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Items: 1 to 20 of 52

1.

Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data.

Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA; CAAPA Consortium..

Bioinformatics. 2016 Dec 29. pii: btw786. doi: 10.1093/bioinformatics/btw786. [Epub ahead of print]

2.

Discovery and functional characterization of a neomorphic PTEN mutation.

Costa HA, Leitner MG, Sos ML, Mavrantoni A, Rychkova A, Johnson JR, Newton BW, Yee MC, De La Vega FM, Ford JM, Krogan NJ, Shokat KM, Oliver D, Halaszovich CR, Bustamante CD.

Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13976-81. doi: 10.1073/pnas.1422504112. Epub 2015 Oct 26.

3.

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes.

Shringarpure SS, Carroll A, De La Vega FM, Bustamante CD.

PLoS One. 2015 Jun 25;10(6):e0129277. doi: 10.1371/journal.pone.0129277. eCollection 2015.

4.

Clinical pertinence metric enables hypothesis-independent genome-phenome analysis for neurologic diagnosis.

Segal MM, Abdellateef M, El-Hattab AW, Hilbush BS, De La Vega FM, Tromp G, Williams MS, Betensky RA, Gleeson J.

J Child Neurol. 2015 Jun;30(7):881-8. doi: 10.1177/0883073814545884. Epub 2014 Aug 24.

5.

Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data.

Cleary JG, Braithwaite R, Gaastra K, Hilbush BS, Inglis S, Irvine SA, Jackson A, Littin R, Nohzadeh-Malakshah S, Rathod M, Ware D, Trigg L, De La Vega FM.

J Comput Biol. 2014 Jun;21(6):405-19. doi: 10.1089/cmb.2014.0029.

PMID:
24874280
6.

Nucleosome regulatory dynamics in response to TGFβ.

Enroth S, Andersson R, Bysani M, Wallerman O, Termén S, Tuch BB, De La Vega FM, Heldin CH, Moustakas A, Komorowski J, Wadelius C.

Nucleic Acids Res. 2014 Jun;42(11):6921-34. doi: 10.1093/nar/gku326. Epub 2014 Apr 25.

7.

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.

8.

Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities.

Craig DW, O'Shaughnessy JA, Kiefer JA, Aldrich J, Sinari S, Moses TM, Wong S, Dinh J, Christoforides A, Blum JL, Aitelli CL, Osborne CR, Izatt T, Kurdoglu A, Baker A, Koeman J, Barbacioru C, Sakarya O, De La Vega FM, Siddiqui A, Hoang L, Billings PR, Salhia B, Tolcher AW, Trent JM, Mousses S, Von Hoff D, Carpten JD.

Mol Cancer Ther. 2013 Jan;12(1):104-16. doi: 10.1158/1535-7163.MCT-12-0781. Epub 2012 Nov 19.

9.

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.

10.

Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population.

Gusev A, Shah MJ, Kenny EE, Ramachandran A, Lowe JK, Salit J, Lee CC, Levandowsky EC, Weaver TN, Doan QC, Peckham HE, McLaughlin SF, Lyons MR, Sheth VN, Stoffel M, De La Vega FM, Friedman JM, Breslow JL, Pe'er I.

Genetics. 2012 Feb;190(2):679-89. doi: 10.1534/genetics.111.134874. Epub 2011 Nov 30.

11.

An Aboriginal Australian genome reveals separate human dispersals into Asia.

Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E.

Science. 2011 Oct 7;334(6052):94-8. doi: 10.1126/science.1211177. Epub 2011 Sep 22.

12.

Genomics for the world.

Bustamante CD, Burchard EG, De la Vega FM.

Nature. 2011 Jul 13;475(7355):163-5. doi: 10.1038/475163a. No abstract available.

13.

A new expectation-maximization statistical test for case-control association studies considering rare variants obtained by high-throughput sequencing.

Gordon D, Finch SJ, De La Vega FM.

Hum Hered. 2011;71(2):113-25. doi: 10.1159/000325590. Epub 2011 Jul 6. Erratum in: Hum Hered. 2011;72(1):53. De La Vega, Francisco [corrected to De La Vega, Francisco M].

PMID:
21734402
14.

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.

15.

Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples.

Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK.

Investig Genet. 2011 Jan 5;2(1):1. doi: 10.1186/2041-2223-2-1.

16.
17.

Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss.

Mitrovich QM, Tuch BB, De La Vega FM, Guthrie C, Johnson AD.

Science. 2010 Nov 5;330(6005):838-41. doi: 10.1126/science.1194554.

18.

The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation.

Tuch BB, Mitrovich QM, Homann OR, Hernday AD, Monighetti CK, De La Vega FM, Johnson AD.

PLoS Genet. 2010 Aug 19;6(8):e1001070. doi: 10.1371/journal.pgen.1001070.

19.

A cost-effective statistical method to correct for differential genotype misclassification when performing case-control genetic association.

Londono D, Haynes C, De La Vega FM, Finch SJ, Gordon D.

Hum Hered. 2010;70(2):102-8. doi: 10.1159/000314470. Epub 2010 Jul 3.

PMID:
20606457
20.

Development of personalized tumor biomarkers using massively parallel sequencing.

Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, Antipova A, Lee C, McKernan K, De La Vega FM, Kinzler KW, Vogelstein B, Diaz LA Jr, Velculescu VE.

Sci Transl Med. 2010 Feb 24;2(20):20ra14. doi: 10.1126/scitranslmed.3000702.

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