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Methods of integrating data to uncover genotype-phenotype interactions

Nature reviews. Genetics, 2015-02, Vol.16 (2), p.85-97

2015

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ATHENA: the analysis tool for heritable and environmental network associations

Bioinformatics, 2014-03, Vol.30 (5), p.698-705

2014

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Exome genotyping and linkage analysis identifies two novel linked regions and replicates two others for myopia in Ashkenazi Jewish families

BMC medical genetics, 2019-01, Vol.20 (1), p.27-27, Article 27

2019

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What makes a good prediction? Feature importance and beginning to open the black box of machine learning in genetics

Human genetics, 2022-09, Vol.141 (9), p.1515-1528

2022

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Genome-wide association study of plasma efavirenz pharmacokinetics in AIDS Clinical Trials Group protocols implicates several CYP2B6 variants

Pharmacogenetics and genomics, 2012-12, Vol.22 (12), p.858-867

2012

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Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies

Pharmacogenomics, 2012-01, Vol.13 (2), p.213-222

2012

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Genetic Association Reveals Protection against Recurrence of Clostridium difficile Infection with Bezlotoxumab Treatment

mSphere, 2020-05, Vol.5 (3)

2020

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ATHENA: a tool for meta-dimensional analysis applied to genotypes and gene expression data to predict HDL cholesterol levels

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2013, p.385

2013

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Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using biofilter, and gene-environment interactions using the Phenx Toolkit

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2015, p.495

2015

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Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2013, p.147

2013

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Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER

Journal of neurovirology, 2012-12, Vol.18 (6), p.511-520

2012

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Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)

BioData mining, 2015-12, Vol.8 (1), p.41-41, Article 41

2015

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Analysis of sequence data to identify potential risk variants for oral clefts in multiplex families

Molecular genetics & genomic medicine, 2017-09, Vol.5 (5), p.570-579

2017

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Comparison of parametric and machine methods for variable selection in simulated Genetic Analysis Workshop 19 data

BMC proceedings, 2016, Vol.10 (Suppl 7), p.147-152, Article 52

2016

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Machine learning and data mining in complex genomic data--a review on the lessons learned in Genetic Analysis Workshop 19

BMC genetics, 2016-02, Vol.17 Suppl 2 (S2), p.1, Article S1

2016

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Genetic Association Reveals Protection against Recurrence of italic toggle="yes">Clostridium difficile /italic> Infection with Bezlotoxumab Treatment

mSphere, 2020-06, Vol.5 (3)

2020

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Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals

BioData mining, 2017-07, Vol.10 (1), p.25-20, Article 25

2017

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Initialization parameter sweep in ATHENA: optimizing neural networks for detecting gene-gene interactions in the presence of small main effects

Proceedings of the 12th annual conference on Genetic and evolutionary computation, 2010, p.203-210

2010

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Comparison of Methods for Meta-dimensional Data Analysis Using in Silico and Biological Data Sets

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 2012, p.134-143

2012

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ATHENA Optimization: The Effect of Initial Parameter Settings across Different Genetic Models

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 2011, Vol.6623, p.48-58

2011

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Evaluation of Parameter Contribution to Neural Network Size and Fitness in ATHENA for Genetic Analysis

Genetic Programming Theory and Practice XI, 2014, p.211-224

2014

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Meta-Dimensional Analysis of Phenotypes Using the Analysis Tool for Heritable and Environmental Network Associations (ATHENA): Challenges with Building Large Networks

Genetic Programming Theory and Practice X, 2013, p.103-115

2013

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Extended clinical and immunological phenotype and transplant outcome in CD27 and CD70 deficiency

Blood, 2020-12, Vol.136 (23), p.2638-2655

2020

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Use of MRP8/14 in clinical practice as a predictor of outcome after methotrexate withdrawal in patients with juvenile idiopathic arthritis

Clinical rheumatology, 2022-09, Vol.41 (9), p.2825-2830

2022

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Methods of integrating data to uncover genotype-phenotype interactions

ATHENA: the analysis tool for heritable and environmental network associations

Exome genotyping and linkage analysis identifies two novel linked regions and replicates two others for myopia in Ashkenazi Jewish families

What makes a good prediction? Feature importance and beginning to open the black box of machine learning in genetics

Genome-wide association study of plasma efavirenz pharmacokinetics in AIDS Clinical Trials Group protocols implicates several CYP2B6 variants

Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies

Genetic Association Reveals Protection against Recurrence of Clostridium difficile Infection with Bezlotoxumab Treatment

ATHENA: a tool for meta-dimensional analysis applied to genotypes and gene expression data to predict HDL cholesterol levels

Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using biofilter, and gene-environment interactions using the Phenx Toolkit

Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit

Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER

Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)

Analysis of sequence data to identify potential risk variants for oral clefts in multiplex families

Comparison of parametric and machine methods for variable selection in simulated Genetic Analysis Workshop 19 data

Machine learning and data mining in complex genomic data--a review on the lessons learned in Genetic Analysis Workshop 19

Genetic Association Reveals Protection against Recurrence of italic toggle="yes">Clostridium difficile /italic> Infection with Bezlotoxumab Treatment

Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals

Initialization parameter sweep in ATHENA: optimizing neural networks for detecting gene-gene interactions in the presence of small main effects

Comparison of Methods for Meta-dimensional Data Analysis Using in Silico and Biological Data Sets

ATHENA Optimization: The Effect of Initial Parameter Settings across Different Genetic Models

Evaluation of Parameter Contribution to Neural Network Size and Fitness in ATHENA for Genetic Analysis

Meta-Dimensional Analysis of Phenotypes Using the Analysis Tool for Heritable and Environmental Network Associations (ATHENA): Challenges with Building Large Networks

Extended clinical and immunological phenotype and transplant outcome in CD27 and CD70 deficiency

Use of MRP8/14 in clinical practice as a predictor of outcome after methotrexate withdrawal in patients with juvenile idiopathic arthritis

Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy

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