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Gibson Group

Biological sequence analysis

Publications

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

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, Forman-Kay JD, Fornasari MS, Gibson TJ, Gomes GW, Gradinaru CC, Head-Gordon T, Jensen MR, Lemke EA, Longhi S, Marino-Buslje C, Minervini G, Mittag T, Monzon AM, Pappu RV, Parisi G, Ricard-Blum S, Ruff KM, Salladini E, Skepö M, Svergun D, Vallet SD, Varadi M, Tompa P, Tosatto SCE, Piovesan D

Nucleic acids research 2020

33305318. doi:10.1093/nar/gkaa1021.

ELM–the eukaryotic linear motif resource in 2020.

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

Nucleic acids research 2019

31680160. doi:10.1093/nar/gkz1030.

An intrinsically disordered proteins community for ELIXIR.

Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE.

2019

doi:10.12688/f1000research.20136.1.

CiliaCarta: An integrated and validated compendium of ciliary genes.

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, Wheway G, van Reeuwijk J, Scheel JF, Knapp B, Mans DA, Franco B, Képès F, van Wijk E, Toedt G, Slaats GG, Omran H, Kremer H, Koutroumpas K, Szymanska K, Nguyen TT, Ueffing M, van Beersum SEC, Schmidts M, Letteboer SJF, Oud MM, Giles RH, Szklarczyk R, Beales PL, Lu Q, Johnson CA, Blacque OE, Russell RB, Gibson TJ, Roepman R, Hernandez-Hernandez V, Wolfrum U, Boldt K, Huynen MA

PloS one 2019

31095607. doi:10.1371/journal.pone.0216705.

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 research 2017

29136216. doi:10.1093/nar/gkx1077.

Degrons in cancer.

Mészáros B, Kumar M, Gibson TJ, Uyar B, Dosztányi Z

Science signaling 2017

28292960. doi:10.1126/scisignal.aak9982.

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJ, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJ, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, Roepman R, UK10K Rare Diseases Group

Nature communications 2016

27173435. doi:10.1038/ncomms11491.

An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes.

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, Horn N, Boldt K, Parry DA, Letteboer SJ, Roosing S, Adams M, Bell SM, Bond J, Higgins J, Morrison EE, Tomlinson DC, Slaats GG, van Dam TJ, Huang L, Kessler K, Giessl A, Logan CV, Boyle EA, Shendure J, Anazi S, Aldahmesh M, Al Hazzaa S, Hegele RA, Ober C, Frosk P, Mhanni AA, Chodirker BN, Chudley AE, Lamont R, Bernier FP, Beaulieu CL, Gordon P, Pon RT, Donahue C, Barkovich AJ, Wolf L, Toomes C, Thiel CT, Boycott KM, McKibbin M, Inglehearn CF, UK10K Consortium, University of Washington Center for Mendelian Genomics, Stewart F, Omran H, Huynen MA, Sergouniotis PI, Alkuraya FS, Parboosingh JS, Innes AM, Willoughby CE, Giles RH, Webster AR, Ueffing M, Blacque O, Gleeson JG, Wolfrum U, Beales PL, Gibson T, Doherty D, Mitchison HM, Roepman R, Johnson CA

Nature cell biology 2015

26167768. doi:10.1038/ncb3201.

FEBS-EMBO Concurrent Session (lecture): CS III-6-3 SynBac: designer minimal baculovirus genome for drug discovery.

Thimiri Govinda Raj DB, Garzoni F, Gavin AC, Gibson T, Berger I

2014

doi:10.1111/febs.12917.

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 research 2013

24214962. doi:10.1093/nar/gkt1047.

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

Molecular bioSystems 2012

21909575. doi:10.1039/c1mb05231d.

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 research 2012

22110040. doi:10.1093/nar/gkr1064.

A community standard format for the representation of protein affinity reagents

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, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H

Molecular & cellular proteomics : MCP 2010

19674966. doi:10.1074/mcp.m900185-mcp200.

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 research 2010

19920119. doi:10.1093/nar/gkp1016.

Clustal W and Clustal X version 2.0

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

Bioinformatics (Oxford, England) 2007

17846036. doi:10.1093/bioinformatics/btm404.

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

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, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M

Nature methods 2007

17195019. doi:10.1038/nmeth0107-13.

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

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, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ

Nucleic acids research 2003

12824381. doi:10.1093/nar/gkg545.

Sequence analysis, dotplot, aligning sequences, indels and gap-penalty

Gibson T, Bork P

1999

doi:.

Assignment of α-Helices in Multiply Aligned Protein Sequences — Applications to DNA Binding Motifs

Gibson TJ

1992

doi:.


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