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Professor Damian Smedley

Damian

Professor of Computational Genomics

Centre: Clinical Pharmacology and Precision Medicine

Email: d.smedley@qmul.ac.uk
Website: https://whri-phenogenomics.github.io/index.html

Profile

Professor Smedley’s research focusses on utilising clinical and model organism phenotype data to better understand human disease.

As a principal investigator for the International Mouse Phenotyping Consortium (IMPC), his team analyses the genotype to phenotype associations emerging from this comprehensive effort to produce the first catalogue of mammalian gene function by knocking out and systematically phenotyping every protein-coding gene in the mouse. A similar approach is taken in human cellular systems as a PI in the Molecular phenotypes of null alleles in cells (MorPhic) project. Utilising phenotype comparison methods developed with his co-PIs in the Monarch Initiative, his team is able to automatically identify new animal models of known disease genes as well as suggest new candidates for diseases where the causative variants have not yet been identified in human. 

This work is extended upon in the Exomiser software package, also developed in conjunction with his collaborators in the Monarch Initiative. Exomiser automates the filtering and prioritisation of coding and non-coding variants called from whole exome or genome sequencing of rare disease families using novel methodologies to prioritise the genes based on the similarity of the patient’s phenotypes to reference knowledge of genotype to phenotype associations from human disease and animal models. This software is widely used by academic researchers, diagnostic laboratories, commercial offering and in large-scale disease sequencing projects such as the US Undiagnosed Disease Network, the UK’s 100,000 Genomes Project as well as being a key component of the ISO-accredited interpretation pipeline for the NHS Genomic Medicine Service.

The team is contributing to a better understanding of the role of missense variants and post-translational modifications in rare disease as part of the MRC-funded human functional genomics initiative. Finally, as part of the Horizon Europe funded NextGen grant the team investigates federated machine learning approaches on multiomics data.

Research

Group members

Julius Jacobsen, Pilar Cacheiro, Valentina Cipriani, Letizia Vestito, Carlo Kroll, Yasemin Bridges, Gabriel Marengo, Diego Pava, Marta Delfino, Krishna Amin, Emma Magavern.

Summary 

Professor Smedley’s research focusses on utilising clinical and model organism phenotype data to better understand human disease.

As a principal investigator for the International Mouse Phenotyping Consortium (IMPC), his team analyses the genotype to phenotype associations emerging from this comprehensive effort to produce the first catalogue of mammalian gene function by knocking out and systematically phenotyping every protein-coding gene in the mouse. Utilising phenotype comparison methods developed with his co-PIs in the Monarch Initiative, his team is able to automatically identify new animal models of known disease genes as well as suggest new candidates for diseases where the causative variants have not yet been identified in human. 

This work is extended upon in the Exomiser software package, also developed in conjunction with his collaborators in the Monarch Initiative. Exomiser automates the filtering and prioritisation of coding and non-coding variants called from whole exome or genome sequencing of rare disease families using novel methodologies to prioritise the genes based on the similarity of the patient’s phenotypes to reference knowledge of genotype to phenotype associations from human disease and animal models. This software is widely used by academic researchers, diagnostic laboratories, commercial offering and in large-scale disease sequencing projects such as the US Undiagnosed Disease Network, the UK’s 100,000 Genomes Project as well as being a key component of the ISO-accredited interpretation pipeline for the NHS Genomic Medicine Service.

Publications

  • Vestito L, Cipriani V, Smedley D (2025). 3 Computational genomics and bioinformatics. nameOfConference


    QMRO: qmroHref
  • Danis D, Bamshad MJ, Bridges Y et al. (2025). A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery. nameOfConference


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  • Beckwith MA, Danis D, Bridges Y et al. (2025). Leveraging clinical intuition to improve accuracy of phenotype-driven prioritization. nameOfConference


  • Elrick H, Peterson KA, Willis BJ et al. (publicationYear). Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines. nameOfConference


  • Cacheiro P, Pava D, Parkinson H et al. (2024). Computational identification of disease models through cross-species phenotype comparison. nameOfConference


  • Benkirane M, Bonhomme M, Morsy H et al. (2024). De novo and inherited monoallelic variants in TUBA4A cause ataxia and spasticity. nameOfConference


  • Bridges Y, de Souza V, Cortes KG et al. (publicationYear). Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. nameOfConference


  • Danis D, Bamshad MJ, Bridges Y et al. (publicationYear). A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery. nameOfConference


  • Stenton SL, O’Leary MC, Lemire G et al. (publicationYear). Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project. nameOfConference


  • Cacheiro P, Lawson S, Van den Veyver IB et al. (2024). Lethal phenotypes in Mendelian disorders. nameOfConference


  • Duyzend MH, Cacheiro P, Jacobsen JOB et al. (2024). Improving prenatal diagnosis through standards and aggregation. nameOfConference


  • Putman TE, Schaper K, Matentzoglu N et al. (2024). The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. nameOfConference


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  • Gargano MA, Matentzoglu N, Coleman B et al. (2024). The Human Phenotype Ontology in 2024: phenotypes around the world. nameOfConference


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  • Magavern EF, Jacobs B, Warren H et al. (2023). CYP2C19 genotype prevalence and association with recurrent myocardial infarction in British-South Asians treated with clopidogrel. nameOfConference


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  • Magavern EF, Van Heel DA, Smedley D et al. (2023). SLCO1B1*5 is protective against non-senile cataracts in cohort prescribed statins: analysis in a British-South Asian cohort. nameOfConference


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  • Jeffries L, Mis EK, McWalter K et al. (2024). Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections. nameOfConference


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  • Magavern EF, Team GHR, Smedley D et al. (2023). Factor V Leiden, estrogen, and multimorbidity association with venous thromboembolism in a British-South Asian cohort. nameOfConference


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  • Park J, Tucci A, Cipriani V et al. (2023). Heterozygous UCHL1 loss-of-function variants cause a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy. nameOfConference


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  • Magavern EF, Jacobs B, Warren H et al. (2023). CYP2C19 Genotype Prevalence and Association With Recurrent Myocardial Infarction in British–South Asians Treated With Clopidogrel. nameOfConference


  • Magavern EF, van Heel DA, Team GHR et al. (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. nameOfConference


  • Stenton SL, O’Leary M, Lemire G et al. (publicationYear). Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project. nameOfConference


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  • Dominik N, Magri S, Currò R et al. (2023). Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis. nameOfConference


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  • Vetro A, Pelorosso C, Balestrini S et al. (2023). Stretch-activated ion channel TMEM63B associates with developmental and epileptic encephalopathies and progressive neurodegeneration. nameOfConference


  • Pavinato L, Stanic J, Barzasi M et al. (2023). Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder. nameOfConference


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  • Crane-Smith Z, De Castro SCP, Nikolopoulou E 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. nameOfConference


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  • Magavern EF, van Heel DA, Smedley D et al. (2023). SLCO1B1*5 is protective against non-senile cataracts in cohort prescribed statins: analysis in a British-South Asian cohort. nameOfConference


  • Stefancsik R, Balhoff JP, Balk MA et al. (2023). The Ontology of Biological Attributes (OBA)—computational traits for the life sciences. nameOfConference


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  • Cacheiro P, Spielmann N, Mashhadi HH et al. (2023). Knockout mice represent an important tool for the multisystemic study of human monogenic heart disease. nameOfConference


  • Cacheiro P, Smedley D (2023). Essential genes: a cross-species perspective. nameOfConference


  • Chee JM, Lanoue L, Clary D et al. (publicationYear). Genome-wide screening reveals the genetic basis of mammalian embryonic eye development. nameOfConference


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  • Stefancsik R, Balhoff JP, Balk MA et al. (publicationYear). The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences. nameOfConference


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  • Chen Z, Tucci A, Cipriani V et al. (2023). Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia. nameOfConference


  • Aragam KG, Jiang T, Goel A et al. (2022). Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants. nameOfConference


  • Higgins K, Moore BA, Berberovic Z et al. (publicationYear). Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes. nameOfConference


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  • Morsy H, Benkirane M, Cali E et al. (2023). Expanding SPTAN1 monoallelic variant associated disorders: From epileptic encephalopathy to pure spastic paraplegia and ataxia. nameOfConference


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  • Groza T, Gomez FL, Mashhadi HH et al. (2023). The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. nameOfConference


  • Cacheiro P, Westerberg CH, Mager J et al. (publicationYear). Mendelian gene identification through mouse embryo viability screening. nameOfConference


  • Moreno-Ruiz N, Lao O, Aróstegui JI et al. (2022). Assessing the digenic model in rare disorders using population sequencing data. nameOfConference


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  • Park J, Tucci A, Cipriani V et al. (2022). Heterozygous UCHL1 loss-of-function variants cause a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy. nameOfConference


  • Kelly C, Szabo A, Pontikos N et al. (2022). Phenotype-aware prioritisation of rare Mendelian disease variants. nameOfConference


  • Dhombres F, Morgan P, Chaudhari BP et al. (2022). Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. nameOfConference


  • Gibson JT, Sadeghi-Alavijeh O, Gale DP et al. (publicationYear). Pathogenicity of missense variants affecting the collagen IV α5 carboxy non-collagenous domain in X-linked Alport syndrome. nameOfConference


  • Jacobsen JOB, Baudis M, Baynam GS et al. (2022). The GA4GH Phenopacket schema defines a computable representation of clinical data. nameOfConference


    QMRO: qmroHref
  • Chen Z, Cipriani V, Zhang D et al. (2022). 022  Functional genomics and transcriptomics further characterise and potentially improve diagnostic yield of hereditary ataxias. nameOfConference


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  • Jacobsen JOB, Kelly C, Cipriani V et al. (2022). Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. nameOfConference


  • Jayadev R, Morais MRPT, Ellingford JM et al. (2022). A basement membrane discovery pipeline uncovers network complexity, regulators, and human disease associations. nameOfConference


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  • Seaby EG, Smedley D, Tavares ALT et al. (2022). A gene-to-patient approach uplifts novel disease gene discovery and identifies 18 putative novel disease genes. nameOfConference


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  • Danis D, Jacobsen JOB, Balachandran P et al. (2022). SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing. nameOfConference


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  • Jacobsen JOB, Kelly C, Cipriani V et al. (2022). Phenotype‐driven approaches to enhance variant prioritization and diagnosis of rare disease. nameOfConference


  • Spielmann N, Miller G, Oprea TI et al. (2022). Publisher Correction: Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy. nameOfConference


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  • Chin H-L, Gazzaz N, Huynh S et al. (2022). The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice. nameOfConference


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  • Lesurf R, Said A, Akinrinade O et al. (publicationYear). Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. nameOfConference


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  • Ibañez K, Polke J, Hagelstrom RT 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. nameOfConference


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  • Spielmann N, Miller G, Oprea TI et al. (2022). Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy. nameOfConference


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  • Gibson JT, Huang M, Shenelli Croos Dabrera M et al. (publicationYear). Genotype–phenotype correlations for COL4A3–COL4A5 variants resulting in Gly substitutions in Alport syndrome. nameOfConference


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  • Laurie S, Piscia D, Matalonga L et al. (2022). The RD‐Connect Genome‐Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases. nameOfConference


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  • Mitchison HM, Smedley D (2022). Primary ciliary dyskinesia: a big data genomics approach. nameOfConference


  • Owen N, Toms M, Young RM et al. (2022). Identification of 4 novel human ocular coloboma genes ANK3, BMPR1B, PDGFRA, and CDH4 through evolutionary conserved vertebrate gene analysis. nameOfConference


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  • Bacq A, Roussel D, Bonduelle T et al. (2022). Cardiac Investigations in Sudden Unexpected Death in DEPDC5‐Related Epilepsy. nameOfConference


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  • Pilehvar MT, Bernard A, Smedley D et al. (2022). PheneBank: a literature-based database of phenotypes. nameOfConference


  • Smedley D, Smith KR, Martin AR et al. (2021). 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report. nameOfConference


  • Danis D, Jacobsen JOB, Carmody LC et al. (2021). Interpretable prioritization of splice variants in diagnostic next-generation sequencing. nameOfConference


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  • Ocansey S, Pullen D, Atkinson P et al. (2022). Biallelic DNAJC3 variants in a neuroendocrine developmental disorder with insulin dysregulation. nameOfConference


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


  • Wotton JM, Peterson E, Flenniken AM et al. (2022). Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen. nameOfConference


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  • Konopka T, Ng S, Smedley D (publicationYear). Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base. nameOfConference


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  • Silvennoinen K, Puvirajasinghe C, Hudgell K et al. (2021). Late diagnoses of Dravet syndrome: How many individuals are we missing?. nameOfConference


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  • Danis D, Jacobsen JOB, Carmody LC et al. (2021). Interpretable prioritization of splice variants in diagnostic next-generation sequencing. nameOfConference


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  • Cousin MA, Creighton BA, Breau KA et al. (2021). Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. nameOfConference


  • Chopra M, McEntagart M, Clayton-Smith J et al. (2021). Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism. nameOfConference


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  • Zou X, Koh GCC, Nanda AS et al. (2021). A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. nameOfConference


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  • Jones CL, Degasperi A, Grandi V et al. (publicationYear). Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma. nameOfConference


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  • Pagnamenta AT, Kaiyrzhanov R, Zou Y et al. (2021). An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy. nameOfConference


  • Haselimashhadi H, Mason JC, Mallon A-M et al. (publicationYear). OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data. nameOfConference


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  • Köhler S, Gargano M, Matentzoglu N et al. (2021). The Human Phenotype Ontology in 2021. nameOfConference


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  • Poulter JA, Gravett MSC, Taylor RL et al. (2021). New variants and in silico analyses in GRK1 associated Oguchi disease. nameOfConference


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  • Dewan R, Chia R, Ding J et al. (2021). Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. nameOfConference


  • Parry DA, Martin CA, Greene P et al. (2020). Heterozygous lamin B1 and lamin B2 variants cause primary microcephaly and define a novel laminopathy. nameOfConference


  • Bourinaris T, Smedley D, Cipriani V et al. (publicationYear). Identification of UBAP1 mutations in juvenile hereditary spastic paraplegia in the 100,000 Genomes Project. nameOfConference


  • Chen Z, Yan Yau W, Jaunmuktane Z et al. (publicationYear). Neuronal intranuclear inclusion disease is genetically heterogeneous. nameOfConference


  • Vig A, Poulter JA, Ottaviani D et al. (2020). DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration. nameOfConference


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  • Robinson PN, Ravanmehr V, Jacobsen JOB et al. (2020). Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. nameOfConference


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  • Wei W, Pagnamenta AT, Gleadall N et al. (publicationYear). Author Correction: Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans. nameOfConference


  • Turro E, Astle WJ, Megy K et al. (2020). Whole-genome sequencing of patients with rare diseases in a national health system. nameOfConference


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  • Tolchin D, Yeager JP, Prasad P et al. (2020). De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas. nameOfConference


  • Cipriani V, Pontikos N, Arno G et al. (publicationYear). An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data. nameOfConference


  • Wei W, Pagnamenta AT, Gleadall N et al. (publicationYear). Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans. nameOfConference


  • Freeman TM, Wang D, Harris J et al. (2020). Genomic loci susceptible to systematic sequencing bias in clinical whole genomes. nameOfConference


  • Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A et al. (2020). Mutational signature in colorectal cancer caused by genotoxic pks+E. coli. nameOfConference


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  • Lloyd KCK, Adams DJ, Baynam G et al. (2020). The Deep Genome Project. nameOfConference


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  • Cacheiro P, Muñoz-Fuentes V, Murray SA et al. (2020). Human and mouse essentiality screens as a resource for disease gene discovery. nameOfConference


  • Konopka T, Smedley D (publicationYear). Incremental data integration for tracking genotype-disease associations. nameOfConference


  • Zhang T, Xie P, Dong Y et al. (publicationYear). High-throughput discovery of genetic determinants of circadian misalignment. nameOfConference


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  • Hong Y, Nanthapisal S, Omoyinmi E et al. (publicationYear). Secondary C1q Deficiency in Activated PI3Kδ Syndrome Type 2. nameOfConference


  • Shefchek KA, Harris NL, Gargano M et al. (2020). The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. nameOfConference


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  • Martin AR, Williams E, Foulger RE et al. (2019). PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. nameOfConference


  • Haselimashhadi H, Mason JC, Munoz-Fuentes V et al. (2020). Soft windowing application to improve analysis of high-throughput phenotyping data. nameOfConference


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  • Wheway G, Ambrose JC, Baple EL et al. (publicationYear). Corrigendum: Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project. nameOfConference


  • Moore BA, Flenniken AM, Clary D et al. (publicationYear). Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function. nameOfConference


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  • Köhler S, Øien NC, Buske OJ et al. (2019). Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. nameOfConference


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  • Cacheiro P, Haendel MA, Smedley D (2019). New models for human disease from the International Mouse Phenotyping Consortium. nameOfConference


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  • Wheway G, Consortium GER, Mitchison HM et al. (publicationYear). Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project. nameOfConference


  • Moore BA, Leonard BC, Sebbag L et al. (publicationYear). Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts. nameOfConference


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  • Muñoz-Fuentes V, Cacheiro P, Meehan TF et al. (2019). Correction to: The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. nameOfConference


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  • Moore BA, Leonard BC, Sebbag L et al. (publicationYear). Identification of genes required for eye development by high-throughput screening of mouse knockouts. nameOfConference


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  • Köhler S, Carmody L, Vasilevsky N et al. (2019). Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. nameOfConference


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  • Arachchi H, Wojcik MH, Weisburd B et al. (2018). matchbox: An open‐source tool for patient matching via the Matchmaker Exchange. nameOfConference


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  • Thomas ERA, Devereau A, Brittain H 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 society human genetics

    DOI: doi

  • Muñoz-Fuentes V, Cacheiro P, Meehan TF et al. (2018). The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. nameOfConference


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  • Turnbull C, Scott RH, Thomas E et al. (publicationYear). The 100 000 Genomes Project: bringing whole genome sequencing to the NHS. nameOfConference


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  • Brown SDM, Holmes CC, Mallon A-M et al. (2018). High-throughput mouse phenomics for characterizing mammalian gene function. nameOfConference


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  • Muñoz‐Fuentes V, Meehan TF, Lloyd KK et al. (2018). The IMPC: A Global Scientific Infrastructure for Understanding the Role of Genes in Complex Traits. nameOfConference


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  • Rozman J, Rathkolb B, Oestereicher MA et al. (publicationYear). Identification of genetic elements in metabolism by high-throughput mouse phenotyping. nameOfConference


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  • Bowl MR, Simon MM, Ingham NJ et al. (2017). A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.. nameOfConference


  • Jacobsen JOB, Smedley D, Robinson P (publicationYear). Exomiser and Genomiser. nameOfConference


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  • Kaloff C, Anastassiadis K, Ayadi A et al. (2016). Genome wide conditional mouse knockout resources. nameOfConference


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  • Meehan TF, Conte N, West DB et al. (2017). Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. nameOfConference


  • Karp NA, Mason J, Beaudet AL et al. (publicationYear). Prevalence of sexual dimorphism in mammalian phenotypic traits. nameOfConference


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  • Gall T, Valkanas E, Bello C et al. (publicationYear). Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. nameOfConference


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  • Taylor RL, Arno G, Poulter JA et al. (2017). Association of Steroid 5α-Reductase Type 3 Congenital Disorder of Glycosylation With Early-Onset Retinal Dystrophy. nameOfConference


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  • Cipriani V, Pontikos N, Arno G et al. (2017). An Improved Bioinformatics Tool for Rare Disease Variant Prioritization: The Exomiser 9.0.1 in Clinical Practice. nameOfConference

    DOI: doi

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  • Jacobsen JOB, Smedley D, Robinson PN (2017). Exomiser and genomiser. nameOfConference


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  • Mungall CJ, McMurry JA, Köhler S et al. (2017). The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.. nameOfConference


  • Köhler S, Vasilevsky NA, Engelstad M et al. (2017). The Human Phenotype Ontology in 2017. nameOfConference


  • Links AE, Draper D, Lee E et al. (publicationYear). Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience. nameOfConference


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  • Smedley D, Schubach M, Jacobsen JOB et al. (2016). A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. nameOfConference


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  • McMurry JA, Köhler S, Washington NL et al. (2016). Navigating the Phenotype Frontier: The Monarch Initiative. nameOfConference


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  • Haendel M, Papatheodorou I, Oellrich A et al. (2016). Tools for exploring mouse models of human disease. nameOfConference


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  • Bone WP, Washington NL, Buske OJ et al. (2016). Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. nameOfConference


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  • Smedley D, Jacobsen JOB, Jäger M et al. (2015). Next-generation diagnostics and disease-gene discovery with the Exomiser. nameOfConference


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  • Collier N, Groza T, Smedley D et al. (2015). PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. nameOfConference


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  • Mungall CJ, Washington NL, Nguyen-Xuan J et al. (2015). Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. nameOfConference


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  • Ring N, Meehan TF, Blake A et al. (2015). A mouse informatics platform for phenotypic and translational discovery. nameOfConference


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  • Tuck E, Estabel J, Oellrich A et al. (2015). A gene expression resource generated by genome-wide lacZ profiling in the mouse. nameOfConference


    QMRO: qmroHref
  • Smedley D, Robinson PN (publicationYear). Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. nameOfConference


    QMRO: qmroHref
  • Haendel MA, Vasilevsky N, Brush M et al. (2015). Disease insights through cross-species phenotype comparisons. nameOfConference


    QMRO: qmroHref
  • Karp NA, Meehan TF, Morgan H et al. (publicationYear). Applying the ARRIVE Guidelines to an In Vivo Database. nameOfConference


    QMRO: qmroHref
  • Smedley D, Haider S, Durinck S et al. (2015). The BioMart community portal: an innovative alternative to large, centralized data repositories. nameOfConference


    QMRO: qmroHref
  • Papatheodorou I, Oellrich A, Smedley D (2015). Linking gene expression to phenotypes via pathway information. nameOfConference


    QMRO: qmroHref
  • Groza T, Köhler S, Doelken S et al. (2015). Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora. nameOfConference


    QMRO: qmroHref
  • Oellrich A, Collier N, Smedley D et al. (publicationYear). Generation of Silver Standard Concept Annotations from Biomedical Texts with Special Relevance to Phenotypes. nameOfConference


    QMRO: qmroHref
  • Consortium I (2015). INFRAFRONTIER—providing mutant mouse resources as research tools for the international scientific community. nameOfConference


    QMRO: qmroHref
  • Smedley D, Kohler S, Bone W et al. (2014). Use of animal models for exome prioritization of rare disease genes. nameOfConference


    QMRO: qmroHref
  • Köhler S, Schoeneberg U, Czeschik JC et al. (2014). Clinical interpretation of CNVs with cross-species phenotype data. nameOfConference


    QMRO: qmroHref
  • Ibn-Salem J, Köhler S, Love MI et al. (2014). Deletions of chromosomal regulatory boundaries are associated with congenital disease. nameOfConference


    QMRO: qmroHref
  • Zemojtel T, Köhler S, Mackenroth L et al. (2014). Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. nameOfConference


    QMRO: qmroHref
  • Smedley D, Köhler S, Czeschik JC et al. (2014). Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases. nameOfConference


    QMRO: qmroHref
  • Oellrich A, Jacobsen J, Papatheodorou I et al. (2014). Using association rule mining to determine promising secondary phenotyping hypotheses. nameOfConference


    QMRO: qmroHref
  • Oellrich A, Koehler S, Washington N et al. (2014). The influence of disease categories on gene candidate predictions from model organism phenotypes. nameOfConference


    QMRO: qmroHref
  • Liakath-Ali K, Vancollie VE, Heath E et al. (publicationYear). Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen. nameOfConference


    QMRO: qmroHref
  • Jäger M, Wang K, Bauer S et al. (2014). Jannovar: A Java Library for Exome Annotation. nameOfConference


    QMRO: qmroHref
  • Oellrich A, Smedley D (2014). Linking tissues to phenotypes using gene expression profiles. nameOfConference


    QMRO: qmroHref
  • Köhler S, Doelken SC, Mungall CJ et al. (2014). The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. nameOfConference


    QMRO: qmroHref
  • Koscielny G, Yaikhom G, Iyer V et al. (2014). The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. nameOfConference


    QMRO: qmroHref
  • Robinson PN, Köhler S, Oellrich A et al. (2014). Improved exome prioritization of disease genes through cross-species phenotype comparison. nameOfConference


    QMRO: qmroHref
  • Smedley D, Oellrich A, Köhler S et al. (2013). PhenoDigm: analyzing curated annotations to associate animal models with human diseases. nameOfConference


    QMRO: qmroHref
  • Chen C-K, Symmons O, Uslu VV et al. (2013). TRACER: a resource to study the regulatory architecture of the mouse genome. nameOfConference


    QMRO: qmroHref
  • Oetting WS, Robinson PN, Greenblatt MS et al. (2013). Getting Ready for the Human Phenome Project: The 2012 Forum of the Human Variome Project. nameOfConference


    QMRO: qmroHref
  • Köhler S, Doelken SC, Ruef BJ et al. (2013). Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. nameOfConference


    QMRO: qmroHref
  • Doelken SC, Köhler S, Mungall CJ 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. nameOfConference


    QMRO: qmroHref
  • Murray SA, Eppig JT, Smedley D et al. (2012). Erratum to: Beyond knockouts: cre resources for conditional mutagenesis. nameOfConference


    QMRO: qmroHref
  • Bradley A, Anastassiadis K, Ayadi A et al. (2012). The mammalian gene function resource: the international knockout mouse consortium. nameOfConference


    QMRO: qmroHref
  • Murray SA, Eppig JT, Smedley D et al. (2012). Beyond knockouts: cre resources for conditional mutagenesis. nameOfConference


    QMRO: qmroHref
  • Chandras C, Zouberakis M, Salimova E et al. (2012). CreZOO—the European virtual repository of Cre and other targeted conditional driver strains. nameOfConference


    QMRO: qmroHref
  • Chen C, Mungall CJ, Gkoutos GV et al. (2012). MouseFinder: Candidate disease genes from mouse phenotype data. nameOfConference


    QMRO: qmroHref
  • Guberman JM, Ai J, Arnaiz O et al. (2011). BioMart Central Portal: an open database network for the biological community. nameOfConference


    QMRO: qmroHref
  • Oakley DJ, Iyer V, Skarnes WC et al. (2011). BioMart as an integration solution for the International Knockout Mouse Consortium. nameOfConference


    QMRO: qmroHref
  • Gaudet P, Bairoch A, Field D et al. (2011). Towards BioDBcore: a community-defined information specification for biological databases. nameOfConference


    QMRO: qmroHref
  • Smedley D, Salimova E, Rosenthal N (2011). Cre recombinase resources for conditional mouse mutagenesis. nameOfConference


    QMRO: qmroHref
  • Gaudet P, Bairoch A, Field D et al. (2011). Towards BioDBcore: a community-defined information specification for biological databases. nameOfConference


    QMRO: qmroHref
  • Schofield PN, Eppig J, Huala E et al. (2010). Sustaining the Data and Bioresource Commons. nameOfConference


    QMRO: qmroHref
  • Ringwald M, Iyer V, Mason JC et al. (2011). The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. nameOfConference


    QMRO: qmroHref
  • Smedley D, Schofield P, Chen C-K et al. (2010). Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. nameOfConference


    QMRO: qmroHref
  • Zouberakis M, Chandras C, Swertz M et al. (2010). Mouse Resource Browser—a database of mouse databases. nameOfConference


    QMRO: qmroHref
  • Chen Y, Cunningham F, Rios D et al. (2010). Ensembl variation resources. nameOfConference


    QMRO: qmroHref
  • Swertz MA, van der Velde KJ, Tesson BM et al. (2010). XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. nameOfConference


    QMRO: qmroHref
  • Gruenberger M, Alberts R, Smedley D et al. (2010). Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics. nameOfConference


    QMRO: qmroHref
  • Smedley D, Kasprzyk A (2006). Database Management. nameOfConference


    QMRO: qmroHref
  • Flicek P, Aken BL, Ballester B et al. (2010). Ensembl's 10th year. nameOfConference


    QMRO: qmroHref
  • Chandras C, Weaver T, Zouberakis M et al. (2009). Models for financial sustainability of biological databases and resources. nameOfConference


    QMRO: qmroHref
  • Wilkinson P, Sengerova J, Matteoni R et al. (2010). EMMA—mouse mutant resources for the international scientific community. nameOfConference


    QMRO: qmroHref
  • Smedley DP, Armstrong G, Ellar DJ (1997). Channel activity caused by a Bacillus thuringiensis δ-endotoxin preparation depends on the method of activation. nameOfConference


    QMRO: qmroHref
  • Haider S, Ballester B, Smedley D et al. (2009). BioMart Central Portal—unified access to biological data. nameOfConference


    QMRO: qmroHref
  • Smedley D, Haider S, Ballester B et al. (2009). BioMart – biological queries made easy. nameOfConference


    QMRO: qmroHref
  • Hubbard TJP, Aken BL, Ayling S et al. (2009). Ensembl 2009. nameOfConference


    QMRO: qmroHref
  • Hancock JM, Schofield PN, Chandras C et al. (2008). CASIMIR: Coordination and Sustainability of International Mouse Informatics Resources. 2008 8th IEEE International Conference on BioInformatics and BioEngineering


    QMRO: qmroHref
  • Swertz MA, Smedley D, Wolstencroft K et al. (2008). Towards dynamic database infrastructures for mouse genetics. 2008 8th IEEE International Conference on BioInformatics and BioEngineering


    QMRO: qmroHref
  • Smedley D, Swertz MA, Wolstencroft K et al. (2008). Solutions for data integration in functional genomics: a critical assessment and case study. nameOfConference


    QMRO: qmroHref
  • Flicek P, Aken BL, Beal K et al. (2008). Ensembl 2008. nameOfConference


    QMRO: qmroHref
  • Hubbard TJP, Aken BL, Beal K et al. (2007). Ensembl 2007. nameOfConference


    QMRO: qmroHref
  • Birney E, Andrews D, Caccamo M et al. (2006). Ensembl 2006. nameOfConference


    QMRO: qmroHref
  • Hubbard T, Andrews D, Caccamo M et al. (2004). Ensembl 2005. nameOfConference


    QMRO: qmroHref
  • Consortium IHGS (2004). Finishing the euchromatic sequence of the human genome. nameOfConference


    QMRO: qmroHref
  • Birney E, Andrews TD, Bevan P et al. (2004). An Overview of Ensembl. nameOfConference


    QMRO: qmroHref
  • Parkinson J, Charon C, Baker BS et al. (2004). Variation at the IRF2 Gene and Susceptibility to Psoriasis in Chromosome 4q-Linked Families. nameOfConference


    QMRO: qmroHref
  • Kasprzyk A, Keefe D, Smedley D et al. (2004). EnsMart: A Generic System for Fast and Flexible Access to Biological Data. nameOfConference


    QMRO: qmroHref
  • Birney E (2004). Ensembl 2004. nameOfConference


    QMRO: qmroHref
  • Hide W, Smedley D, McCarthy M et al. (2003). Application of eVOC: controlled vocabularies for unifying gene expression data. nameOfConference


    QMRO: qmroHref
  • McCarthy MI, Smedley D, Hide W (2003). New methods for finding disease-susceptibility genes: impact and potential. nameOfConference


    QMRO: qmroHref
  • Huntley D, Hummerich H, Smedley D et al. (2003). GANESH: Software for Customized Annotation of Genome Regions. nameOfConference


    QMRO: qmroHref
  • Kelso J, Visagie J, Theiler G et al. (2003). eVOC: A Controlled Vocabulary for Unifying Gene Expression Data. nameOfConference


    QMRO: qmroHref
  • HITMAN GA, McCarthy MI, Levy JC 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.. nameOfConference


    QMRO: qmroHref
  • HITMAN GA, Hattersley AT, Wiltshire S 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.. nameOfConference


    QMRO: qmroHref
  • Sorour A, Brito-Babapulle V, Smedley D et al. (2000). Unusual Breakpoint Distribution of 8p Abnormalities in T-Prolymphocytic Leukemia A Study with YACS Mapping to 8p11–p12. nameOfConference


    QMRO: qmroHref
  • Smedley D, Sidhar S, Birdsall S et al. (2000). Characterization of chromosome 1 abnormalities in malignant melanomas. nameOfConference


    QMRO: qmroHref
  • Smedley D, Demiroglu A, Abdul-Rauf M et al. (1999). ZNF198-FGFR1 Transforms Ba/F3 Cells to Growth Factor Independence and Results in High Level Tyrosine Phosphorylation of STATS 1 and 5. nameOfConference


    QMRO: qmroHref
  • Lu Y, Birdsall S, Summersgill B et al. (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. nameOfConference


    QMRO: qmroHref
  • Smedley D, Hamoudi R, Lu Y-J et al. (1999). Cloning and Mapping of Members of the MYM Family. nameOfConference


    QMRO: qmroHref
  • Kulkarni S, Reiter A, Smedley D et al. (1999). The Genomic Structure of ZNF198 and Location of Breakpoints in the t(8;13) Myeloproliferative Syndrome. nameOfConference


    QMRO: qmroHref
  • Smedley D, Somers G, Venter D et al. (1998). Characterization of a t(8;13)(p11;q11‐12) in an atypical myeloproliferative disorder. nameOfConference


    QMRO: qmroHref
  • Smedley D, Hamoudi R, Clark J 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. nameOfConference


    QMRO: qmroHref
  • Clark J, Lu Y-J, Sidhar SK et al. (1997). Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma. nameOfConference


    QMRO: qmroHref
  • 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. nameOfConference


    QMRO: qmroHref

Sponsors

Collaborators

Internal

External

  • Prof Peter Robinson (Berlin Institute of Health, Germany)
  • Dr. Chris Mungall (Lawrence Berkeley National Laboratory, USA)
  • Prof. Melissa Haendel (University of Colorado, USA)
  • Dr. Helen Parkinson (EBI, UK)
  • Dr. Matthew Child (Imperial College, UK)

News

100,000 Genomes Project paper publication press (Nov 2021):

Disclosures

No disclosures

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