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Items: 1 to 50 of 151

1.

Ontology-based prediction of cancer driver genes.

Althubaiti S, Karwath A, Dallol A, Noor A, Alkhayyat SS, Alwassia R, Mineta K, Gojobori T, Beggs AD, Schofield PN, Gkoutos GV, Hoehndorf R.

Sci Rep. 2019 Nov 22;9(1):17405. doi: 10.1038/s41598-019-53454-1.

2.

PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research.

Kafkas Ş, Abdelhakim M, Hashish Y, Kulmanov M, Abdellatif M, Schofield PN, Hoehndorf R.

Sci Data. 2019 Jun 3;6(1):79. doi: 10.1038/s41597-019-0090-x.

3.

Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice.

Cooper TK, Silva KA, Kennedy VE, Alghamdi S, Hoehndorf R, Sundberg BA, Schofield PN, Sundberg JP.

Vet Pathol. 2019 Sep;56(5):799-806. doi: 10.1177/0300985819844822. Epub 2019 May 6.

PMID:
31060453
4.

Big data in radiation biology and epidemiology; an overview of the historical and contemporary landscape of data and biomaterial archives.

Schofield PN, Kulka U, Tapio S, Grosche B.

Int J Radiat Biol. 2019 Jul;95(7):861-878. doi: 10.1080/09553002.2019.1589026. Epub 2019 Apr 8. Review.

PMID:
30888231
5.

Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies.

Alghamdi SM, Sundberg BA, Sundberg JP, Schofield PN, Hoehndorf R.

Sci Rep. 2019 Mar 11;9(1):4025. doi: 10.1038/s41598-019-40368-1.

6.

DeepPVP: phenotype-based prioritization of causative variants using deep learning.

Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.

BMC Bioinformatics. 2019 Feb 6;20(1):65. doi: 10.1186/s12859-019-2633-8.

7.

SURVEY ON DATA MANAGEMENT IN RADIATION PROTECTION RESEARCH.

Madas BG, Schofield PN.

Radiat Prot Dosimetry. 2019 May 1;183(1-2):233-236. doi: 10.1093/rpd/ncy250.

PMID:
30534952
8.

A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals.

Elmore SA, Cardiff R, Cesta MF, Gkoutos GV, Hoehndorf R, Keenan CM, McKerlie C, Schofield PN, Sundberg JP, Ward JM.

ILAR J. 2018 Dec 1;59(1):29-39. doi: 10.1093/ilar/ily005.

PMID:
30476141
9.

Ontology-based validation and identification of regulatory phenotypes.

Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.

Bioinformatics. 2018 Sep 1;34(17):i857-i865. doi: 10.1093/bioinformatics/bty605.

10.

The tubercular badger and the uncertain curve:- The need for a multiple stressor approach in environmental radiation protection.

Mothersill C, Abend M, Bréchignac F, Copplestone D, Geras'kin S, Goodman J, Horemans N, Jeggo P, McBride W, Mousseau TA, O'Hare A, Papineni RVL, Powathil G, Schofield PN, Seymour C, Sutcliffe J, Austin B.

Environ Res. 2019 Jan;168:130-140. doi: 10.1016/j.envres.2018.09.031. Epub 2018 Sep 26.

11.

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants.

Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.

Sci Rep. 2018 Oct 2;8(1):14681. doi: 10.1038/s41598-018-32876-3.

12.

Living inside the box: environmental effects on mouse models of human disease.

Sundberg JP, Schofield PN.

Dis Model Mech. 2018 Oct 1;11(10). pii: dmm035360. doi: 10.1242/dmm.035360. Review.

13.

Nail abnormalities identified in an ageing study of 30 inbred mouse strains.

Linn SC, Mustonen AM, Silva KA, Kennedy VE, Sundberg BA, Bechtold LS, Alghamdi S, Hoehndorf R, Schofield PN, Sundberg JP.

Exp Dermatol. 2019 Apr;28(4):383-390. doi: 10.1111/exd.13759. Epub 2018 Sep 4.

PMID:
30074290
14.

When a duck is not a duck; a new interdisciplinary synthesis for environmental radiation protection.

Mothersill C, Abend M, Bréchignac F, Iliakis G, Impens N, Kadhim M, Møller AP, Oughton D, Powathil G, Saenen E, Seymour C, Sutcliffe J, Tang FR, Schofield PN.

Environ Res. 2018 Apr;162:318-324. doi: 10.1016/j.envres.2018.01.022. Epub 2018 Feb 4.

15.

Integrating phenotype ontologies with PhenomeNET.

Rodríguez-García MÁ, Gkoutos GV, Schofield PN, Hoehndorf R.

J Biomed Semantics. 2017 Dec 19;8(1):58. doi: 10.1186/s13326-017-0167-4.

16.

Evolving paradigms for the biological response to low dose ionizing radiation; the role of epigenetics.

Schofield PN, Kondratowicz M.

Int J Radiat Biol. 2018 Aug;94(8):769-781. doi: 10.1080/09553002.2017.1388548. Epub 2017 Dec 1. Review.

PMID:
29157078
17.

Systematic screening for skin, hair, and nail abnormalities in a large-scale knockout mouse program.

Sundberg JP, Dadras SS, Silva KA, Kennedy VE, Garland G, Murray SA, Sundberg BA, Schofield PN, Pratt CH.

PLoS One. 2017 Jul 10;12(7):e0180682. doi: 10.1371/journal.pone.0180682. eCollection 2017.

18.

Semantic prioritization of novel causative genomic variants.

Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R.

PLoS Comput Biol. 2017 Apr 17;13(4):e1005500. doi: 10.1371/journal.pcbi.1005500. eCollection 2017 Apr.

19.

The anatomy of phenotype ontologies: principles, properties and applications.

Gkoutos GV, Schofield PN, Hoehndorf R.

Brief Bioinform. 2018 Sep 28;19(5):1008-1021. doi: 10.1093/bib/bbx035.

20.

Reproducibility of histopathological findings in experimental pathology of the mouse: a sorry tail.

Ward JM, Schofield PN, Sundberg JP.

Lab Anim (NY). 2017 Mar 22;46(4):146-151. doi: 10.1038/laban.1214.

21.

Using AberOWL for fast and scalable reasoning over BioPortal ontologies.

Slater L, Gkoutos GV, Schofield PN, Hoehndorf R.

J Biomed Semantics. 2016 Aug 8;7(1):49. doi: 10.1186/s13326-016-0090-0.

22.

Show and tell: disclosure and data sharing in experimental pathology.

Schofield PN, Ward JM, Sundberg JP.

Dis Model Mech. 2016 Jun 1;9(6):601-5. doi: 10.1242/dmm.026054. Review.

23.

DermO; an ontology for the description of dermatologic disease.

Fisher HM, Hoehndorf R, Bazelato BS, Dadras SS, King LE Jr, Gkoutos GV, Sundberg JP, Schofield PN.

J Biomed Semantics. 2016 Jun 13;7:38. doi: 10.1186/s13326-016-0085-x.

24.

Mouse genome-wide association study identifies polymorphisms on chromosomes 4, 11, and 15 for age-related cardiac fibrosis.

Li Q, Berndt A, Sundberg BA, Silva KA, Kennedy VE, Cario CL, Richardson MA, Chase TH, Schofield PN, Uitto J, Sundberg JP.

Mamm Genome. 2016 Jun;27(5-6):179-90. doi: 10.1007/s00335-016-9634-y. Epub 2016 Apr 28.

25.

Datamining with Ontologies.

Hoehndorf R, Gkoutos GV, Schofield PN.

Methods Mol Biol. 2016;1415:385-97. doi: 10.1007/978-1-4939-3572-7_19.

PMID:
27115643
26.

Approaches to Investigating Complex Genetic Traits in a Large-Scale Inbred Mouse Aging Study.

Sundberg JP, Berndt A, Sundberg BA, Silva KA, Kennedy V, Smith RS, Cooper TK, Schofield PN.

Vet Pathol. 2016 Mar;53(2):456-67. doi: 10.1177/0300985815612556.

27.

The Vital Role of Pathology in Improving Reproducibility and Translational Relevance of Aging Studies in Rodents.

Treuting PM, Snyder JM, Ikeno Y, Schofield PN, Ward JM, Sundberg JP.

Vet Pathol. 2016 Mar;53(2):244-9. doi: 10.1177/0300985815620629. Epub 2016 Jan 20.

28.

Genetic determinants of fibro-osseous lesions in aged inbred mice.

Berndt A, Ackert-Bicknell C, Silva KA, Kennedy VE, Sundberg BA, Cates JM, Schofield PN, Sundberg JP.

Exp Mol Pathol. 2016 Feb;100(1):92-100. doi: 10.1016/j.yexmp.2015.11.018. Epub 2015 Nov 14.

29.

Sustaining large-scale infrastructure to promote pre-competitive biomedical research: lessons from mouse genomics.

Mishra A, Schofield PN, Bubela TM.

N Biotechnol. 2016 Mar 25;33(2):280-94. doi: 10.1016/j.nbt.2015.10.002. Epub 2015 Nov 10.

30.

Excavating the Genome: Large-Scale Mutagenesis Screening for the Discovery of New Mouse Models.

Sundberg JP, Dadras SS, Silva KA, Kennedy VE, Murray SA, Denegre JM, Schofield PN, King LE Jr, Wiles MV, Pratt CH.

J Investig Dermatol Symp Proc. 2015 Nov;17(2):27-9. doi: 10.1038/jidsymp.2015.36. Review.

31.

Best behaviour? Ontologies and the formal description of animal behaviour.

Gkoutos GV, Hoehndorf R, Tsaprouni L, Schofield PN.

Mamm Genome. 2015 Oct;26(9-10):540-7. doi: 10.1007/s00335-015-9590-y. Epub 2015 Jul 28. Review.

PMID:
26215546
32.

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN.

Am J Hum Genet. 2015 Jul 2;97(1):111-24. doi: 10.1016/j.ajhg.2015.05.020. Epub 2015 Jun 25.

33.

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases.

Hoehndorf R, Schofield PN, Gkoutos GV.

Sci Rep. 2015 Jun 8;5:10888. doi: 10.1038/srep10888.

34.

The role of ontologies in biological and biomedical research: a functional perspective.

Hoehndorf R, Schofield PN, Gkoutos GV.

Brief Bioinform. 2015 Nov;16(6):1069-80. doi: 10.1093/bib/bbv011. Epub 2015 Apr 10.

35.

Similarity-based search of model organism, disease and drug effect phenotypes.

Hoehndorf R, Gruenberger M, Gkoutos GV, Schofield PN.

J Biomed Semantics. 2015 Feb 19;6:6. doi: 10.1186/s13326-015-0001-9. eCollection 2015.

36.

Dsp rul: a spontaneous mouse mutation in desmoplakin as a model of Carvajal-Huerta syndrome.

Herbert Pratt C, Potter CS, Fairfield H, Reinholdt LG, Bergstrom DE, Harris BS, Greenstein I, Dadras SS, Liang BT, Schofield PN, Sundberg JP.

Exp Mol Pathol. 2015 Apr;98(2):164-72. doi: 10.1016/j.yexmp.2015.01.015. Epub 2015 Feb 7.

37.

Aber-OWL: a framework for ontology-based data access in biology.

Hoehndorf R, Slater L, Schofield PN, Gkoutos GV.

BMC Bioinformatics. 2015 Jan 28;16:26. doi: 10.1186/s12859-015-0456-9.

38.

Deletions of chromosomal regulatory boundaries are associated with congenital disease.

Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN.

Genome Biol. 2014 Sep 4;15(9):423. doi: 10.1186/s13059-014-0423-1.

39.

Identifying mouse models for skin cancer using the Mouse Tumor Biology Database.

Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Schofield PN, Bult CJ, Eppig JT, Sundberg JP.

Exp Dermatol. 2014 Oct;23(10):761-3. doi: 10.1111/exd.12512.

40.

Inbred mouse strains reveal biomarkers that are pro-longevity, antilongevity or role switching.

Moeller M, Hirose M, Mueller S, Roolf C, Baltrusch S, Ibrahim S, Junghanss C, Wolkenhauer O, Jaster R, Köhling R, Kunz M, Tiedge M, Schofield PN, Fuellen G.

Aging Cell. 2014 Aug;13(4):729-38. doi: 10.1111/acel.12226. Epub 2014 May 23.

41.

In silico approaches and the role of ontologies in aging research.

Fuellen G, Boerries M, Busch H, de Grey A, Hahn U, Hiller T, Hoeflich A, Jansen L, Janssens GE, Kaleta C, Meinema AC, Schäuble S, Simm A, Schofield PN, Smith B, Sühnel J, Vera J, Wagner W, Wönne EC, Wuttke D.

Rejuvenation Res. 2013 Dec;16(6):540-6. doi: 10.1089/rej.2013.1517.

42.

Analyzing gene expression data in mice with the Neuro Behavior Ontology.

Hoehndorf R, Hancock JM, Hardy NW, Mallon AM, Schofield PN, Gkoutos GV.

Mamm Genome. 2014 Feb;25(1-2):32-40. doi: 10.1007/s00335-013-9481-z. Epub 2013 Nov 1.

PMID:
24177753
43.

Mouse model phenotypes provide information about human drug targets.

Hoehndorf R, Hiebert T, Hardy NW, Schofield PN, Gkoutos GV, Dumontier M.

Bioinformatics. 2014 Mar 1;30(5):719-25. doi: 10.1093/bioinformatics/btt613. Epub 2013 Oct 24.

44.

The mouse pathology ontology, MPATH; structure and applications.

Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV.

J Biomed Semantics. 2013 Sep 13;4(1):18. doi: 10.1186/2041-1480-4-18.

45.

An integrative, translational approach to understanding rare and orphan genetically based diseases.

Hoehndorf R, Schofield PN, Gkoutos GV.

Interface Focus. 2013 Apr 6;3(2):20120055. doi: 10.1098/rsfs.2012.0055.

46.

The Cinderella effect: searching for the best fit between mouse models and human diseases.

Sundberg JP, Roopenian DC, Liu ET, Schofield PN.

J Invest Dermatol. 2013 Nov;133(11):2509-2513. doi: 10.1038/jid.2013.238. Epub 2013 Jun 27.

47.

Systematic analysis of experimental phenotype data reveals gene functions.

Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV.

PLoS One. 2013 Apr 16;8(4):e60847. doi: 10.1371/journal.pone.0060847. Print 2013.

48.

Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project.

Oetting WS, Robinson PN, Greenblatt MS, Cotton RG, Beck T, Carey JC, Doelken SC, Girdea M, Groza T, Hamilton CM, Hamosh A, Kerner B, MacArthur JA, Maglott DR, Mons B, Rehm HL, Schofield PN, Searle BA, Smedley D, Smith CL, Bernstein IT, Zankl A, Zhao EY.

Hum Mutat. 2013 Apr;34(4):661-6. doi: 10.1002/humu.22293.

49.

The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.

Gkoutos GV, Schofield PN, Hoehndorf R.

Int Rev Neurobiol. 2012;103:69-87. doi: 10.1016/B978-0-12-388408-4.00004-6. Review.

PMID:
23195121
50.

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.

Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE.

Dis Model Mech. 2013 Mar;6(2):358-72. doi: 10.1242/dmm.010322. Epub 2012 Oct 25.

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