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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)
10.1038/s41467-020-15336-3
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.
10.1038/s41586-020-2080-8
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)
10.3390/genes11040460
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.
10.1093/bioinformatics/btz744
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)
10.1186/s13059-020-1931-9
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)
10.1038/s41467-020-14284-2
https://qmro.qmul.ac.uk/xmlui/handle/123456789/63299
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.
10.1101/gr.255349.119
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)
10.1371/journal.pgen.1008577
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.
10.1093/nar/gkz997
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.
10.1038/s41588-019-0528-2
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.
10.1007/s00335-019-09804-5
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.
10.1007/s10592-019-01144-w
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.
10.1093/nar/gky1105
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)
10.3389/fgene.2019.00569
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,
10.1038/s42003-019-0349-y
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)
10.3389/fgene.2019.00127
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)
10.1038/s41467-017-01995-2
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.
10.1002/humu.23655
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.
10.1007/s10592-018-1072-9
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.
10.1038/s41576-018-0005-2
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,
10.1136/bmj.k1687
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.
10.1038/s41467-017-00595-4
https://qmro.qmul.ac.uk/xmlui/handle/123456789/34503
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.
10.1038/ng.3901
https://qmro.qmul.ac.uk/xmlui/handle/123456789/25144
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,
10.1038/ncomms15475
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.
10.1001/jamaophthalmol.2017.0046
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)
10.3389/fmed.2017.00062
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.
10.1093/nar/gkw1039
https://qmro.qmul.ac.uk/xmlui/handle/123456789/18234
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.
10.1093/nar/gkw1128
https://qmro.qmul.ac.uk/xmlui/handle/123456789/34605
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.
10.1016/j.ajhg.2016.07.005
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.
10.1534/genetics.116.188870
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.
10.1038/gim.2015.137
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.
10.1016/j.ddmod.2017.08.002
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.
10.1016/j.ddmod.2017.07.004
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)
10.3389/fmed.2016.00039
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.
10.1242/dmm.021238
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.
10.1007/s00335-015-9599-2
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.
10.1007/s00335-015-9577-8
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.
10.1002/humu.22857
Smedley D, Robinson PN(2015). Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Medicine vol. 7, (1)
10.1186/s13073-015-0199-2
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)
10.1371/journal.pbio.1002151
Papatheodorou I, Oellrich A, Smedley D(2015). Linking gene expression to phenotypes via pathway information. Journal of Biomedical Semantics vol. 6, (1)
10.1186/s13326-015-0013-5
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.
10.1093/nar/gku1193
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)
10.1371/journal.pone.0116040
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,
10.1093/database/bav005
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.
10.1038/nprot.2015.124
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)
10.1093/database/bav104
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.
10.1093/nar/gkv350
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,
10.1186/1750-1172-9-S1-O19
Oellrich A, Jacobsen J, Papatheodorou I, Smedley D(2014). Using association rule mining to determine promising secondary phenotyping hypotheses. Bioinformatics vol. 30, (12)
10.1093/bioinformatics/btu260
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,
10.1038/ncomms4540
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.
10.1101/gr.160325.113
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,
10.12688/f1000research.2-30.v2
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.
10.1136/jmedgenet-2014-102633
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)
10.1186/s13059-014-0423-1
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)
10.1126/scitranslmed.3009262
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.
10.1002/humu.22531
Oellrich A, Smedley D(2014). Linking tissues to phenotypes using gene expression profiles. Database vol. 2014,
10.1093/database/bau017
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)
10.1093/nar/gkt1026
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)
10.1093/nar/gkt977
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,
10.1186/2041-1480-5-S1-S4
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.
10.1093/bioinformatics/btu508
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,
10.1093/database/bat025
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)
10.1186/1471-2164-14-215
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.
10.1002/humu.22293
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.
10.1242/dmm.010322
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,
10.12688/f1000research.2-30.v1
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)
10.1007/s00335-012-9434-y
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.
10.1007/s00335-012-9422-2
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,
10.1093/database/bas029
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.
10.1002/humu.22051
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.
10.1007/s00335-012-9430-2
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,
10.1093/database/bar041
Oakley DJ, Iyer V, Skarnes WC, Smedley D(2011). BioMart as an integration solution for the International Knockout Mouse Consortium. Database vol. 2011,
10.1093/database/bar028
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,
10.1093/database/baq027
Smedley D, Salimova E, Rosenthal N(2011). Cre recombinase resources for conditional mouse mutagenesis. Methods vol. 53, (4) 411-416.
10.1016/j.ymeth.2010.12.027
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)
10.1093/nar/gkq879
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)
10.1093/nar/gkq1173
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.
10.1126/science.1191506
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)
10.1186/1471-2164-11-293
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,
10.1186/1756-0500-3-16
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)
10.1186/gb-2010-11-3-r27
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,
10.1093/database/baq014
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,
10.1093/database/baq010
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)
10.1093/nar/gkp972
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)
10.1093/nar/gkp799
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)
10.1093/nar/gkp265
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A(2009). BioMart - Biological queries made easy. BMC Genomics vol. 10,
10.1186/1471-2164-10-22
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)
10.1093/nar/gkn828
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,
10.1093/database/bap017
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.
10.1109/BIBE.2008.4696712
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.
10.1093/bib/bbn040
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.
10.1109/BIBE.2008.4696715
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)
10.1093/nar/gkm988
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)
10.1093/nar/gkl996
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)
10.1093/nar/gkj133
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.)
10.1093/nar/gki138
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.
10.1101/gr.1860604
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.
10.1101/gr.1645104
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.)
10.1093/nar/gkh038
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.
10.1046/j.0022-202X.2004.22135.x
McCarthy MI, Smedley D, Hide W(2003). New methods for finding disease-susceptibility genes: Impact and potential. Genome Biology vol. 4, (10)
10.1186/gb-2003-4-10-119
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.
10.1101/gr.698103
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.
10.1101/gr.985203
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.
10.1016/j.crvi.2003.09.030
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.
10.2337/diabetes.52.5.1300
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.
10.1086/323249
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.
10.1016/S0165-4608(00)00239-9
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.
10.1002/(SICI)1098-2264(200005)28:1<121::AID-GCC14>3.0.CO;2-O
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.
10.1038/sj.neo.7900035
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.
10.1006/geno.1999.5918
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.
10.1002/(SICI)1096-9896(199903)187:4<490::AID-PATH274>3.0.CO;2-X
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.
10.1006/geno.1998.5634
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.
10.1093/hmg/7.4.637
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.
10.1002/(SICI)1098-2264(199801)21:1<70::AID-GCC9>3.0.CO;2-5
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.
10.1038/sj.onc.1201394
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