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181views more  BMCBI 2008»
11 years 6 months ago
Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270
Background: Genome-wide association studies (GWAS) aim to identify genetic variants (usually single nucleotide polymorphisms [SNPs]) across the entire human genome that are associ...
Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming M. ...
191views more  JCB 2007»
11 years 8 months ago
Bayesian Haplotype Inference via the Dirichlet Process
The problem of inferring haplotypes from genotypes of single nucleotide polymorphisms (SNPs) is essential for the understanding of genetic variation within and among populations, ...
Eric P. Xing, Michael I. Jordan, Roded Sharan
115views more  TCBB 2008»
11 years 8 months ago
Highly Scalable Genotype Phasing by Entropy Minimization
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. SNPs accoun...
Alexander Gusev, Ion I. Mandoiu, Bogdan Pasaniuc
160views ECommerce» more  EC 2007»
11 years 8 months ago
Agent-Based Model of Genotype Editing
Evolutionary algorithms rarely deal with ontogenetic, non-inherited alteration of genetic information because they are based on a direct genotype-phenotype mapping. In contrast, i...
Chien-Feng Huang, Jasleen Kaur, Ana Gabriela Magui...
94views more  BMCBI 2006»
11 years 8 months ago
Dynamic variable selection in SNP genotype autocalling from APEX microarray data
Background: Single nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide
Mohua Podder, William J. Welch, Ruben H. Zamar, Sc...
138views more  BMCBI 2008»
11 years 8 months ago
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
Background: The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organ...
Shu-Yi Su, Jonathan White, David J. Balding, Lachl...
135views more  BMCBI 2010»
11 years 8 months ago
A classification approach for genotyping viral sequences based on multidimensional scaling and linear discriminant analysis
Background: Accurate classification into genotypes is critical in understanding evolution of divergent viruses. Here we report a new approach, MuLDAS, which classifies a query seq...
Ji Woong Kim, Yongju Ahn, Kichan Lee, Sung-Hee Par...
137views more  BMCBI 2007»
11 years 8 months ago
GEVALT: An integrated software tool for genotype analysis
Background: Genotype information generated by individual and international efforts carries the promise of revolutionizing disease studies and the association of phenotypes with al...
Ofir Davidovich, Gad Kimmel, Ron Shamir
218views Optimization» more  GECCO 2010»
12 years 6 days ago
Cartesian genetic programming
This paper presents a new form of Genetic Programming called Cartesian Genetic Programming in which a program is represented as an indexed graph. The graph is encoded in the form o...
Julian Francis Miller, Simon L. Harding
145views Combinatorics» more  CPM 2004»
12 years 1 months ago
Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs
The perfect phylogeny model for haplotype evolution has been successfully applied to haplotype resolution from genotype data. In this study we explore the application of the perfe...
Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, It...