Gibson TeamPublications

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SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.
Davey, N.E., Cowan, J.L., Shields, D.C., Gibson, T.J., Coldwell, M.J. & Edwards, R.J.
Nucleic Acids Res. 2012 Nov 1;40(21):10628-41. doi: 10.1093/nar/gks854. Epub 2012Sep 12. PubMed

A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins.
Jiang, K., Toedt, G., Montenegro Gouveia, S., Davey, N.E., Hua, S., van der Vaart, B., Grigoriev, I., Larsen, J., Pedersen, L.B., Bezstarosti, K., Lince-Faria, M., Demmers, J., Steinmetz, M.O., Gibson, T.J. & Akhmanova, A.
Curr Biol. 2012 Oct 9;22(19):1800-7. doi: 10.1016/j.cub.2012.07.047. Epub 2012Aug 9. PubMed

RACK1 research - ships passing in the night?
Gibson, T.J.
FEBS Lett. 2012 Aug 14;586(17):2787-9. doi: 10.1016/j.febslet.2012.04.048. Epub2012 May 8. PubMed

Linear motifs: lost in (pre)translation.
Weatheritt, R.J. & Gibson, T.J.
Trends Biochem Sci. 2012 Aug;37(8):333-41. doi: 10.1016/j.tibs.2012.05.001. Epub2012 Jun 15. PubMed

Prion infected rhesus monkeys to study differential transcription of Alu DNA elements and editing of Alu transcripts in neuronal cells and blood cells.
Kiesel, P., Bodemer, W., Gibson, T.J., Zischler, H. & Kaup, F.J.
J Med Primatol. 2012 Jun;41(3):176-82. doi: 10.1111/j.1600-0684.2012.00535.x.Epub 2012 Mar 2. PubMed

iELM--a web server to explore short linear motif-mediated interactions.
Weatheritt, R.J., Jehl, P., Dinkel, H. & Gibson, T.J.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W364-9. doi: 10.1093/nar/gks444.Epub 2012 May 25. PubMed

Linear motifs confer functional diversity onto splice variants.
Weatheritt, R.J., Davey, N.E. & Gibson, T.J.
Nucleic Acids Res. 2012 Aug;40(15):7123-31. doi: 10.1093/nar/gks442. Epub 2012May 25. PubMed

Motif switches: decision-making in cell regulation.
Van Roey, K., Gibson, T.J. & Davey, N.E.
Curr Opin Struct Biol. 2012 Jun;22(3):378-85. doi: 10.1016/j.sbi.2012.03.004.Epub 2012 Apr 3. PubMed

The identification of short linear motif-mediated interfaces within the human interactome.
Weatheritt, R.J., Luck, K., Petsalaki, E., Davey, N.E. & Gibson, T.J.
Bioinformatics. 2012 Apr 1;28(7):976-82. doi: 10.1093/bioinformatics/bts072. Epub2012 Feb 10. PubMed

Attributes of short linear motifs.
Davey, N.E., Van Roey, K., Weatheritt, R.J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H. & Gibson, T.J.
Mol Biosyst. 2012 Jan;8(1):268-81. doi: 10.1039/c1mb05231d. Epub 2011 Sep 12. PubMed

ELM--the database of eukaryotic linear motifs.
Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A., Jodicke, L., Dammert, M.A., 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, R.J., Steinmetz, M.O., Meiselbach, H., Diella, F. & Gibson, T.J.
Nucleic Acids Res. 2012 Jan 1;40(D1):D242-D251. Epub 2011 Nov 21. PubMed

A comparative analysis to study editing of small noncoding BC200- and Alu transcripts in brain of prion-inoculated rhesus monkeys (M. Mulatta).
Kiesel, P., Kues, A., Kaup, F.J., Bodemer, W., Gibson, T.J. & Zischler, H.
J Toxicol Environ Health A. 2012;75(7):391-401. doi:10.1080/15287394.2012.670896. PubMed

Possible editing of Alu transcripts in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD).
Kiesel, P., Gibson, T.J., Ciesielczyk, B., Bodemer, M., Kaup, F.J., Bodemer, W., Zischler, H. & Zerr, I.
J Toxicol Environ Health A. 2011 Jan;74(2-4):88-95. PubMed

Phospho.ELM: a database of phosphorylation sites--update 2011.
Dinkel, H., Chica, C., Via, A., Gould, C.M., Jensen, L.J., Gibson, T.J. & Diella, F.
Nucleic Acids Res. 2011 Jan;39(Database issue):D261-7. Epub 2010 Nov 9. PubMed

From sequence to structural analysis in protein phosphorylation motifs.
Via, A., Diella, F., Gibson, T.J. & Helmer-Citterich, M.
Front Biosci. 2011 Jan 1;16:1261-75. PubMed

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soding, J., Thompson, J.D. & Higgins, D.G.
Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. PubMed

How viruses hijack cell regulation.
Davey, N.E., Trave, G. & Gibson, T.J.
Trends Biochem Sci. 2011 Mar;36(3):159-69. Epub 2010 Dec 9 PubMed

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction.
Croset, V., Rytz, R., Cummins, S.F., Budd, A., Brawand, D., Kaessmann, H., Gibson, T.J. & Benton, R.
PLoS Genet. 2010 Aug 19;6(8). pii: e1001064. PubMed

EpiC: an open resource for exploring epitopes to aid antibody-based experiments.
Haslam, N.J. & Gibson, T.J.
J Proteome Res. 2010 Jul 2;9(7):3759-63. PubMed

Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD).
Kiesel, P., Gibson, T.J., Ciesielczyk, B., Bodemer, M., Kaup, F.J., Bodemer, W., Zischler, H. & Zerr, I.
Prion. 2010 Apr-Jun;4(2):87-93. Epub 2010 Apr 5. PubMed

ELM: the status of the 2010 eukaryotic linear motif resource.
Gould, C.M., Diella, F., Via, A., Puntervoll, P., Gemund, C., Chabanis-Davidson, S., Michael, S., Sayadi, A., Bryne, J.C., Chica, C., Seiler, M., Davey, N.E., Haslam, N., Weatheritt, R.J., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave, G., Aasland, R., Helmer-Citterich, M., Linding, R. & Gibson, T.J.
Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016.Epub 2009 Nov 17. PubMed

A community standard format for the representation of protein affinity reagents.
Gloriam, D.E., Orchard, S., Bertinetti, D., Bjorling, E., Bongcam-Rudloff, E., Borrebaeck, C.A., Bourbeillon, J., Bradbury, A.R., de Daruvar, A., Dubel, S., Frank, R., Gibson, T.J., Gold, L., Haslam, N., Herberg, F.W., Hiltke, T., Hoheisel, J.D., Kerrien, S., Koegl, M., Konthur, Z., Korn, B., Landegren, U., Montecchi-Palazzi, L., Palcy, S., Rodriguez, H., Schweinsberg, S., Sievert, V., Stoevesandt, O., Taussig, M.J., Ueffing, M., Uhlen, M., van der Maarel, S., Wingren, C., Woollard, P., Sherman, D.J. & Hermjakob, H.
Mol Cell Proteomics. 2010 Jan;9(1):1-10. doi: 10.1074/mcp.M900185-MCP200. Epub2009 Aug 11. PubMed

Cell regulation: determined to signal discrete cooperation.
Gibson, T.J.
Trends Biochem Sci. 2009 Oct;34(10):471-82. Epub 2009 Sep 8. PubMed

Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60.
Corsini, L., Hothorn, M., Stier, G., Rybin, V., Scheffzek, K., Gibson, T.J. & Sattler, M.
J Biol Chem. 2009 Jan 2;284(1):630-9. doi: 10.1074/jbc.M805395200. Epub 2008 Oct29. PubMed

KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors.
Diella, F., Chabanis, S., Luck, K., Chica, C., Ramu, C., Nerlov, C. & Gibson, T.J.
Bioinformatics. 2009 Jan 1;25(1):1-5. Epub 2008 Nov 24. PubMed

A structure filter for the Eukaryotic Linear Motif Resource.
Via, A., Gould, C.M., Gemund, C., Gibson, T.J. & Helmer-Citterich, M.
BMC Bioinformatics. 2009 Oct 24;10:351. PubMed

Phosphorylation of s776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors.
de Chiara, C., Menon, R.P., Strom, M., Gibson, T.J. & Pastore, A.
PLoS One. 2009 Dec 23;4(12):e8372. PubMed

Evidence for the concerted evolution between short linear protein motifs and their flanking regions.
Chica, C., Diella, F. & Gibson, T.J.
PLoS One. 2009 Jul 8;4(7):e6052. PubMed

Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation.
Schallus, T., Jaeckh, C., Feher, K., Palma, A.S., Liu, Y., Simpson, J.C., Mackeen, M., Stier, G., Gibson, T.J., Feizi, T., Pieler, T. & Muhle-Goll, C.
Mol Biol Cell. 2008 Aug;19(8):3404-14. Epub 2008 Jun 4. PubMed

A careful disorderliness in the proteome: sites for interaction and targets for future therapies.
Russell, R.B. & Gibson, T.J.
FEBS Lett. 2008 Apr 9;582(8):1271-5. doi: 10.1016/j.febslet.2008.02.027. Epub2008 Feb 20. PubMed

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.
Michael, S., Trave, G., Ramu, C., Chica, C. & Gibson, T.J.
Bioinformatics. 2008 Feb 15;24(4):453-7. Epub 2008 Jan 9. PubMed

Phospho.ELM: a database of phosphorylation sites--update 2008.
Diella, F., Gould, C.M., Chica, C., Via, A. & Gibson, T.J.
Nucleic Acids Res. 2008 Jan;36(Database issue):D240-4. Epub 2007 Oct 25. PubMed

A new protein linear motif benchmark for multiple sequence alignment software.
Perrodou, E., Chica, C., Poch, O., Gibson, T.J. & Thompson, J.D.
BMC Bioinformatics. 2008 Apr 25;9:213. PubMed

Understanding eukaryotic linear motifs and their role in cell signaling and regulation.
Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Trave, G. & Gibson, T.J.
Front Biosci. 2008 May 1;13:6580-603. PubMed

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Chica, C., Labarga, A., Gould, C.M., Lopez, R. & Gibson, T.J.
BMC Bioinformatics. 2008 May 6;9:229. PubMed

Clustal W and Clustal X version 2.0.
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. & Higgins, D.G.
Bioinformatics. 2007 Nov 1;23(21):2947-8. Epub 2007 Sep 10. PubMed

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Taussig, M.J., Stoevesandt, O., Borrebaeck, C.A., Bradbury, A.R., Cahill, D., Cambillau, C., de Daruvar, A., Dubel, S., Eichler, J., Frank, R., Gibson, T.J., Gloriam, D., Gold, L., Herberg, F.W., Hermjakob, H., Hoheisel, J.D., Joos, T.O., Kallioniemi, O., Koegll, M., Konthur, Z., Korn, B., Kremmer, E., Krobitsch, S., Landegren, U., van der Maarel, S., McCafferty, J., Muyldermans, S., Nygren, P.A., Palcy, S., Pluckthun, A., Polic, B., Przybylski, M., Saviranta, P., Sawyer, A., Sherman, D.J., Skerra, A., Templin, M., Ueffing, M. & Uhlen, M.
Nat Methods. 2007 Jan;4(1):13-7. PubMed

Systematic discovery of new recognition peptides mediating protein interaction networks.
Neduva, V., Linding, R., Su-Angrand, I., Stark, A., de Masi, F., Gibson, T.J., Lewis, J.D., Serrano, L. & Russell, R.B.
PLoS Biol. 2005 Dec;3(12):e405. Epub 2005 Nov 15. PubMed

Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei.
Michel, K., Budd, A., Pinto, S., Gibson, T.J. & Kafatos, F.C.
EMBO Rep 2005 Sep;6(9):891-7. PubMed

Patterns and clusters within the PSM column in TiBS, 1992-2004.
McEntyre, J.R. & Gibson, T.J.
Trends Biochem Sci 2004 Dec;29(12):627-33. PubMed

The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre.
Menon, R.P., Gibson, T.J. & Pastore, A.
J Mol Biol 2004 Oct 8;343(1):43-53. PubMed

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins.
Diella, F., Cameron, S., Gemund, C., Linding, R., Via, A., Kuster, B., Sicheritz-Ponten, T., Blom, N. & Gibson, T.J.
BMC Bioinformatics 2004 Jun 22;5(1):79. PubMed

Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300.
Ragvin, A., Valvatne, H., Erdal, S., Arskog, V., Tufteland, K.R., Breen, K., OYan, A.M., Eberharter, A., Gibson, T.J., Becker, P.B. & Aasland, R.
J Mol Biol 2004 Apr 2;337(4):773-88. PubMed

Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?
Budd, A., Blandin, S., Levashina, E.A. & Gibson, T.J.
Genome Biol 2004;5(6):R38. Epub 2004 May 26. PubMed

Protein disorder prediction. Implications for structural proteomics.
Linding, R., Jensen, L.J., Diella, F., Bork, P., Gibson, T.J. & Russell, R.B.
Structure (Camb) 2003 Nov;11(11):1453-9. PubMed

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M., Ausiello, G., Brannetti, B., Costantini, A., Ferre, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, L., Kuster, B., Helmer-Citterich, M., Hunter, W.N., Aasland, R. & Gibson, T.J.
Nucleic Acids Res 2003 Jul 1;31(13):3625-30. PubMed

Multiple sequence alignment with the Clustal series of programs.
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. & Thompson, J.D.
Nucleic Acids Res 2003 Jul 1;31(13):3497-500. PubMed

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.
Bimpikis, K., Budd, A., Linding, R. & Gibson, T.J.
Nucleic Acids Res 2003 Jul 1;31(13):3792-4. PubMed

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Huynen, M.A., Snel, B., Bork, P. & Gibson, T.J.
Hum Mol Genet 2001 Oct 1;10(21):2463-8. PubMed

The gene mutated in ataxia-ocular apraxia 1 encodes the new HIT/Zn-finger protein aprataxin.
Moreira, M.C., Barbot, C., Tachi, N., Kozuka, N., Uchida, E., Gibson, T., Mendonca, P., Costa, M., Barros, J., Yanagisawa, T., Watanabe, M., Ikeda, Y., Aoki, M., Nagata, T., Coutinho, P., Sequeiros, J. & Koenig, M.
Nat Genet 2001 Oct;29(2):189-93. PubMed

The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.
Bottomley, M.J., Collard, M.W., Huggenvik, J.I., Liu, Z., Gibson, T.J. & Sattler, M.
Nat Struct Biol 2001 Jul;8(7):626-33. PubMed

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries.
Gemund, C., Ramu, C., Altenberg-Greulich, B. & Gibson, T.J.
Nucleic Acids Res 2001 Mar 15;29(6):1272-7. PubMed

RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein SINE proliferation drives PrP overproduction.
Gibson, T.J.
Genome Biol 2001;2(7):Preprint 0006. PubMed

Object-oriented parsing of biological databases with python.
Ramu, C., Gemund, C. & Gibson, T.J.
Bioinformatics 2000 Jul;16(7):628-38 PubMed

An estimate of large-scale sequencing accuracy.
Hill, F., Gemund, C., Benes, V., Ansorge, W. & Gibson, T.J.
EMBO Rep. 2000 Jul;1(1):29-31. PubMed

Homology-based method for identification of protein repeats using statistical significance estimates.
Andrade, M.A., Ponting, C.P., Gibson, T.J. & Bork, P.
J Mol Biol 2000 May 5;298(3):521-37 PubMed

Evidence in favour of ancient octaploidy in the vertebrate genome.
Gibson, T.J. & Spring, J.
Biochem Soc Trans 2000 Feb;28(2):259-64. PubMed

Assignment of the 1H, 15N, and 13C resonances of the C-terminal domain of frataxin, the protein responsible for Friedreich ataxia
Musco, G., de Tommasi, T., Stier, G., Kolmerer, B., Bottomley, M., Adinolfi, S., Muskett, F.W., Gibson, T.J., Frenkiel, T.A. & Pastore, A.
J Biomol NMR 1999 Sep;15(1):87-8 PubMed

Formin defines a large family of morphoregulatory genes and functions in establishment of the polarising region.
Zeller, R., Haramis, A.G., Zuniga, A., McGuigan, C., Dono, R., Davidson, G., Chabanis, S. & Gibson, T.
Cell Tissue Res 1999 Mar 29 296(1) 85-93 PubMed

Multiple sequence alignment with Clustal X.
Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G. & Gibson, T.J.
Trends Biochem Sci 1998 Oct 23(10) 403-405 PubMed

A new method for isolating tyrosine kinase substrates used to identify fish, an SH3 and PX domain-containing protein, and Src substrate.
Lock, P., Abram, C.L., Gibson, T. & Courtneidge, S.A.
EMBO J 1998 Aug 3 17(15) 4346-4357 PubMed

The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor
Gibson, T.J., Ramu, C., Gemund, C. & Aasland, R.
Trends Biochem Sci 1998 Jul 23(7) 242-244 PubMed

Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins.
Gibson, T.J. & Spring, J.
This is a review article.
Trends Genet 1998 Feb 14(2) 46-49 PubMed

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G.
Nucleic Acids Res 1997 Dec 15;25(24):4876-82 PubMed

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G.
Nucleic Acids Res 1997 Dec 15 25(24) 4876-4882 PubMed

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.
Birney, E., Thompson, J.D. & Gibson, T.J.
Nucleic Acids Res 1996 Jul 15;24(14):2730-9 PubMed

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson, J.D., Higgins, D.G. & Gibson, T.J.
Nucleic Acids Res 1994 Nov 11;22(22):4673-80 PubMed