2020
Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ and Davey NE.
"The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification."
Database (Oxford). 2020 Jan 1;2020:baaa040..
Balasuriya N, Davey NE Johnson JL, Liu H, Biggar KK, Cantley LC, Li SS and O'Donoghue P.
"Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1)."
J Biol Chem. 2020 Jun 12;295(24):8120-8134..
Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE.
"An intrinsically disordered proteins community for ELIXIR."
F1000Res. 2019 Oct 15;8:ELIXIR-1753..
Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE , Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D.
"DisProt: intrinsic protein disorder annotation in 2020."
Nucleic Acids Res. 2020 Jan 8;48(D1):D269-D276..
Kumar M, Gouw M, Michael S, Sámano-Sánchez H, Pancsa R, Glavina J, Diakogianni A, Valverde JA, Bukirova D, Čalyševa J, Palopoli N, Davey NE , Chemes LB, Gibson TJ.
"ELM-the eukaryotic linear motif resource in 2020."
Nucleic Acids Res. 2020 Jan 8;48(D1):D296-D306..
Wigington CP, Roy J, Damle NP, Yadav VK, Blikstad C, Resch E, Wong CJ, Mackay DR, Wang JT, Krystkowiak I, Stearns T, Gingras AC, Ullman KS, Ivarsson Y, Davey NE and Cyert MS.
"Systematic discovery of Short Linear Motifs decodes calcineurin phosphatase signaling."
Mol Cell. 2020 Jul 16;79(2):342-358.e12..
2019
Smith RJ*, Cordeiro MH*; Davey NE, Vallardi G, Ciliberto A, Gross F and Saurin AT.
"PP1 and PP2A use opposite phospho-dependencies to control distinct processes at the kinetochore."
Cell Rep. 2019 Aug 20;28(8):2206-2219.e8..
Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA and Barbar E.
"Systematic identification of recognition motifs for the hub protein LC8."
Life Sci Alliance. 2019 Jul 2;2(4).
Sebaa R, Johnson J, Pileggi C, Norgren M, Xuan J, Sai Y, Tong Q, Krystkowiak I, Bondy-Chorney E, Davey NE, Krogan N, Downey M and Harper ME.
"SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1."
Mol Metab. 2019 Jul;25:35-49.
Davey NE.
"The functional importance of structure in unstructured protein regions."
Curr Opin Struct Biol. 2019 Jun;56:155-163.
2018
Krystkowiak I, Manguy J and Davey NE.
"PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants."
Nucleic Acids Res. 2018 Jul 2;46(W1):W235-W241.
Bentley-DeSousa A, Holinier C, Moteshareie H, Tseng YC, Kajjo S, Nwosu C, Amodeo GF, Bondy-Chorney E, Sai Y, Rudner A, Golshani A, Davey NE and Downey M.
"A screen for candidate targets of lysine polyphosphorylation uncovers new links to ribosome biogenesis."
Cell Rep. 2018 Mar 27;22(13):3427-3439
Chhabra S, Fischer P, Takeuchi K, Dubey A, Ziareka JJ, Boeszoermenyi A, Mathieu D, Bermel W, Davey NE, Wagner G, and Arthanari H.
"15N-Detection Harnesses the Slow Relaxation Property of Nitrogen: Delivering Enhanced Resolution for Intrinsically Disordered Proteins."
Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1710-E1719
Kruse T, Biedenkopf N, Hertz EPT, Dietzel E, Stalmann G, López-Méndez B, Davey NE, Nilsson J and Becker S.
"The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30."
Mol Cell. 2018 Jan 4;69(1):136-145.e6.
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, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H and Gibson TJ.
"The eukaryotic linear motif resource - 2018 update."
Nucleic Acids Res. 2018 Jan 4;46(D1):D428-D434.
2017
Krystkowiak I and Davey NE.
"SLiMSearch - a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions."
Nucleic Acids Res. 2017 Jul 3;45(W1):W464-W469.
Manguy J, Jehl P, Dillon ET, Davey NE, Shields DC and Holton TA.
"Peptigram: A Web-Based Application for Peptidomics Data Visualization."
J Proteome Res. 2017 Feb 3;16(2):712-719.
Piovesan D, Tabaro F, Miceti I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidovic R, Dosztanyi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini W, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljkovic N, Ventura S, Vranken W, Warholm P, Uversky VM, Dunker AK, Longhi S, Tompa P and Tosatto SCE.
"DisProt 7.0: a major update of the database of disordered proteins."
Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124.
Davey NE*, Seo M*, Yadav VK*, Nim S, Jeon J, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM and Ivarsson Y.
"Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome."
FEBS J. 2017 Feb;284(3):485-498
2016
Di Fiore B, Wurzenberger C, Davey NE and Pines J.
"The Mitotic Checkpoint Complex Requires an Evolutionary Conserved Cassette to Bind and Inhibit Active APC/C."
Mol Cell. 2016 Dec 15;64(6):1144-1153.
Davey NE and Morgan DO.
"Building a regulatory network with short linear sequence motifs – lessons from the degrons of the anaphase-promoting complex."
Mol Cell. 2016 Oct 6;64(1):12-23.
Thrane Hertz EP*, Kruse T*, Davey NE, López-Méndez B, Otti Sigurðsson J, Montoya G, Olsen JV, Nilsson J.
"A conserved binding motif provides substrate specificity to the PP2A-B56 phosphatase"
Mol Cell. 2016 Aug 18;63(4):686-95.
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 Res. 2016 Jul 8;44(W1):W11-5.
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, Knudsen AC, Mäder C, Merrill S, Staudt A, Thiel V, Welti L, Davey NE, Diella F, Gibson TJ.
"ELM 2016 - data update and new functionality of the eukaryotic linear motif resource."
Nucleic Acids Res. 2016 Jan 4;44(D1):D294-300.
2015
Van Roey K, Davey NE.
"Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation."
Cell Commun Signal. 2015 Dec 1;13:45.
Davey NE, Cyert MS, Moses AM.
"Short linear motifs - ex nihilo evolution of protein regulation."
Cell Commun Signal. 2015 Nov 21;13(1):43.
Di Fiore B*, Davey NE*, Hagting A, Izawa D, Mansfeld J, Gibson TJ, Pines J.
"The ABBA motif binds APC/C activators to enhance the Spindle Assembly Checkpoint and promote Cyclin A destruction."
Dev Cell. 2015 Feb 9;32(3):358-72.
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."
Mol Cell Proteomics. 2015 Jan;14(1):162-76.
2014
Davey NE*, Satagopam VP*, Santiago-Mozos S*, Villacorta-Martin C, Bharat TAM, Schneider R, and Briggs JAG.
"The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data."
PLoS Comput Biol. 2014 Dec 4;10(12):e1003951.
Lu D, Ying Hsiao J, Davey NE, Van Voorhis VA, Foster SA, Tang C and Morgan DO.
"Multiple mechanisms determine the timing of APC/C substrate degradation in mitosis."
J Cell Biol. 2014 Oct 13;207(1):23-39.
Tompa P, Davey NE, Gibson TJ and Babu MM.
"A million peptide motifs for the molecular biologist."
Mol. Cell. 2014 Jul 17;55(2):161-9.
Uyar B, Weatheritt RJ, Dinkel H, Davey NE and Gibson TJ.
"Proteome-wide Analysis of Human Disease Mutations in Short Linear Motifs: Neglected Players in Cancer?"
Mol. Biosystems. 2014 Aug 26;10(10):2626-42
Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ and Davey NE.
"Short linear motifs: Ubiquitous and functionally diverse protein interaction modules directing cell regulation."
Chem Rev. 2014 Jul 9;114(13):6733-78
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, Chemes LB, Glavina J, Sánchez IE, Diella F and Gibson TJ.
"The eukaryotic linear motif resource ELM: 10 years and counting."
Nucleic Acids Res. 2014 Jan 1; 42(1):D259-66.
2013
Pushker R, Mooney C, Davey NE, Jacqué JM and Shields DC.
"Marked variability in the extent of protein disorder within and between viral families."
PLoS One. 2013; 8(4):e60724.
Van Roey K, Dinkel H, Weatheritt RJ, Gibson TJ and Davey NE.
"The switches.ELM resource: a compendium of conditional regulatory interaction interfaces."
Sci Signal. 2013 Apr 2;6(269):rs7.
2012
Perfetto L*, Gherardini PF*, Davey NE, Diella F, Helmer-Citterich M and Cesareni G.
"Exploring the diversity of SPRY/B30.2-mediated interactions."
Trends Biochem Sci. 2012 Nov 16.
Naumer M, Sonntag F, Schmidt K, Nieto K, Panke C, Davey NE, Popa-Wagner R and Kleinschmidt JA.
"Properties of the adeno-associated virus assembly-activating protein."
J Virol. 2012 Dec;86(23):13038-48.
Stavropoulos I, Khaldi N, Davey NE, O'Brien K, Martin F and Shields DC.
"Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins."
PLoS One. 2012; 7(9):e44389.
Vijayakumar V, Guerrero AN, Davey NE, Lebrilla CB, Shields DC and Khaldi N.
"EnzymePredictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins."
J Proteome Res. 2012 Dec 7; 11(12):6056-65.
Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ and Edwards RJ.
"SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions."
Nucleic Acids Res. 2012 Nov 1;40(21):10628
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 and Akhmanova A.
"A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins."
Curr Biol. 2012 Oct 9;22(19):1800-7.
Weatheritt R, Davey NE and Gibson TJ.
"Linear Motifs confer functional diversity onto splice variants."
Nucleic Acids Res. 2012 Aug;40(15):7123-31
Bharat TA, Davey NE*, Ulbrich P*, Riches JD, de Marco A, Rumlova M, Sachse K, Ruml T and Briggs JA.
"Structure of the immature retroviral capsid at 7Å resolution by cryo-electron microscopy."
Nature. 2012 Jul 19;487(7407):385-9.
Castello A*, Fischer B*, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys D, Preiss T, Steinmetz LM, Krijgsveld J and Hentze MW.
"Insights into RNA biology from a mammalian cell mRNA interactome."
Cell. 2012 Jun 8;149(6):1393-406.
Van Roey K, Gibson TJ and Davey NE.
"Motif switches: decision-making in cell regulation."
Curr Opin Struct Biol. 2012 Jun;22(3):378-85. 3.
Weatheritt RJ, Luck K, Petsalaki E, Davey NE and Gibson TJ.
"The identification of short linear motif-mediated interfaces within the human interactome."
Bioinformatics. 2012 Apr 1;28(7):976-982.
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, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F and Gibson TJ.
"ELM--the database of eukaryotic linear motifs."
Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51.
Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H and Gibson TJ.
"Attributes of short linear motifs."
Mol Biosyst. 2012 Jan;8(1):268-81.
Edwards RJ, Davey NE, O'Brien K and Shields DC.
"Interactome-wide prediction of short, disordered protein interaction motifs in humans."
Mol Biosyst. 2012 Jan;8(1):282-95.
2011
Bharat TA, Riches JD, Kolesnikova L, Welsch S, Krähling V, Davey NE, Parsy ML, Becker S and Briggs JA.
"Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells."
PLoS Biol. 2011 Nov;9(11):e1001196.
Davey NE, Haslam NJ, Shields DC and Edwards RJ.
"SLiMSearch 2.0: biological context for short linear motifs in proteins."
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W56-60.
Davey NE, Travé G and Gibson TJ.
"How viruses hijack cell regulation."
Trends Biochem Sci. 2011 Mar;36(3):159-69.
2010
de Marco A, Davey NE, Ulbrich P, Phillips JM, Lux V, Riches JD, Fuzik T, Ruml T, Kräusslich HG, Vogt VM and Briggs JA.
"Conserved and variable features of Gag structure and arrangement in immature retrovirus particles."
J Virol. 2010 Nov;84(22):11729-36.
Davey NE, Edwards RJ and Shields DC.
"Computational identification and analysis of protein short linear motifs."
Front Biosci. 2010 Jun 1;15:801-25.
Davey NE, Haslam NJ, Shields DC and Edwards RJ.
"SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs."
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W534-9.
Davey NE, Edwards RJ and Shields DC.
"Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins."
BMC Bioinformatics. 2010 Jan 7;11:14.
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, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R and Gibson TJ.
"ELM: the status of the 2010 eukaryotic linear motif resource."
Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80
Davey NE, Haslam NJ, Shields DC and Edwards RJ.
"SLiMSearch: a webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context."
PRIB. 2010 6282: 50–61.
2009
Davey NE, Shields DC and Edwards RJ.
"Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery."
Bioinformatics. 2009 Feb 15;25(4):443-50.
2008
Casey FP, Davey NE, Baran I, Varekova RS and Shields DC.
"Web server to identify similarity of amino acid motifs to compounds (SAAMCO)."
J Chem Inf Model. 2008 Jul;48(7):1524-9.
Edwards RJ, Davey NE and Shields DC.
"CompariMotif: quick and easy comparisons of sequence motifs."
Bioinformatics. 2008 May 15;24(10):1307-9.
2007
Edwards RJ, Davey NE and Shields DC.
"SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins."
PLoS One. 2007 Oct 3;2(10):e967.
Davey NE*, Edwards RJ* and Shields DC.
"The SLiMDisc server: short, linear motif discovery in proteins."
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W455-9.
2006
Parthasarathi L, Devocelle M, Søndergaard C, Baran I, O'Dushlaine CT, Davey NE, Edwards RJ, Moran N, Kenny D and Shields DC.
"Absolute net charge and the biological activity of oligopeptides."
J Chem Inf Model. 2006 Sep-Oct;46(5):2183-90.
Davey NE, Shields DC and Edwards RJ.
"SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent."
Nucleic Acids Res. 2006 Jul 19;34(12):3546-54.