Publications – Gibson Group

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, Chemes LB, Gibson TJ

Nucleic acids research, 2021

doi:10.1093/nar/gkab975.

Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications.

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

Science signaling, 2021

doi:10.1126/scisignal.abd0334.

How to annotate and submit a short linear motif to the Eukaryotic Linear Motif resource.

Gouw M, Alvarado-Valverde J, Čalyševa J, Diella F, Kumar M, Michael S, Van Roey K, Dinkel H, Gibson TJ

Methods in molecular biology (Clifton, N.J.), 2020

doi:10.1007/978-1-0716-0524-0_4.

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

doi:10.1093/nar/gkaa1021.

Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection.

Laursen L, Čalyševa J, Gibson TJ, Jemth P

Molecular biology and evolution, 2020

doi:10.1093/molbev/msaa198.

Mimicry of short linear motifs by bacterial pathogens: a drugging opportunity.

Sámano-Sánchez H, Gibson TJ

Trends in biochemical sciences, 2020

doi:10.1016/j.tibs.2020.03.003.

PDBe-KB: a community-driven resource for structural and functional annotations.

PDBe-KB consortium

Nucleic acids research, 2020

doi:10.1093/nar/gkz853.

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

doi:10.1093/nar/gkz1030.

The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification.

Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ, Davey NE

Database : the journal of biological databases and curation, 2020

doi:10.1093/database/baaa040.

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.

F1000Res , 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

doi:10.1371/journal.pone.0216705.

Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors.

Pabis M, Corsini L, Vincendeau M, Tripsianes K, Gibson TJ, Brack-Werner R, Sattler M

Nucleic acids research, 2019

doi:10.1093/nar/gkz185.

Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1

Schiklenk C, Petrova B, Kschonsak M, Hassler M, Klein C, Gibson TJ, Haering CH

2018

doi:10.1083/jcb.201711097.

Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity.

Palopoli N, González Foutel NS, Gibson TJ, Chemes LB

Protein engineering, design & selection : PEDS, 2018

doi:10.1093/protein/gzx068.

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

doi:10.1093/nar/gkx1077.

CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals.

Ruiz-Velasco M, Kumar M, Lai MC, Bhat P, Solis-Pinson AB, Reyes A, Kleinsorg S, Noh KM, Gibson TJ, Zaugg JB

Cell systems, 2017

doi:10.1016/j.cels.2017.10.018.

The Gene Ontology of eukaryotic cilia and flagella.

Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J

Cilia, 2017

doi:10.1186/s13630-017-0054-8.

Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq

Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mücke N, Wilmanns M, Gibson TJ, Barabas O.

2017

doi:10.1038/s41598-017-10085-8.

Exploring Short Linear Motifs Using the ELM Database and Tools.

Gouw M, Sámano-Sánchez H, Van Roey K, Diella F, Gibson TJ, Dinkel H

Current protocols in bioinformatics, 2017

doi:10.1002/cpbi.26.

Metabolic shifts in residual breast cancer drive tumor recurrence

Havas KM, Milchevskaya V, Radic K, Alladin A, Kafkia E, Garcia M, Stolte J, Klaus B, Rotmensz N, Gibson TJ, Burwinkel B, Schneeweiss A, Pruneri G, Patil KR, Sotillo R, Jechlinger M

The Journal of clinical investigation, 2017

doi:10.1172/JCI89914.

Degrons in cancer.

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

Science signaling, 2017

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

doi:10.1038/ncomms11491.

Hunting for Cis-Regulatory Elements in Proteins.

Gibson TJ, Kumar M

Cell systems, 2016

doi:10.1016/j.cels.2016.02.011.

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

Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Behrendt A, Dahl SL, Damerell V, Diebel S, Kalman S, Klein S, Knudsen AC, Mäder C, Merrill S, Staudt A, Thiel V, Welti L, Davey NE, Diella F, Gibson TJ

Nucleic acids research, 2015

doi:10.1093/nar/gkv1291.

Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad.

Gibson TJ, Dinkel H, Van Roey K, Diella F

Cell communication and signaling : CCS, 2015

doi:10.1186/s12964-015-0121-y.

NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish.

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, Ueffing M, Gibson TJ, Roepman R, Boldt K, Kremer H, van Wijk E

PLoS genetics, 2015

doi:10.1371/journal.pgen.1005574.

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

doi:10.1038/ncb3201.

The ABBA Motif Binds APC/C Activators and Is Shared by APC/C Substrates and Regulators.

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

Developmental cell, 2015

doi:10.1016/j.devcel.2015.01.003.

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

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

Molecular bioSystems, 2014

doi:10.1039/c4mb00290c.

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.

Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems

Weatheritt RJ, Gibson TJ, Babu MM

Nature structural & molecular biology, 2014

doi:10.1038/nsmb.2876.

A million peptide motifs for the molecular biologist

Tompa P, Davey NE, Gibson TJ, Babu MM

Molecular cell, 2014

doi:10.1016/j.molcel.2014.05.032.

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

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

Chemical reviews, 2014

doi:10.1021/cr400585q.

Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry.

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

Molecular & cellular proteomics : MCP, 2014

doi:10.1074/mcp.o113.033233.

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

doi:10.1093/nar/gkt1047.

Drift and conservation of differential exon usage across tissues in primate species

Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W

Proceedings of the National Academy of Sciences of the United States of America, 2013

doi:10.1073/pnas.1307202110.

The transience of transient overexpression

Gibson TJ, Seiler M, Veitia RA

Nature methods, 2013

doi:10.1038/nmeth.2534.

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

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

Science signaling, 2013

doi:10.1126/scisignal.2003345.

Capturing cooperative interactions with the PSI-MI format

Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ

Database : the journal of biological databases and curation, 2013

doi:10.1093/database/bat066.

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

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

Nucleic acids research, 2012

doi:10.1093/nar/gks854.

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

Jiang K, Toedt G, Montenegro Gouveia S, Davey NE, Hua S, van der Vaart B, Grigoriev I, Larsen J, Pedersen LB, Bezstarosti K, Lince-Faria M, Demmers J, Steinmetz MO, Gibson TJ, Akhmanova A

Current biology : CB, 2012

doi:10.1016/j.cub.2012.07.047.

RACK1 research - ships passing in the night?

Gibson TJ

FEBS letters, 2012

doi:10.1016/j.febslet.2012.04.048.

Linear motifs confer functional diversity onto splice variants

Weatheritt RJ, Davey NE, Gibson TJ

Nucleic acids research, 2012

doi:10.1093/nar/gks442.

Linear motifs: lost in (pre)translation

Weatheritt RJ, Gibson TJ

Trends in biochemical sciences, 2012

doi:10.1016/j.tibs.2012.05.001.

iELM--a web server to explore short linear motif-mediated interactions

Weatheritt RJ, Jehl P, Dinkel H, Gibson TJ

Nucleic acids research, 2012

doi:10.1093/nar/gks444.

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, Zischler H, Kaup FJ

Journal of medical primatology, 2012

doi:10.1111/j.1600-0684.2012.00535.x.

Motif switches: decision-making in cell regulation

Van Roey K, Gibson TJ, Davey NE

Current opinion in structural biology, 2012

doi:10.1016/j.sbi.2012.03.004.

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

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

Bioinformatics (Oxford, England), 2012

doi:10.1093/bioinformatics/bts072.

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

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

doi:10.1093/nar/gkr1064.

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 FJ, Bodemer W, Gibson TJ, Zischler H

Journal of toxicology and environmental health. Part A, 2012

doi:10.1080/15287394.2012.670896.

How viruses hijack cell regulation

Davey NE, Travé G, Gibson TJ

Trends in biochemical sciences, 2011

doi:10.1016/j.tibs.2010.10.002.

Phospho.ELM: a database of phosphorylation sites--update 2011

Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F

Nucleic acids research, 2011

doi:10.1093/nar/gkq1104.

Possible editing of Alu transcripts in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD)

Kiesel P, Gibson TJ, Ciesielczyk B, Bodemer M, Kaup FJ, Bodemer W, Zischler H, Zerr I

Journal of toxicology and environmental health. Part A, 2011

doi:10.1080/15287394.2011.529057.

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG

Molecular systems biology, 2011

doi:10.1038/msb.2011.75.

From sequence to structural analysis in protein phosphorylation motifs

Via A, Diella F, Gibson TJ, Helmer-Citterich M

Frontiers in bioscience (Landmark edition), 2011

doi:10.2741/3787.

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction

Croset V, Rytz R, Cummins SF, Budd A, Brawand D, Kaessmann H, Gibson TJ, Benton R

PLoS genetics, 2010

doi:10.1371/journal.pgen.1001064.

EpiC: an open resource for exploring epitopes to aid antibody-based experiments

Haslam NJ, Gibson TJ

Journal of proteome research, 2010

doi:10.1021/pr100029f.

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

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

doi:10.1093/nar/gkp1016.

Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD)

Kiesel P, Gibson TJ, Ciesielczyk B, Bodemer M, Kaup FJ, Bodemer W, Zischler H, Zerr I

Prion, 2010

doi:10.4161/pri.4.2.11965.

Cell regulation: determined to signal discrete cooperation

Gibson TJ

Trends in biochemical sciences, 2009

doi:10.1016/j.tibs.2009.06.007.

Evidence for the concerted evolution between short linear protein motifs and their flanking regions

Chica C, Diella F, Gibson TJ

PloS one, 2009

doi:10.1371/journal.pone.0006052.

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 TJ, Sattler M

The Journal of biological chemistry, 2009

doi:10.1074/jbc.m805395200.

Phosphorylation of S776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors

de Chiara C, Menon RP, Strom M, Gibson TJ, Pastore A

PloS one, 2009

doi:10.1371/journal.pone.0008372.

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 TJ

Bioinformatics (Oxford, England), 2009

doi:10.1093/bioinformatics/btn594.

A structure filter for the Eukaryotic Linear Motif Resource

Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M

BMC bioinformatics, 2009

doi:10.1186/1471-2105-10-351.

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, Fehér K, Palma AS, Liu Y, Simpson JC, Mackeen M, Stier G, Gibson TJ, Feizi T, Pieler T, Muhle-Goll C

Molecular biology of the cell, 2008

doi:10.1091/mbc.e08-04-0354.

A careful disorderliness in the proteome: sites for interaction and targets for future therapies

Russell RB, Gibson TJ

FEBS letters, 2008

doi:10.1016/j.febslet.2008.02.027.

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation

Michael S, Travé G, Ramu C, Chica C, Gibson TJ

Bioinformatics (Oxford, England), 2008

doi:10.1093/bioinformatics/btm624.

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences

Chica C, Labarga A, Gould CM, López R, Gibson TJ

BMC bioinformatics, 2008

doi:10.1186/1471-2105-9-229.

Phospho.ELM: a database of phosphorylation sites--update 2008

Diella F, Gould CM, Chica C, Via A, Gibson TJ

Nucleic acids research, 2008

doi:10.1093/nar/gkm772.

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

Diella F, Haslam N, Chica C, Budd A, Michael S, Brown NP, Trave G, Gibson TJ

Frontiers in bioscience : a journal and virtual library, 2008

doi:10.2741/3175.

A new protein linear motif benchmark for multiple sequence alignment software

Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD

BMC bioinformatics, 2008

doi:10.1186/1471-2105-9-213.

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

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

doi:10.1038/nmeth0107-13.

Systematic discovery of new recognition peptides mediating protein interaction networks

Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB

PLoS biology, 2005

doi:10.1371/journal.pbio.0030405.

Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei

Michel K, Budd A, Pinto S, Gibson TJ, Kafatos FC

EMBO reports, 2005

doi:10.1038/sj.embor.7400478.

Patterns and clusters within the PSM column in TiBS, 1992-2004

McEntyre JR, Gibson TJ

Trends in biochemical sciences, 2004

doi:10.1016/j.tibs.2004.10.006.

The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre

Menon RP, Gibson TJ, Pastore A

Journal of molecular biology, 2004

doi:10.1016/j.jmb.2004.08.024.

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins

Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ

BMC bioinformatics, 2004

doi:10.1186/1471-2105-5-79.

Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300

Ragvin A, Valvatne H, Erdal S, Arskog V, Tufteland KR, Breen K, ØYan AM, Eberharter A, Gibson TJ, Becker PB, Aasland R

Journal of molecular biology, 2004

doi:10.1016/j.jmb.2004.01.051.

Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?

Budd A, Blandin S, Levashina EA, Gibson TJ

Genome biology, 2004

doi:10.1186/gb-2004-5-6-r38.

Protein disorder prediction: implications for structural proteomics

Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB

Structure (London, England : 1993), 2003

doi:10.1016/j.str.2003.10.002.

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 TJ

Nucleic acids research, 2003

doi:10.1093/nar/gkg535.

Multiple sequence alignment with the Clustal series of programs

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD

Nucleic acids research, 2003

doi:10.1093/nar/gkg500.

GlobPlot: Exploring protein sequences for globularity and disorder

Linding R, Russell RB, Neduva V, Gibson TJ

Nucleic acids research, 2003

doi:10.1093/nar/gkg519.

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

doi:10.1093/nar/gkg545.

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

Huynen MA, Snel B, Bork P, Gibson TJ

Human molecular genetics, 2001

doi:10.1093/hmg/10.21.2463.

The gene mutated in ataxia-ocular apraxia 1 encodes the new HIT/Zn-finger protein aprataxin

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, Sequeiros J, Koenig M

Nature genetics, 2001

doi:10.1038/ng1001-189.

The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation

Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M

Nature structural biology, 2001

doi:10.1038/89675.

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries

Gemünd C, Ramu C, Altenberg-Greulich B, Gibson TJ

Nucleic acids research, 2001

doi:10.1093/nar/29.6.1272.

RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein SINE proliferation drives PrP overproduction

Gibson TJ

Genome biology, 2001

doi:10.1186/gb-2001-2-7-preprint0006.

An estimate of large-scale sequencing accuracy

Hill F, Gemünd C, Benes V, Ansorge W, Gibson TJ

EMBO reports, 2000

doi:10.1093/embo-reports/kvd015.

Towards a structural understanding of Friedreich's ataxia: the solution structure of frataxin

Musco G, Stier G, Kolmerer B, Adinolfi S, Martin S, Frenkiel T, Gibson T, Pastore A

Structure (London, England : 1993), 2000

doi:10.1016/s0969-2126(00)00158-1.

Object-oriented parsing of biological databases with Python

Ramu C, Gemünd C, Gibson TJ

Bioinformatics (Oxford, England), 2000

doi:10.1093/bioinformatics/16.7.628.

Homology-based method for identification of protein repeats using statistical significance estimates

Andrade MA, Ponting CP, Gibson TJ, Bork P

Journal of molecular biology, 2000

doi:10.1006/jmbi.2000.3684.

Evidence in favour of ancient octaploidy in the vertebrate genome

Gibson TJ, Spring J

Biochemical Society transactions, 2000

doi:10.1042/bst0280259.

Dissecting FMR1, the protein responsible for fragile X syndrome, in its structural and functional domains

Adinolfi S, Bagni C, Musco G, Gibson T, Mazzarella L, Pastore A

RNA (New York, N.Y.), 1999

doi:10.1017/s1355838299990647.

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 FW, Gibson TJ, Frenkiel TA, Pastore A

Journal of biomolecular NMR, 1999

doi:10.1023/a:1008398832619.

Formin defines a large family of morphoregulatory genes and functions in establishment of the polarising region

Zeller R, Haramis AG, Zuniga A, McGuigan C, Dono R, Davidson G, Chabanis S, Gibson T

Cell and tissue research, 1999

doi:10.1007/s004410051269.

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

Gibson T, Bork P

1999

doi:.

Multiple sequence alignment with Clustal X

Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ

Trends in biochemical sciences, 1998

doi:10.1016/s0968-0004(98)01285-7.

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 CL, Gibson T, Courtneidge SA

The EMBO journal, 1998

doi:10.1093/emboj/17.15.4346.

The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor

Gibson TJ, Ramu C, Gemünd C, Aasland R

Trends in biochemical sciences, 1998

doi:10.1016/s0968-0004(98)01231-6.

Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins

Gibson TJ, Spring J

Trends in genetics : TIG, 1998

doi:10.1016/s0168-9525(97)01367-x.

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG

Nucleic acids research, 1997

doi:10.1093/nar/25.24.4876.

The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome

Musco G, Kharrat A, Stier G, Fraternali F, Gibson TJ, Nilges M, Pastore A

NATURE STRUCTURAL BIOLOGY, 1997

doi:10.1038/nsb0997-712.

Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction

Gibson TJ, Koonin EV, Musco G, Pastore A, Bork P

Trends in neurosciences, 1996

doi:10.1016/s0166-2236(96)20054-2.

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames

Birney E, Thompson JD, Gibson TJ

Nucleic acids research, 1996

doi:10.1093/nar/24.14.2730.

Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome.

Musco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, Gibson TJ, Pastore A

Cell, 1996

doi:10.1016/S0092-8674(00)81100-9.

The SANT domain: A putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional corepressor N-CoR and TFIIIB

Aasland R, Stewart AF, Gibson T

TRENDS IN BIOCHEMICAL SCIENCES, 1996

doi:10.1016/0968-0004(96)30009-1.

Applying motif and profile searches

Bork P, Gibson TJ

Methods in enzymology, 1996

doi:10.1016/s0076-6879(96)66013-3.

Using CLUSTAL for multiple sequence alignments

Higgins DG, Thompson JD, Gibson TJ

COMPUTER METHODS FOR MACROMOLECULAR SEQUENCE ANALYSIS, 1996

doi:.

Dystrophin and utrophin: the missing links!

Winder SJ, Gibson TJ, Kendrick-Jones J

FEBS letters, 1995

doi:10.1016/0014-5793(95)00398-S.

Structure of the dsRNA binding domain of E. coli RNase III.

Kharrat A, Macias MJ, Gibson TJ, Nilges M, Pastore A

The EMBO journal, 1995

doi:10.1002/j.1460-2075.1995.tb07363.x.

The PHD finger: implications for chromatin-mediated transcriptional regulation.

Aasland R, Gibson TJ, Stewart AF

Trends in biochemical sciences, 1995

doi:10.1016/S0968-0004(00)88957-4.

The KH module has an alpha beta fold.

Castiglone Morelli MA, Stier G, Gibson T, Joseph C, Musco G, Pastore A, Travè G

FEBS letters, 1995

doi:10.1016/0014-5793(94)01422-W.

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Thompson JD, Higgins DG, Gibson TJ

Nucleic acids research, 1994

doi:10.1093/nar/22.22.4673.

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.

Muhle-Goll C, Gibson T, Schuck P, Schubert D, Nalis D, Nilges M, Pastore A

Biochemistry, 1994

doi:10.1021/bi00203a027.

PH domain: the first anniversary.

Gibson TJ, Hyvönen M, Musacchio A, Saraste M, Birney E

Trends in biochemical sciences, 1994

doi:10.1016/0968-0004(94)90108-2.

Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases.

Gibson TJ, Thompson JD

Nucleic acids research, 1994

doi:10.1093/nar/22.13.2552.

The evolution of titin and related giant muscle proteins.

Higgins DG, Labeit S, Gautel M, Gibson TJ

Journal of molecular evolution, 1994

doi:10.1007/BF00163156.

Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107.

Gibson TJ, Thompson JD, Blocker A, Kouzarides T

Nucleic acids research, 1994

doi:10.1093/nar/22.6.946.

Improved sensitivity of profile searches through the use of sequence weights and gap excision.

Thompson JD, Higgins DG, Gibson TJ

Computer applications in the biosciences : CABIOS, 1994

doi:.

Non-muscle and smooth muscle myosin light chain kinases: no end in sight.

Gibson TJ, Higgins DG

DNA sequence : the journal of DNA sequencing and mapping, 1993

doi:.

KH domains within the FMR1 sequence suggest that fragile X syndrome stems from a defect in RNA metabolism.

Gibson TJ, Rice PM, Thompson JD, Heringa J

Trends in biochemical sciences, 1993

doi:10.1016/0968-0004(93)90068-X.

The PH domain: a common piece in the structural patchwork of signalling proteins.

Musacchio A, Gibson T, Rice P, Thompson J, Saraste M

Trends in biochemical sciences, 1993

doi:10.1016/0968-0004(93)90071-T.

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.

Gibson TJ, Thompson JD, Heringa J

FEBS letters, 1993

doi:10.1016/0014-5793(93)80152-K.

Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins.

Gibson TJ, Thompson JD, Abagyan RA

Protein engineering, 1993

doi:10.1093/protein/6.1.41.

Mechanisms for the transformation of myeloid and erythroid cells by the nuclear oncogene V-myb.

Frampton J, Gibson T, Lim F, McNagny K, Metz T, Ness S, Graf T

Leukemia, 1992

doi:.

Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis

Nardelli J, Gibson T, Charnay P

Nucleic acids research, 1992

doi:10.1093/nar/20.16.4137.

SH3--an abundant protein domain in search of a function.

Musacchio A, Gibson T, Lehto VP, Saraste M

FEBS letters, 1992

doi:10.1016/0014-5793(92)80901-R.

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

Gibson TJ

1992

doi:.

Proposed structure for the DNA-binding domain of the Myb oncoprotein based on model building and mutational analysis.

Frampton J, Gibson TJ, Ness SA, Döderlein G, Graf T

Protein engineering, 1991

doi:10.1093/protein/4.8.891.

Rop/helix-loop-helix similarity.

Gibson TJ, Sibbald PR, Rice P

DNA sequence : the journal of DNA sequencing and mapping, 1991

doi:.

The solution structure of a leucine-zipper motif peptide

Saudek V, Pastore A, Morelli MA, Frank R, Gausepohl H, Gibson T

Protein engineering, 1991

doi:10.1093/protein/4.5.519.

Evidence that nebulin is a protein-ruler in muscle thin filaments.

Labeit S, Gibson T, Lakey A, Leonard K, Zeviani M, Knight P, Wardale J, Trinick J

FEBS letters, 1991

doi:10.1016/0014-5793(91)80503-U.

Solution structure of the basic region from the transcriptional activator GCN4

Saudek V, Pasley HS, Gibson T, Gausepohl H, Frank R, Pastore A

Biochemistry, 1991

doi:10.1021/bi00219a022.

Base sequence discrimination by zinc-finger DNA-binding domains

Nardelli J, Gibson TJ, Vesque C, Charnay P

Nature, 1991

doi:10.1038/349175a0.

Solution structure of the DNA-binding domain of the yeast transcriptional activator protein GCN4

Saudek V, Pastore A, Castiglione Morelli MA, Frank R, Gausepohl H, Gibson T, Weih F, Roesch P

Protein engineering, 1990

doi:10.1093/protein/4.1.3.

Catalytic RNA and the origin of genetic systems.

Lamond AI, Gibson TJ

Trends in genetics : TIG, 1990

doi:10.1016/0168-9525(90)90148-Y.

A regular pattern of two types of 100-residue motif in the sequence of titin

Labeit S, Barlow DP, Gautel M, Gibson T, Holt J, Hsieh CL, Francke U, Leonard K, Wardale J, Whiting A

Nature, 1990

doi:10.1038/345273a0.

Protruding domain of tomato bushy stunt virus coat protein is a hitherto unrecognized class of jellyroll conformation.

Gibson TJ, Argos P

Journal of molecular biology, 1990

doi:10.1016/0022-2836(90)90298-Z.

Metabolic complexity in the RNA world and implications for the origin of protein synthesis

Gibson TJ, Lamond AI

Journal of molecular evolution, 1990

doi:10.1007/bf02102448.

DNA-binding domain ancestry

Frampton J, Leutz A, Gibson TJ, Graf T

NATURE, 1989

doi:10.1038/342134a0.

The phototrophic bacterium Rhodopseudomonas capsulata sp108 encodes an indigenous class A beta-lactamase.

Campbell JI, Scahill S, Gibson T, Ambler RP

The Biochemical journal, 1989

doi:10.1042/bj2600803.

A model for the tertiary structure of the 28 residue DNA-binding motif ('zinc finger') common to many eukaryotic transcriptional regulatory proteins.

Gibson TJ, Postma JP, Brown RS, Argos P

Protein engineering, 1988

doi:10.1093/protein/2.3.209.

Lorist2, a cosmid with transcriptional terminators insulating vector genes from interference by promoters within the insert: effect on DNA yield and cloned insert frequency.

Gibson TJ, Coulson AR, Sulston JE, Little PF

Gene, 1987

doi:10.1016/0378-1119(87)90016-3.

Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression.

Gibson TJ, Rosenthal A, Waterston RH

Gene, 1987

doi:10.1016/0378-1119(87)90017-5.

Coding content and expression of the EBV B95-8 genome in the region from base 62,248 to base 82,920.

Gibson TJ, Barrell BG, Farrell PJ

Virology, 1986

doi:10.1016/0042-6822(86)90379-X.

The BamHI F region of the B95-8 Epstein-Barr virus genome.

Hudson GS, Gibson TJ, Barrell BG

Virology, 1985

doi:10.1016/0042-6822(85)90230-2.

Structure of murine complement component C3. II. Nucleotide sequence of cloned complementary DNA coding for the alpha chain.

Wetsel RA, Lundwall A, Davidson F, Gibson T, Tack BF, Fey GH

The Journal of biological chemistry, 1984

doi:.

Homology between two EBV early genes and HSV ribonucleotide reductase and 38K genes.

Gibson T, Stockwell P, Ginsburg M, Barrell B

Nucleic acids research, 1984

doi:10.1093/nar/12.12.5087.

Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination.

Biggin MD, Gibson TJ, Hong GF

Proceedings of the National Academy of Sciences of the United States of America, 1983

doi:10.1073/pnas.80.13.3963.

DNA sequence and expression of the B95-8 Epstein-Barr virus genome.

Baer R, Bankier AT, Biggin MD, Deininger PL, Farrell PJ, Gibson TJ, Hatfull G, Hudson GS, Satchwell SC, Séguin C

Nature, 1984

doi:10.1038/310207a0.

Preparation of large numbers of plasmid DNA samples in microtiter plates by the alkaline lysis method.

Gibson TJ, Sulston JE

Gene analysis techniques, 1987

doi:10.1016/0735-0651(87)90016-1.