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Results: 1 to 20 of 31

1.

Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing.

Bhattacharjee A, Sokolsky T, Wyman SK, Reese MG, Puffenberger E, Strauss K, Morton H, Parad RB, Naylor EW.

Genet Med. 2015 May;17(5):337-47. doi: 10.1038/gim.2014.117. Epub 2014 Sep 25.

PMID:
25255367
2.

A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD.

Nat Biotechnol. 2014 Jul;32(7):663-9. doi: 10.1038/nbt.2895. Epub 2014 May 18.

3.

Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data.

Kennedy B, Kronenberg Z, Hu H, Moore B, Flygare S, Reese MG, Jorde LB, Yandell M, Huff C.

Curr Protoc Hum Genet. 2014 Apr 24;81:6.14.1-6.14.25. doi: 10.1002/0471142905.hg0614s81.

4.

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.

5.

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.

6.

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.

7.

Clinical analysis of genome next-generation sequencing data using the Omicia platform.

Coonrod EM, Margraf RL, Russell A, Voelkerding KV, Reese MG.

Expert Rev Mol Diagn. 2013 Jul;13(6):529-40. doi: 10.1586/14737159.2013.811907.

8.

VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.

Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M.

Genet Epidemiol. 2013 Sep;37(6):622-34. doi: 10.1002/gepi.21743. Epub 2013 Jul 8.

9.

Assuring the quality of next-generation sequencing in clinical laboratory practice.

Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM.

Nat Biotechnol. 2012 Nov;30(11):1033-6. doi: 10.1038/nbt.2403. No abstract available.

10.

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD.

Am J Hum Genet. 2012 Oct 5;91(4):660-71. doi: 10.1016/j.ajhg.2012.08.025.

11.

A probabilistic disease-gene finder for personal genomes.

Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG.

Genome Res. 2011 Sep;21(9):1529-42. doi: 10.1101/gr.123158.111. Epub 2011 Jun 23.

12.

Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics.

Moore B, Hu H, Singleton M, De La Vega FM, Reese MG, Yandell M.

Genet Med. 2011 Mar;13(3):210-7. doi: 10.1097/GIM.0b013e31820ed321.

13.

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.

14.

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP.

Genome Res. 2009 Sep;19(9):1527-41. doi: 10.1101/gr.091868.109. Epub 2009 Jun 22.

15.

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

Yandell M, Moore B, Salas F, Mungall C, MacBride A, White C, Reese MG.

PLoS Comput Biol. 2008 Nov;4(11):e1000218. doi: 10.1371/journal.pcbi.1000218. Epub 2008 Nov 7.

16.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.

Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.

17.

EGASP: Introduction.

Reese MG, Guigó R.

Genome Biol. 2006;7 Suppl 1:S1.1-3. Epub 2006 Aug 7. No abstract available.

18.

EGASP: collaboration through competition to find human genes.

Guigó R, Reese MG.

Nat Methods. 2005 Aug;2(8):575-7.

PMID:
16094379
19.

Improved use of SNP information to detect the role of genes.

Jannot AS, Essioux L, Reese MG, Clerget-Darpoux F.

Genet Epidemiol. 2003 Sep;25(2):158-67.

PMID:
12916024
20.
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