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Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.
Zhuang Z, Gusev A, Cho J, Pe'er I. Zhuang Z, et al. PLoS One. 2012;7(10):e47618. doi: 10.1371/journal.pone.0047618. Epub 2012 Oct 11. PLoS One. 2012. PMID: 23071825 Free PMC article.
In doing so, we extend GERMLINE, a method to detect IBD from exome sequencing data by finding small slices of matching alleles between pairs of individuals and extending them into full IBD segments. ...We hypothesize that the variable coverage and platform biases of exome …
In doing so, we extend GERMLINE, a method to detect IBD from exome sequencing data by finding small slices of matching alleles betwee …
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. Gusev A, et al. Genetics. 2012 Feb;190(2):679-89. doi: 10.1534/genetics.111.134874. Epub 2011 Nov 30. Genetics. 2012. PMID: 22135348 Free PMC article.
We ascertained a pilot data set of whole-genome sequences from seven Kosraean individuals, with average 5× coverage. This assay identified 5,735,306 unique sites of which 1,212,831 were previously unknown. ...This study presents whole-genome analysis of a homogenous …
We ascertained a pilot data set of whole-genome sequences from seven Kosraean individuals, with average 5× coverage. This assay ident …
Highly scalable genotype phasing by entropy minimization.
Gusev A, Măndoiu II, Paşaniuc B. Gusev A, et al. IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):252-61. doi: 10.1109/TCBB.2007.70223. IEEE/ACM Trans Comput Biol Bioinform. 2008. PMID: 18451434
A Single Nucleotide Polymorphism (SNP) is a position in the genome at which two or more of the possible four nucleotides occur in a large percentage of the population. ...A description of the SNPs in a chromosome is called a haplotype. At
A Single Nucleotide Polymorphism (SNP) is a position in the genome at which two or more of the possible four nucleotides occur
The architecture of long-range haplotypes shared within and across populations.
Gusev A, Palamara PF, Aponte G, Zhuang Z, Darvasi A, Gregersen P, Pe'er I. Gusev A, et al. Mol Biol Evol. 2012 Feb;29(2):473-86. doi: 10.1093/molbev/msr133. Epub 2011 Oct 6. Mol Biol Evol. 2012. PMID: 21984068 Free PMC article.
Homologous long segments along the genomes of close or remote relatives that are identical by descent (IBD) from a common ancestor provide clues for recent events in human genetics. ...We show that the frequency of IBD pairs is population dependent and can be used to clust …
Homologous long segments along the genomes of close or remote relatives that are identical by descent (IBD) from a common ancestor pr …
DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation.
Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe'er I. Gusev A, et al. Am J Hum Genet. 2011 Jun 10;88(6):706-717. doi: 10.1016/j.ajhg.2011.04.023. Epub 2011 May 27. Am J Hum Genet. 2011. PMID: 21620352 Free PMC article.
Rare variants affecting phenotype pose a unique challenge for human genetics. Although genome-wide association studies have successfully detected many common causal variants, they are underpowered in identifying disease variants that are too rare or population-specific to …
Rare variants affecting phenotype pose a unique challenge for human genetics. Although genome-wide association studies have successfu …
HLA type inference via haplotypes identical by descent.
Setty MN, Gusev A, Pe'er I. Setty MN, et al. J Comput Biol. 2011 Mar;18(3):483-93. doi: 10.1089/cmb.2010.0258. J Comput Biol. 2011. PMID: 21385049
The human leukocyte antigen (HLA) genes play a major role in adaptive immune response and are used to differentiate self antigens from non-self ones. ...We analyze performance of the method in a previously typed subset of the HapMap population, achieving accuracy of …
The human leukocyte antigen (HLA) genes play a major role in adaptive immune response and are used to differentiate self antigens fro …
Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population.
Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Kang HM, Newton-Cheh C, Daly MJ, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL, Pe'er I. Kenny EE, et al. Hum Mol Genet. 2011 Feb 15;20(4):827-39. doi: 10.1093/hmg/ddq510. Epub 2010 Nov 30. Hum Mol Genet. 2011. PMID: 21118897 Free PMC article.
Further, we leveraged shared identity-by-descent genetic segments in the region of the uric acid locus to fine-map the signal, refining the known locus by a factor of 4. Finally, we report a novel associations for height (rs17629022, P< 2.1 × 10⁻⁸)....
Further, we leveraged shared identity-by-descent genetic segments in the region of the uric acid locus to fine-map the signal, refining the …
Whole population, genome-wide mapping of hidden relatedness.
Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I. Gusev A, et al. Genome Res. 2009 Feb;19(2):318-26. doi: 10.1101/gr.081398.108. Epub 2008 Oct 29. Genome Res. 2009. PMID: 18971310 Free PMC article.
We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. ...Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact matches between indiv …
We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of indiv …
Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae.
Kenny EE, Gusev A, Riegel K, Lütjohann D, Lowe JK, Salit J, Maller JB, Stoffel M, Daly MJ, Altshuler DM, Friedman JM, Breslow JL, Pe'er I, Sehayek E. Kenny EE, et al. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13886-91. doi: 10.1073/pnas.0907336106. Epub 2009 Aug 10. Proc Natl Acad Sci U S A. 2009. PMID: 19667188 Free PMC article.
To overcome confounding effects of multiple independent variants at such a locus and narrow the interval for causal allele capture, we developed an approach that maps local shared haplotypes harboring a putative causal variant. ...A single 526-kb haplotype ma …
To overcome confounding effects of multiple independent variants at such a locus and narrow the interval for causal allele capture, w …
Quantifying missing heritability at known GWAS loci.
Gusev A, Bhatia G, Zaitlen N, Vilhjalmsson BJ, Diogo D, Stahl EA, Gregersen PK, Worthington J, Klareskog L, Raychaudhuri S, Plenge RM, Pasaniuc B, Price AL. Gusev A, et al. PLoS Genet. 2013;9(12):e1003993. doi: 10.1371/journal.pgen.1003993. Epub 2013 Dec 26. PLoS Genet. 2013. PMID: 24385918 Free PMC article.
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