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Purcell S, Daly MJ, Sham PC. WHAP: haplotype-based
association analysis.Bioinformatics. 2006 Nov
21; PMID: 17118959.
Van Bodegraven AA, Curley CR, Hunt KA, Monsuur
AJ, Linskens RK, Onnie CM, Crusius JB, Annese
V, Latiano A, Silverberg MS, Bitton A, Fisher
SA, Steinhart AH, Forbes A, Sanderson J, Prescott
NJ, Strachan DP, Playford RJ, Mathew CG, Wijmenga
C, Daly MJ, Rioux JD, Van Heel DA. Genetic Variation
in Myosin IXB Is Associated With Ulcerative Colitis.
Gastroenterology. 2006 Sep 8; PMID: 17087940.
Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg
MS, Daly MJ, Steinhart AH, Abraham C, Regueiro
M, Griffiths A, Dassopoulos T, Bitton A, Yang
H, Targan S, Datta LW, Kistner EO, Schumm LP,
Lee AT, Gregersen PK, Barmada MM, Rotter JI, Nicolae
DL, Cho JH. A genome-wide association study identifies
IL23R as an inflammatory bowel disease gene. Science.
2006 Dec 1;314(5804):1461-3. PMID: 17068223.
Lyon HN, Florez JC, Bersaglieri T, Saxena R,
Winckler W, Almgren P, Lindblad U, Tuomi T, Gaudet
D, Zhu X, Cooper R, Ardlie KG, Daly MJ, Altshuler
D, Groop L, Hirschhorn JN. Common variants in
the ENPP1 gene are not reproducibly associated
with diabetes or obesity. Diabetes. 2006 Nov;
55(11):3180-4. PMID: 17065359.
de Bakker PI, Burtt NP, Graham RR, Guiducci C,
Yelensky R, Drake JA, Bersaglieri T, Penney KL,
Butler J, Young S, Onofrio RC, Lyon HN, Stram
DO, Haiman CA, Freedman ML, Zhu X, Cooper R, Groop
L, Kolonel LN, Henderson BE, Daly MJ, Hirschhorn
JN, Altshuler D. Transferability of tag SNPs in
genetic association studies in multiple populations.
Nat Genet. 2006 Nov;38(11):1298-1303. PMID: 17057720.
Mutsuddi M, Morris DW, Waggoner SG, Daly MJ,
Scolnick EM, Sklar P. Analysis of high-resolution
HapMap of DTNBP1 (Dysbindin) suggests no consistency
between reported common variant associations and
schizophrenia.Am J Hum Genet. 2006 Nov;79(5):903-9.
PMID: 17033966.
Wiltshire S, de Bakker PI, Daly MJ. The value
of gene-based selection of tag SNPs in genome-wide
association studies. Eur J Hum Genet. 2006 Nov;14(11):1209-14.
PMID: 16804554.
Saxena R, Gianniny L, Burtt NP, Lyssenko V, Giuducci
C, Sjogren M, Florez JC, Almgren P, Isomaa B,
Orho-Melander M, Lindblad U, Daly MJ, Tuomi T,
Hirschhorn JN, Ardlie KG, Groop LC, Altshuler
D. Common single nucleotide polymorphisms in TCF7L2
are reproducibly associated with type 2 diabetes
and reduce the insulin response to glucose in
nondiabetic individuals. Diabetes. 2006 Oct;55(10):2890-5.
PMID: 17003358.
de Bakker PI, McVean G, Sabeti PC, Miretti MM,
Green T, Marchini J, Ke X, Monsuur AJ, Whittaker
P, Delgado M, Morrison J, Richardson A, Walsh
EC, Gao X, Galver L, Hart J, Hafler DA, Pericak-Vance
M, Todd JA, Daly MJ, Trowsdale J, Wijmenga C,
Vyse TJ, Beck S, Murray SS, Carrington M, Gregory
S, Deloukas P, Rioux JD. A high-resolution HLA
and SNP haplotype map for disease association
studies in the extended human MHC. Nat Genet.
2006 Oct;38(10):1166-72. PMID: 16998491.
Maller J, George S, Purcell S, Fagerness J, Altshuler
D, Daly MJ, Seddon JM. Common variation in three
genes, including a noncoding variant in CFH, strongly
influences risk of age-related macular degeneration.
Nat Genet. 2006 Sep;38(9):1055-9. PMID: 16936732.
Giallourakis C, Cao Z, Green T, Wachtel H, Xie
X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.
A molecular-properties-based approach to understanding
PDZ domain proteins and PDZ ligands.Genome Res.
2006 Aug;16(8):1056-72.PMID: 16825666.
Fisher SA, Hampe J, Onnie CM, Daly MJ, Curley
C, Purcell S, Sanderson J, Mansfield J, Annese
V, Forbes A, Lewis CM, Schreiber S, Rioux JD,
Mathew CG. Direct or indirect association in a
complex disease: the role of SLC22A4 and SLC22A5
functional variants in Crohn disease. Hum Mutat.
2006 Aug;27(8):778-85.PMID: 16835882.
Ishiguro K, Green T, Rapley J, Wachtel H, Giallourakis
C, Landry A, Cao Z, Lu N, Takafumi A, Goto H,
Daly MJ, Xavier RJ. Ca2+/calmodulin-dependent
protein kinase II is a modulator of CARMA1-mediated
NF-kappaB activation. Mol Cell Biol. 2006 Jul;26(14):5497-508.PMID:
16809782.
Saxena R, de Bakker PI, Singer K, Mootha V, Burtt
N, Hirschhorn JN, Gaudet D, Isomaa B, Daly MJ,
Groop L, Ardlie KG, Altshuler D. Comprehensive
association testing of common mitochondrial DNA
variation in metabolic disease. Am J Hum Genet.
2006 Jul;79(1):54-61. PMID: 16773565.
Pe'er I, de Bakker PI, Maller J, Yelensky R,
Altshuler D, Daly MJ. Evaluating and improving
power in whole-genome association studies using
fixed marker sets. Nat Genet. 2006 Jun;38(6):663-7.
PMID: 16715096.
Tello-Ruiz MK, Curley C, DelMonte T, Giallourakis
C, Kirby A, Miller K, Wild G, Cohen A, Langelier
D, Latiano A, Wedemeyer N, Lander E, Schreiber
S, Annese V, Daly MJ, Rioux JD. Haplotype-based
association analysis of 56 functional candidate
genes in the IBD6 locus on chromosome 19.Eur J
Hum Genet. 2006 Jun;14(6):780-90.PMID: 16570073.
Salmela E, Taskinen O, Seppanen JK, Sistonen
P, Daly MJ, Lahermo P, Savontaus ML, Kere J. Subpopulation
difference scanning: a strategy for exclusion
mapping of susceptibility genes. J Med Genet.
2006 Jul;43(7):590-7.PMID: 16443857.
Graham RR, Kozyrev SV, Baechler EC, Reddy MV,
Plenge RM, Bauer JW, Ortmann WA, Koeuth T, Gonzalez
Escribano MF; Argentine and Spanish Collaborative
Groups; Pons-Estel B, Petri M, Daly M, Gregersen
PK, Martin J, Altshuler D, Behrens TW, Alarcon-Riquelme
ME. A common haplotype of interferon regulatory
factor 5 (IRF5) regulates splicing and expression
and is associated with increased risk of systemic
lupus erythematosus. Nat Genet. 2006 May;38(5):550-5.
PMID: 16642019.
Pe'er I, Chretien YR, de Bakker PI, Barrett JC,
Daly MJ, Altshuler DM. Biases and reconciliation
in estimates of linkage disequilibrium in the
human genome. Am J Hum Genet. 2006 Apr;78(4):588-603.
PMID: 16532390.
Yan BS, Kirby A, Shebzukhov YV, Daly MJ, Kramnik
I. Genetic architecture of tuberculosis resistance
in a mouse model of infection. Genes Immun. 2006
Apr;7(3):201-10.PMID: 16452998.
Friedrichs F, Brescianini S, Annese V, Latiano
A, Berger K, Kugathasan S, Broeckel U, Nikolaus
S, Daly MJ, Schreiber S, Rioux JD, Stoll M. Evidence
of transmission ratio distortion of DLG5 R30Q
variant in general and implication of an association
with Crohn disease in men. Hum Genet. 2006 Apr;119(3):305-11.
PMID: 16446977.
Sun MW, Lee JY, de Bakker PI, Burtt NP, Almgren
P, Rastam L, Tuomi T, Gaudet D, Daly MJ, Hirschhorn
JN, Altshuler D, Groop L, Florez JC. Free Full
Text Haplotype structures and large-scale association
testing of the 5' AMP-activated protein kinase
genes PRKAA2, PRKAB1, and PRKAB2 [corrected] with
type 2 diabetes. Diabetes. 2006 Mar;55(3):849-55.
Erratum in: Diabetes. 2006 Jun;55(6):1904.PMID:
16505254.
Bonnen PE, Pe'er I, Plenge RM, Salit J, Lowe
JK, Shapero MH, Lifton RP, Breslow JL, Daly MJ,
Reich DE, Jones KW, Stoffel M, Altshuler D, Friedman
JM. Evaluating potential for whole-genome studies
in Kosrae, an isolated population in Micronesia.Nat
Genet. 2006 Feb;38(2):214-7. PMID: 16429162.
Florez JC, Wiltshire S, Agapakis CM, Burtt NP,
de Bakker PI, Almgren P, Bengtsson Bostrom K,
Tuomi T, Gaudet D, Daly MJ, Hirschhorn JN, McCarthy
MI, Altshuler D, Groop L. High-density haplotype
structure and association testing of the insulin-degrading
enzyme (IDE) gene with type 2 diabetes in 4,206
people. Diabetes. 2006 Jan;55(1):128-35.PMID:
16380485.
Crawford GE, Holt IE, Whittle J, Webb BD, Tai
D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg
D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg
TG, Collins FS. Genome-wide mapping of DNase hypersensitive
sites using massively parallel signature sequencing
(MPSS). Genome Res. 2006 Jan;16(1):123-31. PMID:
16344561.
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC,
Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee
C, Daly MJ, Altshuler DM; International HapMap
Consortium. Common deletion polymorphisms in the
human genome. Nat Genet. 2006 Jan;38(1):86-92.PMID:
16468122.
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