Hongyu Zhao

Hongyu Zhao, Raymond J Carroll, Ruiyan Luo, 2015, Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.

ProteomicsBrowser: MS/proteomics data visualization and investigation

Hongyu Zhao, Angus C Nairn, Gang Peng, 2018, Bioinform..

Experiments with obstacle and terrain avoidance of autonomous underwater vehicle

Lei Gao, Hongyu Zhao, Yiqun Wang, 2015, OCEANS 2015 - MTS/IEEE Washington.

Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies

Hongyu Zhao, Shuang Song, Wei Jiang, 2020, PLoS Comput. Biol..

On calculating the probability of a set of orthologous sequences

Liang Chen, Dirk F Moore, Weichung Joe Shih, 2009, Advances and applications in bioinformatics and chemistry : AABC.

Variance Estimation and Confidence Intervals from High-dimensional Genome-wide Association Studies Through Misspecified Mixed Model Analysis

Debashis Paul, Hongyu Zhao, Cecilia Dao, 2021, 2101.06638.

Conditional Functional Graphical Models

Hongyu Zhao, Lexin Li, Dingjue Ji, 2021, Journal of the American Statistical Association.

A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data

Naftali Kaminski, Hongyu Zhao, Taylor Adams, 2021, BMC Bioinform..

Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics

Hongyu Zhao, Qiongshi Lu, Wei Jiang, 2021, Briefings Bioinform..

Estimating genetic correlation jointly using individual-level and summary-level GWAS data

Hongyu Zhao, Qiongshi Lu, Wei Jiang, 2021 .

Transformation and differential abundance analysis of microbiome data incorporating phylogeny

Hongyu Zhao, Tao Wang, Chao Zhou, 2021, Bioinform..

Protein–DNA interaction mapping using genomic tiling path microarrays in Drosophila

Hongyu Zhao, Giacomo Cavalli, Kevin P White, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

Qian Wang, Hongyu Zhao, Qiongshi Lu, 2015, bioRxiv.

Genotyping Error Detection in Samples of Unrelated Individuals without Replicate Genotyping

Dabao Zhang, Hongyu Zhao, Nianjun Liu, 2008, Human Heredity.

Greedy outcome weighted tree learning of optimal personalized treatment rules

Shuangge Ma, Hongyu Zhao, Ruoqing Zhu, 2017, Biometrics.

Increased peripheral blood expression of electron transport chain genes in bipolar depression.

Rajita Sinha, Hongyu Zhao, Zubin Bhagwagar, 2010, Bipolar disorders.

Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS

Qian Wang, Can Yang, Hongyu Zhao, 2015, Human Genetics.

T cell-intrinsic role of IL-6 signaling in primary and memory responses

Yan Gao, Hongyu Zhao, Xiting Yan, 2014, eLife.

CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS.

Hongyu Zhao, Mengjie Chen, Hongyu Zhao, 2013, The annals of applied statistics.

Acute Drug-Induced Vascular Injury in Beagle Dogs: Pathology and Correlating Genomic Expression

Hongyu Zhao, Aiping Lin, Bradley E. Enerson, 2006, Toxicologic pathology.

Genetic Analysis of Variation in Transcription Factor Binding in Yeast

Wei Zheng, Hongyu Zhao, Lars M. Steinmetz, 2010, Nature.

A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing

Qian Wang, Hongyu Zhao, Qiongshi Lu, 2015, Front. Genet..

Adaptive clinical trial designs to detect interaction between treatment and a dichotomous biomarker

Hongyu Zhao, Feifang Hu, Hongjian Zhu, 2013 .

High-dimensional genome-wide association study and misspecified mixed model analysis

Can Yang, Debashis Paul, Hongyu Zhao, 2014, 1404.2355.

Implications of pleiotropy: challenges and opportunities for mining Big Data in biomedicine

Qian Wang, Can Yang, Hongyu Zhao, 2015, Front. Genet..

DNA-protein binding and gene expression patterns

Hongyu Zhao, Ning Sun, Ning Sun, 2003 .

Genome-wide Association Study of Cannabis Dependence Severity, Novel Risk Variants, and Shared Genetic Risks.

Qian Wang, Hongyu Zhao, Joel Gelernter, 2016, JAMA psychiatry.

Improving mass spectrometry peak detection using multiple peak alignment results.

Zengyou He, Hongyu Zhao, Hongyu Zhao, 2008, Journal of proteome research.

Rare independent mutations in renal salt handling genes contribute to blood pressure variation

Hongyu Zhao, Daniel Levy, Weizhen Ji, 2008, Nature Genetics.

Improved risk prediction for Crohn's disease with a multi-locus approach.

Judy H Cho, Hongyu Zhao, Michel Georges, 2011, Human molecular genetics.

Statistical Power of Model Selection Strategies for Genome-Wide Association Studies

Hongyu Zhao, Zheyang Wu, Hongyu Zhao, 2009, PLoS genetics.

Haplotype block structures show significant variation among populations

Hongyu Zhao, Nianjun Liu, Anthony J Brookes, 2004, Genetic epidemiology.

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

Hongyu Zhao, Ligeng Ma, Matthew Holford, 2009, Nature Genetics.

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

Yongmei Cheng, Wei Chen, Hongyu Zhao, 2013, PloS one.

Detecting Epistatic SNPs Associated with Complex Diseases via a Bayesian Classification Tree Search Method

Hongyu Zhao, Judy Cho, Min Chen, 2011, Annals of human genetics.

Light Control of Arabidopsis Development Entails Coordinated Regulation of Genome Expression and Cellular Pathways

Hongyu Zhao, Xing Wang Deng, Janet Hager, 2001, The Plant Cell Online.

Haplotype Frequency Estimation in the Presence of Genotyping Errors

Hongyu Zhao, Guohua Zou, Hongyu Zhao, 2003, Human Heredity.

The impact of sample size and marker selection on the study of haplotype structures

Hongyu Zhao, Hongyu Zhao, J. Stephens, 2004, Human Genomics.

Shrinkage‐based Diagonal Discriminant Analysis and Its Applications in High‐Dimensional Data

Tiejun Tong, Hongyu Zhao, Herbert Pang, 2009, Biometrics.

On the Convergence of the EM Algorithm: A Data-Adaptive Analysis

Can Yang, Hongyu Zhao, Chong Wu, 2016, 1611.00519.

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.

Jian Wang, Lars Bolund, Ning Su, 2005, Genome research.

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

Kei-Hoi Cheung, Jiehuan Sun, Hongyu Zhao, 2015, Scientific Reports.

SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data

Hongyu Zhao, Murat Gunel, Mengjie Chen, 2013, PloS one.

Evidence for association between multiple complement pathway genes and AMD

Hongyu Zhao, Valentin Dinu, Hongyu Zhao, 2007, Genetic epidemiology.

On optimal pooling designs to identify rare variants through massive resequencing

Murim Choi, Hongyu Zhao, Xiting Yan, 2011, Genetic epidemiology.

A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data

Hongyu Zhao, Mingfeng Li, Zhixiang Lin, 2016, Statistical applications in genetics and molecular biology.

FTO gene SNPs associated with extreme obesity in cases, controls and extremely discordant sister pairs

Hongyu Zhao, Hongyu Zhao, R. A. Price, 2008, BMC Medical Genetics.

A non-parametric approach to population structure inference using multilocus genotypes

Hongyu Zhao, Nianjun Liu, Hongyu Zhao, 2006, Human Genomics.

Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation

William Wheeler, Hongyu Zhao, John P. Ferguson, 2012, European Journal of Human Genetics.

Association of Gamma-Aminobutyric Acid A Receptor α2 Gene (GABRA2) with Alcohol Use Disorder

Hongyu Zhao, Joel Gelernter, Arvis Sulovari, 2014, Neuropsychopharmacology.

On high-dimensional misspecified mixed model analysis in genome-wide association study

Can Yang, Debashis Paul, Hongyu Zhao, 2016 .

Handbook of Statistical Bioinformatics

Bernhard Schölkopf, Hongyu Zhao, Henry Horng-Shing Lu, 2011 .

Disease-drug pairs revealed by computational genomic connectivity mapping on GBA1 deficient, Gaucher disease mice

Hongyu Zhao, Ling-Ling Zhu, Tony Yuen, 2012, Biochemical and Biophysical Research Communications.

A Genome-Wide Association Study on Obesity and Obesity-Related Traits

Hongyu Zhao, Struan F. A. Grant, Joseph T. Glessner, 2011, PloS one.

Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality

Hongyu Zhao, Gang Peng, John H. Krystal, 2018, Clinical Epigenetics.

Metabolic Regulation of Gene Expression by Histone Lysine β‐hydroxybutyrylation

Hongyu Zhao, Chao Peng, Dongjun Chung, 2016, Molecular cell.

Parametric and Nonparametric FDR Estimation Revisited

Hongyu Zhao, Zhong Guan, Hongyu Zhao, 2006, Biometrics.

On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals

Xiaofeng Zhu, Hongyu Zhao, Hongyu Zhao, 2003, Genetic epidemiology.

iFad: an integrative factor analysis model for drug-pathway association inference

Hongyu Zhao, Haisu Ma, 2012 .

Ovarian Cancer Classification Based on Mass Spectrometry Analysis of Sera

Hongyu Zhao, David Fishman, Gil Mor, 2006 .

The impacts of errors in individual genotyping and DNA pooling on association studies

Hongyu Zhao, Guohua Zou, Hongyu Zhao, 2004, Genetic epidemiology.

Haplotype analysis in population genetics and association studies.

Hongyu Zhao, Ruth Pfeiffer, Mitchell H Gail, 2003, Pharmacogenomics.

Genomewide linkage scan for opioid dependence and related traits.

Hongyu Zhao, Joel Gelernter, Marsha Wilcox, 2006, American journal of human genetics.

Differentially co-expressed genes in postmortem prefrontal cortex of individuals with alcohol use disorders: influence on alcohol metabolism-related pathways

Hongyu Zhao, Joel Gelernter, Fan Wang, 2014, Human Genetics.

Gene Regulation Network Inference With Joint Sparse Gaussian Graphical Models

Hongyu Zhao, Hyonho Chun, Hongyu Zhao, 2015, Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.

Leveraging Functional Annotations in Genetic Risk Prediction for Human Complex Diseases

Hongyu Zhao, Qiongshi Lu, Yiming Hu, 2016 .

Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.

Mark Gerstein, Nathaniel Echols, Hongyu Zhao, 2004, Journal of molecular biology.

Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease

Qian Wang, Wei Liu, Hongyu Zhao, 2016, bioRxiv.

Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment

Hongyu Zhao, Joel Gelernter, Hongyu Zhao, 2005, BMC Genetics.

Gene hunting of the Genetic Analysis Workshop 16 rheumatoid arthritis data using rough set theory

Chatchawit Aporntewan, Hongyu Zhao, Zheyang Wu, 2009, BMC proceedings.

The genetics of functional disability in schizophrenia and bipolar illness: Methods and initial results for VA cooperative study #572

Hongyu Zhao, Mary Brophy, Philip D. Harvey, 2014, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

On Estimation of Allele Frequencies via Next-Generation DNA Resequencing with Barcoding

Hongyu Zhao, Hongyu Zhao, Joon Sang Lee, 2013, Statistics in biosciences.

Family‐Based Association Tests for Different Family Structures Using Pooled DNA

Hongyu Zhao, Guohua Zou, Hongyu Zhao, 2005, Annals of human genetics.

A New Approach for the Joint Analysis of Multiple Chip-Seq Libraries with Application to Histone Modification

Judy H Cho, Hongyu Zhao, John P Ferguson, 2012, Statistical applications in genetics and molecular biology.

Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers

Debashis Ghosh, Bin Zhu, Hongyu Zhao, 2017, Scientific Reports.

Asymptotic efficiency and finite-sample properties of the generalized profiling estimation of parameters in ordinary differential equations

Hongyu Zhao, Xin Qi, Hongyu Zhao, 2009, 0903.3400.

On the use of DNA pooling to estimate haplotype frequencies

Hongyu Zhao, Kenneth K Kidd, Hongyu Zhao, 2003, Genetic epidemiology.

Exploring the genetic architecture of alcohol dependence in African-Americans via analysis of a genomewide set of common variants

Can Yang, Hongyu Zhao, Henry R. Kranzler, 2013, Human Genetics.

Integrating GWASs and human protein interaction networks identifies a gene subnetwork underlying alcohol dependence.

Hongyu Zhao, Eric Boerwinkle, Joel Gelernter, 2013, American journal of human genetics.

Bias‐Corrected Diagonal Discriminant Rules for High‐Dimensional Classification

Tiejun Tong, Hongyu Zhao, Hongyu Zhao, 2010, Biometrics.

A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus

Hongyu Zhao, Trefor Jenkins, David Goldman, 1998, Human Genetics.

Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data

Inyoung Kim, Hongyu Zhao, Herbert Pang, 2015, Statistics in biosciences.

Phylogeny-based tumor subclone identification using a Bayesian feature allocation model

Hongyu Zhao, Joshua L. Warren, Hongyu Zhao, 2018, The Annals of Applied Statistics.

Detection boundary and Higher Criticism approach for rare and weak genetic effects

Jiashun Jin, Hongyu Zhao, Zheyang Wu, 2014, 1407.8382.

Practical Issues in Building Risk-Predicting Models for Complex Diseases

Hongyu Zhao, Jia Kang, Hongyu Zhao, 2010, Journal of biopharmaceutical statistics.

Microarrays

Hongyu Zhao, Terry Speed, Hongyu Zhao, 2009, Statistical methods in medical research.

A statistical framework for cross-tissue transcriptome-wide association analysis

Hongyu Zhao, Qiongshi Lu, Yiming Hu, 2018, bioRxiv.

Prediction of pattern recognition receptor family using pseudo-amino acid composition.

Hongyu Zhao, Jia He, Qing-Bin Gao, 2012, Biochemical and biophysical research communications.

Protein interaction predictions from diverse sources.

Inyoung Kim, Hongyu Zhao, Hongyu Zhao, 2008, Drug discovery today.

Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

Yufeng Shen, Alessandro Giardini, Hongyu Zhao, 2017, Nature Genetics.

Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data

Hongyu Zhao, Christopher A. Fragoso, Christopher Heffelfinger, 2015, Genetics.

Estimating DNA methylation levels by joint modeling of multiple methylation profiles from microarray data.

Tao Wang, Hongyu Zhao, Mengjie Chen, 2016, Biometrics.

MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence.

Wei Chen, Yongmei Cheng, Hongyu Zhao, 2013, Journal of microbiological methods.

Bayesian Analysis of iTRAQ Data with Nonrandom Missingness: Identification of Differentially Expressed Proteins

Hongyu Zhao, Ruiyan Luo, Christopher M Colangelo, 2009, Statistics in biosciences.

Nonparametric estimator of false discovery rate based on Bernšteǐn polynomials

Hongyu Zhao, Zhong Guan, Hongyu Zhao, 2008 .

Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use

Hongyu Zhao, Joel Gelernter, Amei Amei, 2019, bioRxiv.

Identifying Gene–Environment and Gene–Gene Interactions Using a Progressive Penalization Approach

Shuangge Ma, Hongyu Zhao, Hongyu Zhao, 2014, Genetic epidemiology.

Haplotype-association analysis.

Kui Zhang, Hongyu Zhao, Nianjun Liu, 2008, Advances in genetics.

Expression of the type 3 InsP3 receptor is a final common event in the development of hepatocellular carcinoma

Hongyu Zhao, Jianlei Gu, Yung-Chi Cheng, 2019, Gut.

Interacting genetic loci on chromosomes 20 and 10 influence extreme human obesity.

Hongyu Zhao, Chuanhui Dong, Hongyu Zhao, 2003, American journal of human genetics.

On the Convergence of the EM Algorithm: From the Statistical Perspective

Can Yang, Hongyu Zhao, Chong Wu, 2016 .

Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies

Hongyu Zhao, Walter McMurray, Kathryn Stone, 2005, Current protocols in bioinformatics.

Controlling Population Structure in Human Genetic Association Studies with Samples of Unrelated Individuals.

Hongyu Zhao, Nianjun Liu, David B Allison, 2011, Statistics and its interface.

Flexible and scalable genotyping-by-sequencing strategies for population studies

Hongyu Zhao, Christopher A. Fragoso, Christopher Heffelfinger, 2014, BMC Genomics.

Analyzing cellular biochemistry in terms of molecular networks.

Mark Gerstein, Dov Greenbaum, Yu Xia, 2003, Annual review of biochemistry.

Genome-Wide Association Study of Opioid Dependence: Multiple Associations Mapped to Calcium and Potassium Pathways

Hongyu Zhao, Henry R. Kranzler, Lindsay A. Farrer, 2014, Biological Psychiatry.

Genomewide association study of cocaine dependence and related traits: FAM53B identified as a risk gene

Hongyu Zhao, Henry R. Kranzler, Joel Gelernter, 2013, Molecular Psychiatry.

A powerful approach to estimating annotation-stratified genetic covariance using GWAS summary statistics

Hongyu Zhao, Qiongshi Lu, Yiming Hu, 2017, bioRxiv.

Sample size needed to detect gene-gene interactions using association designs.

Hongyu Zhao, Hongyu Zhao, Shuang Wang, 2003, American journal of epidemiology.

Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development

Hongyu Zhao, Xing Wang Deng, Ligeng Ma, 2003, Development.

Phylogenetic Indian Buffet Process: Theory and Applications in Integrative Analysis of Cancer Genomics

Hongyu Zhao, Chao Gao, Mengjie Chen, 2013 .

Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction

Wei Liu, Hongyu Zhao, Qiongshi Lu, 2017, PLoS genetics.

Mediated pleiotropy between psychiatric disorders and autoimmune disorders revealed by integrative analysis of multiple GWAS

Can Yang, Qian Wang, Hongyu Zhao, 2015, bioRxiv.

Bayesian Methods for Predicting Interacting Protein Pairs Using Domain Information

Inyoung Kim, Hongyu Zhao, Hongyu Zhao, 2007, Biometrics.

Statistical Analysis Reveals Co-Expression Patterns of Many Pairs of Genes in Yeast Are Jointly Regulated by Interacting Loci

Hongyu Zhao, Minghua Deng, Wei Zheng, 2013, PLoS genetics.

A penalized linear mixed model for genomic prediction using pedigree structures

Can Yang, Hongyu Zhao, Mengjie Chen, 2014, BMC Proceedings.

De novo mutations in histone modifying genes in congenital heart disease

Murim Choi, Hongyu Zhao, Alexander E. Lopez, 2013, Nature.

Assessing reliability of gene clusters from gene expression data

Hongyu Zhao, Kui Zhang, Hongyu Zhao, 2000, Functional & Integrative Genomics.

Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma.

Hongyu Zhao, Xiting Yan, Carole Holm, 2016, Annals of the American Thoracic Society.

Test of Association for Quantitative Traits in General Pedigrees: The Quantitative Pedigree Disequilibrium Test

Hongyu Zhao, Fengzhu Sun, Kui Zhang, 2001, Genetic epidemiology.

Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains

Hongyu Zhao, Liang Chen, 2004, BMC Genomics.

Improving genetic risk prediction by leveraging pleiotropy

Can Yang, Hongyu Zhao, Joel Gelernter, 2013, Human Genetics.

MALDI-MS data analysis for disease biomarker discovery.

Weichuan Yu, Hongyu Zhao, Kenneth R Williams, 2006, Methods in molecular biology.

Practical Population Group Assignment with Selected Informative Markers: Characteristics and Properties of Bayesian Clustering via Structure

Hongyu Zhao, Joel Gelernter, Hongyu Zhao, 2022 .

A statistical framework for cross-tissue transcriptome-wide association analysis

Hongyu Zhao, Qiongshi Lu, Yiming Hu, 2018, Nature Genetics.

Semantic Web-Based Integration of Cancer Pathways and Allele Frequency Data

Kei-Hoi Cheung, Hongyu Zhao, Kenneth K. Kidd, 2009, Cancer informatics.

Two-Stage Designs in Case–Control Association Analysis

Yijun Zuo, Hongyu Zhao, Guohua Zou, 2006, Genetics.

Information assessment on predicting protein-protein interactions BMC Bioinformatics 2004

Mark Gerstein, Ronald Jansen, Hongyu Zhao, 2004 .

Serum protein markers for early detection of ovarian cancer.

Hongyu Zhao, Gil Mor, Yinglei Lai, 2005, Proceedings of the National Academy of Sciences of the United States of America.

A genome wide association study of plasma uric acid levels in obese cases and never-overweight controls

Hongyu Zhao, Joseph T. Glessner, Hakon Hakonarson, 2013, Obesity.