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MaCH-Admix: Genotype Imputation for Admixed Populations

by Eric Yi Liu, Mingyao Li, Wei Wang, Yun Li , 2012
"... ABSTRACT: Imputation in admixed populations is an important problem but challenging due to the complex linkage disequilibrium (LD) pattern. The emergence of large reference panels such as that from the 1,000 Genomes Project enables more accurate imputation in general, and in particular for admixed p ..."
Abstract - Cited by 23 (3 self) - Add to MetaCart
hidden Markov model and specific to each target individual. These methods fall into two categories: identity-by-state (IBS) based and ancestry-weighted approach. We evaluated the performance on individuals from recently admixed populations. Our target samples include 8,421 African Americans and 3

Genetic Epidemiology 00: 1–13 (2012) MaCH-Admix: Genotype Imputation for Admixed Populations

by Eric Yi Liu, Mingyao Li, Wei Wang, Yun Li
"... Imputation in admixed populations is an important problem but challenging due to the complex linkage disequilibrium (LD) pattern. The emergence of large reference panels such as that from the 1,000 Genomes Project enables more accurate imputation in general, and in particular for admixed populations ..."
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hidden Markov model and specific to each target individual. These methods fall into two categories: identity-by-state (IBS) based and ancestry-weighted approach. We evaluated the performance on individuals from recently admixed populations. Our target samples include 8,421 African Americans and 3

A Novel Approach to Structure Alignment

by Mattias Ohlsson, Carsten Peterson, Markus Ringnér, Richard Blankenbecler - Protein Sci , 2000
"... Motivation: Aligning protein structures is a highly relevant task. It enables the study of functional and ancestry relationships between proteins and is very important for homology and threading methods in structure prediction. Existing methods typically only partially explore the space of possible ..."
Abstract - Cited by 3 (0 self) - Add to MetaCart
-valued atomic coordinates. (2) Minimization of the error function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation/translation of atomic coordinates is performed, weighted with the corresponding assignment variables. The approach

A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies. PloS one 6: e24220

by Nirmala Akula, Ancha Baranova, Donald Seto, Jeffrey Solka, Michael A. Nalls, Andrew Singleton, Luigi Ferrucci, Toshiko Tanaka, Stefania B, Yoon Shin Cho, Young Jin Kim, Control Consortium, Francis J. Mcmahon , 2011
"... Genome-wide association studies (GWAS) are a valuable approach to understanding the genetic basis of complex traits. One of the challenges of GWAS is the translation of genetic association results into biological hypotheses suitable for further investigation in the laboratory. To address this challe ..."
Abstract - Cited by 12 (0 self) - Add to MetaCart
Genome-wide association studies (GWAS) are a valuable approach to understanding the genetic basis of complex traits. One of the challenges of GWAS is the translation of genetic association results into biological hypotheses suitable for further investigation in the laboratory. To address

Efficient learning of microbial genotype-phenotype association rules

by Norman J Macdonald, Robert G Beiko - Bioinformatics , 2010
"... Motivation: Finding biologically causative genotype-phenotype associations from whole-genome data is difficult due to the large gene feature space to mine, the potential for interactions among genes and phylogenetic correlations between genomes. Associations within phylogentically distinct organisms ..."
Abstract - Cited by 5 (0 self) - Add to MetaCart
the dependence among samples by modeling shared ancestry using conditional mutual information, and demonstrate its complementary nature to traditional mining approaches. Availability: Software implemented for this study is available under the Creative Commons Attribution 3.0 license from the author at

Running Head: Structure Alignment of Proteins

by Mattias Ohlsson, Carsten Peterson, Markus Ringnér, Richard Blankenbecler , 2000
"... Background: Aligning protein structures is a highly relevant task. It enables the study of functional and ancestry relationships between proteins and is very important for homology and threading methods in structure prediction. Existing methods typically only partially explore the space of possible ..."
Abstract - Add to MetaCart
-valued atomic coordinates. (2) Minimization of the error function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation/translation of atomic coordinates is performed, weighted with the corresponding assignment variables. The approach

A Nonlinear Hierarchical Model for Estimating Prevalence Rates with Small Samples

by unknown authors
"... Estimating prevalence rates with small weighted sam-ples, especially for rare diseases is a challenging task. We encountered such a situation in the recent Na-tional Latino and Asian American Study (NLAAS) on mental health. Due to small sizes of the weighted samples in various age groups, the standa ..."
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Estimating prevalence rates with small weighted sam-ples, especially for rare diseases is a challenging task. We encountered such a situation in the recent Na-tional Latino and Asian American Study (NLAAS) on mental health. Due to small sizes of the weighted samples in various age groups

Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats.

by A M Casa , Ae S E Mitchell , Ae M T Hamblin , H Sun , Ae J E Bowers , Ae A H Paterson , C F Aquadro , Ae S Kresovich - Theor. Appl. Genet. , 2005
"... Abstract Although molecular markers and DNA sequence data are now available for many crop species, our ability to identify genetic variation associated with functional or adaptive diversity is still limited. In this study, our aim was to quantify and characterize diversity in a panel of cultivated ..."
Abstract - Cited by 8 (0 self) - Add to MetaCart
of these loci mapped in or near genomic regions associated with domestication-related QTLs (i.e., shattering, seed weight, and rhizomatousness). We anticipate that such population genetics-based statistical approaches will be useful for re-evaluating extant SSR data for mining interesting genomic regions from

ORIGINAL COMMUNICATION Evidence-Based Anatomy KAISSAR YAMMINE* The Foot and Hand Clinic at Emirates Hospital and The Center for Evidence-Based Sports And Orthopedic

by United Arab Emirates
"... Anatomy is a descriptive basic medical science that is no longer considered a research-led discipline. Many publications in clinical anatomy are prevalence studies treating clinically relevant anatomical variations and reporting their fre-quencies and/or associations with variables such as age, sex, ..."
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, side, laterality, and ancestry. This article discusses the need to make sense of the available lit-erature. A new concept, evidence-based anatomy (EBA), is proposed to find, appraise, and synthetize the results reported in such publications. It consists in applying evidence-based principles

INVESTIGATION Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium

by Po-ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K. Pickrell, David Reich, Bonnie Berger
"... ABSTRACT Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in ..."
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in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD
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