protein short linear motifs'. Frontiers in bioscience a journal and virtual library, 15 :801-825. [Details]
Davey, Norman and Edwards, Richard and Shields, Denis (2010) 'Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins'. BMC bioinformatics, 11 (1):14. [Details]
Davey, Norman E and Shields, Denis C and Edwards, Richard J (2009) 'Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery'. Bioinformatics, 25 (4):443-450. [Details]
Edwards, Richard J and Davey, Norman E and Shields, Denis C (2008) 'CompariMotif: quick and easy comparisons of sequence motifs'. Bioinformatics, 24 (10):1307-1309. [Details]
Casey, Fergal P and Davey, Norman E and Baran, Ivan and Varekova, Radka Svobodova and Shields, Denis C (2008) 'Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO)'. Journal of chemical information and modeling, 48 (7):1524-1529. [Details]
Edwards, Richard J and Davey, Norman E and Shields, Denis C (2007) 'SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins'. PLoS One, 2 (10):e967. [Details]
Davey, Norman E and Shields, Denis C and Edwards, Richard J (2006) 'SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent'. Nucleic acids research, 34 (12):3546-3554. [Details]
Parthasarathi, Laavanya and Devocelle, Marc and S\ondergaard, Chresten and Baran, Ivan and O'Dushlaine, Colm T and Davey, Norman E and Edwards, Richard J and Moran, Niamh and Kenny, Dermot and Shields, Denis C (2006) 'Absolute net charge and the biological activity of oligopeptides'. Journal of chemical information and modeling, 46 (5):2183-2190. [Details]
                                                                                             

Research

Research Interests

One third of the human proteome is intrinsically disordered. Various estimates have suggested that there may be upwards of one hundred thousand interaction interfaces in these regions. However, to date, few functional elements within these regions have been characterised. The majority of known interfaces in disordered regions belong to a class of compact, degenerate and convergently evolvable interaction modules known as Short, Linear Motifs (SLiMs).

"Understanding the role of short linear motifs in cell regulation"

Our research focuses on the role of intrinsically disordered regions in directing cell regulation. Specifically, we attempt to utilise evolutionary, proteomic and genomic data to gain a better understanding of the function and regulation of SLiM-mediated interaction interfaces. We apply this information to discover novel motifs, and novel mechanisms regulating the conditional functionality of these motifs. Our work is funded by a Science Foundation Ireland Starting Investigator Research Grant (SIRG) grant.

Research Projects

Sponsor : Science Foundation Ireland (SFI)
Title : Decoding the regulatory landscape of the intrinsically disordered proteome
Start Date / End Date : 01-SEP-14 / 01-SEP-18