Norman Davey - Publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://www.embl.de/research/units/scb/gibson/members/index.php?s_personId=5193

50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Krystkowiak I, Manguy J, Davey NE. PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants. Nucleic Acids Research. PMID 29873773 DOI: 10.1093/nar/gky426  0.96
2017 Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, et al. MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Research. PMID 29136219 DOI: 10.1093/nar/gkx1071  0.4
2017 Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, et al. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Research. PMID 29136216 DOI: 10.1093/nar/gkx1077  0.88
2016 Manguy J, Jehl P, Dillon ET, Davey NE, Shields DC, Holton TA. Peptigram: A Web-Based Application for Peptidomics Data Visualization. Journal of Proteome Research. PMID 27997202 DOI: 10.1021/acs.jproteome.6b00751  1
2016 Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27965415 DOI: 10.1093/nar/gkw1279  0.4
2016 Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27899601 DOI: 10.1093/nar/gkw1056  0.4
2016 Jehl P, Manguy J, Shields DC, Higgins DG, Davey NE. ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Research. PMID 27085803 DOI: 10.1093/nar/gkw265  1
2015 Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Communication and Signaling : Ccs. 13: 45. PMID 26626130 DOI: 10.1186/s12964-015-0123-9  1
2015 Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Behrendt A, Dahl SL, Damerell V, Diebel S, Kalman S, Klein S, ... ... Davey NE, et al. ELM 2016-data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Research. PMID 26615199 DOI: 10.1093/nar/gkv1291  1
2015 Davey NE, Cyert MS, Moses AM. Short linear motifs - ex nihilo evolution of protein regulation. Cell Communication and Signaling : Ccs. 13: 43. PMID 26589632 DOI: 10.1186/s12964-015-0120-z  1
2015 Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP. Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1. Molecular & Cellular Proteomics : McP. 14: 162-76. PMID 25381059 DOI: 10.1074/mcp.M114.043141  1
2014 Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA. The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data. Plos Computational Biology. 10: e1003951. PMID 25474213 DOI: 10.1371/journal.pcbi.1003951  1
2014 Lu D, Hsiao JY, Davey NE, Van Voorhis VA, Foster SA, Tang C, Morgan DO. Multiple mechanisms determine the order of APC/C substrate degradation in mitosis. The Journal of Cell Biology. 207: 23-39. PMID 25287299 DOI: 10.1083/jcb.201402041  1
2014 Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ. Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? Molecular Biosystems. 10: 2626-42. PMID 25057855 DOI: 10.1039/c4mb00290c  1
2014 Tompa P, Davey NE, Gibson TJ, Babu MM. A million peptide motifs for the molecular biologist. Molecular Cell. 55: 161-9. PMID 25038412 DOI: 10.1016/j.molcel.2014.05.032  1
2014 Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chemical Reviews. 114: 6733-78. PMID 24926813 DOI: 10.1021/cr400585q  1
2014 Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, et al. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Research. 42: D259-66. PMID 24214962 DOI: 10.1093/nar/gkt1047  1
2013 Pushker R, Mooney C, Davey NE, Jacqué JM, Shields DC. Marked variability in the extent of protein disorder within and between viral families. Plos One. 8: e60724. PMID 23620725 DOI: 10.1371/journal.pone.0060724  1
2013 Van Roey K, Dinkel H, Weatheritt RJ, Gibson TJ, Davey NE. The switches.ELM resource: a compendium of conditional regulatory interaction interfaces. Science Signaling. 6: rs7. PMID 23550212 DOI: 10.1126/scisignal.2003345  1
2013 Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G. Exploring the diversity of SPRY/B30.2-mediated interactions. Trends in Biochemical Sciences. 38: 38-46. PMID 23164942 DOI: 10.1016/j.tibs.2012.10.001  1
2012 Vijayakumar V, Guerrero AN, Davey N, Lebrilla CB, Shields DC, Khaldi N. EnzymePredictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins. Journal of Proteome Research. 11: 6056-65. PMID 23098558 DOI: 10.1021/pr300721f  1
2012 Naumer M, Sonntag F, Schmidt K, Nieto K, Panke C, Davey NE, Popa-Wagner R, Kleinschmidt JA. Properties of the adeno-associated virus assembly-activating protein. Journal of Virology. 86: 13038-48. PMID 23015698 DOI: 10.1128/JVI.01675-12  1
2012 Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Research. 40: 10628-41. PMID 22977176 DOI: 10.1093/nar/gks854  1
2012 Stavropoulos I, Khaldi N, Davey NE, O'Brien K, Martin F, Shields DC. Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins. Plos One. 7: e44389. PMID 22962613 DOI: 10.1371/journal.pone.0044389  1
2012 Jiang K, Toedt G, Montenegro Gouveia S, Davey NE, Hua S, van der Vaart B, Grigoriev I, Larsen J, Pedersen LB, Bezstarosti K, Lince-Faria M, Demmers J, Steinmetz MO, Gibson TJ, Akhmanova A. A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins. Current Biology : Cb. 22: 1800-7. PMID 22885064 DOI: 10.1016/j.cub.2012.07.047  1
2012 Bharat TA, Davey NE, Ulbrich P, Riches JD, de Marco A, Rumlova M, Sachse C, Ruml T, Briggs JA. Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy. Nature. 487: 385-9. PMID 22722831 DOI: 10.1038/nature11169  1
2012 Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell. 149: 1393-406. PMID 22658674 DOI: 10.1016/j.cell.2012.04.031  1
2012 Weatheritt RJ, Davey NE, Gibson TJ. Linear motifs confer functional diversity onto splice variants. Nucleic Acids Research. 40: 7123-31. PMID 22638587 DOI: 10.1093/nar/gks442  1
2012 Van Roey K, Gibson TJ, Davey NE. Motif switches: decision-making in cell regulation. Current Opinion in Structural Biology. 22: 378-85. PMID 22480932 DOI: 10.1016/j.sbi.2012.03.004  1
2012 Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ. The identification of short linear motif-mediated interfaces within the human interactome. Bioinformatics (Oxford, England). 28: 976-82. PMID 22328783 DOI: 10.1093/bioinformatics/bts072  1
2012 Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, et al. ELM--the database of eukaryotic linear motifs. Nucleic Acids Research. 40: D242-51. PMID 22110040 DOI: 10.1093/nar/gkr1064  1
2012 Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ. Attributes of short linear motifs. Molecular Biosystems. 8: 268-81. PMID 21909575 DOI: 10.1039/c1mb05231d  1
2012 Edwards RJ, Davey NE, O'Brien K, Shields DC. Interactome-wide prediction of short, disordered protein interaction motifs in humans. Molecular Biosystems. 8: 282-95. PMID 21879107 DOI: 10.1039/c1mb05212h  1
2011 Bharat TA, Riches JD, Kolesnikova L, Welsch S, Krähling V, Davey N, Parsy ML, Becker S, Briggs JA. Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells. Plos Biology. 9: e1001196. PMID 22110401 DOI: 10.1371/journal.pbio.1001196  1
2011 Mooney C, Davey N, Martin AJ, Walsh I, Shields DC, Pollastri G. In silico protein motif discovery and structural analysis. Methods in Molecular Biology (Clifton, N.J.). 760: 341-53. PMID 21780007 DOI: 10.1007/978-1-61779-176-5_21  1
2011 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Research. 39: W56-60. PMID 21622654 DOI: 10.1093/nar/gkr402  1
2011 Davey NE, Travé G, Gibson TJ. How viruses hijack cell regulation. Trends in Biochemical Sciences. 36: 159-69. PMID 21146412 DOI: 10.1016/j.tibs.2010.10.002  1
2010 de Marco A, Davey NE, Ulbrich P, Phillips JM, Lux V, Riches JD, Fuzik T, Ruml T, Kräusslich HG, Vogt VM, Briggs JA. Conserved and variable features of Gag structure and arrangement in immature retrovirus particles. Journal of Virology. 84: 11729-36. PMID 20810738 DOI: 10.1128/JVI.01423-10  1
2010 Davey NE, Edwards RJ, Shields DC. Computational identification and analysis of protein short linear motifs. Frontiers in Bioscience (Landmark Edition). 15: 801-25. PMID 20515727 DOI: 10.2741/3647  1
2010 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Research. 38: W534-9. PMID 20497999 DOI: 10.1093/nar/gkq440  1
2010 Davey NE, Edwards RJ, Shields DC. Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. Bmc Bioinformatics. 11: 14. PMID 20055997 DOI: 10.1186/1471-2105-11-14  1
2010 Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, et al. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Research. 38: D167-80. PMID 19920119 DOI: 10.1093/nar/gkp1016  1
2010 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMSearch: A webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6282: 50-61. DOI: 10.1007/978-3-642-16001-1_5  1
2009 Davey NE, Shields DC, Edwards RJ. Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics (Oxford, England). 25: 443-50. PMID 19136552 DOI: 10.1093/bioinformatics/btn664  1
2008 Casey FP, Davey NE, Baran I, Varekova RS, Shields DC. Web server to identify similarity of amino acid motifs to compounds (SAAMCO). Journal of Chemical Information and Modeling. 48: 1524-9. PMID 18570372 DOI: 10.1021/ci8000474  1
2008 Edwards RJ, Davey NE, Shields DC. CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics (Oxford, England). 24: 1307-9. PMID 18375965 DOI: 10.1093/bioinformatics/btn105  1
2007 Edwards RJ, Davey NE, Shields DC. SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. Plos One. 2: e967. PMID 17912346 DOI: 10.1371/journal.pone.0000967  1
2007 Davey NE, Edwards RJ, Shields DC. The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Research. 35: W455-9. PMID 17576682 DOI: 10.1093/nar/gkm400  1
2006 Parthasarathi L, Devocelle M, Søndergaard C, Baran I, O'Dushlaine CT, Davey NE, Edwards RJ, Moran N, Kenny D, Shields DC. Absolute net charge and the biological activity of oligopeptides. Journal of Chemical Information and Modeling. 46: 2183-90. PMID 16995748 DOI: 10.1021/ci0600760  1
2006 Davey NE, Shields DC, Edwards RJ. SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Research. 34: 3546-54. PMID 16855291 DOI: 10.1093/nar/gkl486  1
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