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Research

Publications: Dr Damian Smedley

Wei W, Pagnamenta AT, Gleadall N, Sanchis-Juan A, Stephens J, Broxholme J, Tuna S, Odhams CA et al. ( 2020 ) . Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans . Nature Communications vol. 11 , ( 1 )
Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A, van Hoeck A, Wood HM, Nomburg J, Gurjao C, Manders F et al. ( 2020 ) . Mutational signature in colorectal cancer caused by genotoxic pks <sup>+</sup> E. coli . Nature vol. 580 , ( 7802 ) 269 - 273 .
Cipriani V, Pontikos N, Arno G, Sergouniotis PI, Lenassi E, Thawong P, Danis D, Michaelides M et al. ( 2020 ) . An improved phenotype-driven tool for rare mendelian variant prioritization: Benchmarking exomiser on real patient whole-exome data . Genes vol. 11 , ( 4 )
Haselimashhadi H, Mason JC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J et al. ( 2020 ) . Soft windowing application to improve analysis of high-throughput phenotyping data . Bioinformatics vol. 36 , ( 5 ) 1492 - 1500 .
Lloyd KCK, Adams DJ, Baynam G, Beaudet AL, Bosch F, Boycott KM, Braun RE, Caulfield M et al. ( 2020 ) . The Deep Genome Project . Genome Biology vol. 21 , ( 1 )
Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H et al. ( 2020 ) . Human and mouse essentiality screens as a resource for disease gene discovery . Nature Communications vol. 11 , ( 1 )
Freeman TM, Wang D, Harris J, Ambrose JC, Arumugam P, Baple EL, Bleda M, Boardman-Pretty F et al. ( 2020 ) . Genomic loci susceptible to systematic sequencing bias in clinical whole genomes . Genome Research vol. 30 , ( 3 ) 415 - 426 .
Zhang T, Xie P, Dong Y, Liu Z, Zhou F, Pan D, Huang Z, Zhai Q et al. ( 2020 ) . High-throughput discovery of genetic determinants of circadian misalignment . PLoS Genetics vol. 16 , ( 1 )
Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T et al. ( 2020 ) . The Monarch Initiative in 2019: An integrative data and analytic platform connecting phenotypes to genotypes across species . Nucleic Acids Research vol. 48 , ( D1 ) D704 - D715 .
Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR et al. ( 2019 ) . PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels . Nature Genetics vol. 51 , ( 11 ) 1560 - 1565 .
Cacheiro P, Haendel MA, Smedley D, Meehan T, Mason J, Mashhadi HH, Muñoz-Fuentes V, Tocchini G et al. ( 2019 ) . New models for human disease from the International Mouse Phenotyping Consortium . Mammalian Genome vol. 30 , ( 5-6 ) 143 - 150 .
Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Beaudet AL, Brown SDM, Dickinson ME, Flenniken AM et al. ( 2019 ) . Correction to: The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation (Conservation Genetics, (2018), 19, 4, (995-1005), 10.1007/s10592-018-1072-9) . Conservation Genetics vol. 20 , ( 1 ) 135 - 136 .
Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL et al. ( 2019 ) . Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources . Nucleic Acids Research vol. 47 , ( D1 ) D1018 - D1027 .
Wheway G, Mitchison HM, Ambrose JC, Baple EL, Bleda M, Boardman-Pretty F, Boissiere JM, Boustred CR et al. ( 2019 ) . Corrigendum: Opportunities and challenges for molecular understanding of ciliopathies - The 100,000 Genomes Project (Frontiers in Genetics DOI: 10.3389/fgene.2019.00127) . Frontiers in Genetics vol. 10 , ( MAY )
Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L et al. ( 2019 ) . Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts . Communications biology vol. 2 ,
Wheway G, Mitchison HM, Ambrose JC, Baple EL, Bleda M, Boardman-Pretty F, Boissiere JM, Boustred CR et al. ( 2019 ) . Opportunities and challenges for molecular understanding of ciliopathies–the 100,000 genomes project . Frontiers in Genetics vol. 10 , ( MAR )
Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M et al. ( 2018 ) . Identification of genetic elements in metabolism by high-throughput mouse phenotyping . Nature Communications vol. 9 , ( 1 )
Arachchi H, Wojcik MH, Weisburd B, Jacobsen JOB, Valkanas E, Baxter S, Byrne AB, O'Donnell-Luria AH et al. ( 2018 ) . matchbox: An open-source tool for patient matching via the Matchmaker Exchange . Human Mutation vol. 39 , ( 12 ) 1827 - 1834 .
Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A et al. ( 2018 ) . The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation . Conservation Genetics vol. 19 , ( 4 ) 995 - 1005 .
Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells S ( 2018 ) . High-throughput mouse phenomics for characterizing mammalian gene function . Nature Reviews Genetics vol. 19 , ( 6 ) 357 - 370 .
Turnbull C, Scott RH, Thomas E, Jones L, Murugaesu N, Pretty FB, Halai D, Baple E et al. ( 2018 ) . The 100 000 Genomes Project: Bringing whole genome sequencing to the NHS . BMJ (Online) vol. 361 ,
Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J et al. ( 2017 ) . A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction . Nat Commun vol. 8 , ( 1 ) 886 - 886 .
Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I et al. ( 2017 ) . Disease model discovery from 3,328 gene knockouts by the International Mouse Phenotyping Consortium . Nature Genetics vol. 49 , ( 8 ) 1231 - 1238 .
Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ et al. ( 2017 ) . Prevalence of sexual dimorphism in mammalian phenotypic traits . Nature Communications vol. 8 ,
Taylor RL, Arno G, Poulter JA, Khan KN, Morarji J, Hull S, Pontikos N, Martin AR et al. ( 2017 ) . Association of steroid 5α-reductase type 3 congenital disorder of glycosylation with early-onset retinal dystrophy . JAMA Ophthalmology vol. 135 , ( 4 ) 339 - 347 .
Gall T, Valkanas E, Bello C, Markello T, Adams C, Bone WP, Brandt AJ, Brazill JM et al. ( 2017 ) . Defining disease, diagnosis, and translational medicine within a homeostatic perturbation paradigm: The National Institutes of Health undiagnosed diseases program experience . Frontiers in Medicine vol. 4 , ( MAY )
Jacobsen JOB, Smedley D, Robinson PN ( 2017 ) . Exomiser and genomiser . Computational Exome and Genome Analysis ,
Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM et al. ( 2017 ) . The human phenotype ontology in 2017 . Nucleic Acids Research vol. 45 , ( D1 ) D865 - D876 .
Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T et al. ( 2016 ) . The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species . Nucleic Acids Res vol. 45 , ( D1 ) D712 - D722 .
Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H et al. ( 2016 ) . A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease . American Journal of Human Genetics vol. 99 , ( 3 ) 595 - 606 .
McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T et al. ( 2016 ) . Navigating the phenotype frontier: The monarch initiative . Genetics vol. 203 , ( 4 ) 1491 - 1495 .
Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M et al. ( 2016 ) . Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency . Genetics in Medicine vol. 18 , ( 6 ) 608 - 617 .
Kaloff C, Anastassiadis K, Ayadi A, Baldock R, Beig J, Birling MC, Bradley A, Brown SDM et al. ( 2016 ) . Genome wide conditional mouse knockout resources . Drug Discovery Today: Disease Models vol. 20 , 3 - 12 .
Haendel M, Papatheodorou I, Oellrich A, Mungall CJ, Washington N, Lewis SE, Robinson PN, Smedley D ( 2016 ) . Tools for exploring mouse models of human disease . Drug Discovery Today: Disease Models vol. 20 , 21 - 26 .
Links AE, Draper D, Lee E, Guzman J, Valivullah Z, Maduro V, Lebedev V, Didenko M et al. ( 2016 ) . Distributed cognition and process management enabling individualized translational research: The NIH undiagnosed diseases program experience . Frontiers in Medicine vol. 3 , ( OCT )
Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C et al. ( 2015 ) . A gene expression resource generated by genome-wide lacZ profiling in the mouse . DMM Disease Models and Mechanisms vol. 8 , ( 11 ) 1467 - 1478 .
Ring N, Meehan TF, Blake A, Brown J, Chen CK, Conte N, Di Fenza A, Fiegel T et al. ( 2015 ) . A mouse informatics platform for phenotypic and translational discovery . Mammalian Genome vol. 26 , ( 9-10 ) 413 - 421 .
Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N et al. ( 2015 ) . Disease insights through cross-species phenotype comparisons . Mammalian Genome vol. 26 , ( 9-10 ) 548 - 555 .
Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K et al. ( 2015 ) . Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery . Human Mutation vol. 36 , ( 10 ) 979 - 984 .
Smedley D, Robinson PN ( 2015 ) . Phenotype-driven strategies for exome prioritization of human Mendelian disease genes . Genome Medicine vol. 7 , ( 1 )
Karp NA, Meehan TF, Morgan H, Mason JC, Blake A, Kurbatova N, Smedley D, Jacobsen J et al. ( 2015 ) . Applying the ARRIVE Guidelines to an In Vivo Database . PLoS Biology vol. 13 , ( 5 )
Papatheodorou I, Oellrich A, Smedley D ( 2015 ) . Linking gene expression to phenotypes via pathway information . Journal of Biomedical Semantics vol. 6 , ( 1 )
Meehan TF, Chen CK, Koscielny G, Relac M, Wilkinson P, Flicek P, Parkinson H, Bottomley J et al. ( 2015 ) . INFRAFRONTIER-providing mutant mouse resources as research tools for the international scientific community . Nucleic Acids Research vol. 43 , ( D1 ) D1171 - D1175 .
Oellrich A, Collier N, Smedley D, Groza T ( 2015 ) . Generation of silver standard concept annotations from Biomedical texts with special relevance to phenotypes . PLoS ONE vol. 10 , ( 1 )
Groza T, Köhler S, Doelken S, Collier N, Oellrich A, Smedley D, Couto FM, Baynam G et al. ( 2015 ) . Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora . Database vol. 2015 ,
Smedley D, Jacobsen JOB, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T et al. ( 2015 ) . Next-generation diagnostics and disease-gene discovery with the Exomiser . Nature Protocols vol. 10 , ( 12 ) 2004 - 2015 .
Collier N, Groza T, Smedley D, Robinson PN, Oellrich A, Rebholz-Schuhmann D ( 2015 ) . PhenoMiner: From text to a database of phenotypes associated with OMIM diseases . Database vol. 2015 , ( 1 )
Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH et al. ( 2015 ) . The BioMart community portal: An innovative alternative to large, centralized data repositories . Nucleic Acids Research vol. 43 , ( W1 ) W589 - W598 .
Smedley D, Kohler S, Bone W, Oellrich A, Jacobsen J, Wang K, Mungall C, Washington N et al. ( 2014 ) . Use of animal models for exome prioritization of rare disease genes . Orphanet Journal of Rare Diseases . vol. 9 ,
Oellrich A, Jacobsen J, Papatheodorou I, Smedley D ( 2014 ) . Using association rule mining to determine promising secondary phenotyping hypotheses . Bioinformatics vol. 30 , ( 12 )
Liakath-Ali K, Vancollie VE, Heath E, Smedley DP, Estabel J, Sunter D, Ditommaso T, White JK et al. ( 2014 ) . Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen . Nature Communications vol. 5 ,
Robinson PN, Köhler S, Oellrich A, Genetics SM, Wang K, Mungall CJ, Lewis SE, Washington N et al. ( 2014 ) . Improved exome prioritization of disease genes through cross-species phenotype comparison . Genome Research vol. 24 , ( 2 ) 340 - 348 .
Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P et al. ( 2014 ) . Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research . F1000Research vol. 2 ,
Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D et al. ( 2014 ) . Clinical interpretation of CNVs with cross-species phenotype data . Journal of Medical Genetics vol. 51 , ( 11 ) 766 - 772 .
Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL et al. ( 2014 ) . Deletions of chromosomal regulatory boundaries are associated with congenital disease . Genome biology vol. 15 , ( 9 )
Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S et al. ( 2014 ) . Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome . Science Translational Medicine vol. 6 , ( 252 )
Jäger M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN ( 2014 ) . Jannovar: A Java Library for Exome Annotation . Human Mutation vol. 35 , ( 5 ) 548 - 555 .
Oellrich A, Smedley D ( 2014 ) . Linking tissues to phenotypes using gene expression profiles . Database vol. 2014 ,
Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, Brown DL et al. ( 2014 ) . The Human Phenotype Ontology project: Linking molecular biology and disease through phenotype data . Nucleic Acids Research vol. 42 , ( D1 )
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK et al. ( 2014 ) . The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data . Nucleic Acids Research vol. 42 , ( D1 )
Oellrich A, Koehler S, Washington N, Mungall C, Lewis S, Haendel M, Robinson PN, Smedley D et al. ( 2014 ) . The influence of disease categories on gene candidate predictions from model organism phenotypes . Journal of Biomedical Semantics vol. 5 ,
Smedley D, Köhler S, Czeschik JC, Amberger J, Bocchini C, Hamosh A, Veldboer J, Zemojtel T et al. ( 2014 ) . Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases . Bioinformatics vol. 30 , ( 22 ) 3215 - 3222 .
Smedley D, Oellrich A, Köhler S, Ruef B, Westerfield M, Robinson P, Lewis S, Mungall C ( 2013 ) . PhenoDigm: Analyzing curated annotations to associate animal models with human diseases . Database vol. 2013 ,
Chen CK, Symmons O, Uslu VV, Tsujimura T, Ruf S, Smedley D, Spitz F ( 2013 ) . TRACER: A resource to study the regulatory architecture of the mouse genome . BMC Genomics vol. 14 , ( 1 )
Oetting WS, Robinson PN, Greenblatt MS, Cotton RG, Beck T, Carey JC, Doelken SC, Girdea M et al. ( 2013 ) . Getting Ready for the Human Phenome Project: The 2012 Forum of the Human Variome Project . Human Mutation . vol. 34 , 661 - 666 .
Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S et al. ( 2013 ) . Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish . DMM Disease Models and Mechanisms vol. 6 , ( 2 ) 358 - 372 .
Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P et al. ( 2013 ) . Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research . F1000Research vol. 2 ,
Murray SA, Eppig JT, Smedley D, Simpson EM, Rosenthal N ( 2012 ) . Erratum: Beyond knockouts: Cre resources for conditional mutagenesis (Mammalian Genome (2012) 23 (791) (DOI 10.1007/s00335-012-9430-2)) . Mammalian Genome vol. 23 , ( 11-12 )
Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD et al. ( 2012 ) . The mammalian gene function resource: The International Knockout Mouse Consortium . Mammalian Genome vol. 23 , ( 9-10 ) 580 - 586 .
Chandras C, Zouberakis M, Salimova E, Smedley D, Rosenthal N, Aidinis V ( 2012 ) . CreZOO-The European virtual repository of Cre and other targeted conditional driver strains . Database vol. 2012 ,
Chen CK, Mungall CJ, Gkoutos GV, Doelken SC, Kohler S, Ruef BJ, Smith C, Westerfield M et al. ( 2012 ) . Mousefinder: Candidate disease genes from mouse phenotype data . Human Mutation vol. 33 , ( 5 ) 858 - 866 .
Murray SA, Eppig JT, Smedley D, Simpson EM, Rosenthal N ( 2012 ) . Beyond knockouts: Cre resources for conditional mutagenesis . Mammalian Genome vol. 23 , ( 9-10 ) 587 - 599 .
Guberman JM, Ai J, Arnaiz O, Baran J, Blake A, Baldock R, Chelala C, Croft D et al. ( 2011 ) . BioMart Central Portal: An open database network for the biological community . Database vol. 2011 ,
Oakley DJ, Iyer V, Skarnes WC, Smedley D ( 2011 ) . BioMart as an integration solution for the International Knockout Mouse Consortium . Database vol. 2011 ,
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA et al. ( 2011 ) . Towards BioDBcore: A community-defined information specification for biological databases . Database vol. 2011 ,
Smedley D, Salimova E, Rosenthal N ( 2011 ) . Cre recombinase resources for conditional mouse mutagenesis . Methods vol. 53 , ( 4 ) 411 - 416 .
Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT et al. ( 2011 ) . The IKMC web portal: A central point of entry to data and resources from the International Knockout Mouse Consortium . Nucleic Acids Research vol. 39 , ( SUPPL. 1 )
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA et al. ( 2011 ) . Towards BioDBcore: A community-defined information specification for biological databases . Nucleic Acids Research vol. 39 , ( SUPPL. 1 )
Schofield PN, Eppig J, Huala E, De Angelis MH, Harvey M, Davidson D, Weaver T, Brown S et al. ( 2010 ) . Sustaining the data and bioresource commons . Science vol. 330 , ( 6004 ) 592 - 593 .
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S et al. ( 2010 ) . Ensembl variation resources . BMC Genomics vol. 11 , ( 1 )
Gruenberger M, Alberts R, Smedley D, Swertz M, Schofield P, Schughart K ( 2010 ) . Towards the integration of mouse databases - Definition and implementation of solutions to two use-cases in mouse functional genomics . BMC Research Notes vol. 3 ,
Swertz MA, Velde KJVD, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M et al. ( 2010 ) . XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments . Genome Biology vol. 11 , ( 3 )
Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R, Birney E et al. ( 2010 ) . Finding and sharing: new approaches to registries of databases and services for the biomedical sciences . Database : the journal of biological databases and curation vol. 2010 ,
Zouberakis M, Chandras C, Swertz M, Smedley D, Gruenberger M, Bard J, Schughart K, Rosenthal N et al. ( 2010 ) . Mouse Resource Browser--a database of mouse databases . Database : the journal of biological databases and curation vol. 2010 ,
Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P et al. ( 2009 ) . Ensembl's 10th year . Nucleic Acids Research vol. 38 , ( SUPPL.1 )
Wilkinson P, Sengerova J, Matteoni R, Chen CK, Soulat G, Ureta-Vidal A, Fessele S, Hagn M et al. ( 2009 ) . EMMA-Mouse mutant resources for the international scientific community . Nucleic Acids Research vol. 38 , ( SUPPL.1 )
Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A ( 2009 ) . BioMart central portal - Unified access to biological data . Nucleic Acids Research vol. 37 , ( SUPPL. 2 )
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A ( 2009 ) . BioMart - Biological queries made easy . BMC Genomics vol. 10 ,
Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y et al. ( 2009 ) . Ensembl 2009 . Nucleic Acids Research vol. 37 , ( SUPPL. 1 )
Chandras C, Weaver T, Zouberakis M, Smedley D, Schughart K, Rosenthal N, Hancock JM, Kollias G et al. ( 2009 ) . Models for financial sustainability of biological databases and resources . Database vol. 2009 ,
Hancock JM, Schofield PN, Chandras C, Zouberakis M, Aidinis V, Smedley D, Rosenthal N, Schughart K ( 2008 ) . CASIMIR: Coordination and sustainability of international mouse informatics resources . 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 .
Smedley D, Swertz MA, Wolstencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P ( 2008 ) . Solutions for data integration in functional genomics: A critical assessment and case study . Briefings in Bioinformatics vol. 9 , ( 6 ) 532 - 544 .
Swertz MA, Smedley D, Wolstencroft K, Alberts R, Zouberakis M, Aidinis V, Schughart K, Schofield PN et al. ( 2008 ) . Towards dynamic database infrastructures for mouse genetics . 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 .
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G et al. ( 2008 ) . Ensembl 2008 . Nucleic Acids Research vol. 36 , ( SUPPL. 1 )
Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G et al. ( 2007 ) . Ensembl 2007 . Nucleic Acids Research vol. 35 , ( SUPPL. 1 )
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F et al. ( 2006 ) . Ensembl 2006 . Nucleic acids research vol. 34 , ( Database issue )
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G et al. ( 2005 ) . Ensembl 2005 . Nucleic Acids Research vol. 33 , ( DATABASE ISS. )
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J et al. ( 2004 ) . An overview of Ensembl . Genome Research vol. 14 , ( 5 ) 925 - 928 .
Kasprzk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P et al. ( 2004 ) . EnsMart: A generic system for fast and flexible access to biological data . Genome Research vol. 14 , ( 1 ) 160 - 169 .
Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G et al. ( 2004 ) . Ensembl 2004 . Nucleic Acids Research vol. 32 , ( DATABASE ISS. )
Parkinson J, Charon C, Baker BS, Powles AV, Rogers S, Caird A, Smedley D, Halford S et al. ( 2004 ) . Variation at the IRF2 gene and susceptibility to psoriasis in chromosome 4q-linked families . Journal of Investigative Dermatology vol. 122 , ( 3 ) 640 - 643 .
McCarthy MI, Smedley D, Hide W ( 2003 ) . New methods for finding disease-susceptibility genes: Impact and potential . Genome Biology vol. 4 , ( 10 )
Huntley D, Hummerich H, Smedley D, Kittivoravitkul S, McCarthy M, Little P, Sergot M ( 2003 ) . GANESH: Software for customized annotation of genome regions . Genome Research vol. 13 , ( 9 ) 2195 - 2202 .
Kelso J, Visagie J, Theiler G, Christoffels A, Bardien S, Smedley D, Otgaar D, Greyling G et al. ( 2003 ) . eVOC: A controlled vocabulary for unifying gene expression data . Genome Research vol. 13 , ( 6 A ) 1222 - 1230 .
Hide W, Smedley D, McCarthy M, Kelso J ( 2003 ) . Application of eVOC: Controlled vocabularies for unifying gene expression data . Comptes Rendus - Biologies vol. 326 , ( 10-11 ) 1089 - 1096 .
HITMAN GA, McCarthy MI, Levy JC, Frayling TM, Smedley D, Groves CJ, Wiltshire S, Owen KR et al. ( 2003 ) . Association and haplotype analysis of the insulin-degrading enzyme (IDE) gene, a strong positional and biological candidate for type 2 diabetes susceptibility . Diabetes vol. 52 , 1300 - 1305 .
HITMAN GA, Hattersley AT, Wiltshire S, Bottazzo GF, Simecek N, Prestwich P, Rao PV, Wishart M et al. ( 2001 ) . A genomewide scan for loci predisposing to type 2 diabetes in a U.K. population (the Diabetes UK Warren 2 repository): analysis of 573 pedigrees provides independent replication of a susceptibility locus on chromosome 1q . Am. J. Hum. Genet vol. 69 , 553 - 569 .
Sorour A, Brito-Babapulle V, Smedley D, Yuille M, Catovsky D ( 2000 ) . Unusual breakpoint distribution of 8p abnormalities in T-prolymphocytic leukemia: A study with YACS mapping to 8p11-p12 . Cancer Genetics and Cytogenetics vol. 121 , ( 2 ) 128 - 132 .
Smedley D, Sidhar S, Birdsall S, Bennett D, Herlyn M, Cooper C, Shipley J ( 2000 ) . Characterization of chromosome 1 abnormalities in malignant melanomas . Genes Chromosomes and Cancer vol. 28 , ( 1 ) 121 - 125 .
Smedley D, Demiroglu A, Abdul-Rauf M, Heath C, Cooper C, Shipley J, Cross NCP ( 1999 ) . ZNF198-FGFR1 Transforms Ba/F3 Cells to Growth Factor Independence and Results in High Level Tyrosine Phosphorylation of STATS 1 and 5 . Neoplasia vol. 1 , ( 4 ) 349 - 355 .
Smedley D, Hamoudi R, Lu YJ, Cooper C, Shipley J ( 1999 ) . Cloning and mapping of members of the MYM family . Genomics vol. 60 , ( 2 ) 244 - 247 .
Lu YJ, Birdsall S, Summersgill B, Smedley D, Osin P, Fisher C, Shipley J ( 1999 ) . Dual colour fluorescence in situ hybridization to paraffin-embedded samples to deduce the presence of the der(X)t(X;18)(P11.2;q11.2) and involvement of either the SSX1 or SSX2 gene: A diagnostic and prognostic aid for synovial sarcoma . Journal of Pathology vol. 187 , ( 4 ) 490 - 496 .
Kulkarni S, Reiter A, Smedley D, Goldman JM, Cross NCP ( 1999 ) . The genomic structure of ZNF198 and location of breakpoints in the t(8;13) myeloproliferative syndrome . Genomics vol. 55 , ( 1 ) 118 - 121 .
Smedley D, Hamoudi R, Clark J, Warren W, Abdul-Rauf M, Somers G, Venter D, Fagan K et al. ( 1998 ) . The t(8;13)(p11;q11-12) rearrangement associated with an atypical myeloproliferative disorder fuses the fibroblast growth factor receptor 1 gene to a novel gene RAMP . Human Molecular Genetics vol. 7 , ( 4 ) 637 - 642 .
Smedley D, Somers G, Venter D, Chow CW, Cooper C, Shipley J ( 1998 ) . Characterization of a t(8;13)(p11;q11-12) in an atypical myeloproliferative disorder . Genes Chromosomes and Cancer vol. 21 , ( 1 ) 70 - 73 .
Clark J, Lu YJ, Sidhar SK, Parker C, Gill S, Smedley D, Hamoudi R, Linehan WM et al. ( 1997 ) . Fusion of splicing factor genes PSF and NonO (p54(nrb)) to the TFE3 gene in papillary renal cell carcinoma . Oncogene vol. 15 , ( 18 ) 2233 - 2239 .