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Items: 1 to 50 of 57

1.

Systematic identification of recognition motifs for the hub protein LC8.

Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E.

Life Sci Alliance. 2019 Jul 2;2(4). pii: e201900366. doi: 10.26508/lsa.201900366. Print 2019 Aug.

2.

SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1.

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, Harper ME.

Mol Metab. 2019 Jul;25:35-49. doi: 10.1016/j.molmet.2019.04.008. Epub 2019 Apr 17.

3.

The functional importance of structure in unstructured protein regions.

Davey NE.

Curr Opin Struct Biol. 2019 Apr 16;56:155-163. doi: 10.1016/j.sbi.2019.03.009. [Epub ahead of print] Review.

4.

PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.

Krystkowiak I, Manguy J, Davey NE.

Nucleic Acids Res. 2018 Jul 2;46(W1):W235-W241. doi: 10.1093/nar/gky426.

5.

A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis.

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, Downey M.

Cell Rep. 2018 Mar 27;22(13):3427-3439. doi: 10.1016/j.celrep.2018.02.104.

6.

15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins.

Chhabra S, Fischer P, Takeuchi K, Dubey A, Ziarek JJ, Boeszoermenyi A, Mathieu D, Bermel W, Davey NE, Wagner G, Arthanari H.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1710-E1719. doi: 10.1073/pnas.1717560115. Epub 2018 Feb 5.

7.

The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30.

Kruse T, Biedenkopf N, Hertz EPT, Dietzel E, Stalmann G, López-Méndez B, Davey NE, Nilsson J, Becker S.

Mol Cell. 2018 Jan 4;69(1):136-145.e6. doi: 10.1016/j.molcel.2017.11.034. Epub 2017 Dec 28.

8.

The eukaryotic linear motif resource - 2018 update.

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, Gibson TJ.

Nucleic Acids Res. 2018 Jan 4;46(D1):D428-D434. doi: 10.1093/nar/gkx1077.

9.

SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions.

Krystkowiak I, Davey NE.

Nucleic Acids Res. 2017 Jul 3;45(W1):W464-W469. doi: 10.1093/nar/gkx238.

10.

Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome.

Davey NE, Seo MH, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y.

FEBS J. 2017 Feb;284(3):485-498. doi: 10.1111/febs.13995. Epub 2017 Jan 18.

11.

Peptigram: A Web-Based Application for Peptidomics Data Visualization.

Manguy J, Jehl P, Dillon ET, Davey NE, Shields DC, Holton TA.

J Proteome Res. 2017 Feb 3;16(2):712-719. doi: 10.1021/acs.jproteome.6b00751. Epub 2016 Dec 20.

PMID:
27997202
12.

Corrigendum: DisProt 7.0: a major update of the database of disordered proteins.

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, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13. No abstract available.

13.

The Mitotic Checkpoint Complex Requires an Evolutionary Conserved Cassette to Bind and Inhibit Active APC/C.

Di Fiore B, Wurzenberger C, Davey NE, Pines J.

Mol Cell. 2016 Dec 15;64(6):1144-1153. doi: 10.1016/j.molcel.2016.11.006. Epub 2016 Dec 8.

14.

DisProt 7.0: a major update of the database of disordered proteins.

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, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. doi: 10.1093/nar/gkw1056. Epub 2016 Nov 28. Erratum in: Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124.

15.

Building a Regulatory Network with Short Linear Sequence Motifs: Lessons from the Degrons of the Anaphase-Promoting Complex.

Davey NE, Morgan DO.

Mol Cell. 2016 Oct 6;64(1):12-23. doi: 10.1016/j.molcel.2016.09.006. Review.

16.

A Conserved Motif Provides Binding Specificity to the PP2A-B56 Phosphatase.

Hertz EPT, Kruse T, Davey NE, López-Méndez B, Sigurðsson JO, Montoya G, Olsen JV, Nilsson J.

Mol Cell. 2016 Aug 18;63(4):686-695. doi: 10.1016/j.molcel.2016.06.024. Epub 2016 Jul 21.

17.

ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences.

Jehl P, Manguy J, Shields DC, Higgins DG, Davey NE.

Nucleic Acids Res. 2016 Jul 8;44(W1):W11-5. doi: 10.1093/nar/gkw265. Epub 2016 Apr 16.

18.

Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation.

Van Roey K, Davey NE.

Cell Commun Signal. 2015 Dec 1;13:45. doi: 10.1186/s12964-015-0123-9. Review.

19.

ELM 2016--data update and new functionality of the eukaryotic linear motif resource.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D294-300. doi: 10.1093/nar/gkv1291. Epub 2015 Nov 28.

20.

Short linear motifs - ex nihilo evolution of protein regulation.

Davey NE, Cyert MS, Moses AM.

Cell Commun Signal. 2015 Nov 21;13:43. doi: 10.1186/s12964-015-0120-z. Review.

21.

The ABBA motif binds APC/C activators and is shared by APC/C substrates and regulators.

Di Fiore B, Davey NE, Hagting A, Izawa D, Mansfeld J, Gibson TJ, Pines J.

Dev Cell. 2015 Feb 9;32(3):358-372. doi: 10.1016/j.devcel.2015.01.003.

22.

The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data.

Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA.

PLoS Comput Biol. 2014 Dec 4;10(12):e1003951. doi: 10.1371/journal.pcbi.1003951. eCollection 2014 Dec.

23.

Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1.

Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP.

Mol Cell Proteomics. 2015 Jan;14(1):162-76. doi: 10.1074/mcp.M114.043141. Epub 2014 Nov 7.

24.

Multiple mechanisms determine the order of APC/C substrate degradation in mitosis.

Lu D, Hsiao JY, Davey NE, Van Voorhis VA, Foster SA, Tang C, Morgan DO.

J Cell Biol. 2014 Oct 13;207(1):23-39. doi: 10.1083/jcb.201402041. Epub 2014 Oct 6.

25.

Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?

Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ.

Mol Biosyst. 2014 Oct;10(10):2626-42. doi: 10.1039/c4mb00290c.

26.

A million peptide motifs for the molecular biologist.

Tompa P, Davey NE, Gibson TJ, Babu MM.

Mol Cell. 2014 Jul 17;55(2):161-9. doi: 10.1016/j.molcel.2014.05.032. Review.

27.

Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation.

Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE.

Chem Rev. 2014 Jul 9;114(13):6733-78. doi: 10.1021/cr400585q. Epub 2014 Jun 13. Review. No abstract available.

PMID:
24926813
28.

The eukaryotic linear motif resource ELM: 10 years and counting.

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, Gibson TJ.

Nucleic Acids Res. 2014 Jan;42(Database issue):D259-66. doi: 10.1093/nar/gkt1047. Epub 2013 Nov 7.

29.

Marked variability in the extent of protein disorder within and between viral families.

Pushker R, Mooney C, Davey NE, Jacqué JM, Shields DC.

PLoS One. 2013 Apr 19;8(4):e60724. doi: 10.1371/journal.pone.0060724. Print 2013.

30.

The switches.ELM resource: a compendium of conditional regulatory interaction interfaces.

Van Roey K, Dinkel H, Weatheritt RJ, Gibson TJ, Davey NE.

Sci Signal. 2013 Apr 2;6(269):rs7. doi: 10.1126/scisignal.2003345.

PMID:
23550212
31.

Exploring the diversity of SPRY/B30.2-mediated interactions.

Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G.

Trends Biochem Sci. 2013 Jan;38(1):38-46. doi: 10.1016/j.tibs.2012.10.001. Epub 2012 Nov 17. Review.

PMID:
23164942
32.

Properties of the adeno-associated virus assembly-activating protein.

Naumer M, Sonntag F, Schmidt K, Nieto K, Panke C, Davey NE, Popa-Wagner R, Kleinschmidt JA.

J Virol. 2012 Dec;86(23):13038-48. doi: 10.1128/JVI.01675-12. Epub 2012 Sep 26.

33.

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.

Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ.

Nucleic Acids Res. 2012 Nov;40(21):10628-41. doi: 10.1093/nar/gks854. Epub 2012 Sep 12.

34.

Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins.

Stavropoulos I, Khaldi N, Davey NE, O'Brien K, Martin F, Shields DC.

PLoS One. 2012;7(9):e44389. doi: 10.1371/journal.pone.0044389. Epub 2012 Sep 4.

35.

A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins.

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.

Curr Biol. 2012 Oct 9;22(19):1800-7. doi: 10.1016/j.cub.2012.07.047. Epub 2012 Aug 9.

36.

Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy.

Bharat TA, Davey NE, Ulbrich P, Riches JD, de Marco A, Rumlova M, Sachse C, Ruml T, Briggs JA.

Nature. 2012 Jul 19;487(7407):385-9. doi: 10.1038/nature11169.

PMID:
22722831
37.

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.

Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW.

Cell. 2012 Jun 8;149(6):1393-406. doi: 10.1016/j.cell.2012.04.031. Epub 2012 May 31.

38.

Linear motifs confer functional diversity onto splice variants.

Weatheritt RJ, Davey NE, Gibson TJ.

Nucleic Acids Res. 2012 Aug;40(15):7123-31. doi: 10.1093/nar/gks442. Epub 2012 May 25.

39.

Motif switches: decision-making in cell regulation.

Van Roey K, Gibson TJ, Davey NE.

Curr Opin Struct Biol. 2012 Jun;22(3):378-85. doi: 10.1016/j.sbi.2012.03.004. Epub 2012 Apr 3. Review.

PMID:
22480932
40.

The identification of short linear motif-mediated interfaces within the human interactome.

Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ.

Bioinformatics. 2012 Apr 1;28(7):976-82. doi: 10.1093/bioinformatics/bts072. Epub 2012 Feb 10.

41.

ELM--the database of eukaryotic linear motifs.

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, Gibson TJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51. doi: 10.1093/nar/gkr1064. Epub 2011 Nov 21.

42.

Attributes of short linear motifs.

Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ.

Mol Biosyst. 2012 Jan;8(1):268-81. doi: 10.1039/c1mb05231d. Epub 2011 Sep 12.

PMID:
21909575
43.

Interactome-wide prediction of short, disordered protein interaction motifs in humans.

Edwards RJ, Davey NE, O'Brien K, Shields DC.

Mol Biosyst. 2012 Jan;8(1):282-95. doi: 10.1039/c1mb05212h. Epub 2011 Aug 30.

PMID:
21879107
44.

SLiMSearch 2.0: biological context for short linear motifs in proteins.

Davey NE, Haslam NJ, Shields DC, Edwards RJ.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W56-60. doi: 10.1093/nar/gkr402. Epub 2011 May 26.

45.

How viruses hijack cell regulation.

Davey NE, Travé G, Gibson TJ.

Trends Biochem Sci. 2011 Mar;36(3):159-69. doi: 10.1016/j.tibs.2010.10.002. Epub 2010 Dec 9.

PMID:
21146412
46.

Conserved and variable features of Gag structure and arrangement in immature retrovirus particles.

de Marco A, Davey NE, Ulbrich P, Phillips JM, Lux V, Riches JD, Fuzik T, Ruml T, Kräusslich HG, Vogt VM, Briggs JA.

J Virol. 2010 Nov;84(22):11729-36. doi: 10.1128/JVI.01423-10. Epub 2010 Sep 1.

47.

Computational identification and analysis of protein short linear motifs.

Davey NE, Edwards RJ, Shields DC.

Front Biosci (Landmark Ed). 2010 Jun 1;15:801-25. Review.

PMID:
20515727
48.

SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs.

Davey NE, Haslam NJ, Shields DC, Edwards RJ.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W534-9. doi: 10.1093/nar/gkq440. Epub 2010 May 23.

49.

Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins.

Davey NE, Edwards RJ, Shields DC.

BMC Bioinformatics. 2010 Jan 7;11:14. doi: 10.1186/1471-2105-11-14.

50.

ELM: the status of the 2010 eukaryotic linear motif resource.

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, Gibson TJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016. Epub 2009 Nov 17.

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