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Items: 42

1.

Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene.

Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R; ClinGen Inborn Errors of Metabolism Working Group.

Hum Mutat. 2018 Nov;39(11):1569-1580. doi: 10.1002/humu.23649.

PMID:
30311390
2.

ClinVar Miner: Demonstrating utility of a Web-based tool for viewing and filtering ClinVar data.

Henrie A, Hemphill SE, Ruiz-Schultz N, Cushman B, DiStefano MT, Azzariti D, Harrison SM, Rehm HL, Eilbeck K.

Hum Mutat. 2018 Aug;39(8):1051-1060. doi: 10.1002/humu.23555. Epub 2018 Jun 21.

3.

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool.

Flygare S, Hernandez EJ, Phan L, Moore B, Li M, Fejes A, Hu H, Eilbeck K, Huff C, Jorde L, G Reese M, Yandell M.

BMC Bioinformatics. 2018 Feb 20;19(1):57. doi: 10.1186/s12859-018-2056-y.

4.

Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia.

Schlaberg R, Ampofo K, Tardif KD, Stockmann C, Simmon KE, Hymas W, Flygare S, Kennedy B, Blaschke A, Eilbeck K, Yandell M, McCullers JA, Williams DJ, Edwards K, Arnold SR, Bramley A, Jain S, Pavia AT.

J Infect Dis. 2017 Sep 15;216(6):688-696. doi: 10.1093/infdis/jix352.

5.

Settling the score: variant prioritization and Mendelian disease.

Eilbeck K, Quinlan A, Yandell M.

Nat Rev Genet. 2017 Oct;18(10):599-612. doi: 10.1038/nrg.2017.52. Epub 2017 Aug 14. Review.

6.

Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology.

Schlaberg R, Queen K, Simmon K, Tardif K, Stockmann C, Flygare S, Kennedy B, Voelkerding K, Bramley A, Zhang J, Eilbeck K, Yandell M, Jain S, Pavia AT, Tong S, Ampofo K.

J Infect Dis. 2017 May 1;215(9):1407-1415. doi: 10.1093/infdis/jix148.

7.

Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.

Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthey EA, Zaranek AW, Zook JM.

J Mol Diagn. 2017 May;19(3):417-426. doi: 10.1016/j.jmoldx.2016.12.001. Epub 2017 Mar 18.

8.

The development of non-coding RNA ontology.

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M.

Int J Data Min Bioinform. 2016;15(3):214-232.

9.

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.

Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R.

Genome Biol. 2016 May 26;17(1):111. doi: 10.1186/s13059-016-0969-1.

10.

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva Nd, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A.

J Biomed Semantics. 2016 May 10;7:25. doi: 10.1186/s13326-016-0064-2. eCollection 2016.

11.

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M.

J Biomed Semantics. 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. eCollection 2016.

12.

Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.

Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R.

J Clin Microbiol. 2016 Apr;54(4):1000-7. doi: 10.1128/JCM.03060-15. Epub 2016 Jan 27.

13.

The genomic CDS sandbox: An assessment among domain experts.

Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM.

J Biomed Inform. 2016 Apr;60:84-94. doi: 10.1016/j.jbi.2015.12.019. Epub 2016 Jan 15.

14.

miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants.

Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH.

Trends Genet. 2015 Nov;31(11):613-626. doi: 10.1016/j.tig.2015.09.002. Epub 2015 Oct 8. Review.

15.

Building an Ontology for Identity Resolution in Healthcare and Public Health.

Duncan J, Eilbeck K, Narus SP, Clyde S, Thornton S, Staes C.

Online J Public Health Inform. 2015 Jul 1;7(2):e219. doi: 10.5210/ojphi.v7i2.6010. eCollection 2015.

16.

Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

Thibault JC, Roe DR, Eilbeck K, Cheatham TE III, Facelli JC.

SAR QSAR Environ Res. 2015;26(7-9):577-93. doi: 10.1080/1062936X.2015.1076515. Epub 2015 Sep 21. Review.

17.

Improving the Sequence Ontology terminology for genomic variant annotation.

Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K.

J Biomed Semantics. 2015 Jul 31;6:32. doi: 10.1186/s13326-015-0030-4. eCollection 2015.

18.

GFVO: the Genomic Feature and Variation Ontology.

Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M.

PeerJ. 2015 May 5;3:e933. doi: 10.7717/peerj.933. eCollection 2015.

19.

A high-throughput next-generation sequencing assay for the mitochondrial genome.

Dames S, Eilbeck K, Mao R.

Methods Mol Biol. 2015;1264:77-88. doi: 10.1007/978-1-4939-2257-4_8.

PMID:
25631005
20.

A proposed clinical decision support architecture capable of supporting whole genome sequence information.

Welch BM, Loya SR, Eilbeck K, Kawamoto K.

J Pers Med. 2014 Apr 4;4(2):176-99. doi: 10.3390/jpm4020176.

21.

Birth of identity: understanding changes to birth certificates and their value for identity resolution.

Duncan J, Narus SP, Clyde S, Eilbeck K, Thornton S, Staes C.

J Am Med Inform Assoc. 2015 Apr;22(e1):e120-9. doi: 10.1136/amiajnl-2014-002774. Epub 2014 Jul 30.

PMID:
25080533
22.

OMIT: dynamic, semi-automated ontology development for the microRNA domain.

Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M.

PLoS One. 2014 Jul 15;9(7):e100855. doi: 10.1371/journal.pone.0100855. eCollection 2014.

23.

Technical desiderata for the integration of genomic data with clinical decision support.

Welch BM, Eilbeck K, Del Fiol G, Meyer LJ, Kawamoto K.

J Biomed Inform. 2014 Oct;51:3-7. doi: 10.1016/j.jbi.2014.05.014. Epub 2014 Jun 12.

24.

Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.

Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M.

Am J Hum Genet. 2014 Apr 3;94(4):599-610. doi: 10.1016/j.ajhg.2014.03.010.

25.

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM.

Genome Biol. 2014 Mar 25;15(3):R53. doi: 10.1186/gb-2014-15-3-r53.

26.

Clinical decision support for whole genome sequence information leveraging a service-oriented architecture: a prototype.

Welch BM, Rodriguez-Loya S, Eilbeck K, Kawamoto K.

AMIA Annu Symp Proc. 2014 Nov 14;2014:1188-97. eCollection 2014.

27.

Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System.

Eilbeck KL, Lipstein J, McGarvey S, Staes CJ.

AMIA Annu Symp Proc. 2014 Nov 14;2014:496-505. eCollection 2014.

28.

Integrating precision medicine in the study and clinical treatment of a severely mentally ill person.

O'Rawe JA, Fang H, Rynearson S, Robison R, Kiruluta ES, Higgins G, Eilbeck K, Reese MG, Lyon GJ.

PeerJ. 2013 Oct 3;1:e177. doi: 10.7717/peerj.177. eCollection 2013.

29.

The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders.

Dames S, Chou LS, Xiao Y, Wayman T, Stocks J, Singleton M, Eilbeck K, Mao R.

J Mol Diagn. 2013 Jul;15(4):526-34. doi: 10.1016/j.jmoldx.2013.03.005. Epub 2013 May 9.

PMID:
23665194
30.

A standard variation file format for human genome sequences.

Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K.

Genome Biol. 2010;11(8):R88. doi: 10.1186/gb-2010-11-8-r88. Epub 2010 Aug 26.

31.

SOBA: sequence ontology bioinformatics analysis.

Moore B, Fan G, Eilbeck K.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W161-4. doi: 10.1093/nar/gkq426. Epub 2010 May 21.

32.

Evolution of the Sequence Ontology terms and relationships.

Mungall CJ, Batchelor C, Eilbeck K.

J Biomed Inform. 2011 Feb;44(1):87-93. doi: 10.1016/j.jbi.2010.03.002. Epub 2010 Mar 10.

33.

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis.

Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH.

Hum Mol Genet. 2010 Feb 15;19(4):707-19. doi: 10.1093/hmg/ddp521. Epub 2009 Nov 18.

34.

Quantitative measures for the management and comparison of annotated genomes.

Eilbeck K, Moore B, Holt C, Yandell M.

BMC Bioinformatics. 2009 Feb 23;10:67. doi: 10.1186/1471-2105-10-67.

35.

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.

Bioinformatics. 2008 Dec 1;24(23):2767-72. doi: 10.1093/bioinformatics/btn528. Epub 2008 Oct 20.

36.

Sequence ontology annotation guide.

Eilbeck K, Lewis SE.

Comp Funct Genomics. 2004;5(8):642-7. doi: 10.1002/cfg.446.

37.

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S.

Nat Biotechnol. 2007 Nov;25(11):1251-5.

38.

The Sequence Ontology: a tool for the unification of genome annotations.

Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M.

Genome Biol. 2005;6(5):R44. Epub 2005 Apr 29.

39.

The Gene Ontology (GO) database and informatics resource.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

40.

The sequence of the human genome.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X.

Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.

PMID:
11181995
41.

Conceptual modelling of genomic information.

Paton NW, Khan SA, Hayes A, Moussouni F, Brass A, Eilbeck K, Goble CA, Hubbard SJ, Oliver SG.

Bioinformatics. 2000 Jun;16(6):548-57.

PMID:
10980152
42.

INTERACT: an object oriented protein-protein interaction database.

Eilbeck K, Brass A, Paton N, Hodgman C.

Proc Int Conf Intell Syst Mol Biol. 1999:87-94.

PMID:
10786290

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