Toby J. Gibson - Publications

Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 

132 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
2021 Mészáros B, Sámano-Sánchez H, Alvarado-Valverde J, Čalyševa J, Martínez-Pérez E, Alves R, Shields DC, Kumar M, Rippmann F, Chemes LB, Gibson TJ. Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. Science Signaling. 14. PMID 33436497 DOI: 10.1126/scisignal.abd0334  0.4
2020 Gouw M, Alvarado-Valverde J, Čalyševa J, Diella F, Kumar M, Michael S, Van Roey K, Dinkel H, Gibson TJ. How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. Methods in Molecular Biology (Clifton, N.J.). 2141: 73-102. PMID 32696353 DOI: 10.1007/978-1-0716-0524-0_4  0.52
2020 Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ, Davey NE. The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database : the Journal of Biological Databases and Curation. 2020. PMID 32507889 DOI: 10.1093/Database/Baaa040  0.52
2019 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, et al. An intrinsically disordered proteins community for ELIXIR. F1000research. 8. PMID 31824649 DOI: 10.12688/F1000Research.20136.1  0.52
2019 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 Research. PMID 31680160 DOI: 10.1093/Nar/Gkz1030  0.52
2019 van Dam TJP, Kennedy J, van der Lee R, de Vrieze E, Wunderlich KA, Rix S, Dougherty GW, Lambacher NJ, Li C, Jensen VL, Leroux MR, Hjeij R, Horn N, Texier Y, Wissinger Y, ... ... Gibson TJ, et al. CiliaCarta: An integrated and validated compendium of ciliary genes. Plos One. 14: e0216705. PMID 31095607 DOI: 10.1371/Journal.Pone.0216705  0.52
2017 Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 6: 10. PMID 29177046 DOI: 10.1186/S13630-017-0054-8  0.52
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, ... ... Gibson TJ, et al. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Research. PMID 29136216 DOI: 10.1093/Nar/Gkx1077  0.52
2017 Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mücke N, Wilmanns M, Gibson TJ, Barabas O. Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. Scientific Reports. 7: 9903. PMID 28852099 DOI: 10.1038/S41598-017-10085-8  0.48
2017 Gouw M, Sámano-Sánchez H, Van Roey K, Diella F, Gibson TJ, Dinkel H. Exploring Short Linear Motifs Using the ELM Database and Tools. Current Protocols in Bioinformatics. 58: 8.22.1-8.22.35. PMID 28654726 DOI: 10.1002/Cpbi.26  0.52
2017 Mészáros B, Kumar M, Gibson TJ, Uyar B, Dosztányi Z. Degrons in cancer. Science Signaling. 10. PMID 28292960 DOI: 10.1126/Scisignal.Aak9982  0.52
2016 Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TT, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, ... ... Gibson TJ, et al. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature Communications. 7: 11491. PMID 27173435 DOI: 10.1038/ncomms11491  1
2016 Gibson TJ, Kumar M. Hunting for Cis-Regulatory Elements in Proteins. Cell Systems. 2: 68-70. PMID 27135160 DOI: 10.1016/J.Cels.2016.02.011  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, ... ... Gibson TJ, 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 Gibson TJ, Dinkel H, Van Roey K, Diella F. Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Communication and Signaling : Ccs. 13: 42. PMID 26581338 DOI: 10.1186/S12964-015-0121-Y  1
2015 Dona M, Bachmann-Gagescu R, Texier Y, Toedt G, Hetterschijt L, Tonnaer EL, Peters TA, van Beersum SE, Bergboer JG, Horn N, de Vrieze E, Slijkerman RW, van Reeuwijk J, Flik G, Keunen JE, ... ... Gibson TJ, et al. NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish. Plos Genetics. 11: e1005574. PMID 26485514 DOI: 10.1371/Journal.Pgen.1005574  1
2015 Wheway G, Schmidts M, Mans DA, Szymanska K, Nguyen TT, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA, Sorusch N, Abdelhamed ZA, Natarajan S, Herridge W, van Reeuwijk J, ... ... Gibson T, et al. An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. Nature Cell Biology. PMID 26167768 DOI: 10.1038/Ncb3201  1
2014 Weatheritt RJ, Gibson TJ, Babu MM. Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems. Nature Structural & Molecular Biology. 21: 833-9. PMID 25150862 DOI: 10.1038/Nsmb.2876  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 Texier Y, Toedt G, Gorza M, Mans DA, van Reeuwijk J, Horn N, Willer J, Katsanis N, Roepman R, Gibson TJ, Ueffing M, Boldt K. Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry. Molecular & Cellular Proteomics : McP. 13: 1382-91. PMID 24563533 DOI: 10.1074/Mcp.O113.033233  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, ... ... Gibson TJ, 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 Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ. Capturing cooperative interactions with the PSI-MI format. Database : the Journal of Biological Databases and Curation. 2013: bat066. PMID 24067240 DOI: 10.1093/Database/Bat066  1
2013 Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W. Drift and conservation of differential exon usage across tissues in primate species. Proceedings of the National Academy of Sciences of the United States of America. 110: 15377-82. PMID 24003148 DOI: 10.1073/Pnas.1307202110  1
2013 Gibson TJ, Seiler M, Veitia RA. The transience of transient overexpression. Nature Methods. 10: 715-21. PMID 23900254 DOI: 10.1038/Nmeth.2534  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
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 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 Weatheritt RJ, Gibson TJ. Linear motifs: lost in (pre)translation. Trends in Biochemical Sciences. 37: 333-41. PMID 22705166 DOI: 10.1016/J.Tibs.2012.05.001  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 Weatheritt RJ, Jehl P, Dinkel H, Gibson TJ. iELM--a web server to explore short linear motif-mediated interactions. Nucleic Acids Research. 40: W364-9. PMID 22638578 DOI: 10.1093/Nar/Gks444  1
2012 Gibson TJ. RACK1 research - ships passing in the night? Febs Letters. 586: 2787-9. PMID 22580388 DOI: 10.1016/J.Febslet.2012.04.048  1
2012 Kiesel P, Kues A, Kaup FJ, Bodemer W, Gibson TJ, Zischler H. A comparative analysis to study editing of small noncoding BC200- and Alu transcripts in brain of prion-inoculated rhesus monkeys (M. Mulatta). Journal of Toxicology and Environmental Health. Part A. 75: 391-401. PMID 22524594 DOI: 10.1080/15287394.2012.670896  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 Kiesel P, Bodemer W, Gibson T, Zischler H, Kaup FJ. Prion infected rhesus monkeys to study differential transcription of Alu DNA elements and editing of Alu transcripts in neuronal cells and blood cells Journal of Medical Primatology. 41: 176-182. PMID 22380733 DOI: 10.1111/J.1600-0684.2012.00535.X  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, ... ... Gibson TJ, 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
2011 Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology. 7: 539. PMID 21988835 DOI: 10.1038/Msb.2011.75  1
2011 Kiesel P, Gibson TJ, Ciesielczyk B, Bodemer M, Kaup FJ, Bodemer W, Zischler H, Zerr I. Possible editing of Alu transcripts in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD). Journal of Toxicology and Environmental Health. Part A. 74: 88-95. PMID 21218337 DOI: 10.1080/15287394.2011.529057  1
2011 Via A, Diella F, Gibson TJ, Helmer-Citterich M. From sequence to structural analysis in protein phosphorylation motifs. Frontiers in Bioscience (Landmark Edition). 16: 1261-75. PMID 21196230 DOI: 10.2741/3787  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
2011 Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Research. 39: D261-7. PMID 21062810 DOI: 10.1093/Nar/Gkq1104  1
2010 Croset V, Rytz R, Cummins SF, Budd A, Brawand D, Kaessmann H, Gibson TJ, Benton R. Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. Plos Genetics. 6: e1001064. PMID 20808886 DOI: 10.1371/Journal.Pgen.1001064  1
2010 Haslam NJ, Gibson TJ. EpiC: an open resource for exploring epitopes to aid antibody-based experiments. Journal of Proteome Research. 9: 3759-63. PMID 20496950 DOI: 10.1021/Pr100029F  1
2010 Kiesel P, Gibson TJ, Ciesielczyk B, Bodemer M, Kaup FJ, Bodemer W, Zischler H, Zerr I. Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD). Prion. 4: 87-93. PMID 20424511 DOI: 10.4161/Pri.4.2.11965  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, ... ... Gibson TJ, 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 Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, et al. A community standard format for the representation of protein affinity reagents. Molecular & Cellular Proteomics : McP. 9: 1-10. PMID 19674966 DOI: 10.1074/Mcp.M900185-Mcp200  1
2009 de Chiara C, Menon RP, Strom M, Gibson TJ, Pastore A. Phosphorylation of S776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors. Plos One. 4: e8372. PMID 20037628 DOI: 10.1371/Journal.Pone.0008372  1
2009 Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M. A structure filter for the Eukaryotic Linear Motif Resource. Bmc Bioinformatics. 10: 351. PMID 19852836 DOI: 10.1186/1471-2105-10-351  1
2009 Gibson TJ. Cell regulation: determined to signal discrete cooperation. Trends in Biochemical Sciences. 34: 471-82. PMID 19744855 DOI: 10.1016/J.Tibs.2009.06.007  1
2009 Chica C, Diella F, Gibson TJ. Evidence for the concerted evolution between short linear protein motifs and their flanking regions. Plos One. 4: e6052. PMID 19584925 DOI: 10.1371/Journal.Pone.0006052  1
2009 Diella F, Chabanis S, Luck K, Chica C, Ramu C, Nerlov C, Gibson TJ. KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. Bioinformatics (Oxford, England). 25: 1-5. PMID 19033273 DOI: 10.1093/Bioinformatics/Btn594  1
2009 Corsini L, Hothorn M, Stier G, Rybin V, Scheffzek K, Gibson TJ, Sattler M. Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60. The Journal of Biological Chemistry. 284: 630-9. PMID 18974054 DOI: 10.1074/Jbc.M805395200  1
2009 Haslam N, Gibson T. EpiC: A resource for integrating information and analyses to enable selection of epitopes for antibody based experiments Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5647: 173-181. DOI: 10.1007/978-3-642-02879-3_14  1
2008 Schallus T, Jaeckh C, Fehér K, Palma AS, Liu Y, Simpson JC, Mackeen M, Stier G, Gibson TJ, Feizi T, Pieler T, Muhle-Goll C. Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation. Molecular Biology of the Cell. 19: 3404-14. PMID 18524852 DOI: 10.2210/Pdb2Jwp/Pdb  1
2008 Diella F, Haslam N, Chica C, Budd A, Michael S, Brown NP, Trave G, Gibson TJ. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Frontiers in Bioscience : a Journal and Virtual Library. 13: 6580-603. PMID 18508681 DOI: 10.2741/3175  1
2008 Chica C, Labarga A, Gould CM, López R, Gibson TJ. A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. Bmc Bioinformatics. 9: 229. PMID 18460207 DOI: 10.1186/1471-2105-9-229  1
2008 Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD. A new protein linear motif benchmark for multiple sequence alignment software. Bmc Bioinformatics. 9: 213. PMID 18439277 DOI: 10.1186/1471-2105-9-213  1
2008 Russell RB, Gibson TJ. A careful disorderliness in the proteome: sites for interaction and targets for future therapies. Febs Letters. 582: 1271-5. PMID 18284921 DOI: 10.1016/J.Febslet.2008.02.027  1
2008 Michael S, Travé G, Ramu C, Chica C, Gibson TJ. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation. Bioinformatics (Oxford, England). 24: 453-7. PMID 18184688 DOI: 10.1093/Bioinformatics/Btm624  1
2008 Diella F, Gould CM, Chica C, Via A, Gibson TJ. Phospho.ELM: a database of phosphorylation sites--update 2008. Nucleic Acids Research. 36: D240-4. PMID 17962309 DOI: 10.1093/Nar/Gkm772  1
2007 Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England). 23: 2947-8. PMID 17846036 DOI: 10.1093/Bioinformatics/Btm404  1
2007 Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, et al. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nature Methods. 4: 13-7. PMID 17195019 DOI: 10.1038/Nmeth0107-13  1
2005 Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB. Systematic discovery of new recognition peptides mediating protein interaction networks. Plos Biology. 3: e405. PMID 16279839 DOI: 10.1371/Journal.Pbio.0030405  1
2005 Michel K, Budd A, Pinto S, Gibson TJ, Kafatos FC. Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei. Embo Reports. 6: 891-7. PMID 16113656 DOI: 10.1038/Sj.Embor.7400478  1
2004 McEntyre JR, Gibson TJ. Patterns and clusters within the PSM column in TiBS, 1992-2004. Trends in Biochemical Sciences. 29: 627-33. PMID 15544947 DOI: 10.1016/J.Tibs.2004.10.006  1
2004 Menon RP, Gibson TJ, Pastore A. The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre. Journal of Molecular Biology. 343: 43-53. PMID 15381419 DOI: 10.1016/J.Jmb.2004.08.024  1
2004 Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ. Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. Bmc Bioinformatics. 5: 79. PMID 15212693 DOI: 10.1186/1471-2105-5-79  1
2004 Budd A, Blandin S, Levashina EA, Gibson TJ. Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? Genome Biology. 5: R38. PMID 15186489 DOI: 10.1186/Gb-2004-5-6-R38  1
2004 Ragvin A, Valvatne H, Erdal S, Arskog V, Tufteland KR, Breen K, ØYan AM, Eberharter A, Gibson TJ, Becker PB, Aasland R. Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300. Journal of Molecular Biology. 337: 773-88. PMID 15033350 DOI: 10.1016/J.Jmb.2004.01.051  1
2003 Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure (London, England : 1993). 11: 1453-9. PMID 14604535 DOI: 10.1016/J.Str.2003.10.002  1
2003 Bimpikis K, Budd A, Linding R, Gibson TJ. BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases. Nucleic Acids Research. 31: 3792-4. PMID 12824420 DOI: 10.1093/Nar/Gkg535  1
2003 Linding R, Russell RB, Neduva V, Gibson TJ. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Research. 31: 3701-8. PMID 12824398 DOI: 10.1093/Nar/Gkg519  1
2003 Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, ... ... Gibson TJ, et al. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research. 31: 3625-30. PMID 12824381 DOI: 10.1093/Nar/Gkg545  1
2003 Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research. 31: 3497-500. PMID 12824352 DOI: 10.1093/Nar/Gkg500  1
2002 Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 2.3. PMID 18792934 DOI: 10.1002/0471250953.Bi0203S00  1
2001 Huynen MA, Snel B, Bork P, Gibson TJ. The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. Human Molecular Genetics. 10: 2463-8. PMID 11689493 DOI: 10.1093/Hmg/10.21.2463  1
2001 Moreira MC, Barbot C, Tachi N, Kozuka N, Uchida E, Gibson T, Mendonça P, Costa M, Barros J, Yanagisawa T, Watanabe M, Ikeda Y, Aoki M, Nagata T, Coutinho P, et al. The gene mutated in ataxia-ocular apraxia 1 encodes the new HIT/Zn-finger protein aprataxin Nature Genetics. 29: 189-193. PMID 11586300 DOI: 10.1038/Ng1001-189  1
2001 Gibson TJ. RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein SINE proliferation drives PrP overproduction. Genome Biology. 2: Preprint 0006. PMID 11521680 DOI: 10.1186/Gb-2001-2-7-Preprint0006  1
2001 Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M. The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation. Nature Structural Biology. 8: 626-33. PMID 11427895 DOI: 10.1038/89675  1
2001 Gemünd C, Ramu C, Altenberg-Greulich B, Gibson TJ. Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries. Nucleic Acids Research. 29: 1272-7. PMID 11238992 DOI: 10.1093/Nar/29.6.1272  1
2000 Hill F, Gemünd C, Benes V, Ansorge W, Gibson TJ. An estimate of large-scale sequencing accuracy. Embo Reports. 1: 29-31. PMID 11256620 DOI: 10.1093/Embo-Reports/Kvd015  1
2000 Ramu C, Gemünd C, Gibson TJ. Object-oriented parsing of biological databases with Python. Bioinformatics (Oxford, England). 16: 628-38. PMID 11038333 DOI: 10.1093/Bioinformatics/16.7.628  1
2000 Musco G, Stier G, Kolmerer B, Adinolfi S, Martin S, Frenkiel T, Gibson T, Pastore A. Towards a structural understanding of Friedreich's ataxia: Solution structure of frataxin Structure. 8: 695-707. PMID 10903947 DOI: 10.1016/S0969-2126(00)00158-1  1
2000 Gibson TJ, Spring J. Evidence in favour of ancient octaploidy in the vertebrate genome. Biochemical Society Transactions. 28: 259-64. PMID 10816139 DOI: 10.1042/Bst0280259  1
2000 Andrade MA, Ponting CP, Gibson TJ, Bork P. Homology-based method for identification of protein repeats using statistical significance estimates. Journal of Molecular Biology. 298: 521-37. PMID 10772867 DOI: 10.1006/Jmbi.2000.3684  1
1999 Musco G, de Tommasi T, Stier G, Kolmerer B, Bottomley M, Adinolfi S, Muskett FW, Gibson TJ, Frenkiel TA, Pastore A. Assignment of the 1H, 15N, and 13C resonances of the C-terminal domain of frataxin, the protein responsible for Friedreich ataxia. Journal of Biomolecular Nmr. 15: 87-8. PMID 10549137 DOI: 10.1023/A:1008398832619  1
1999 Adinolfi S, Bagni C, Musco G, Gibson T, Mazzarella L, Pastore A. Dissecting FMR1, the protein responsible for fragile X syndrome, in its structural and functional domains. Rna (New York, N.Y.). 5: 1248-58. PMID 10496225 DOI: 10.1017/S1355838299990647  1
1999 Zeller R, Haramis AG, Zuniga A, McGuigan C, Dono R, Davidson G, Chabanis S, Gibson T. Formin defines a large family of morphoregulatory genes and functions in establishment of the polarising region Cell and Tissue Research. 296: 85-93. PMID 10199968 DOI: 10.1007/S004410051269  1
1998 Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences. 23: 403-5. PMID 9810230 DOI: 10.1016/S0968-0004(98)01285-7  1
1998 Gibson TJ, Ramu C, Gemünd C, Aasland R. The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor. Trends in Biochemical Sciences. 23: 242-4. PMID 9697411 DOI: 10.1016/S0968-0004(98)01231-6  1
1998 Lock P, Abram CL, Gibson T, Courtneidge SA. A new method for isolating tyrosine kinase substrates used to identify Fish, an SH3 and PX domain-containing protein, and Src substrate Embo Journal. 17: 4346-4357. PMID 9687503 DOI: 10.1093/Emboj/17.15.4346  1
1998 Gibson TJ, Spring J. Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins. Trends in Genetics : Tig. 14: 46-9; discussion 49-. PMID 9520595 DOI: 10.1016/S0168-9525(97)01367-X  1
1997 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 25: 4876-82. PMID 9396791 DOI: 10.1093/Nar/25.24.4876  1
1997 Musco G, Kharrat A, Stier G, Fraternali F, Gibson TJ, Nilges M, Pastore A. The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome. Nature Structural Biology. 4: 712-6. PMID 9302998 DOI: 10.1038/Nsb0997-712  1
1996 Gibson TJ, Koonin EV, Musco G, Pastore A, Bork P. Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction. Trends in Neurosciences. 19: 465-8. PMID 8931268 DOI: 10.1016/S0166-2236(96)20054-2  1
1996 Aasland R, Stewart AF, Gibson T. The SANT domain: A putative DNA binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB Trends in Biochemical Sciences. 21: 87-88. PMID 8882580 DOI: 10.1016/S0968-0004(96)30009-1  1
1996 Birney E, Thompson JD, Gibson TJ. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Research. 24: 2730-9. PMID 8759004 DOI: 10.1093/Nar/24.14.2730  1
1996 Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Methods in Enzymology. 266: 383-402. PMID 8743695 DOI: 10.1016/S0076-6879(96)66024-8  1
1996 Bork P, Gibson TJ. Applying motif and profile searches. Methods in Enzymology. 266: 162-84. PMID 8743684 DOI: 10.1016/S0076-6879(96)66013-3  1
1996 Winder SJ, Gibson TJ, Kendrick-Jones J. Low probability of dystrophin and utrophin coiled coil regions forming dimers. Biochemical Society Transactions. 24: 280S. PMID 8736938 DOI: 10.1042/Bst024280S  1
1996 Musco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, Gibson TJ, Pastore A. Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. Cell. 85: 237-45. PMID 8612276 DOI: 10.1016/S0092-8674(00)81100-9  1
1995 Castiglione Morelli MA, Stier G, Gibson T, Joseph C, Musco G, Pastore A, Travè G. The KH module has an αβ fold Febs Letters. 358: 193-198. PMID 7828735 DOI: 10.1016/0014-5793(94)01422-W  1
1995 Aasland R, Gibson TJ, Stewart AF. The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends in Biochemical Sciences. 20: 56-9. PMID 7701562 DOI: 10.1016/S0968-0004(00)88957-4  1
1995 Winder SJ, Gibson TJ, Kendrick-Jones J. Dystrophin and utrophin: the missing links! Febs Letters. 369: 27-33. PMID 7641878 DOI: 10.1016/0014-5793(95)00398-S  1
1995 Kharrat A, Macias MJ, Gibson TJ, Nilges M, Pastore A. Structure of the dsRNA binding domain of E. coli RNase III. The Embo Journal. 14: 3572-84. PMID 7628457 DOI: 10.1002/J.1460-2075.1995.Tb07363.X  1
1994 Thompson JD, Higgins DG, Gibson TJ. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Computer Applications in the Biosciences : Cabios. 10: 19-29. PMID 8193951 DOI: 10.1093/Bioinformatics/10.1.19  1
1994 Gibson TJ, Thompson JD, Blocker A, Kouzarides T. Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107. Nucleic Acids Research. 22: 946-52. PMID 8152925 DOI: 10.1093/Nar/22.6.946  1
1994 Gibson TJ, Thompson JD. Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases. Nucleic Acids Research. 22: 2552-6. PMID 8041617 DOI: 10.1093/Nar/22.13.2552  1
1994 Higgins DG, Labeit S, Gautel M, Gibson TJ. The evolution of titin and related giant muscle proteins. Journal of Molecular Evolution. 38: 395-404. PMID 8007007 DOI: 10.1007/Bf00163156  1
1994 Gibson TJ, Hyvönen M, Musacchio A, Saraste M, Birney E. PH domain: the first anniversary. Trends in Biochemical Sciences. 19: 349-53. PMID 7985225 DOI: 10.1016/0968-0004(94)90108-2  1
1994 Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research. 22: 4673-80. PMID 7984417 DOI: 10.1093/Nar/22.22.4673  1
1993 Gibson TJ, Thompson JD, Abagyan RA. Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Engineering. 6: 41-50. PMID 8433970 DOI: 10.1093/Protein/6.1.41  1
1993 Gibson TJ, Higgins DG. Non-muscle and smooth muscle myosin light chain kinases: no end in sight. Dna Sequence : the Journal of Dna Sequencing and Mapping. 3: 333-5. PMID 8400365 DOI: 10.3109/10425179309020833  1
1993 Gibson TJ, Rice PM, Thompson JD, Heringa J. KH domains within the FMR1 sequence suggest that fragile X syndrome stems from a defect in RNA metabolism. Trends in Biochemical Sciences. 18: 331-3. PMID 7694397 DOI: 10.1016/0968-0004(93)90068-X  1
1991 Nardelli J, Gibson TJ, Vesque C, Charnay P. Base sequence discrimination by zinc-finger DNA-binding domains. Nature. 349: 175-8. PMID 1898772 DOI: 10.1038/349175A0  1
1991 Frampton J, Gibson TJ, Ness SA, Döderlein G, Graf T. Proposed structure for the DNA-binding domain of the Myb oncoprotein based on model building and mutational analysis. Protein Engineering. 4: 891-901. PMID 1817253 DOI: 10.1093/Protein/4.8.891  1
1990 Gibson TJ, Argos P. Protruding domain of tomato bushy stunt virus coat protein is a hitherto unrecognized class of jellyroll conformation. Journal of Molecular Biology. 212: 7-9. PMID 2319600 DOI: 10.1016/0022-2836(90)90298-Z  1
1990 Lamond AI, Gibson TJ. Catalytic RNA and the origin of genetic systems. Trends in Genetics : Tig. 6: 145-9. PMID 2195724 DOI: 10.1016/0168-9525(90)90148-Y  1
1990 Gibson TJ, Lamond AI. Metabolic complexity in the RNA world and implications for the origin of protein synthesis. Journal of Molecular Evolution. 30: 7-15. PMID 1690303 DOI: 10.1007/Bf02102448  1
1989 Frampton J, Leutz A, Gibson TJ, Graf T. DNA-binding domain ancestry [15] Nature. 342: 134. PMID 2572967 DOI: 10.1038/342134A0  1
1988 Gibson TJ, Postma JP, Brown RS, Argos P. A model for the tertiary structure of the 28 residue DNA-binding motif ('zinc finger') common to many eukaryotic transcriptional regulatory proteins. Protein Engineering. 2: 209-18. PMID 3148934 DOI: 10.1093/Protein/2.3.209  1
1987 Gibson TJ, Sulston JE. Preparation of large numbers of plasmid DNA samples in microtiter plates by the alkaline lysis method. Gene Analysis Techniques. 4: 41-4. PMID 3333759 DOI: 10.1016/0735-0651(87)90016-1  1
1987 Gibson TJ, Coulson AR, Sulston JE, Little PF. Lorist2, a cosmid with transcriptional terminators insulating vector genes from interference by promoters within the insert: effect on DNA yield and cloned insert frequency. Gene. 53: 275-81. PMID 3301536 DOI: 10.1016/0378-1119(87)90016-3  1
1987 Gibson TJ, Rosenthal A, Waterston RH. Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression. Gene. 53: 283-6. PMID 3038694 DOI: 10.1016/0378-1119(87)90017-5  1
1986 Gibson TJ, Barrell BG, Farrell PJ. Coding content and expression of the EBV B95-8 genome in the region from base 62,248 to base 82,920. Virology. 152: 136-48. PMID 3012865 DOI: 10.1016/0042-6822(86)90379-X  1
1986 Weston K, Cozens A, Nelson HCM, Fairall L, Amos L, Mengle-Gaw L, Lefebvre FA, Clark MJ, Kenyon C, Bienz M, Breeden L, Schnabel H, Robinson M, Albertson D, Greenwald I, ... ... Gibson TJ, et al. Sexist ads Nature. 321: 106. DOI: 10.1038/321106b0  1
1985 Hudson GS, Gibson TJ, Barrell BG. The BamHI F region of the B95-8 Epstein-Barr virus genome. Virology. 147: 99-109. PMID 2998075 DOI: 10.1016/0042-6822(85)90230-2  1
1984 Baer R, Bankier AT, Biggin MD, Deininger PL, Farrell PJ, Gibson TJ, Hatfull G, Hudson GS, Satchwell SC, Séguin C. DNA sequence and expression of the B95-8 Epstein-Barr virus genome Nature. 310: 207-211. PMID 6087149 DOI: 10.1038/310207A0  1
1983 Biggin MD, Gibson TJ, Hong GF. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proceedings of the National Academy of Sciences of the United States of America. 80: 3963-3965. PMID 6575390 DOI: 10.1073/Pnas.80.13.3963  1
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