| Year |
Citation |
Score |
| 2024 |
Zeke A, Gibson TJ, Dobson L. Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. Plos Computational Biology. 20: e1011902. PMID 38363808 DOI: 10.1371/journal.pcbi.1011902 |
0.363 |
|
| 2024 |
Lee CY, Hubrich D, Varga JK, Schäfer C, Welzel M, Schumbera E, Djokic M, Strom JM, Schönfeld J, Geist JL, Polat F, Gibson TJ, Keller Valsecchi CI, Kumar M, Schueler-Furman O, et al. Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation. Molecular Systems Biology. PMID 38225382 DOI: 10.1038/s44320-023-00005-6 |
0.397 |
|
| 2023 |
Kumar M, Michael S, Alvarado-Valverde J, Zeke A, Lazar T, Glavina J, Nagy-Kanta E, Donagh JM, Kalman ZE, Pascarelli S, Palopoli N, Dobson L, Suarez CF, Van Roey K, Krystkowiak I, ... ... Gibson TJ, et al. ELM-the Eukaryotic Linear Motif resource-2024 update. Nucleic Acids Research. PMID 37962385 DOI: 10.1093/nar/gkad1058 |
0.628 |
|
| 2023 |
Tusnády GE, Zeke A, Kálmán ZE, Fatoux M, Ricard-Blum S, Gibson TJ, Dobson L. LeishMANIAdb: a comparative resource for Leishmania proteins. Database : the Journal of Biological Databases and Curation. 2023. PMID 37935582 DOI: 10.1093/database/baad074 |
0.33 |
|
| 2023 |
Sámano-Sánchez H, Gibson TJ, Chemes LB. Using Linear Motif Database Resources to Identify SH2 Domain Binders. Methods in Molecular Biology (Clifton, N.J.). 2705: 153-197. PMID 37668974 DOI: 10.1007/978-1-0716-3393-9_9 |
0.369 |
|
| 2023 |
Martínez-Pérez E, Pajkos M, Tosatto SCE, Gibson TJ, Dosztanyi Z, Marino-Buslje C. Pipeline for transferring annotations between proteins beyond globular domains. Protein Science : a Publication of the Protein Society. e4655. PMID 37167423 DOI: 10.1002/pro.4655 |
0.348 |
|
| 2022 |
Putta S, Alvarez L, Lüdtke S, Sehr P, Müller GA, Fernandez SM, Tripathi S, Lewis J, Gibson TJ, Chemes LB, Rubin SM. Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family. Structure (London, England : 1993). PMID 35716663 DOI: 10.1016/j.str.2022.05.019 |
0.383 |
|
| 2021 |
Kumar M, Michael S, Alvarado-Valverde J, Mészáros B, Sámano-Sánchez H, Zeke A, Dobson L, Lazar T, Örd M, Nagpal A, Farahi N, Käser M, Kraleti R, Davey NE, Pancsa R, ... ... Gibson TJ, et al. The Eukaryotic Linear Motif resource: 2022 release. Nucleic Acids Research. PMID 34718738 DOI: 10.1093/nar/gkab975 |
0.587 |
|
| 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 |
0.608 |
|
| 2020 |
Lazar T, Martínez-Pérez E, Quaglia F, Hatos A, Chemes LB, Iserte JA, Méndez NA, Garrone NA, Saldaño TE, Marchetti J, Rueda AJV, Bernadó P, Blackledge M, Cordeiro TN, Fagerberg E, ... ... Gibson TJ, et al. PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Research. PMID 33305318 DOI: 10.1093/nar/gkaa1021 |
0.327 |
|
| 2020 |
Laursen L, Čalyševa J, Gibson TJ, Jemth P. Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection. Molecular Biology and Evolution. PMID 32750125 DOI: 10.1093/Molbev/Msaa198 |
0.453 |
|
| 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 |
0.532 |
|
| 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 |
0.574 |
|
| 2020 |
Sámano-Sánchez H, Gibson TJ. Mimicry of Short Linear Motifs by Bacterial Pathogens: A Drugging Opportunity. Trends in Biochemical Sciences. 45: 526-544. PMID 32413327 DOI: 10.1016/J.Tibs.2020.03.003 |
0.369 |
|
| 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 |
0.674 |
|
| 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 |
0.646 |
|
| 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 |
0.357 |
|
| 2019 |
Pabis M, Corsini L, Vincendeau M, Tripsianes K, Gibson TJ, Brack-Werner R, Sattler M. Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors. Nucleic Acids Research. PMID 30892606 DOI: 10.1093/Nar/Gkz185 |
0.394 |
|
| 2018 |
Schiklenk C, Petrova B, Kschonsak M, Hassler M, Klein C, Gibson TJ, Haering CH. Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1. The Journal of Cell Biology. PMID 29735745 DOI: 10.1083/Jcb.201711097 |
0.349 |
|
| 2018 |
Palopoli N, González Foutel NS, Gibson TJ, Chemes LB. Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity. Protein Engineering, Design & Selection : Peds. PMID 29370437 DOI: 10.1093/Protein/Gzx068 |
0.486 |
|
| 2017 |
Ruiz-Velasco M, Kumar M, Lai MC, Bhat P, Solis-Pinson AB, Reyes A, Kleinsorg S, Noh KM, Gibson TJ, Zaugg JB. CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals. Cell Systems. PMID 29199022 DOI: 10.1016/J.Cels.2017.10.018 |
0.405 |
|
| 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 |
0.318 |
|
| 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 |
0.668 |
|
| 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 |
0.547 |
|
| 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 |
0.45 |
|
| 2017 |
Mészáros B, Kumar M, Gibson TJ, Uyar B, Dosztányi Z. Degrons in cancer. Science Signaling. 10. PMID 28292960 DOI: 10.1126/Scisignal.Aak9982 |
0.378 |
|
| 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 |
0.402 |
|
| 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 |
0.607 |
|
| 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 |
0.449 |
|
| 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 |
0.342 |
|
| 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 |
0.343 |
|
| 2015 |
Di Fiore B, Davey NE, Hagting A, Izawa D, Mansfeld J, Gibson TJ, Pines J. The ABBA motif binds APC/C activators and is shared by APC/C substrates and regulators. Developmental Cell. 32: 358-72. PMID 25669885 DOI: 10.1016/J.Devcel.2015.01.003 |
0.553 |
|
| 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 |
0.403 |
|
| 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 |
0.528 |
|
| 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 |
0.568 |
|
| 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 |
0.803 |
|
| 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 |
0.309 |
|
| 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 |
0.798 |
|
| 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 |
0.373 |
|
| 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 |
0.352 |
|
| 2013 |
Gibson TJ, Seiler M, Veitia RA. The transience of transient overexpression. Nature Methods. 10: 715-21. PMID 23900254 DOI: 10.1038/Nmeth.2534 |
0.602 |
|
| 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 |
0.618 |
|
| 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 |
0.732 |
|
| 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 |
0.64 |
|
| 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 |
0.471 |
|
| 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 |
0.642 |
|
| 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 |
0.466 |
|
| 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 |
0.422 |
|
| 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 |
0.598 |
|
| 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 |
0.646 |
|
| 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 |
0.806 |
|
| 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 |
0.789 |
|
| 2012 |
Roepman R, Ueffing M, Kremer H, Huynen M, Gibson T, Katsanis N, Walz G, Wolfrum U, Franco B, Giles R, Beales P, Johnson C, Blacque O, Pontoglio M, Képès F, et al. SYSCILIA, “A systems biology approach to dissect cilia function and its disruption in human genetic disease” Cilia. 1: 41. DOI: 10.1186/2046-2530-1-S1-P41 |
0.326 |
|
| 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 |
0.362 |
|
| 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 |
0.32 |
|
| 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 |
0.387 |
|
| 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 |
0.576 |
|
| 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 |
0.376 |
|
| 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 |
0.676 |
|
| 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 |
0.746 |
|
| 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 |
0.796 |
|
| 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 |
0.76 |
|
| 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 |
0.433 |
|
| 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 |
0.493 |
|
| 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 |
0.389 |
|
| 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 |
0.487 |
|
| 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 |
0.452 |
|
| 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 |
0.443 |
|
| 2009 |
Diella F, Via A, Chica C, Luck K, Gould CM, Gibson TJ. The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3152.1 |
0.448 |
|
| 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 |
0.685 |
|
| 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 |
0.373 |
|
| 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 |
0.788 |
|
| 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 |
0.515 |
|
| 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 |
0.44 |
|
| 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 |
0.433 |
|
| 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 |
0.487 |
|
| 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 |
0.418 |
|
| 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 |
0.49 |
|
| 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 |
0.309 |
|
| 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 |
0.718 |
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| 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 |
0.669 |
|
| 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 |
0.4 |
|
| 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 |
0.469 |
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| 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 |
0.673 |
|
| 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 |
0.665 |
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| 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 |
0.332 |
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| 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 |
0.707 |
|
| 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 |
0.778 |
|
| 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 |
0.735 |
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| 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 |
0.731 |
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| 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 |
0.34 |
|
| 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 |
0.345 |
|
| 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 |
0.372 |
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| 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 |
0.399 |
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| 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 |
0.384 |
|
| 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 |
0.361 |
|
| 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 |
0.347 |
|
| 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 |
0.354 |
|
| 2000 |
Musco G, Tommasi Td, Stier G, Kolmerer B, Bottomle M, Adinolfi S, Musket F, Gibson T, Frenkiel T, Pastore A. Assignment of the 1H, 15N, and 13C Resonances of the C-terminal Domain of Frataxin, the Protein Involved in Friedreich Ataxia. Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr4342 |
0.301 |
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| 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 |
0.407 |
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| 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 |
0.331 |
|
| 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 |
0.304 |
|
| 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 |
0.308 |
|
| 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 |
0.358 |
|
| 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 |
0.348 |
|
| 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 |
0.376 |
|
| 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 |
0.3 |
|
| 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 |
0.407 |
|
| 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 |
0.418 |
|
| 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 |
0.386 |
|
| 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 |
0.394 |
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| 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 |
0.351 |
|
| 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 |
0.357 |
|
| 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 |
0.459 |
|
| 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 |
0.376 |
|
| 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 |
0.371 |
|
| 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 |
0.455 |
|
| 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 |
0.315 |
|
| 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 |
0.379 |
|
| 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 |
0.34 |
|
| 1994 |
Muhle-Goll C, Gibson T, Schuck P, Schubert D, Nalis D, Nilges M, Pastore A. The dimerization stability of the HLH-LZ transcription protein family is modulated by the leucine zippers: a CD and NMR study of TFEB and c-Myc. Biochemistry. 33: 11296-306. PMID 7727380 DOI: 10.1021/Bi00203A027 |
0.394 |
|
| 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 |
0.397 |
|
| 1993 |
Gibson TJ, Thompson JD, Heringa J. The KH domain occurs in a diverse set of RNA-binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid. Febs Letters. 324: 361-6. PMID 8405383 DOI: 10.1016/0014-5793(93)80152-K |
0.395 |
|
| 1993 |
Musacchio A, Gibson T, Rice P, Thompson J, Saraste M. The PH domain: a common piece in the structural pathcwork of signalling proteins Trends in Biochemical Sciences. 18: 343-348. PMID 8236453 DOI: 10.1016/0968-0004(93)90071-T |
0.409 |
|
| 1992 |
Musacchio A, Gibson T, Lehto V, Saraste M. SH3--an abundant protein domain in search of a function. Febs Letters. 307: 55-61. PMID 1639195 DOI: 10.1016/0014-5793(92)80901-R |
0.428 |
|
| 1992 |
Nardelli J, Gibson T, Charnay P. Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis. Nucleic Acids Research. 20: 4137-44. PMID 1508708 DOI: 10.1093/Nar/20.16.4137 |
0.347 |
|
| 1991 |
Labeit S, Gibson T, Lakey A, Leonard K, Zeviani M, Knight P, Wardale J, Trinick J. Evidence that nebulin is a protein-ruler in muscle thin filaments. Febs Letters. 282: 313-6. PMID 2037050 DOI: 10.1016/0014-5793(91)80503-U |
0.419 |
|
| 1991 |
Saudek V, Pasley HS, Gibson T, Gausepohl H, Frank R, Pastore A. Solution structure of the basic region from the transcriptional activator GCN4. Biochemistry. 30: 1310-1317. PMID 1991112 DOI: 10.1021/Bi00219A022 |
0.322 |
|
| 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 |
0.348 |
|
| 1991 |
Saudek V, Pastore A, Morelli MAC, Frank R, Gausepohl H, Gibson T. The solution structure of a leucine-zipper motif peptide. Protein Engineering. 4: 519-529. PMID 1891459 DOI: 10.1093/Protein/4.5.519 |
0.323 |
|
| 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 |
0.392 |
|
| 1991 |
Gibson TJ, Sibbald PR, Rice P. Rop/helix-loop-helix similarity. Dna Sequence : the Journal of Dna Sequencing and Mapping. 1: 213-5. PMID 1773060 DOI: 10.3109/10425179109020773 |
0.302 |
|
| 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 |
0.377 |
|
| 1990 |
Saudek V, Pastore A, Morelli MAC, Frank R, Gausepohl H, Gibson T, Weih F, Roesch P. Solution structure of the DNA-binding domain of the yeast transcriptional activator protein GCN4 Protein Engineering. 4: 3-10. PMID 2290831 DOI: 10.1093/Protein/4.1.3 |
0.351 |
|
| 1990 |
Labeit S, Barlow DP, Gautel M, Gibson T, Holt J, Hsieh C-, Francke U, Leonard K, Wardale J, Whiting A, Trinick J. A regular pattern of two types of 100-residue motif in the sequence of titin. Nature. 345: 273-276. PMID 2129545 DOI: 10.1038/345273A0 |
0.369 |
|
| 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 |
0.327 |
|
| 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 |
0.432 |
|
| 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 |
0.324 |
|
| 1984 |
Gibson T, Stockwell P, Ginsburg M, Barrell B. Homology between two EBV early genes and HSV ribonudeotide reductase and 38K genes Nucleic Acids Research. 12: 5087-5099. PMID 6330697 DOI: 10.1093/Nar/12.12.5087 |
0.303 |
|
| 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 |
0.309 |
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