Adopting Mechanistic Molecular Biology Approaches in Exposome Research for Causal Understanding.

Foreman AL, Warth B, Hessel EVS, Price EJ, Schymanski EL, Cantelli G, Parkinson H, Hecht H, Klánová J, Vlaanderen J, Hilscherova K, Vrijheid M, Vineis P, Araujo R, Barouki R, Vermeulen R, Lanone S, Brunak S, Sebert S, Karjalainen T.

Environ Sci Technol, 2024

doi:10.1021/acs.est.3c07961.

Recent advances in polygenic scores: translation, equitability, methods and FAIR tools.

Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA.

Genome Med, 2024

doi:10.1186/s13073-024-01304-9.

"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.

David R, Rybina A, Burel JM, Heriche JK, Audergon P, Boiten JW, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Grüning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras JL, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, Sánchez-Pla A, Sansone SA, Sarkans U, Serrano-Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P.

EMBO J, 2023

doi:10.15252/embj.2023115008.

eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs.

Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K.

PLoS Genet, 2023

doi:10.1371/journal.pgen.1010932.

Features of a FAIR vocabulary.

Xu F, Juty N, Goble C, Jupp S, Parkinson H, Courtot M.

J Biomed Semantics, 2023

doi:10.1186/s13326-023-00286-8.

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing.

Yaldiz B, Kucuk E, Hampstead J, Hofste T, Pfundt R, Corominas Galbany J, Rinne T, Yntema HG, Hoischen A, Nelen M, Gilissen C, Solve-RD consortium.

Hum Genomics, 2023

doi:10.1186/s40246-023-00485-5.

Clinical, genetic, epidemiologic, evolutionary, and functional delineation of <i>TSPEAR</i>-related autosomal recessive ectodermal dysplasia 14.

Jackson A, Lin SJ, Jones EA, Chandler KE, Orr D, Moss C, Haider Z, Ryan G, Holden S, Harrison M, Burrows N, Jones WD, Loveless M, Petree C, Stewart H, Low K, Donnelly D, Lovell S, Drosou K, Genomics England Research Consortium, Solve-RD consortium, Varshney GK, Banka S.

HGG Adv, 2023

doi:10.1016/j.xhgg.2023.100186.

An atlas of genetic scores to predict multi-omic traits.

Xu Y, Ritchie SC, Liang Y, Timmers PRHJ, Pietzner M, Lannelongue L, Lambert SA, Tahir UA, May-Wilson S, Foguet C, Johansson Å, Surendran P, Nath AP, Persyn E, Peters JE, Oliver-Williams C, Deng S, Prins B, Luan J, Bomba L, Soranzo N, Di Angelantonio E, Pirastu N, Tai ES, van Dam RM, Parkinson H, Davenport EE, Paul DS, Yau C, Gerszten RE, Mälarstig A, Danesh J, Sim X, Langenberg C, Wilson JF, Butterworth AS, Inouye M.

Nature, 2023

doi:10.1038/s41586-023-05844-9.

Virtual Fly Brain-An interactive atlas of the <i>Drosophila</i> nervous system.

Court R, Costa M, Pilgrim C, Millburn G, Holmes A, McLachlan A, Larkin A, Matentzoglu N, Kir H, Parkinson H, Brown NH, O'Kane CJ, Armstrong JD, Jefferis GSXE, Osumi-Sutherland D.

Front Physiol, 2023

doi:10.3389/fphys.2023.1076533.

Genome-wide screening reveals the genetic basis of mammalian embryonic eye development.

Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ, Bosch F, Braun RE, Brown SDM, Chin HG, Dickinson ME, Hsu CW, Dobbie M, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Mammano F, Nutter LMJ, Parkinson H, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, International Mouse Phenotyping Consortium, Brooks B, McKerlie C, Lloyd KCK, Westerberg H, Moshiri A.

BMC Biol, 2023

doi:10.1186/s12915-022-01475-0.

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing.

Denommé-Pichon AS, Matalonga L, de Boer E, Jackson A, Benetti E, Banka S, Bruel AL, Ciolfi A, Clayton-Smith J, Dallapiccola B, Duffourd Y, Ellwanger K, Fallerini C, Gilissen C, Graessner H, Haack TB, Havlovicova M, Hoischen A, Jean-Marçais N, Kleefstra T, López-Martín E, Macek M, Mencarelli MA, Moutton S, Pfundt R, Pizzi S, Posada M, Radio FC, Renieri A, Rooryck C, Ryba L, Safraou H, Schwarz M, Tartaglia M, Thauvin-Robinet C, Thevenon J, Tran Mau-Them F, Trimouille A, Votypka P, de Vries BBA, Willemsen MH, Zurek B, Verloes A, Philippe C, Solve-RD DITF-ITHACA, Solve-RD SNV-indel Working Group, Solve-RD Consortia, Orphanomix Group, Vitobello A, Vissers LELM, Faivre L.

Genet Med, 2023

doi:10.1016/j.gim.2023.100018.

COVoc and COVTriage: novel resources to support literature triage.

Caucheteur D, May Pendlington Z, Roncaglia P, Gobeill J, Mottin L, Matentzoglu N, Agosti D, Osumi-Sutherland D, Parkinson H, Ruch P.

Bioinformatics, 2023

doi:10.1093/bioinformatics/btac800.

PDCM Finder: an open global research platform for patient-derived cancer models.

Perova Z, Martinez M, Mandloi T, Gomez FL, Halmagyi C, Follette A, Mason J, Newhauser S, Begley DA, Krupke DM, Bult C, Parkinson H, Groza T.

Nucleic Acids Res, 2023

doi:10.1093/nar/gkac1021.

The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.

Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JAL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert SA, Inouye M, Parkinson H, Harris LW.

Nucleic Acids Res, 2023

doi:10.1093/nar/gkac1010.

The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease.

Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, Cacheiro P, Frost A, Keskivali-Bond P, Vardal B, McCoy A, Cheng TK, Santos L, Wells S, Smedley D, Mallon AM, Parkinson H.

Nucleic Acids Res, 2023

doi:10.1093/nar/gkac972.

Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes.

Higgins K, Moore BA, Berberovic Z, Adissu HA, Eskandarian M, Flenniken AM, Shao A, Imai DM, Clary D, Lanoue L, Newbigging S, Nutter LMJ, Adams DJ, Bosch F, Braun RE, Brown SDM, Dickinson ME, Dobbie M, Flicek P, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Chin HG, Mammano F, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, IMPC Consortium, Lloyd KCK, McKerlie C, Moshiri A.

Sci Rep, 2022

doi:10.1038/s41598-022-19710-7.

Mendelian gene identification through mouse embryo viability screening.

Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LMJ, Muñoz-Fuentes V, Hsu CW, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Haseli Mashhadi H, Parkinson H, Mallon AM, International Mouse Phenotyping Consortium, Genomics England Research Consortium, Smedley D.

Genome Med, 2022

doi:10.1186/s13073-022-01118-7.

A community driven GWAS summary statistics standard

Hayhurst J, Buniello A, Harris L, Mosaku A, Chang C, Gignoux CR, Hatzikotoulas K, Karim MA, Lambert SA, Lyon M, McMahon A, Okada Y, Pirastu N, Rayner NW, Schwartzentruber J, Vaughan R, Verma S, Wilder SP, Cunningham F, Hindorff L, Wiley K, Parkinson H, Barroso I.

2022

doi:10.1101/2022.07.15.500230.

Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen.

Wotton JM, Peterson E, Flenniken AM, Bains RS, Veeraragavan S, Bower LR, Bubier JA, Parisien M, Bezginov A, Haselimashhadi H, Mason J, Moore MA, Stewart ME, Clary DA, Delbarre DJ, Anderson LC, D'Souza A, Goodwin LO, Harrison ME, Huang Z, Mckay M, Qu D, Santos L, Srinivasan S, Urban R, Vukobradovic I, Ward CS, Willett AM, Braun RE, Brown SDM, Dickinson ME, Heaney JD, Kumar V, Lloyd KCK, Mallon AM, McKerlie C, Murray SA, Nutter LMJ, Nutter LMJ, Parkinson H, Seavitt JR, Wells S, Samaco RC, Chesler EJ, Smedley D, Diatchenko L, Baumbauer KM, Young EE, Bonin RP, Mandillo S, White JK, International Mouse Phenotyping Consortium.

Pain, 2022

doi:10.1097/j.pain.0000000000002481.

Features of a FAIR vocabulary

Xu F, Juty N, Goble C, Jupp S, Parkinson H, Courtot M.

2022

doi:10.21203/rs.3.rs-1465079/v1.

Mondo: Unifying diseases for the world, by the world

Vasilevsky NA, Matentzoglu NA, Toro S, Flack JE, Hegde H, Unni DR, Alyea GF, Amberger JS, Babb L, Balhoff JP, Bingaman TI, Burns GA, Buske OJ, Callahan TJ, Carmody LC, Cordo PC, Chan LE, Chang GS, Christiaens SL, Dumontier M, Failla LE, Flowers MJ, Garrett HA, Goldstein JL, Gration D, Groza T, Hanauer M, Harris NL, Hilton JA, Himmelstein DS, Hoyt CT, Kane MS, Köhler S, Lagorce D, Lai A, Larralde M, Lock A, López Santiago I, Maglott DR, Malheiro AJ, Meldal BHM, Munoz-Torres MC, Nelson TH, Nicholas FW, Ochoa D, Olson DP, Oprea TI, Osumi-Sutherland D, Parkinson H, Pendlington ZM, Rath A, Rehm HL, Remennik L, Riggs ER, Roncaglia P, Ross JE, Shadbolt MF, Shefchek KA, Similuk MN, Sioutos N, Smedley D, Sparks R, Stefancsik R, Stephan R, Storm AL, Stupp D, Stupp GS, Sundaramurthi JC, Tammen I, Tay D, Thaxton CL, Valasek E, Valls-Margarit J, Wagner AH, Welter D, Whetzel PL, Whiteman LL, Wood V, Xu CH, Zankl A, Zhang XA, Chute CG, Robinson PN, Mungall CJ, Hamosh A, Haendel MA.

2022

doi:10.1101/2022.04.13.22273750.

The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization.

Dudová Z, Conte N, Mason J, Stuchlík D, Peša R, Halmagyi C, Perova Z, Mosaku A, Thorne R, Follette A, Pivarč Ľ, Šašinka R, Usman M, Neuhauser S, Begley DA, Krupke DM, Frassà M, Fiori A, Corsi R, Vezzadini L, Isella C, Bertotti A, Bult C, Parkinson H, Medico E, Meehan T, Křenek A.

BMC Genomics, 2022

doi:10.1186/s12864-022-08367-1.

Mendelian gene identification through mouse embryo viability screening

Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LM, Muñoz-Fuentes V, Hsu C, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Mashhadi HH, Parkinson H, Mallon A, Smedley D, International Mouse Phenotyping Consortium, Genomics England Research Consortium.

2022

doi:10.1101/2022.01.07.22268899.

The European Genome-phenome Archive in 2021.

Freeberg MA, Fromont LA, D'Altri T, Romero AF, Ciges JI, Jene A, Kerry G, Moldes M, Ariosa R, Bahena S, Barrowdale D, Barbero MC, Fernandez-Orth D, Garcia-Linares C, Garcia-Rios E, Haziza F, Juhasz B, Llobet OM, Milla G, Mohan A, Rueda M, Sankar A, Shaju D, Shimpi A, Singh B, Thomas C, de la Torre S, Uyan U, Vasallo C, Flicek P, Guigo R, Navarro A, Parkinson H, Keane T, Rambla J.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1059.

The European Variation Archive: a FAIR resource of genomic variation for all species.

Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S, Flicek P, Parkinson H, Keane TM.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab960.

Pleiotropy data resource as a primer for investigating co-morbidities/multi-morbidities and their role in disease.

Muñoz-Fuentes V, Haselimashhadi H, Santos L, Westerberg H, Parkinson H, Mason J.

Mamm Genome, 2022

doi:10.1007/s00335-021-09917-w.

Workshop proceedings: GWAS summary statistics standards and sharing.

MacArthur JAL, Buniello A, Harris LW, Hayhurst J, McMahon A, Sollis E, Cerezo M, Hall P, Lewis E, Whetzel PL, Bahcall OG, Barroso I, Carroll RJ, Inouye M, Manolio TA, Rich SS, Hindorff LA, Wiley K, Parkinson H.

Cell Genom, 2021

doi:10.1016/j.xgen.2021.100004.

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Udara Liyanage I, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O'Connor BD, Oesterle S, Ogishima S, Wang VO, Paglione LAD, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E.

Cell Genom, 2021

doi:10.1016/j.xgen.2021.100029.

Sequencing-based genome-wide association studies reporting standards.

McMahon A, Lewis E, Buniello A, Cerezo M, Hall P, Sollis E, Parkinson H, Hindorff LA, Harris LW, MacArthur JAL.

Cell Genom, 2021

doi:10.1016/j.xgen.2021.100005.

The Data Use Ontology to streamline responsible access to human biomedical datasets.

Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M, Burdett T, Clissold H, Donnelly S, Dyke SOM, Freeberg MA, Haendel MA, Hata C, Holub P, Jeanson F, Jene A, Kawashima M, Kawashima S, Konopko M, Kyomugisha I, Li H, Linden M, Rodriguez LL, Morita M, Mulder N, Muller J, Nagaie S, Nasir J, Ogishima S, Ota Wang V, Paglione LD, Pandya RN, Parkinson H, Philippakis AA, Prasser F, Rambla J, Reinold K, Rushton GA, Saltzman A, Saunders G, Sofia HJ, Spalding JD, Swertz MA, Tulchinsky I, van Enckevort EJ, Varma S, Voisin C, Yamamoto N, Yamasaki C, Zass L, Guidry Auvil JM, Nyrönen TH, Courtot M.

Cell Genom, 2021

doi:10.1016/j.xgen.2021.100028.

Impact of Essential Genes on the Success of Genome Editing Experiments Generating 3,313 New Genetically Engineered Mouse Lines

Elrick H, Peterson KA, Willis BJ, Lanza DG, Acar EF, Ryder EJ, Teboul L, Kasparek P, Birling M, Adams DJ, Bradley A, Braun RE, Brown SD, Caulder A, Codner GF, DeMayo FJ, Dickinson ME, Doe B, Duddy G, Gertsenstein M, Goodwin LO, Hérault Y, Lintott LG, Lloyd KCK, Lorenzo I, Mackenzie M, Mallon A, McKerlie C, Parkinson H, Ramirez-Solis R, Seavitt JR, Sedlacek R, Skarnes WC, Smedley D, Wells S, White JK, Wood JA, Murray SA, Heaney JD, Nutter LMJ, International Mouse Phenotyping Consortium.

2021

doi:10.1101/2021.10.06.463037.

Desiderata for the development of next-generation electronic health record phenotype libraries.

Chapman M, Mumtaz S, Rasmussen LV, Karwath A, Gkoutos GV, Gao C, Thayer D, Pacheco JA, Parkinson H, Richesson RL, Jefferson E, Denaxas S, Curcin V.

Gigascience, 2021

doi:10.1093/gigascience/giab059.

A compendium of uniformly processed human gene expression and splicing quantitative trait loci.

Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates AD, Zerbino DR, Alasoo K.

Nat Genet, 2021

doi:10.1038/s41588-021-00924-w.

Correction: Solving unsolved rare neurological diseases-a Solve-RD viewpoint.

Schüle R, Timmann D, Erasmus CE, Reichbauer J, Wayand M, Solve-RD-DITF-RND, van de Warrenburg B, Schöls L, Wilke C, Bevot A, Zuchner S, Beltran S, Laurie S, Matalonga L, Graessner H, Synofzik M, Solve-RD Consortium.

Eur J Hum Genet, 2021

doi:10.1038/s41431-021-00935-5.

Correction to: Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Matalonga L, Hernández-Ferrer C, Piscia D, Solve-RD SNV-indel working group, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Solve-RD DITF-GENTURIS, Solve-RD DITF-ITHACA, Solve-RD DITF-euroNMD, Solve-RD DITF-RND, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S, Solve-RD Consortium.

Eur J Hum Genet, 2021

doi:10.1038/s41431-021-00934-6.

Correction to: Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

Zurek B, Ellwanger K, Vissers LELM, Schüle R, Synofzik M, Töpf A, de Voer RM, Laurie S, Matalonga L, Gilissen C, Ossowski S, 't Hoen PAC, Vitobello A, Schulze-Hentrich JM, Riess O, Brunner HG, Brookes AJ, Rath A, Bonne G, Gumus G, Verloes A, Hoogerbrugge N, Evangelista T, Harmuth T, Swertz M, Spalding D, Hoischen A, Beltran S, Graessner H, Solve-RD consortium.

Eur J Hum Genet, 2021

doi:10.1038/s41431-021-00936-4.

Solving patients with rare diseases through programmatic reanalysis of genome-phenome data.

Matalonga L, Hernández-Ferrer C, Piscia D, Solve-RD SNV-indel working group, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Solve-RD DITF-GENTURIS, Solve-RD DITF-ITHACA, Solve-RD DITF-euroNMD, Solve-RD DITF-RND, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S, Solve-RD Consortia.

Eur J Hum Genet, 2021

doi:10.1038/s41431-021-00852-7.

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

Zurek B, Ellwanger K, Vissers LELM, Schüle R, Synofzik M, Töpf A, de Voer RM, Laurie S, Matalonga L, Gilissen C, Ossowski S, 't Hoen PAC, Vitobello A, Schulze-Hentrich JM, Riess O, Brunner HG, Brookes AJ, Rath A, Bonne G, Gumus G, Verloes A, Hoogerbrugge N, Evangelista T, Harmuth T, Swertz M, Spalding D, Hoischen A, Beltran S, Graessner H, Solve-RD consortium.

Eur J Hum Genet, 2021

doi:10.1038/s41431-021-00859-0.

REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.

Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A.

Nat Methods, 2021

doi:10.1038/s41592-021-01166-8.

Solving unsolved rare neurological diseases-a Solve-RD viewpoint.

Schüle R, Timmann D, Erasmus CE, Reichbauer J, Wayand M, Solve-RD-DITF-RND, van de Warrenburg B, Schöls L, Wilke C, Bevot A, Zuchner S, Beltran S, Laurie S, Matalonga L, Graessner H, Synofzik M, Solve-RD Consortium.

Eur J Hum Genet, 2021

doi:10.1038/s41431-021-00901-1.

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups.

Nature, 2021

doi:10.1038/s41586-021-03287-8.

The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation.

Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JAL, Inouye M.

Nat Genet, 2021

doi:10.1038/s41588-021-00783-5.

Improving reporting standards for polygenic scores in risk prediction studies.

Wand H, Lambert SA, Tamburro C, Iacocca MA, O'Sullivan JW, Sillari C, Kullo IJ, Rowley R, Dron JS, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis K, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJW, Goddard KAB, Kraft P, MacArthur JAL, Inouye M, Wojcik GL.

Nature, 2021

doi:10.1038/s41586-021-03243-6.

Author Correction: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH, PDXNET Consortium, EurOPDX Consortium.

Nat Genet, 2021

doi:10.1038/s41588-021-00811-4.

ELIXIR-EXCELERATE: establishing Europe's data infrastructure for the life science research of the future.

Harrow J, Hancock J, ELIXIR-EXCELERATE Community, Blomberg N.

EMBO J, 2021

doi:10.15252/embj.2020107409.

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH, PDXNET Consortium, EurOPDX Consortium.

Nat Genet, 2021

doi:10.1038/s41588-020-00750-6.

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.

Ghoussaini M, Mountjoy E, Carmona M, Peat G, Schmidt EM, Hercules A, Fumis L, Miranda A, Carvalho-Silva D, Buniello A, Burdett T, Hayhurst J, Baker J, Ferrer J, Gonzalez-Uriarte A, Jupp S, Karim MA, Koscielny G, Machlitt-Northen S, Malangone C, Pendlington ZM, Roncaglia P, Suveges D, Wright D, Vrousgou O, Papa E, Parkinson H, MacArthur JAL, Todd JA, Barrett JC, Schwartzentruber J, Hulcoop DG, Ochoa D, McDonagh EM, Dunham I.

Nucleic Acids Res, 2021

doi:10.1093/nar/gkaa840.

OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data.

Haselimashhadi H, Mason JC, Mallon AM, Smedley D, Meehan TF, Parkinson H.

PLoS One, 2020

doi:10.1371/journal.pone.0242933.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density.

Swan AL, Schütt C, Rozman J, Del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P, Grallert H, Werner T, Teperino R, Becker L, Miller G, Moshiri A, Seavitt JR, Cissell DD, Meehan TF, Acar EF, Lelliott CJ, Flenniken AM, Champy MF, Sorg T, Ayadi A, Braun RE, Cater H, Dickinson ME, Flicek P, Gallegos J, Ghirardello EJ, Heaney JD, Jacquot S, Lally C, Logan JG, Teboul L, Mason J, Spielmann N, McKerlie C, Murray SA, Nutter LMJ, Odfalk KF, Parkinson H, Prochazka J, Reynolds CL, Selloum M, Spoutil F, Svenson KL, Vales TS, Wells SE, White JK, Sedlacek R, Wurst W, Lloyd KCK, Croucher PI, Fuchs H, Williams GR, Bassett JHD, Gailus-Durner V, Herault Y, Mallon AM, Brown SDM, Mayer-Kuckuk P, Hrabe de Angelis M, IMPC Consortium.

PLoS Genet, 2020

doi:10.1371/journal.pgen.1009190.

LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, LifeTime Community Working Groups.

Nature, 2020

doi:10.1038/s41586-020-2715-9.

The Polygenic Score Catalog: an open database for reproducibility and systematic evaluation

Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, Abraham G, Chapman M, Parkinson H, Danesh J, MacArthur JA, Inouye M.

2020

doi:10.1101/2020.05.20.20108217.

Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.

Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC.

J Alzheimers Dis, 2020

doi:10.3233/jad-200207.

OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic Data

Haselimashhadi H, Mason JC, Mallon A, Smedley D, Meehan TF, Parkinson H.

2020

doi:10.1101/2020.05.13.091157.

Improving reporting standards for polygenic scores in risk prediction studies

Wand H, Lambert SA, Tamburro C, Iacocca MA, O’Sullivan JW, Sillari C, Kullo IJ, Rowley R, Dron JS, Brockman D, Venner E, McCarthy MI, Antoniou AC, Easton DF, Hegele RA, Khera AV, Chatterjee N, Kooperberg C, Edwards K, Vlessis K, Kinnear K, Danesh JN, Parkinson H, Ramos EM, Roberts MC, Ormond KE, Khoury MJ, Janssens ACJ, Goddard KA, Kraft P, MacArthur JAL, Inouye M, Wojcik G.

2020

doi:10.1101/2020.04.23.20077099.

The Deep Genome Project.

Lloyd KCK, Adams DJ, Baynam G, Beaudet AL, Bosch F, Boycott KM, Braun RE, Caulfield M, Cohn R, Dickinson ME, Dobbie MS, Flenniken AM, Flicek P, Galande S, Gao X, Grobler A, Heaney JD, Herault Y, de Angelis MH, Lupski JR, Lyonnet S, Mallon AM, Mammano F, MacRae CA, McInnes R, McKerlie C, Meehan TF, Murray SA, Nutter LMJ, Obata Y, Parkinson H, Pepper MS, Sedlacek R, Seong JK, Shiroishi T, Smedley D, Tocchini-Valentini G, Valle D, Wang CL, Wells S, White J, Wurst W, Xu Y, Brown SDM.

Genome Biol, 2020

doi:10.1186/s13059-020-1931-9.

Human and mouse essentiality screens as a resource for disease gene discovery.

Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D, Genomics England Research Consortium, International Mouse Phenotyping Consortium.

Nat Commun, 2020

doi:10.1038/s41467-020-14284-2.

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Sakthivel MP, Kuzmin I, Trevanion SJ, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates A, Zerbino DR, Alasoo K.

2020

doi:10.1101/2020.01.29.924266.

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.

Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Elixir Core Data Resource Forum, Blomberg N, Durinx C, McEntyre J.

Bioinformatics, 2020

doi:10.1093/bioinformatics/btz959.

High-throughput discovery of genetic determinants of circadian misalignment.

Zhang T, Xie P, Dong Y, Liu Z, Zhou F, Pan D, Huang Z, Zhai Q, Gu Y, Wu Q, Tanaka N, Obata Y, Bradley A, Lelliott CJ, Sanger Institute Mouse Genetics Project, Nutter LMJ, McKerlie C, Flenniken AM, Champy MF, Sorg T, Herault Y, Angelis MH, Durner VG, Mallon AM, Brown SDM, Meehan T, Parkinson HE, Smedley D, Lloyd KCK, Yan J, Gao X, Seong JK, Wang CL, Sedlacek R, Liu Y, Rozman J, Yang L, Xu Y.

PLoS Genet, 2020

doi:10.1371/journal.pgen.1008577.

Soft windowing application to improve analysis of high-throughput phenotyping data.

Haselimashhadi H, Mason JC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu CW, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy MF, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SDM, Smedley D, Flicek P, Mallon AM, Parkinson H, Meehan TF.

Bioinformatics, 2020

doi:10.1093/bioinformatics/btz744.

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022.

Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S.

Nat Rev Genet, 2019

doi:10.1038/s41576-019-0178-3.

Leveraging European infrastructures to access 1 million human genomes by 2022.

Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S.

Nat Rev Genet, 2019

doi:10.1038/s41576-019-0156-9.

Correction to: The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Beaudet AL, Brown SDM, Dickinson ME, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Heaney JD, Hrabé de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE, the IMPC consortium.

Conserv Genet, 2019

doi:10.1007/s10592-019-01144-w.

Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function.

Moore BA, Flenniken AM, Clary D, Moshiri AS, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, McKerlie C, International Mouse Phenotyping Consortium, Thomasy SM, Lloyd KCK, Murphy CJ, Moshiri A.

Sci Rep, 2019

doi:10.1038/s41598-019-47286-2.

Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank

Denaxas S, Parkinson H, Fitzpatrick N, Sudlow C, Hemingway H.

2019

doi:10.1101/685156.

Human and mouse essentiality screens as a resource for disease gene discovery

Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LM, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu C, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon A, Lloyd KK, Brown SD, Parkinson H, Meehan TF, Smedley D, on behalf of the Genomics England Research Consortium and the International Mouse Phenotyping Consortium.

2019

doi:10.1101/678250.

Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data

Haselimashhadi H, Jeremy MC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J, Flenniken AM, King R, Straiton E, Seavitt JR, Gaspero A, Garza A, Christianson AE, Hsu C, Reynolds CL, Lanza DG, Lorenzo I, Green JR, Gallegos JJ, Bohat R, Samaco RC, Veeraragavan S, Kim JK, Miller G, Fuchs H, Garrett L, Becker L, Kang YK, Clary D, Cho SY, Tamura M, Tanaka N, Soo KD, Bezginov A, About GB, Champy M, Vasseur L, Leblanc S, Meziane H, Selloum M, Reilly PT, Spielmann N, Maier H, Gailus-Durner V, Sorg T, Hiroshi M, Yuichi O, Heaney JD, Dickinson ME, Wolfgang W, Tocchini-Valentini GP, Lloyd KCK, McKerlie C, Seong JK, Yann H, de Angelis MH, Brown SD, Smedley D, Flicek P, Mallon A, Parkinson H, Meehan TF.

2019

doi:10.1101/656678.

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Blomberg N, Durinx C, McEntyre J, ELIXIR Core Data Resource Forum.

2019

doi:10.1101/598318.

Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts.

Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, International Mouse Phenotyping Consortium, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Kent Lloyd KC, Murphy CJ, Moshiri A.

Commun Biol, 2019

doi:10.1038/s42003-019-0349-y.

PDX Finder: A portal for patient-derived tumor xenograft model discovery.

Conte N, Mason JC, Halmagyi C, Neuhauser S, Mosaku A, Yordanova G, Chatzipli A, Begley DA, Krupke DM, Parkinson H, Meehan TF, Bult CC.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky984.

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.

Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky1120.

BioSamples database: an updated sample metadata hub.

Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D, Harrison P, Whetzel PL, Parkinson H, Burdett T.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky1061.

The Gene Ontology Resource: 20 years and still GOing strong.

The Gene Ontology Consortium.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky1055.

Identification of genes required for eye development by high-throughput screening of mouse knockouts.

Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, International Mouse Phenotyping Consortium, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Lloyd KCK, Murphy CJ, Moshiri A.

Commun Biol, 2018

doi:10.1038/s42003-018-0226-0.

Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data.

Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC.

Genes (Basel), 2018

doi:10.3390/genes9120593.

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation.

Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE, IMPC consortium.

Conserv Genet, 2018

doi:10.1007/s10592-018-1072-9.

PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery

Conte N, Mason J, Halmagyi C, Neuhauser SB, Mosaku A, Begley DA, Krupke DM, Parkinson H, Meehan TF, Bult CJ.

2018

doi:10.1101/291443.

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog.

Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JAL.

Genome Biol, 2018

doi:10.1186/s13059-018-1396-2.

Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.

Osumi-Sutherland DJ, Ponta E, Courtot M, Parkinson H, Badi L.

J Biomed Semantics, 2018

doi:10.1186/s13326-018-0175-z.

Harmonising phenomics information for a better interoperability in the rare disease field.

Maiella S, Olry A, Hanauer M, Lanneau V, Lourghi H, Donadille B, Rodwell C, Köhler S, Seelow D, Jupp S, Parkinson H, Groza T, Brudno M, Robinson PN, Rath A.

Eur J Med Genet, 2018

doi:10.1016/j.ejmg.2018.01.013.

Identification of genetic elements in metabolism by high-throughput mouse phenotyping.

Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R, Meehan TF, Mason J, Haselimashhadi H, IMPC Consortium, Hough T, Mallon AM, Wells S, Santos L, Lelliott CJ, White JK, Sorg T, Champy MF, Bower LR, Reynolds CL, Flenniken AM, Murray SA, Nutter LMJ, Svenson KL, West D, Tocchini-Valentini GP, Beaudet AL, Bosch F, Braun RB, Dobbie MS, Gao X, Herault Y, Moshiri A, Moore BA, Kent Lloyd KC, McKerlie C, Masuya H, Tanaka N, Flicek P, Parkinson HE, Sedlacek R, Seong JK, Wang CL, Moore M, Brown SD, Tschöp MH, Wurst W, Klingenspor M, Wolf E, Beckers J, Machicao F, Peter A, Staiger H, Häring HU, Grallert H, Campillos M, Maier H, Fuchs H, Gailus-Durner V, Werner T, Hrabe de Angelis M.

Nat Commun, 2018

doi:10.1038/s41467-017-01995-2.

A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.

Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH.

Stem Cell Reports, 2018

doi:10.1016/j.stemcr.2017.12.002.

Comparison, alignment, and synchronization of cell line information between CLO and EFO.

Ong E, Sarntivijai S, Jupp S, Parkinson H, He Y.

BMC Bioinformatics, 2017

doi:10.1186/s12859-017-1979-z.

Corrigendum: High-throughput discovery of novel developmental phenotypes.

Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA.

Nature, 2017

doi:10.1038/nature24643.

PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.

Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ.

Cancer Res, 2017

doi:10.1158/0008-5472.can-17-0582.

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.

Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S, Bower LR, Clary DA, Meziane H, Reilly P, Minowa O, Kelsey L, International Mouse Phenotyping Consortium, Tocchini-Valentini GP, Gao X, Bradley A, Skarnes WC, Moore M, Beaudet AL, Justice MJ, Seavitt J, Dickinson ME, Wurst W, de Angelis MH, Herault Y, Wakana S, Nutter LMJ, Flenniken AM, McKerlie C, Murray SA, Svenson KL, Braun RE, West DB, Lloyd KCK, Adams DJ, White J, Karp N, Flicek P, Smedley D, Meehan TF, Parkinson HE, Teboul LM, Wells S, Steel KP, Mallon AM, Brown SDM.

Nat Commun, 2017

doi:10.1038/s41467-017-00595-4.

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

Morales J, Bowler EH, Buniello A, Cerezo M, Hall P, Harris LW, Hastings E, Junkins HA, Malangone C, McMahon AC, Milano A, Welter D, Burdett T, Cunningham F, Flicek P, Parkinson H, Hindorff LA, MacArthur JAL.

2017

doi:10.1101/129395.

Building bridges between cellular and molecular structural biology.

Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ.

Elife, 2017

doi:10.7554/elife.25835.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol, 2017

doi:10.1371/journal.pbio.2001414.

Prevalence of sexual dimorphism in mammalian phenotypic traits.

Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL, International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK.

Nat Commun, 2017

doi:10.1038/ncomms15475.

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, International Mouse Phenotyping Consortium, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KCK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SDM, Smedley D.

Nat Genet, 2017

doi:10.1038/ng.3901.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hermjakob H, Hériché J, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone S, Sariyar M, Snoep JL, Stanford NJ, Soiland-Reyes S, Swainston N, Washington N, Williams AR, Wimalaratne S, Winfree L, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

2017

doi:10.1101/117812.

Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience.

De Sousa PA, Steeg R, Wachter E, Bruce K, King J, Hoeve M, Khadun S, McConnachie G, Holder J, Kurtz A, Seltmann S, Dewender J, Reimann S, Stacey G, O'Shea O, Chapman C, Healy L, Zimmermann H, Bolton B, Rawat T, Atkin I, Veiga A, Kuebler B, Serano BM, Saric T, Hescheler J, Brüstle O, Peitz M, Thiele C, Geijsen N, Holst B, Clausen C, Lako M, Armstrong L, Gupta SK, Kvist AJ, Hicks R, Jonebring A, Brolén G, Ebneth A, Cabrera-Socorro A, Foerch P, Geraerts M, Stummann TC, Harmon S, George C, Streeter I, Clarke L, Parkinson H, Harrison PW, Faulconbridge A, Cherubin L, Burdett T, Trigueros C, Patel MJ, Lucas C, Hardy B, Predan R, Dokler J, Brajnik M, Keminer O, Pless O, Gribbon P, Claussen C, Ringwald A, Kreisel B, Courtney A, Allsopp TE.

Stem Cell Res, 2017

doi:10.1016/j.scr.2017.03.002.

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).

MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H.

Nucleic Acids Res, 2017

doi:10.1093/nar/gkw1133.

Open Targets: a platform for therapeutic target identification and validation.

Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.

Nucleic Acids Res, 2017

doi:10.1093/nar/gkw1055.

The human-induced pluripotent stem cell initiative-data resources for cellular genetics.

Streeter I, Harrison PW, Faulconbridge A, The HipSci Consortium, Flicek P, Parkinson H, Clarke L.

Nucleic Acids Res, 2017

doi:10.1093/nar/gkw928.

High-throughput discovery of novel developmental phenotypes.

Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie SM, Fuchs H, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Newbigging S, Nutter LM, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Jackson Laboratory, Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS), Charles River Laboratories, MRC Harwell, Toronto Centre for Phenogenomics, Wellcome Trust Sanger Institute, RIKEN BioResource Center, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SD, Adams DJ, Lloyd KC, McKerlie C, Beaudet AL, Bućan M, Murray SA.

Nature, 2016

doi:10.1038/nature19356.

Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.

Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A.

PLoS One, 2016

doi:10.1371/journal.pone.0157484.

PhenoImageShare: an image annotation and query infrastructure.

Adebayo S, McLeod K, Tudose I, Osumi-Sutherland D, Burdett T, Baldock R, Burger A, Parkinson H.

J Biomed Semantics, 2016

doi:10.1186/s13326-016-0072-2.

The cellular microscopy phenotype ontology.

Jupp S, Malone J, Burdett T, Heriche JK, Williams E, Ellenberg J, Parkinson H, Rustici G.

J Biomed Semantics, 2016

doi:10.1186/s13326-016-0074-0.

The Ontology for Biomedical Investigations.

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.

PLoS One, 2016

doi:10.1371/journal.pone.0154556.

Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.

Jupp S, Burdett T, Welter D, Sarntivijai S, Parkinson H, Malone J.

J Biomed Semantics, 2016

doi:10.1186/s13326-016-0055-3.

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.

Sarntivijai S, Vasant D, Jupp S, Saunders G, Bento AP, Gonzalez D, Betts J, Hasan S, Koscielny G, Dunham I, Parkinson H, Malone J.

J Biomed Semantics, 2016

doi:10.1186/s13326-016-0051-7.

Ten Simple Rules for Selecting a Bio-ontology.

Malone J, Stevens R, Jupp S, Hancocks T, Parkinson H, Brooksbank C.

PLoS Comput Biol, 2016

doi:10.1371/journal.pcbi.1004743.

Reporting phenotypes in mouse models when considering body size as a potential confounder.

Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK, Karp NA.

J Biomed Semantics, 2016

doi:10.1186/s13326-016-0050-8.

Gramene 2016: comparative plant genomics and pathway resources.

Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D.

Nucleic Acids Res, 2016

doi:10.1093/nar/gkv1179.

Tools and data services registry: a community effort to document bioinformatics resources.

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.

Nucleic Acids Res, 2016

doi:10.1093/nar/gkv1116.

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A.

Nucleic Acids Res, 2016

doi:10.1093/nar/gkv1045.

A mouse informatics platform for phenotypic and translational discovery.

Ring N, Meehan TF, Blake A, Brown J, Chen CK, Conte N, Di Fenza A, Fiegel T, Horner N, Jacobsen JO, Karp N, Lawson T, Mason JC, Mason JC, Matthews P, Morgan H, Relac M, Santos L, Smedley D, Sneddon D, Pengelly A, Tudose I, Warren JW, Westerberg H, Yaikhom G, Parkinson H, Mallon AM.

Mamm Genome, 2015

doi:10.1007/s00335-015-9599-2.

Precision medicine: Look to the mice.

Lloyd KC, Meehan T, Beaudet A, Murray S, Svenson K, McKerlie C, West D, Morse I, Parkinson H, Brown S, Mallon AM, Moore M.

Science, 2015

doi:10.1126/science.349.6246.390-a.

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN.

Am J Hum Genet, 2015

doi:10.1016/j.ajhg.2015.05.020.

Applying the ARRIVE Guidelines to an In Vivo Database.

Karp NA, Meehan TF, Morgan H, Mason JC, Mason JC, Blake A, Kurbatova N, Smedley D, Jacobsen J, Mott RF, Iyer V, Matthews P, Melvin DG, Wells S, Flenniken AM, Masuya H, Wakana S, White JK, Lloyd KC, Reynolds CL, Paylor R, West DB, Svenson KL, Chesler EJ, de Angelis MH, Tocchini-Valentini GP, Sorg T, Herault Y, Parkinson H, Mallon AM, Brown SD.

PLoS Biol, 2015

doi:10.1371/journal.pbio.1002151.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol, 2015

doi:10.1371/journal.pbio.1002033.

Gene Ontology Consortium: going forward.

Gene Ontology Consortium.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku1179.

INFRAFRONTIER--providing mutant mouse resources as research tools for the international scientific community.

INFRAFRONTIER Consortium.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku1193.

ArrayExpress update--simplifying data submissions.

Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku1057.

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku1011.

CLO: The cell line ontology.

Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y.

J Biomed Semantics, 2014

doi:10.1186/2041-1480-5-37.

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.

Federhen S, Clark K, Barrett T, Parkinson H, Ostell J, Kodama Y, Mashima J, Nakamura Y, Cochrane G, Karsch-Mizrachi I.

Stand Genomic Sci, 2014

doi:10.4056/sigs.4851102.

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R.

J Biomed Semantics, 2014

doi:10.1186/2041-1480-5-25.

The EBI RDF platform: linked open data for the life sciences.

Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.

Bioinformatics, 2014

doi:10.1093/bioinformatics/btt765.

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.

Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1229.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1270.

Updates to BioSamples database at European Bioinformatics Institute.

Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1081.

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.

Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt977.

ArrayExpress update--trends in database growth and links to data analysis tools.

Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.

Nucleic Acids Res, 2013

doi:10.1093/nar/gks1174.

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.

Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P, Skarnes WC.

Mamm Genome, 2012

doi:10.1007/s00335-012-9428-9.

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.

Bioinformatics, 2012

doi:10.1093/bioinformatics/bts148.

Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.

Adamusiak T, Parkinson H, Muilu J, Roos E, van der Velde KJ, Thorisson GA, Byrne M, Pang C, Gollapudi S, Ferretti V, Hillege H, Brookes AJ, Swertz MA.

Hum Mutat, 2012

doi:10.1002/humu.22070.

The BioSample Database (BioSD) at the European Bioinformatics Institute.

Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H.

Nucleic Acids Res, 2012

doi:10.1093/nar/gkr937.

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.

Nucleic Acids Res, 2012

doi:10.1093/nar/gkr913.

Anatomy ontologies and potential users: bridging the gap.

Travillian RS, Adamusiak T, Burdett T, Gruenberger M, Hancock J, Mallon AM, Malone J, Schofield P, Parkinson H.

J Biomed Semantics, 2011

doi:10.1186/2041-1480-2-s4-s3.

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA.

BMC Bioinformatics, 2011

doi:10.1186/1471-2105-12-218.

Data standards for Omics data: the basis of data sharing and reuse.

Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CA.

Methods Mol Biol, 2011

doi:10.1007/978-1-61779-027-0_2.

Contributions of the EMERALD project to assessing and improving microarray data quality.

Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M.

Biotechniques, 2011

doi:10.2144/000113591.

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.

Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.

Nucleic Acids Res, 2011

doi:10.1093/nar/gkq1040.

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL.

Stand Genomic Sci, 2010

doi:10.4056/sigs.147362.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

BMC Bioinformatics, 2010

doi:10.1186/1471-2105-11-s12-s12.

Large scale comparison of global gene expression patterns in human and mouse.

Zheng-Bradley X, Rung J, Parkinson H, Brazma A.

Genome Biol, 2010

doi:10.1186/gb-2010-11-12-r124.

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.

Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ, Ball CA.

Bioinformatics, 2010

doi:10.1093/bioinformatics/btq462.

Modeling biomedical experimental processes with OBI.

Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J, OBI consortium.

J Biomed Semantics, 2010

doi:10.1186/2041-1480-1-s1-s7.

A global map of human gene expression.

Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A.

Nat Biotechnol, 2010

doi:10.1038/nbt0410-322.

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC.

Genome Biol, 2010

doi:10.1186/gb-2010-11-3-r27.

Modeling sample variables with an Experimental Factor Ontology.

Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H.

Bioinformatics, 2010

doi:10.1093/bioinformatics/btq099.

Gene expression atlas at the European bioinformatics institute.

Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A.

Nucleic Acids Res, 2010

doi:10.1093/nar/gkp936.

Importing ArrayExpress datasets into R/Bioconductor.

Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btp354.

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.

Rayner TF, Rezwan FI, Lukk M, Bradley XZ, Farne A, Holloway E, Malone J, Williams E, Parkinson H.

Bioinformatics, 2009

doi:10.1093/bioinformatics/btn617.

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.

Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.

Nucleic Acids Res, 2009

doi:10.1093/nar/gkn889.

Data storage and analysis in ArrayExpress and Expression Profiler.

Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.

Curr Protoc Bioinformatics, 2008

doi:10.1002/0471250953.bi0713s23.

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.

Nat Biotechnol, 2008

doi:10.1038/nbt1391.

Cancer informatics in the U.K.: the NCRI informatics initiative.

Reddington F, Wilkinson JM, Clark R, Parkinson H, Kerr P, Begent R.

Cancer Inform, 2007

doi:.

Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.

Mouse Phenotype Database Integration Consortium, Hancock JM, Adams NC, Aidinis V, Blake A, Blake A, Bogue M, Brown SD, Chesler EJ, Davidson D, Duran C, Eppig JT, Gailus-Durner V, Gates H, Gkoutos GV, Greenaway S, Hrabé de Angelis M, Kollias G, Leblanc S, Lee K, Lengger C, Maier H, Mallon AM, Masuya H, Melvin DG, Müller W, Parkinson H, Proctor G, Reuveni E, Schofield P, Shukla A, Smith C, Toyoda T, Vasseur L, Wakana S, Walling A, White J, Wood J, Zouberakis M.

Mamm Genome, 2007

doi:10.1007/s00335-007-9004-x.

ArrayExpress--a public database of microarray experiments and gene expression profiles.

Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A.

Nucleic Acids Res, 2007

doi:10.1093/nar/gkl995.

ArrayExpress service for reviewers/editors of DNA microarray papers.

Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI.

Nat Biotechnol, 2006

doi:10.1038/nbt1106-1321.

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.

BMC Bioinformatics, 2006

doi:10.1186/1471-2105-7-489.

Data storage and analysis in ArrayExpress.

Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.

Methods Enzymol, 2006

doi:10.1016/s0076-6879(06)11020-4.

Using ontologies to annotate microarray experiments.

Whetzel PL, Parkinson H, Stoeckert CJ.

Methods Enzymol, 2006

doi:10.1016/s0076-6879(06)11017-4.

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.

OMICS, 2006

doi:10.1089/omi.2006.10.205.

Development of FuGO: an ontology for functional genomics investigations.

Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ, Taylor C, White J, Wood A, FuGO Working Group.

OMICS, 2006

doi:10.1089/omi.2006.10.199.

Annotation of environmental OMICS data: application to the transcriptomics domain.

Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, Bailhache T, Reeves J, Pallett D, Warne J, Nashar K, Parkinson H, Sansone SA, Rocca-Serra P, Stevens R, Snape J, Brass A, Field D.

OMICS, 2006

doi:10.1089/omi.2006.10.172.

The MGED Ontology: a resource for semantics-based description of microarray experiments.

Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ.

Bioinformatics, 2006

doi:10.1093/bioinformatics/btl005.

Wrestling with SUMO and bio-ontologies.

Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.

Nat Biotechnol, 2006

doi:10.1038/nbt0106-21a.

MIAME/Plant - adding value to plant microarrray experiments.

Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee S, Wagner U, Hennig L.

Plant Methods, 2006

doi:10.1186/1746-4811-2-1.

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.

Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M.

Plant Physiol, 2005

doi:10.1104/pp.105.063156.

NCRI informatics initiative.

Begent RH, Kerr P, Parkinson H, Reddington F, Wilkinson JM.

Nat Biotechnol, 2005

doi:10.1038/nbt1005-1212.

The ArrayExpress gene expression database: a software engineering and implementation perspective.

Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.

Bioinformatics, 2005

doi:10.1093/bioinformatics/bti157.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.

Nucleic Acids Res, 2005

doi:10.1093/nar/gki056.

Standards and ontologies for functional genomics 2.

Harris MA, Parkinson H.

Comp Funct Genomics, 2004

doi:10.1002/cfg.448.

The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data.

Parkinson H, Aitken S, Baldock RA, Bard JB, Burger A, Hayamizu TF, Rector A, Ringwald M, Rogers J, Rosse C, Stoeckert CJ, Davidson D.

Comp Funct Genomics, 2004

doi:10.1002/cfg.434.

An open letter on microarray data from the MGED Society.

Microarray Gene Expression Data Mged Society.

Microbiology (Reading), 2004

doi:10.1099/mic.0.27637-0.

Submission of microarray data to public repositories.

Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N.

PLoS Biol, 2004

doi:10.1371/journal.pbio.0020317.

Standards for microarray data: an open letter.

Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N, MGED Society.

Environ Health Perspect, 2004

doi:10.1289/ehp.112-1277123.

The MGED ontology: a framework for describing functional genomics experiments.

Stoeckert CJ, Parkinson H.

Comp Funct Genomics, 2003

doi:10.1002/cfg.234.

Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine.

Harris MA, Parkinson H.

Comp Funct Genomics, 2003

doi:10.1002/cfg.249.

ArrayExpress: a public database of gene expression data at EBI.

Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.

C R Biol, 2003

doi:10.1016/j.crvi.2003.09.026.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA.

Nucleic Acids Res, 2003

doi:10.1093/nar/gkg091.

The European Bioinformatics Institute's data resources.

Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, Stoehr P, Cameron G.

Nucleic Acids Res, 2003

doi:10.1093/nar/gkg066.

The underlying principles of scientific publication.

Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data.

Bioinformatics, 2002

doi:10.1093/bioinformatics/18.11.1409.

Standards for microarray data.

Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J, Microarray Gene Expression Data (MGED) Society.

Science, 2002

doi:10.1126/science.298.5593.539b.

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.

Lombard V, Camon EB, Parkinson HE, Hingamp P, Stoesser G, Redaschi N.

Bioinformatics, 2002

doi:10.1093/bioinformatics/18.5.763.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M.

Nat Genet, 2001

doi:10.1038/ng1201-365.

The EMBL nucleotide sequence database.

Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Lombard V, Lopez R, Parkinson H, Redaschi N, Sterk P, Stoehr P, Tuli MA.

Nucleic Acids Res, 2001

doi:10.1093/nar/29.1.17.

Natural variation in a Drosophila clock gene and temperature compensation.

Sawyer LA, Hennessy JM, Peixoto AA, Rosato E, Parkinson H, Costa R, Kyriacou CP.

Science, 1997

doi:10.1126/science.278.5346.2117.