Publications: Dr Damian Smedley

Danis D, Bamshad MJ, Bridges Y, Caballero-Oteyza A, Cacheiro P, Carmody LC, Chimirri L, Chong JX et al. ( 2024 ) . A corpus of GA4GH phenopackets: case-level phenotyping for genomic diagnostics and discovery . Human Genetics and Genomics Advances vol. 6 , ( 1 )

Beckwith MA, Danis D, Bridges Y, Jacobsen JOB, Smedley D, Robinson PN ( 2024 ) . Leveraging Clinical Intuition to Improve Accuracy of Phenotype-Driven Prioritization . Genetics in Medicine

Elrick H, Peterson KA, Willis BJ, Lanza DG, Acar EF, Ryder EJ, Teboul L, Kasparek P et al. ( 2024 ) . Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines . Scientific Reports vol. 14 , ( 1 )

Cacheiro P, Pava D, Parkinson H, VanZanten M, Wilson R, Gunes O, Consortium TIMP, Smedley D ( 2024 ) . Computational identification of disease models through cross-species phenotype comparison . Disease Models & Mechanisms vol. 17 , ( 6 )

Benkirane M, Bonhomme M, Morsy H, Safgren SL, Marelli C, Chaussenot A, Smedley D, Cipriani V et al. ( 2024 ) . De novo and inherited monoallelic variants in TUBA4A cause ataxia and spasticity . Brain vol. 147 , ( 11 ) 3681 - 3689 .

Bridges Y, de Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N et al. ( 2024 ) . Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework . vol. 5 , ( 06-24 )

Danis D, Bamshad MJ, Bridges Y, Cacheiro P, Carmody LC, Chong JX, Coleman B, Dalgleish R et al. ( 2024 ) . A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery . vol. 5 , ( 06-07 )

Stenton SL, O’Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O’Heir E et al. ( 2024 ) . Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project . Human Genomics vol. 18 , ( 1 )

Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN et al. ( 2024 ) . Lethal phenotypes in Mendelian disorders . Genetics in Medicine vol. 26 , ( 7 )

Duyzend MH, Cacheiro P, Jacobsen JOB, Giordano J, Brand H, Wapner RJ, Talkowski ME, Robinson PN et al. ( 2024 ) . Improving prenatal diagnosis through standards and aggregation . Prenatal Diagnosis vol. 44 , ( 4 ) 454 - 464 .

Putman TE, Schaper K, Matentzoglu N, Rubinetti VP, Alquaddoomi FS, Cox C, Caufield JH, Elsarboukh G et al. ( 2023 ) . The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species . Nucleic Acids Research vol. 52 , ( D1 ) d938 - d949 .

Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM et al. ( 2023 ) . The Human Phenotype Ontology in 2024: phenotypes around the world . Nucleic Acids Research vol. 52 , ( D1 ) d1333 - d1346 .

Jeffries L, Mis EK, McWalter K, Donkervoort S, Brodsky NN, Carpier J-M, Ji W, Ionita C et al. ( 2023 ) . Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections . Genetics in Medicine vol. 26 , ( 2 )

Magavern EF, Team GHR, Smedley D, Caulfield MJ ( 2023 ) . Factor V Leiden, estrogen, and multimorbidity association with venous thromboembolism in a British-South Asian cohort . iScience vol. 26 , ( 10 )

Park J, Tucci A, Cipriani V, Demidov G, Rocca C, Senderek J, Butryn M, Velic A et al. ( 2023 ) . Heterozygous UCHL1 loss-of-function variants cause a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy . Genetics in Medicine vol. 25 , ( 10 )

Magavern EF, Jacobs B, Warren H, Finocchiaro G, Finer S, van Heel DA, Team GHR, Smedley D et al. ( 2023 ) . CYP2C19 Genotype Prevalence and Association With Recurrent Myocardial Infarction in British–South Asians Treated With Clopidogrel . JACC Advances vol. 2 , ( 7 )

Magavern EF, van Heel DA, Team GHR, Smedley D, Caulfield MJ ( 2023 ) . CYP2C19 loss‐of‐function alleles are not associated with higher prevalence of gastrointestinal bleeds in those who have been prescribed antidepressants: Analysis in a British‐South Asian cohort . British Journal of Clinical Pharmacology vol. 89 , ( 11 ) 3432 - 3438 .

Stenton SL, O’Leary M, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O’Heir E et al. ( 2023 ) . Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project . vol. 4 , ( 08-11 )

Dominik N, Magri S, Currò R, Abati E, Facchini S, Corbetta M, Macpherson H, Di Bella D et al. ( 2023 ) . Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis . Brain vol. 146 , ( 12 ) 5060 - 5069 .

Vetro A, Pelorosso C, Balestrini S, Masi A, Hambleton S, Argilli E, Conti V, Giubbolini S et al. ( 2023 ) . Stretch-activated ion channel TMEM63B associates with developmental and epileptic encephalopathies and progressive neurodegeneration . American Journal of Human Genetics vol. 110 , ( 8 ) 1356 - 1376 .

Pavinato L, Stanic J, Barzasi M, Gurgone A, Chiantia G, Cipriani V, Eberini I, Palazzolo L et al. ( 2023 ) . Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder . Genetics in Medicine vol. 25 , ( 11 )

Crane-Smith Z, De Castro SCP, Nikolopoulou E, Wolujewicz P, Smedley D, Lei Y, Mather E, Santos C et al. ( 2023 ) . A non-coding insertional mutation of Grhl2 causes gene over-expression and multiple structural anomalies including cleft palate, spina bifida and encephalocele . Human Molecular Genetics vol. 32 , ( 17 ) 2681 - 2692 .

Magavern EF, van Heel DA, Smedley D, Caulfield MJ ( 2023 ) . SLCO1B1*5 is protective against non-senile cataracts in cohort prescribed statins: analysis in a British-South Asian cohort . The Pharmacogenomics Journal vol. 23 , ( 5 ) 134 - 139 .

Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V et al. ( 2023 ) . The Ontology of Biological Attributes (OBA)—computational traits for the life sciences . Mammalian Genome vol. 34 , ( 3 ) 364 - 378 .

Cacheiro P, Spielmann N, Mashhadi HH, Fuchs H, Gailus-Durner V, Smedley D, de Angelis MH ( 2023 ) . Knockout mice represent an important tool for the multisystemic study of human monogenic heart disease . Disease Models & Mechanisms vol. 16 , ( 5 )

Cacheiro P, Smedley D ( 2023 ) . Essential genes: a cross-species perspective . Mammalian Genome vol. 34 , ( 3 ) 357 - 363 .

Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ et al. ( 2023 ) . Genome-wide screening reveals the genetic basis of mammalian embryonic eye development . BMC Biology vol. 21 , ( 1 )

Stefancsik R, Balhoff JP, Balk MA, Ball R, Bello SM, Caron AR, Chessler E, de Souza V et al. ( 2023 ) . The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences . vol. 4 , ( 02-06 )

Chen Z, Tucci A, Cipriani V, Gustavsson EK, Ibañez K, Reynolds RH, Zhang D, Vestito L et al. ( 2023 ) . Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia . Brain vol. 146 , ( 7 ) 2869 - 2884 .

Aragam KG, Jiang T, Goel A, Kanoni S, Wolford BN, Atri DS, Weeks EM, Wang M et al. ( 2022 ) . Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants . Nature Genetics vol. 54 , ( 12 ) 1803 - 1815 .

Higgins K, Moore BA, Berberovic Z, Adissu HA, Eskandarian M, Flenniken AM, Shao A, Imai DM et al. ( 2022 ) . Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes . Scientific Reports vol. 12 , ( 1 )

Morsy H, Benkirane M, Cali E, Rocca C, Zhelcheska K, Cipriani V, Galanaki E, Maroofian R et al. ( 2022 ) . Expanding SPTAN1 monoallelic variant associated disorders: From epileptic encephalopathy to pure spastic paraplegia and ataxia . Genetics in Medicine vol. 25 , ( 1 ) 76 - 89 .

Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, Cacheiro P, Frost A et al. ( 2022 ) . The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease . Nucleic Acids Research vol. 51 , ( D1 ) d1038 - d1045 .

Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LMJ, Muñoz-Fuentes V, Hsu C-W, Van den Veyver IB et al. ( 2022 ) . Mendelian gene identification through mouse embryo viability screening . Genome Medicine vol. 14 , ( 1 )

Moreno-Ruiz N, Lao O, Aróstegui JI, Laayouni H, Casals F ( 2022 ) . Assessing the digenic model in rare disorders using population sequencing data . European Journal of Human Genetics vol. 30 , ( 12 ) 1439 - 1443 .

Park J, Tucci A, Cipriani V, Demidov G, Rocca C, Senderek J, Butryn M, Velic A et al. ( 2022 ) . Heterozygous UCHL1 loss-of-function variants cause a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy . Genetics in Medicine vol. 24 , ( 10 ) 2079 - 2090 .

Kelly C, Szabo A, Pontikos N, Arno G, Robinson PN, Jacobsen JOB, Smedley D, Cipriani V ( 2022 ) . Phenotype-aware prioritisation of rare Mendelian disease variants . Trends in Genetics vol. 38 , ( 12 ) 1271 - 1283 .

Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U et al. ( 2022 ) . Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology . American Journal of Medical Genetics Part C Seminars in Medical Genetics vol. 190 , ( 2 ) 231 - 242 .

Gibson JT, Sadeghi-Alavijeh O, Gale DP, Rothe H, Savige J ( 2022 ) . Pathogenicity of missense variants affecting the collagen IV α5 carboxy non-collagenous domain in X-linked Alport syndrome . Scientific Reports vol. 12 , ( 1 )

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG et al. ( 2022 ) . The GA4GH Phenopacket schema defines a computable representation of clinical data . Nature Biotechnology vol. 40 , ( 6 ) 817 - 820 .

Chen Z, Cipriani V, Zhang D, Tucci A, Vestito L, Smedley D, Houlden H, Botia J et al. ( 2022 ) . 022  Functional genomics and transcriptomics further characterise and potentially improve diagnostic yield of hereditary ataxias . Journal of Neurology Neurosurgery & Psychiatry vol. 93 , ( 6 ) a107.3 - a1a108 .

Jacobsen JOB, Kelly C, Cipriani V, Robinson PN, Smedley D ( 2022 ) . Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases . Briefings in Bioinformatics vol. 23 , ( 5 )

Jayadev R, Morais MRPT, Ellingford JM, Srinivasan S, Naylor RW, Lawless C, Li AS, Ingham JF et al. ( 2022 ) . A basement membrane discovery pipeline uncovers network complexity, regulators, and human disease associations . Science Advances vol. 8 , ( 20 )

Seaby EG, Smedley D, Tavares ALT, Brittain H, van Jaarsveld RH, Baralle D, Rehm HL, O’Donnell-Luria A et al. ( 2022 ) . A gene-to-patient approach uplifts novel disease gene discovery and identifies 18 putative novel disease genes . Genetics in Medicine vol. 24 , ( 8 ) 1697 - 1707 .

Danis D, Jacobsen JOB, Balachandran P, Zhu Q, Yilmaz F, Reese J, Haimel M, Lyon GJ et al. ( 2022 ) . SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing . Genome Medicine vol. 14 , ( 1 )

Jacobsen JOB, Kelly C, Cipriani V, Consortium GER, Mungall CJ, Reese J, Danis D, Robinson PN et al. ( 2022 ) . Phenotype‐driven approaches to enhance variant prioritization and diagnosis of rare disease . Human Mutation vol. 43 , ( 8 ) 1071 - 1081 .

Spielmann N, Miller G, Oprea TI, Hsu C-W, Fobo G, Frishman G, Montrone C, Haseli Mashhadi H et al. ( 2022 ) . Publisher Correction: Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy . Nature Cardiovascular Research vol. 1 , ( 5 ) 529 - 531 .

Chin H-L, Gazzaz N, Huynh S, Handra I, Warnock L, Moller-Hansen A, Boerkoel P, Jacobsen JOB et al. ( 2022 ) . The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice . Genetics in Medicine vol. 24 , ( 7 ) 1512 - 1522 .

Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G et al. ( 2022 ) . Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy . npj Genomic Medicine vol. 7 , ( 1 )

Ibañez K, Polke J, Hagelstrom RT, Dolzhenko E, Pasko D, Thomas ERA, Daugherty LC, Kasperaviciute D et al. ( 2022 ) . Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study . The Lancet Neurology vol. 21 , ( 3 ) 234 - 245 .

Spielmann N, Miller G, Oprea TI, Hsu C-W, Fobo G, Frishman G, Montrone C, Haseli Mashhadi H et al. ( 2022 ) . Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy . Nature Cardiovascular Research vol. 1 , ( 2 ) 157 - 173 .

Gibson JT, Huang M, Shenelli Croos Dabrera M, Shukla K, Rothe H, Hilbert P, Deltas C, Storey H et al. ( 2022 ) . Genotype–phenotype correlations for COL4A3–COL4A5 variants resulting in Gly substitutions in Alport syndrome . Scientific Reports vol. 12 , ( 1 )

Laurie S, Piscia D, Matalonga L, Corvó A, Fernández‐Callejo M, Garcia‐Linares C, Hernandez‐Ferrer C, Luengo C et al. ( 2022 ) . The RD‐Connect Genome‐Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases . Human Mutation vol. 43 , ( 6 ) 717 - 733 .

Mitchison HM, Smedley D ( 2022 ) . Primary ciliary dyskinesia: a big data genomics approach . The Lancet Respiratory Medicine vol. 10 , ( 5 ) 423 - 425 .

Owen N, Toms M, Young RM, Eintracht J, Sarkar H, Brooks BP, Moosajee M, Consortium GER et al. ( 2022 ) . Identification of 4 novel human ocular coloboma genes ANK3, BMPR1B, PDGFRA, and CDH4 through evolutionary conserved vertebrate gene analysis . Genetics in Medicine vol. 24 , ( 5 ) 1073 - 1084 .

Bacq A, Roussel D, Bonduelle T, Zagaglia S, Maletic M, Ribierre T, Adle‐Biassette H, Marchal C et al. ( 2021 ) . Cardiac Investigations in Sudden Unexpected Death in DEPDC5‐Related Epilepsy . Annals of Neurology vol. 91 , ( 1 ) 101 - 116 .

Pilehvar MT, Bernard A, Smedley D, Collier N ( 2021 ) . PheneBank: a literature-based database of phenotypes . Bioinformatics vol. 38 , ( 4 ) 1179 - 1180 .

Smedley D, Smith KR, Martin AR, Thomas EA, McDonagh EM, Cipriani V, Ellingford JM, Arno G et al. ( 2021 ) . 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report . New England Journal of Medicine vol. 385 , ( 20 ) 1868 - 1880 .

Danis D, Jacobsen JOB, Carmody LC, Gargano MA, McMurry JA, Hegde A, Haendel MA, Valentini G et al. ( 2021 ) . Interpretable prioritization of splice variants in diagnostic next-generation sequencing . American Journal of Human Genetics vol. 108 , ( 11 )

Ocansey S, Pullen D, Atkinson P, Clarke A, Hadonou M, Crosby C, Short J, Lloyd IC et al. ( 2021 ) . Biallelic DNAJC3 variants in a neuroendocrine developmental disorder with insulin dysregulation . Clinical Dysmorphology vol. 31 , ( 1 ) 11 - 17 .

Konopka T, Vestito L, Smedley D ( 2021 ) . Dimensional reduction of phenotypes from 53 000 mouse models reveals a diverse landscape of gene function . Bioinformatics Advances vol. 1 , ( 1 )

Wotton JM, Peterson E, Flenniken AM, Bains RS, Veeraragavan S, Bower LR, Bubier JA, Parisien M et al. ( 2021 ) . Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen . Pain vol. 163 , ( 6 ) 1139 - 1157 .

Konopka T, Ng S, Smedley D ( 2021 ) . Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base . PLOS Computational Biology vol. 17 , ( 8 )

Silvennoinen K, Puvirajasinghe C, Hudgell K, Sidhu MK, Custodio HM, Ambrose JC, Arumugam P, Baple EL et al. ( 2021 ) . Late diagnoses of Dravet syndrome: How many individuals are we missing? . Epilepsia Open vol. 6 , ( 4 ) 770 - 776 .

Danis D, Jacobsen JOB, Carmody LC, Gargano MA, McMurry JA, Hegde A, Haendel MA, Valentini G et al. ( 2021 ) . Interpretable prioritization of splice variants in diagnostic next-generation sequencing . American Journal of Human Genetics vol. 108 , ( 9 ) 1564 - 1577 .

Cousin MA, Creighton BA, Breau KA, Spillmann RC, Torti E, Dontu S, Tripathi S, Ajit D et al. ( 2021 ) . Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome . Nature Genetics vol. 53 , ( 7 ) 1006 - 1021 .

Chopra M, McEntagart M, Clayton-Smith J, Platzer K, Shukla A, Girisha KM, Kaur A, Kaur P et al. ( 2021 ) . Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism . American Journal of Human Genetics vol. 108 , ( 6 ) 1138 - 1150 .

Zou X, Koh GCC, Nanda AS, Degasperi A, Urgo K, Roumeliotis TI, Agu CA, Badja C et al. ( 2021 ) . A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage . Nature Cancer vol. 2 , ( 6 ) 643 - 657 .

Jones CL, Degasperi A, Grandi V, Amarante TD, Mitchell TJ, Nik-Zainal S, Whittaker SJ ( 2021 ) . Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma . Scientific Reports vol. 11 , ( 1 )

Pagnamenta AT, Kaiyrzhanov R, Zou Y, Da'as SI, Maroofian R, Donkervoort S, Dominik N, Lauffer M et al. ( 2021 ) . An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy . Brain

Haselimashhadi H, Mason JC, Mallon A-M, Smedley D, Meehan TF, Parkinson H ( 2020 ) . OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data . PLOS ONE vol. 15 , ( 12 )

Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G et al. ( 2020 ) . The Human Phenotype Ontology in 2021 . Nucleic Acids Research vol. 49 , ( D1 ) d1207 - d1217 .

Poulter JA, Gravett MSC, Taylor RL, Fujinami K, De Zaeytijd J, Bellingham J, Rehman AU, Hayashi T et al. ( 2020 ) . New variants and in silico analyses in GRK1 associated Oguchi disease . Human Mutation vol. 42 , ( 2 ) 164 - 176 .

Dewan R, Chia R, Ding J, Hickman RA, Stein TD, Abramzon Y, Ahmed S, Sabir MS et al. ( 2020 ) . Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis . Neuron vol. 109 , ( 3 ) 448 - 460.e4 .

Parry DA, Martin CA, Greene P, Marsh JA, Ambrose JC, Arumugam P, Baple EL, Bleda M et al. ( 2020 ) . Heterozygous lamin B1 and lamin B2 variants cause primary microcephaly and define a novel laminopathy . Genetics in Medicine

Bourinaris T, Smedley D, Cipriani V, Sheikh I, Athanasiou-Fragkouli A, Chinnery P, Morris H, Real R et al. ( 2020 ) . Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project . European Journal of Human Genetics

Chen Z, Yan Yau W, Jaunmuktane Z, Tucci A, Sivakumar P, Gagliano Taliun SA, Turner C, Efthymiou S et al. ( 2020 ) . Neuronal intranuclear inclusion disease is genetically heterogeneous . Annals of Clinical and Translational Neurology Article acn3.51151 ,

Vig A, Poulter JA, Ottaviani D, Tavares E, Toropova K, Tracewska AM, Mollica A, Kang J et al. ( 2020 ) . DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration . Genetics in Medicine vol. 22 , ( 12 ) 2041 - 2051 .

Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL et al. ( 2020 ) . Interpretable Clinical Genomics with a Likelihood Ratio Paradigm . American Journal of Human Genetics vol. 107 , ( 3 ) 403 - 417 .

Wei W, Pagnamenta AT, Gleadall N, Sanchis-Juan A, Stephens J, Broxholme J, Tuna S, Odhams CA et al. ( 2020 ) . Author Correction: Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans . Nature Communications vol. 11 , ( 1 )

Turro E, Astle WJ, Megy K, Gräf S, Greene D, Shamardina O, Allen HL, Sanchis-Juan A et al. ( 2020 ) . Whole-genome sequencing of patients with rare diseases in a national health system . Nature vol. 583 , ( 7814 ) 96 - 102 .

Tolchin D, Yeager JP, Prasad P, Dorrani N, Russi AS, Martinez-Agosto JA, Haseeb A, Angelozzi M et al. ( 2020 ) . De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas . American Journal of Human Genetics vol. 106 , ( 6 ) 830 - 845 .

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 )

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 )

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 .

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+E. coli . Nature vol. 580 , ( 7802 ) 269 - 273 .

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 )

Konopka T, Smedley D ( 2020 ) . Incremental data integration for tracking genotype-disease associations . PLOS Computational Biology vol. 16 , ( 1 )

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 )

Hong Y, Nanthapisal S, Omoyinmi E, Olbrich P, Neth O, Speckmann C, Lucena JM, Gilmour K et al. ( 2019 ) . Secondary C1q Deficiency in Activated PI3Kδ Syndrome Type 2 . Frontiers in Immunology vol. 10 ,

Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T et al. ( 2019 ) . 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 .

Haselimashhadi H, Mason JC, Munoz-Fuentes V, López-Gómez F, Babalola K, Acar EF, Kumar V, White J et al. ( 2019 ) . Soft windowing application to improve analysis of high-throughput phenotyping data . Bioinformatics vol. 36 , ( 5 ) 1492 - 1500 .

Wheway G, Ambrose JC, Baple EL, Bleda M, Boardman-Pretty F, Boissiere JM, Boustred CR, Caulfield MJ et al. ( 2019 ) . Corrigendum: Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project . Frontiers in Genetics vol. 10 ,

Moore BA, Flenniken AM, Clary D, Moshiri AS, Nutter LMJ, Berberovic Z, Owen C, Newbigging S et al. ( 2019 ) . Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function . Scientific Reports vol. 9 , ( 1 )

Köhler S, Øien NC, Buske OJ, Groza T, Jacobsen JOB, McNamara C, Vasilevsky N, Carmody LC et al. ( 2019 ) . Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics . Current Protocols in Human Genetics vol. 103 , ( 1 )

Cacheiro P, Haendel MA, Smedley D ( 2019 ) . New models for human disease from the International Mouse Phenotyping Consortium . Mammalian Genome vol. 30 , ( 5-6 ) 143 - 150 .

Wheway G, Consortium GER, Mitchison HM, Ambrose JC, Baple EL, Bleda M, Boardman-Pretty F, Boissiere JM et al. ( 2019 ) . Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project . Frontiers in Genetics vol. 10 ,

Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L et al. ( 2019 ) . Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts . Communications Biology vol. 2 , ( 1 )

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 vol. 20 , ( 1 ) 135 - 136 .

Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L et al. ( 2018 ) . Identification of genes required for eye development by high-throughput screening of mouse knockouts . Communications Biology vol. 1 , ( 1 )

Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine J-P, Gargano M, Harris NL et al. ( 2018 ) . Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources . Nucleic Acids Research vol. 47 , ( D1 ) d1018 - d1027 .

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 .

Thomas ERA, Devereau A, Brittain H, Tucci A, Ryten M, Smedley D, Rendon A, Caulfield MJ et al. ( 2018 ) . Widespread uptake of the Human Phenotype Ontology (HPO) in the National Health Service (NHS) in England as part of the 100,000 Genomes Project . EUROPEAN JOURNAL OF HUMAN GENETICS . Conference: european society human genetics vol. 27 , 513 - 513 .

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 .

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 . The BMJ vol. 361 ,

Brown SDM, Holmes CC, Mallon A-M, Meehan TF, Smedley D, Wells S ( 2018 ) . High-throughput mouse phenomics for characterizing mammalian gene function . Nature Reviews Genetics vol. 19 , ( 6 ) 357 - 370 .

Muñoz‐Fuentes V, Meehan TF, Lloyd KK, Mallon A, Smedley D, Parkinson H ( 2018 ) . The IMPC: A Global Scientific Infrastructure for Understanding the Role of Genes in Complex Traits . The FASEB Journal vol. 32 , ( S1 ) 754.1 - 754.1 .

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 )

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 .

Jacobsen JOB, Smedley D, Robinson P ( 2017 ) . Exomiser and Genomiser . Computational Exome and Genome Analysis , Taylor & Francis

Kaloff C, Anastassiadis K, Ayadi A, Baldock R, Beig J, Birling M-C, Bradley A, Brown SDM et al. ( 2017 ) . Genome wide conditional mouse knockout resources . Drug Discovery Today Disease Models vol. 20 , 3 - 12 .

Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen C-K, 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 , ( 1 )

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 ,

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 .

Cipriani V, Pontikos N, Arno G, Webster AR, Moore AT, Carss KJ, Raymond LF, Danis D et al. ( 2017 ) . An Improved Bioinformatics Tool for Rare Disease Variant Prioritization: The Exomiser 9.0.1 in Clinical Practice . HUMAN HEREDITY . vol. 83 , 5 - 6 .

Jacobsen JOB, Smedley D, Robinson PN ( 2017 ) . Exomiser and genomiser . Computational Exome and Genome Analysis ,

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 .

Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM et al. ( 2016 ) . The Human Phenotype Ontology in 2017 . Nucleic Acids Research vol. 45 , ( D1 ) d865 - d876 .

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 ,

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 .

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 .

Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M et al. ( 2015 ) . Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency . Genetics in Medicine vol. 18 , ( 6 ) 608 - 617 .

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 ,

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 .

Ring N, Meehan TF, Blake A, Brown J, Chen C-K, 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 .

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 . Disease Models & Mechanisms vol. 8 , ( 11 ) 1467 - 1478 .

Smedley D, Robinson PN ( 2015 ) . Phenotype-driven strategies for exome prioritization of human Mendelian disease genes . Genome Medicine vol. 7 , ( 1 )

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 .

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 )

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 .

Papatheodorou I, Oellrich A, Smedley D ( 2015 ) . Linking gene expression to phenotypes via pathway information . Journal of Biomedical Semantics vol. 6 , ( 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 , ( 0 )

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 )

Consortium I ( 2014 ) . INFRAFRONTIER—providing mutant mouse resources as research tools for the international scientific community . Nucleic Acids Research vol. 43 , ( D1 ) d1171 - d1175 .

Smedley D, Kohler S, Bone W, Oellrich A, Jacobsen J, Sanger Mouse Genetics Project, Wang K, Mungall C et al. ( 2014 ) . Use of animal models for exome prioritization of rare disease genes . Orphanet Journal of Rare Diseases . vol. 9 ,

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 )

Ibn-Salem J, Köhler S, Love MI, Chung H-R, 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 )

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 .

Oellrich A, Jacobsen J, Papatheodorou I, Project TSMG, Smedley D ( 2014 ) . Using association rule mining to determine promising secondary phenotyping hypotheses . Bioinformatics vol. 30 , ( 12 ) i52 - i59 .

Oellrich A, Koehler S, Washington N, Sanger Mouse Genetic Project, Mungall C, Lewis S, Haendel M, Robinson PN et al. ( 2014 ) . The influence of disease categories on gene candidate predictions from model organism phenotypes . Journal of Biomedical Semantics vol. 5 , ( Suppl 1 )

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 , ( 1 )

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 , ( 0 )

Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, Brown DL et al. ( 2013 ) . The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data . Nucleic Acids Research vol. 42 , ( D1 ) d966 - d974 .

Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen C-K et al. ( 2013 ) . 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 ) d802 - d809 .

Robinson PN, Köhler S, Oellrich A, Project SMG, Wang K, Mungall CJ, Lewis SE, Washington N et al. ( 2013 ) . Improved exome prioritization of disease genes through cross-species phenotype comparison . Genome Research vol. 24 , ( 2 ) 340 - 348 .

Smedley D, Oellrich A, Köhler S, Ruef B, Project SMG, Westerfield M, Robinson P, Lewis S et al. ( 2013 ) . PhenoDigm: analyzing curated annotations to associate animal models with human diseases . Database vol. 2013 , ( 0 )

Chen C-K, 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 .

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 ,

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 . Disease Models & Mechanisms vol. 6 , ( 2 ) 358 - 372 .

Murray SA, Eppig JT, Smedley D, Simpson EM, Rosenthal N ( 2012 ) . Erratum to: Beyond knockouts: cre resources for conditional mutagenesis . Mammalian Genome vol. 23 , ( 11-12 ) 791 - 791 .

Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling M-C, 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 .

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 .

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 , ( 0 )

Chen C, Mungall CJ, Gkoutos GV, Doelken SC, Köhler 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 .

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 , ( 0 )

Oakley DJ, Iyer V, Skarnes WC, Smedley D ( 2011 ) . BioMart as an integration solution for the International Knockout Mouse Consortium . Database vol. 2011 , ( 0 )

Gaudet P, Bairoch A, Field D, Sansone S-A, Taylor C, Attwood TK, Bateman A, Blake JA et al. ( 2011 ) . Towards BioDBcore: a community-defined information specification for biological databases . Database vol. 2011 , ( 0 )

Smedley D, Salimova E, Rosenthal N ( 2010 ) . Cre recombinase resources for conditional mouse mutagenesis . Methods vol. 53 , ( 4 ) 411 - 416 .

Gaudet P, Bairoch A, Field D, Sansone S-A, Taylor C, Attwood TK, Bateman A, Blake JA et al. ( 2010 ) . Towards BioDBcore: a community-defined information specification for biological databases . Nucleic Acids Research vol. 39 , ( suppl_1 ) d7 - d10 .

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 .

Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT et al. ( 2010 ) . 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 ) d849 - d855 .

Smedley D, Schofield P, Chen C-K, 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 vol. 2010 , ( 0 )

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 vol. 2010 , ( 0 )

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 )

Swertz MA, van der Velde KJ, 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 )

Gruenberger M, Alberts R, Smedley D, Swertz M, Schofield P, The CASIMIR consortium, 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 , ( 1 )

Smedley D, Kasprzyk A ( 2009 ) . Database Management . In Silico Technologies in Drug Target Identification and Validation , vol. 20060772 , Taylor & Francis

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 ) d557 - d562 .

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 , ( 0 )

Wilkinson P, Sengerova J, Matteoni R, Chen C-K, 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 ) d570 - d576 .

Smedley DP, Armstrong G, Ellar DJ ( 2009 ) . Channel activity caused by a Bacillus thuringiensis δ-endotoxin preparation depends on the method of activation . Molecular Membrane Biology vol. 14 , ( 1 ) 13 - 18 .

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 ) w23 - w27 .

Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A ( 2009 ) . BioMart – biological queries made easy . BMC Genomics vol. 10 , ( 1 )

Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y et al. ( 2008 ) . Ensembl 2009 . Nucleic Acids Research vol. 37 , ( suppl_1 ) d690 - d697 .

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 . Conference: 2008 8th IEEE International Conference on BioInformatics and BioEngineering1 - 6 .

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 . Conference: 2008 8th IEEE International Conference on BioInformatics and BioEngineering1 - 7 .

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 .

Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G et al. ( 2007 ) . Ensembl 2008 . Nucleic Acids Research vol. 36 , ( suppl_1 ) d707 - d714 .

Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G et al. ( 2006 ) . Ensembl 2007 . Nucleic Acids Research vol. 35 , ( suppl_1 ) d610 - d617 .

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 , ( suppl_1 ) d556 - d561 .

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 , ( suppl_1 ) d447 - d453 .

( 2004 ) . Finishing the euchromatic sequence of the human genome . Nature vol. 431 , ( 7011 ) 931 - 945 .

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 .

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 .

Kasprzyk 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 ( 2004 ) . Ensembl 2004 . Nucleic Acids Research vol. 32 , ( 90001 ) 468d - 4470 .

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 .

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 , ( 6a ) 1222 - 1230 .

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 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, Heatht 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 .

Lu Y, 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 . The Journal of Pathology vol. 187 , ( 4 ) 490 - 496 .

Smedley D, Hamoudi R, Lu Y-J, Cooper C, Shipley J ( 1999 ) . Cloning and Mapping of Members of the MYM Family . Genomics vol. 60 , ( 2 ) 244 - 247 .

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, 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 .

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 .

Clark J, Lu Y-J, Sidhar SK, Parker C, Gill S, Smedley D, Hamoudi R, Linehan WM et al. ( 1997 ) . Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma . Oncogene vol. 15 , ( 18 ) 2233 - 2239 .

Smedley DP, Ellar DJ ( 1996 ) . Mutagenesis of three surface-exposed loops of a Bacillus thuringiensis insecticidal toxin reveals residues important for toxicity, receptor recognition and possibly membrane insertion . Microbiology vol. 142 , ( 7 ) 1617 - 1624 .