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Items: 14

1.

Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray.

Hayeems RZ, Bhawra J, Tsiplova K, Meyn MS, Monfared N, Bowdin S, Stavropoulos DJ, Marshall CR, Basran R, Shuman C, Ito S, Cohn I, Hum C, Girdea M, Brudno M, Cohn RD, Scherer SW, Ungar WJ.

Eur J Hum Genet. 2017 Dec;25(12):1303-1312. doi: 10.1038/s41431-017-0020-3. Epub 2017 Nov 20.

PMID:
29158552
2.

Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience.

Links AE, Draper D, Lee E, Guzman J, Valivullah Z, Maduro V, Lebedev V, Didenko M, Tomlin G, Brudno M, Girdea M, Dumitriu S, Haendel MA, Mungall CJ, Smedley D, Hochheiser H, Arnold AM, Coessens B, Verhoeven S, Bone W, Adams D, Boerkoel CF, Gahl WA, Sincan M.

Front Med (Lausanne). 2016 Oct 12;3:39. eCollection 2016.

3.

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.

Stavropoulos DJ, Merico D, Jobling R, Bowdin S, Monfared N, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Yuen RKC, Szego MJ, Hayeems RZ, Shaul RZ, Brudno M, Girdea M, Frey B, Alipanahi B, Ahmed S, Babul-Hirji R, Porras RB, Carter MT, Chad L, Chaudhry A, Chitayat D, Doust SJ, Cytrynbaum C, Dupuis L, Ejaz R, Fishman L, Guerin A, Hashemi B, Helal M, Hewson S, Inbar-Feigenberg M, Kannu P, Karp N, Kim R, Kronick J, Liston E, MacDonald H, Mercimek-Mahmutoglu S, Mendoza-Londono R, Nasr E, Nimmo G, Parkinson N, Quercia N, Raiman J, Roifman M, Schulze A, Shugar A, Shuman C, Sinajon P, Siriwardena K, Weksberg R, Yoon G, Carew C, Erickson R, Leach RA, Klein R, Ray PN, Meyn MS, Scherer SW, Cohn RD, Marshall CR.

NPJ Genom Med. 2016 Jan 13;1. pii: 15012. doi: 10.1038/npjgenmed.2015.12.

4.

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.

Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D.

Genet Med. 2016 Jun;18(6):608-17. doi: 10.1038/gim.2015.137. Epub 2015 Nov 12.

5.

Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data.

Foong J, Girdea M, Stavropoulos J, Brudno M.

PLoS One. 2015 Oct 5;10(10):e0139656. doi: 10.1371/journal.pone.0139656. eCollection 2015.

6.

The Matchmaker Exchange: a platform for rare disease gene discovery.

Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL.

Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858.

7.

The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles.

Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M.

Hum Mutat. 2015 Oct;36(10):922-7. doi: 10.1002/humu.22850.

8.

PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases.

Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, Trang H, Misyura A, Friedman T, Beaulieu C, Bone WP, Links AE, Washington NL, Haendel MA, Robinson PN, Boerkoel CF, Adams D, Gahl WA, Boycott KM, Brudno M.

Hum Mutat. 2015 Oct;36(10):931-40. doi: 10.1002/humu.22851. Epub 2015 Aug 31.

9.

Phenotyping: targeting genotype's rich cousin for diagnosis.

Baynam G, Walters M, Claes P, Kung S, LeSouef P, Dawkins H, Bellgard M, Girdea M, Brudno M, Robinson P, Zankl A, Groza T, Gillett D, Goldblatt J.

J Paediatr Child Health. 2015 Apr;51(4):381-6. doi: 10.1111/jpc.12705. Epub 2014 Aug 11. Review.

PMID:
25109851
10.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN.

Nucleic Acids Res. 2014 Jan;42(Database issue):D966-74. doi: 10.1093/nar/gkt1026. Epub 2013 Nov 11.

11.

PhenoTips: patient phenotyping software for clinical and research use.

Girdea M, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chénier S, Chitayat D, Faghfoury H, Meyn MS, Ray PN, So J, Stavropoulos DJ, Brudno M.

Hum Mutat. 2013 Aug;34(8):1057-65. doi: 10.1002/humu.22347. Epub 2013 May 24.

PMID:
23636887
12.

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.

13.

Designing Efficient Spaced Seeds for SOLiD Read Mapping.

Noé L, Gîrdea M, Kucherov G.

Adv Bioinformatics. 2010. pii: 708501. doi: 10.1155/2010/708501. Epub 2010 Sep 16.

14.

Back-translation for discovering distant protein homologies in the presence of frameshift mutations.

Girdea M, Noe L, Kucherov G.

Algorithms Mol Biol. 2010 Jan 4;5(1):6. doi: 10.1186/1748-7188-5-6.

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