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2024

Computational identification of disease models through cross-species phenotype comparison
Graphical Abstract: Cell
Cacheiro P, Pava D, Parkinson H, VanZanten M, Wilson R, Gusnes O, The International Mouse Phenotyping Consortium, Smedley D. Dis Model Mech. 2024 1Jun 1;17(6):dmm050604.

Lethal phenotypes in Mendelian disorders
Graphical Abstract: Cell
Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Genet Med. 2024 Apr 13:101141.

Improving prenatal diagnosis through standards and aggregation.
Graphical Abstract: Cell
Duyzend MH, Cacheiro P, Jacobsen JOB, Giordano J, Brand H, Wapner RJ, Talkowski, ME, Robinson, PN, Smedley D. Prenat Diagn. 2024 Apr;44(4):454-464.

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.
Graphical Abstract: Cell
Putman TE ... Jacobsen JOB ... Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC. Nucleic Acids Res. 2024 Jan 5;52(D1):D938-D949.

The Human Phenotype Ontology in 2024: phenotypes around the world.
Graphical Abstract: Cell
Gargano MA ... Jacobsen JOB ... Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlčková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinson PN. Nucleic Acids Res. 2024 Jan 5;52(D1):D1333-D1346.

2023

Factor V Leiden, estrogen, and multimorbidity association with venous thromboembolism in a British-South Asian cohort.
Graphical Abstract: Cell
Magavern EF; Genes & Health Research Team; Smedley D, Caulfield MJ. iScience. 2023 Sep 1;26(10):107795.

CYP2C19 Genotype Prevalence and Association With Recurrent Myocardial Infarction in British-South Asians Treated With Clopidogrel.
Graphical Abstract: Cell
Magavern EF, Jacobs B, Warren H, Finocchiaro G, Finer S, van Heel DA; Genes & Health Research Team; Smedley D, Caulfield MJ. JACC Adv. 2023 Sep;2(7)

Essential genes: a cross-species perspective
Graphical Abstract: Cell
Cacheiro P, Smedley D. Mamm Genome. 2023 Sep;34(3):357-363.

Knockout mice are an important tool for human monogenic heart disease studies
Graphical Abstract: Cell
Cacheiro P, Spielmann N, Mashhadi HH, Fuchs H, Gailus-Durner V, Smedley D, de Angelis MH. Dis Model Mech. 2023 May 1;16(5):dmm049770.

SLCO1B1*5 is protective against non-senile cataracts in cohort prescribed statins: analysis in a British-South Asian cohort
Graphical Abstract: Cell
Magavern EF, van Heel DA; Genes & Health Research Team; Smedley D, Caulfield MJ. Pharmacogenomics J. 2023 Sep;23(5):134-139.

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.
Graphical Abstract: Cell
Magavern EF, van Heel DA; Genes & Health Research Team; Smedley D, Caulfield MJ. Br J Clin Pharmacol. 2023 May 4

The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease.
Graphical Abstract: Cell
Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, Cacheiro P, Frost A, Keskivali-Bond P, Vardal B, McCoy A, Cheng TK, Santos L, Wells S, Smedley D, Mallon AM, Parkinson H. Nucleic Acids Res. 2023 Jan 6;51(D1):D1038-D1045.

2022

Phenotype-aware prioritisation of rare Mendelian disease variants.
Graphical Abstract: Cell
Kelly C, Szabo A, Pontikos N, Arno G, Robinson PN, Jacobsen JOB, Smedley D, Cipriani V. Trends Genet. 2022 Dec;38(12):1271-1283.

Mendelian gene identification through mouse embryo viability screening.
Graphical Abstract: Cell
Cacheiro P, ..., Smedley D. Genome Med. 2022 Oct 13;14(1):119.

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases.
Graphical Abstract: Cell
Jacobsen JOB, Kelly C, Cipriani V, Robinson PN, Smedley D. Brief Bioinform. 2022 Sep 20;23(5):bbac188.

Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease.
Graphical Abstract: Cell
Jacobsen JOB, Kelly C, Cipriani V, Research Consortium GE, Mungall CJ, Reese J, Danis D, Robinson PN, Smedley D. Hum Mutat. 2022 Aug;43(8):1071-1081. doi: 10.1002/humu.24380. Epub 2022 Apr 27.

The GA4GH Phenopacket schema defines a computable representation of clinical data.
Graphical Abstract: Cell
Jacobsen JOB, ..., Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C; GAGH Phenopacket Modeling Consortium; Haendel MA, Robinson PN. Nat Biotechnol. 2022 Jun;40(6):817-820.

Primary ciliary dyskinesia: a big data genomics approach.
Graphical Abstract: Cell
Mitchison HM, Smedley D. Lancet Respir Med. 2022 May;10(5):423-425.

PheneBank: a literature-based database of phenotypes.
Graphical Abstract: Cell
Pilehvar MT, Bernard A, Smedley D, Collier N. Bioinformatics. 2022 Jan 27;38(4):1179-1180.

2021

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report.
Graphical Abstract: Cell
Smedley D, Smith KR, Martin A, Thomas EA, McDonagh EM, Cipriani V et al N Engl J Med. 2021 Nov 11;385(20):1868-1880.

Dimensional reduction of phenotypes from 53 000 mouse models reveals a diverse landscape of gene function.
Graphical Abstract: Cell
Konopka T, Vestito L, Smedley D. Bioinform Adv. 2021 Oct 11;1(1):vbab026.

Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base.
Graphical Abstract: Cell
Konopka T, Ng S, Smedley D. PLoS Comput Biol. 2021 Aug 11;17(8):e1009283.

The Human Phenotype Ontology in 2021.

Graphical Abstract: Cell
Köhler S, ..., Smedley D, Talmy T, Thomas Y, Wiafe SA, Xian J, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217.

2020

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm.
Graphical Abstract: Cell
Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL; UNC Biocuration Core; Karlebach G, Reese J, Holtgrewe M, Köhler S, McMurry JA, Haendel MA, Smedley D. Am J Hum Genet. 2020 Sep 3;107(3):403-417

An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data.
Graphical Abstract: Cell
Cipriani V, Pontikos N, Arno G, Sergouniotis PI, Lenassi E, Thawong P, Danis D, Michaelides M, Webster AR, Moore AT, Robinson PN, Jacobsen JOB, Smedley D. Genes (Basel). 2020 Apr 23;11(4):460.

Human and mouse essentiality screens as a resource for disease gene discovery.
Graphical Abstract: Cell
Cacheiro P, ..., Smedley D; Genomics England Research Consortium; International Mouse Phenotyping Consortium. Nat Commun. 2020 Jan 31;11(1):655.

Incremental data integration for tracking genotype-disease associations.
Graphical Abstract: Cell
Konopka T, Smedley D. PLoS Comput Biol. 2020 Jan 27;16(1):e1007586.

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Graphical Abstract: Cell
Shefchek KA, ..., Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. Nucleic Acids Res. 2020 Jan 8;48(D1):D704-D715.

2014-19

New models for human disease from the International Mouse Phenotyping Consortium
Graphical Abstract: Cell
Cacheiro P, Haendel MA, Smedley D; International Mouse Phenotyping Consortium and the Monarch Initiative. Mamm Genome. 2019 Jun;30(5-6):143-150.

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation.
Graphical Abstract: Cell
Muñoz-Fuentes V, Cacheiro P, ..., Smedley D, Parkinson HE; IMPC consortium. Conserv Genet. 2018;19(4):995-1005.

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.
Graphical Abstract: Cell
Meehan TF, Conte N, West DB, Jacobsen JO, ... , Smedley D. Nat Genet. 2017 Aug;49(8):1231-1238.

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.
Graphical Abstract: Cell
Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN. Am J Hum Genet. 2016 Sep 1;99(3):595-606.

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.
Graphical Abstract: Cell
Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, ..., Smedley D. Genet Med. 2016 Jun;18(6):608-17.

Next-generation diagnostics and disease-gene discovery with the Exomiser.
Graphical Abstract: Cell
Smedley D, Jacobsen JO, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN. Nat Protoc. 2015 Dec;10(12):2004-15.

Phenotype-driven strategies for exome prioritization of human Mendelian disease genes.
Graphical Abstract: Cell
Smedley D, Robinson PN. Genome Med. 2015 Jul 30;7(1):81.

The BioMart community portal: an innovative alternative to large, centralized data repositories.
Graphical Abstract: Cell
Smedley D et al Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98.

Linking gene expression to phenotypes via pathway information.
Graphical Abstract: Cell
Papatheodorou I, Oellrich A, Smedley D. J Biomed Semantics. 2015 Apr 11;6:17.

Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases.
Graphical Abstract: Cell
Smedley D, Köhler S, Czeschik JC, Amberger J, Bocchini C, Hamosh A, Veldboer J, Zemojtel T, Robinson PN. Bioinformatics. 2014 Nov 15;30(22):3215-22.

Using association rule mining to determine promising secondary phenotyping hypotheses.
Graphical Abstract: Cell
Oellrich A, Jacobsen J, Papatheodorou I; Sanger Mouse Genetics Project; Smedley D. Bioinformatics. 2014 Jun 15;30(12):i52-59.

The influence of disease categories on gene candidate predictions from model organism phenotypes.
Graphical Abstract: Cell
Oellrich A, Koehler S, Washington N; Sanger Mouse Genetic Project; Mungall C, Lewis S, Haendel M, Robinson PN, Smedley D. J Biomed Semantics. 2014 Jun 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S4.

Linking tissues to phenotypes using gene expression profiles.
Graphical Abstract: Cell
Oellrich A; Sanger Mouse Genetics Project; Smedley D. Database (Oxford). 2014 Mar 13;2014:bau017.

Improved exome prioritization of disease genes through cross-species phenotype comparison.

Graphical Abstract: Cell
Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project; Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D. Genome Res. 2014 Feb;24(2):340-8.

PhenoDigm: analyzing curated annotations to associate animal models with human diseases.
Graphical Abstract: Cell
Smedley D, Oellrich A, Köhler S, Ruef B; Sanger Mouse Genetics Project; Westerfield M, Robinson P, Lewis S, Mungall C. Database (Oxford). 2013 May 9;2013:bat025.