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Research Output 1998 2020

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Article
2020

Local epigenomic data are more informative than local genome sequence data in predicting enhancer-promoter interactions using neural networks

Xiao, M., Zhuang, Z. & Pan, W., Jan 2020, In : Genes. 11, 1, 41.

Research output: Contribution to journalArticle

Open Access
Epigenomics
Genome
Learning
Genome-Wide Association Study
Genes
2019

An adaptive test for meta-analysis of rare variant association studies

Yang, T., Kim, J., Wu, C., Ma, Y., Wei, P. & Pan, W., Jan 1 2019, (Accepted/In press) In : Genetic epidemiology.

Research output: Contribution to journalArticle

Meta-Analysis
Exome
National Heart, Lung, and Blood Institute (U.S.)
Coronary Artery Disease
Triglycerides

A powerful fine-mapping method for transcriptome-wide association studies

Wu, C. & Pan, W., Jan 1 2019, (Accepted/In press) In : Human Genetics.

Research output: Contribution to journalArticle

Transcriptome
Genes
Linkage Disequilibrium
Schizophrenia
Genome-Wide Association Study
Microscopy
Proteins
Learning
Computational Biology
Datasets
2 Citations (Scopus)

A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data

Zhuang, Z., Shen, X. & Pan, W., Sep 1 2019, In : Bioinformatics. 35, 17, p. 2899-2906 8 p.

Research output: Contribution to journalArticle

DNA sequences
Promoter
DNA Sequence
Cells
Neural Networks
1 Citation (Scopus)

Constrained likelihood for reconstructing a directed acyclic Gaussian graph

Yuan, Y., Shen, X., Pan, W. & Wang, Z., Mar 1 2019, In : Biometrika. 106, 1, p. 109-125 17 p.

Research output: Contribution to journalArticle

Parameter estimation
Error analysis
Maximum likelihood
Computational complexity
Likelihood

Integrating germline and somatic genetics to identify genes associated with lung cancer

Pattee, J., Zhan, X., Xiao, G. & Pan, W., Jan 1 2019, (Accepted/In press) In : Genetic epidemiology.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Lung Neoplasms
Transcriptome
Genes
Neoplasms

Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes

Wu, C. & Pan, W., Oct 1 2019, In : Bioinformatics. 35, 19, p. 3576-3583 8 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Methylation
Genome-Wide Association Study
Schizophrenia
Genome

Likelihood Ratio Tests for a Large Directed Acyclic Graph

Li, C., Shen, X. & Pan, W., Jan 1 2019, In : Journal of the American Statistical Association.

Research output: Contribution to journalArticle

Directed Acyclic Graph
Likelihood Ratio Test
Asymptotic distribution
Pathway
Chi-squared

On High-Dimensional Constrained Maximum Likelihood Inference

Zhu, Y., Shen, X. & Pan, W., Jan 1 2019, In : Journal of the American Statistical Association.

Research output: Contribution to journalArticle

Likelihood Inference
Maximum Likelihood
High-dimensional
Regularization
Nuisance Parameter

Some statistical consideration in transcriptome-wide association studies

for the Alzheimer’s Disease Neuroimaging Initiative, Jan 1 2019, (Accepted/In press) In : Genetic epidemiology.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Transcriptome
Least-Squares Analysis
Gene Expression
Neuroimaging
2018
4 Citations (Scopus)

Adaptive SNP-Set Association Testing in Generalized Linear Mixed Models with Application to Family Studies

Park, J. Y., Wu, C., Basu, S., McGue, M. & Pan, W., Jan 1 2018, In : Behavior genetics. 48, 1, p. 55-66 12 p.

Research output: Contribution to journalArticle

Open Access
family studies
Single Nucleotide Polymorphism
Linear Models
Genome-Wide Association Study
testing
1 Citation (Scopus)

An adaptive gene-based test for methylation data 06 Biological Sciences 0604 Genetics

Wu, C., Park, J. Y., Guan, W. & Pan, W., Sep 17 2018, In : BMC Proceedings. 12, 60.

Research output: Contribution to journalArticle

Open Access
Methylation
Biological Science Disciplines
Cytosine
Guanine
Genes
1 Citation (Scopus)

An adaptive gene-level association test for pedigree data 06 Biological Sciences 0604 Genetics

Park, J. Y., Wu, C. & Pan, W., Sep 17 2018, In : BMC genetics. 19, 68.

Research output: Contribution to journalArticle

Open Access
Biological Science Disciplines
Pedigree
Genes
Single Nucleotide Polymorphism
Linear Models
1 Citation (Scopus)

Improved use of small reference panels for conditional and joint analysis with gwas summary statistics

Deng, Y. & Pan, W., Jun 2018, In : Genetics. 209, 2, p. 401-408 8 p.

Research output: Contribution to journalArticle

Open Access
Genome-Wide Association Study
Linkage Disequilibrium
Genome
Information Dissemination
Confidentiality
3 Citations (Scopus)

Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia

Wu, C. & Pan, W., Apr 2018, In : Genetic epidemiology. 42, 3, p. 303-316 14 p.

Research output: Contribution to journalArticle

Open Access
Quantitative Trait Loci
Genome-Wide Association Study
Schizophrenia
Genes
Transcriptome
4 Citations (Scopus)

Integration of enhancer-promoter interactions with GWAS summary results identifies novel schizophrenia-associated genes and pathways

Wu, C. & Pan, W., Jul 2018, In : Genetics. 209, 3, p. 699-709 11 p.

Research output: Contribution to journalArticle

Open Access
Genome-Wide Association Study
Schizophrenia
Genes
Transcriptome
Body Regions

Significance testing for allelic heterogeneity

Deng, Y. & Pan, W., Sep 2018, In : Genetics. 210, 1, p. 25-32 8 p.

Research output: Contribution to journalArticle

Open Access
Single Nucleotide Polymorphism
Genome-Wide Association Study
HDL Lipoproteins
Schizophrenia
Bayes Theorem
2 Citations (Scopus)

TCM visualizes trajectories and cell populations from single cell data

Gong, W., Kwak, I. Y., Koyano-Nakagawa, N., Pan, W. & Garry, D. J., Dec 1 2018, In : Nature communications. 9, 1, 2749.

Research output: Contribution to journalArticle

Open Access
Gene expression
Visualization
Cells
Trajectories
Throughput
2017
2 Citations (Scopus)

Adaptive testing for association between two random vectors in moderate to high dimensions

Xu, Z., Xu, G. & Pan, W., Nov 2017, In : Genetic epidemiology. 41, 7, p. 599-609 11 p.

Research output: Contribution to journalArticle

Open Access
Noise
Weights and Measures
3 Citations (Scopus)

Adaptive testing for multiple traits in a proportional odds model with applications to detect SNP-brain network associations

for the Alzheimer's Disease Neuroimaging Initiative, Apr 1 2017, In : Genetic epidemiology. 41, 3, p. 259-277 19 p.

Research output: Contribution to journalArticle

Open Access
Single Nucleotide Polymorphism
Brain
Phenotype
Neuroimaging
Sample Size

A novel and efficient algorithm for de novo discovery of mutated driver pathways in cancer

Liu, B., Wu, C., Shen, X. T. & Pan, W., Sep 2017, In : Annals of Applied Statistics. 11, 3, p. 1481-1512 32 p.

Research output: Contribution to journalArticle

Open Access
Driver
Pathway
Cancer
Mutation
Efficient Algorithms
14 Citations (Scopus)

A powerful framework for integrating eqtl and gwas summary data

Xu, Z., Wu, C., Wei, P. & Pan, W., Nov 2017, In : Genetics. 207, 3, p. 893-902 10 p.

Research output: Contribution to journalArticle

Open Access
Genome-Wide Association Study
Genes
Software
Lipids
Datasets
7 Citations (Scopus)

Conditional analysis of multiple quantitative traits based on marginal GWAS summary statistics

Deng, Y. & Pan, W., Jul 2017, In : Genetic epidemiology. 41, 5, p. 427-436 10 p.

Research output: Contribution to journalArticle

Open Access
Genome-Wide Association Study
Single Nucleotide Polymorphism
Linear Models
Cost-Benefit Analysis
Joints
12 Citations (Scopus)
Open Access
Single-Cell Analysis
Gene Expression Profiling
Software
computer programs
cells
10 Citations (Scopus)

Gene- and pathway-based association tests for multiple traits with GWAS summary statistics

Kwak, I. Y. & Pan, W., Jan 1 2017, In : Bioinformatics. 33, 1, p. 64-71 8 p.

Research output: Contribution to journalArticle

Open Access
Genome-Wide Association Study
Pathway
Genes
Statistics
Gene
7 Citations (Scopus)

Imaging-wide association study: Integrating imaging endophenotypes in GWAS

Xu, Z., Wu, C. & Pan, W., Oct 1 2017, In : NeuroImage. 159, p. 159-169 11 p.

Research output: Contribution to journalArticle

Open Access
Endophenotypes
Genome-Wide Association Study
Alzheimer Disease
Transcriptome
Gene Expression
2 Citations (Scopus)

Testing genetic pleiotropy with GWAS summary statistics for marginal and conditional analyses

Deng, Y. & Pan, W., Dec 2017, In : Genetics. 207, 4, p. 1285-1299 15 p.

Research output: Contribution to journalArticle

Open Access
Genetic Pleiotropy
Genome-Wide Association Study
LDL Cholesterol
Lipids
Hydroxymethylglutaryl-CoA Reductase Inhibitors
2016
25 Citations (Scopus)

Adaptive gene-and pathway-trait association testing with GWAS summary statistics

Kwak, I. Y. & Pan, W., Apr 15 2016, In : Bioinformatics. 32, 8, p. 1178-1184 7 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Pathway
Genes
Statistics
Adaptive Test
19 Citations (Scopus)

An adaptive association test for microbiome data

Wu, C., Chen, J., Kim, J. & Pan, W., May 19 2016, In : Genome Medicine. 8, 1, 56.

Research output: Contribution to journalArticle

Microbiota
Joints
Health
6 Citations (Scopus)

An adaptive two-sample test for high-dimensional means

Xu, G., Lin, L., Wei, P. & Pan, W., Sep 1 2016, In : Biometrika. 103, 3, p. 609-624 16 p.

Research output: Contribution to journalArticle

Adaptive Test
Two-sample Test
Genome-Wide Association Study
Chromosomes
Nucleotides
6 Citations (Scopus)

A new algorithm and theory for penalized regression-based clustering

Wu, C., Kwon, S., Shen, X. & Pan, W., Oct 1 2016, In : Journal of Machine Learning Research. 17

Research output: Contribution to journalArticle

Penalized Regression
Method of multipliers
Alternating Direction Method
Clustering
Grouping

Binomial Mixture Model Based Association Testing to Account for Genetic Heterogeneity for GWAS

Xu, Z. & Pan, W., Apr 1 2016, In : Genetic epidemiology. 40, 3, p. 202-209 8 p.

Research output: Contribution to journalArticle

Genetic Heterogeneity
Genome-Wide Association Study
Statistical Models
Single Nucleotide Polymorphism
Gene Frequency
14 Citations (Scopus)

Carotid Atherosclerosis and Stroke in Atrial Fibrillation: The Atherosclerosis Risk in Communities Study

Bekwelem, W., Jensen, P. N., Norby, F. L., Soliman, E. Z., Agarwal, S. K., Lip, G. Y. H., Pan, W., Folsom, A. R., Longstreth, W. T., Alonso, A., Heckbert, S. R. & Chen, L. Y., Jun 1 2016, In : Stroke. 47, 6, p. 1643-1646 4 p.

Research output: Contribution to journalArticle

Carotid Artery Diseases
Atrial Fibrillation
Atherosclerosis
Stroke
Carotid Intima-Media Thickness
6 Citations (Scopus)

Estimation of multiple networks in Gaussian mixture models

Gao, C., Zhu, Y., Shen, X. T. & Pan, W., Jan 1 2016, In : Electronic Journal of Statistics. 10, 1, p. 1133-1154 22 p.

Research output: Contribution to journalArticle

Gaussian Mixture Model
Functional Genomics
Unknown
Gene Networks
Gene Regulation
8 Citations (Scopus)

Integrative and regularized principal component analysis of multiple sources of data

Liu, B., Shen, X. & Pan, W., Jun 15 2016, In : Statistics in Medicine. 35, 13, p. 2235-2250 16 p.

Research output: Contribution to journalArticle

Information Storage and Retrieval
Principal Component Analysis
DNA Methylation
Neoplasms
DNA
1 Citation (Scopus)

Nonlinear joint latent variable models and integrative tumor subtype discovery

Liu, B., Shen, X. T. & Pan, W., Apr 1 2016, In : Statistical Analysis and Data Mining. 9, 2, p. 106-116 11 p.

Research output: Contribution to journalArticle

Latent Variable Models
Joint Model
Tumors
Tumor
Feature extraction
6 Citations (Scopus)

On robust association testing for quantitative traits and rare variants

Wei, P., Cao, Y., Zhang, Y., Xu, Z., Kwak, I. Y., Boerwinkle, E. & Pan, W., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 12, p. 3941-3950 10 p.

Research output: Contribution to journalArticle

Exome
National Heart, Lung, and Blood Institute (U.S.)
Triglycerides
Cohort Studies
Technology
17 Citations (Scopus)

Powerful and adaptive testing for multi-trait and Multi-SNP associations with GWAS and sequencing data

Alzheimer's Disease Neuroimaging Initiative, Jun 2016, In : Genetics. 203, 2, p. 715-731 17 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Alzheimer Disease
Brain
Genes
Chromosomes, Human, Pair 19
2015
3 Citations (Scopus)

A Bayesian partitioning model for the detection of multilocus effects in case-control studies

Ray, D., Li, X., Pan, W., Pankow, J. & Basu, S., Jul 22 2015, In : Human Heredity. 79, 2, p. 69-79 11 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Case-Control Studies
Type 2 Diabetes Mellitus
Single Nucleotide Polymorphism
Atherosclerosis
4 Citations (Scopus)

A cautionary note on using secondary phenotypes in neuroimaging genetic studies

for the Alzheimer's Disease Neuroimaging Initiative, Nov 1 2015, In : NeuroImage. 121, p. 136-145 10 p.

Research output: Contribution to journalArticle

Neuroimaging
Alzheimer Disease
Phenotype
Molecular Epidemiology
Health Services Needs and Demand
22 Citations (Scopus)

An Adaptive Association Test for Multiple Phenotypes with GWAS Summary Statistics

Kim, J., Bai, Y. & Pan, W., Dec 1 2015, In : Genetic epidemiology. 39, 8, p. 651-663 13 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Phenotype
Genotype
Genome
Meta-Analysis
1 Citation (Scopus)

A Novel Statistic for Global Association Testing Based on Penalized Regression

Austin, E., Shen, X. T. & Pan, W., Sep 1 2015, In : Genetic epidemiology. 39, 6, p. 415-426 12 p.

Research output: Contribution to journalArticle

Linkage Disequilibrium
Public Opinion
Genetic Structures
Logistic Models
Hypertension
28 Citations (Scopus)

A Powerful Pathway-Based Adaptive Test for Genetic Association with Common or Rare Variants

Pan, W., Kwak, I. Y. & Wei, P., Jan 1 2015, In : American Journal of Human Genetics. 97, 1, p. 86-98 13 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Genome-Wide Association Study
Genes
Genetic Heterogeneity
6 Citations (Scopus)

Approximate score-based testing with application to multivariate trait association analysis

Alzheimer's Disease Neuroimaging Initiative, Sep 1 2015, In : Genetic epidemiology. 39, 6, p. 469-479 11 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
DNA Sequence Analysis
Software
10 Citations (Scopus)

Highly adaptive tests for group differences in brain functional connectivity

Alzheimer's Disease Neuroimaging Initiative, Jan 1 2015, In : NeuroImage: Clinical. 9, p. 625-639 15 p.

Research output: Contribution to journalArticle

Brain
Alzheimer Disease
Neuroimaging
Uncertainty
Noise
9 Citations (Scopus)

Principal Component Regression and Linear Mixed Model in Association Analysis of Structured Samples: Competitors or Complements?

Zhang, Y. & Pan, W., Mar 1 2015, In : Genetic epidemiology. 39, 3, p. 149-155 7 p.

Research output: Contribution to journalArticle

Linear Models
Genome-Wide Association Study
Population
Environmental Pollution
Principal Component Analysis
8 Citations (Scopus)

Testing for polygenic effects in genome-wide association studies

Pan, W., Chen, Y. M. & Wei, P., May 1 2015, In : Genetic epidemiology. 39, 4, p. 306-316 11 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Single Nucleotide Polymorphism
Viverridae
Schizophrenia
Alcoholism
9 Citations (Scopus)

Testing Group Differences in Brain Functional Connectivity: Using Correlations or Partial Correlations?

Kim, J., Wozniak, J. R., Mueller, B. A. & Pan, W., May 1 2015, In : Brain connectivity. 5, 4, p. 214-231 18 p.

Research output: Contribution to journalArticle

Brain
Public Opinion
Healthy Volunteers
Alzheimer Disease
Magnetic Resonance Imaging
2014
1 Citation (Scopus)

Adjusting for population stratification and relatedness with sequencing data

Zhang, Y. & Pan, W., Jun 17 2014, In : BMC Proceedings. 8, S42.

Research output: Contribution to journalArticle

Genetic Association Studies
Linear Models
Genes
Availability
Genome