H. Deng

发表

Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies

Yu-ping Wang, Junbo Duan, Ji-Gang Zhang, 2013, PloS one.

EPS‐LASSO: test for high‐dimensional regression under extreme phenotype sampling of continuous traits

Yu-Ping Wang, Hui Shen, Jian Fang, 2018, Bioinform..

A Unified Sparse Representation for Sequence Variant Identification for Complex Traits

Yu-ping Wang, H. Deng, S. Cao, 2014, Genetic epidemiology.

Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network

Dongdong Lin, Yu-Ping Wang, Ji-Gang Zhang, 2017, BMC Bioinformatics.

Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence

J. Yun, Yu-ping Wang, Hongzheng Ren, 2020, bioRxiv.

Identification of novel rheumatoid arthritis-associated MiRNA-204-5p from plasma exosomes

H. Deng, S. Lei, F. Deng, 2022, Experimental & molecular medicine.

Metagenomic Profiling, Interaction of Genomics with Meta-genomics

Yu-ping Wang, Ji-Gang Zhang, H. Deng, 2016 .

Class-specific correlations of gene expressions: identification and their effects on clustering analyses.

Ji-Gang Zhang, H. Deng, Jian Li, 2008, American journal of human genetics.

Comprehensive Characterization of Human Genome Variation by High Coverage Whole-Genome Sequencing of Forty Four Caucasians

Hui Shen, Jun Chen, Chao Xu, 2013, PloS one.

Fusing Gene Interaction to Improve Disease Discrimination on Classification Analysis.

Ji-Gang Zhang, H. Deng, Wenlong Tang, 2012, Advancements in genetic engineering.

Low‐, high‐coverage, and two‐stage DNA sequencing in the design of the genetic association study

Hui Shen, Ji-Gang Zhang, Chao Xu, 2017, Genetic epidemiology.

Mutant ZP1 in familial infertility.

H. Deng, C. Papasian, Hongmei Xiao, 2014, The New England journal of medicine.

Gains in power for exhaustive analyses of haplotypes using variable-sized sliding window strategy: a comparison of association-mapping strategies

Yanfang Guo, Jian Li, H. Deng, 2009, European Journal of Human Genetics.

Structure and molecular phylogeny of sasA genes in cyanobacteria: insights into evolution of the prokaryotic circadian system.

E. Nevo, H. Deng, V. Dvornyk, 2004, Molecular biology and evolution.

Multi-omics analyses of drug repurposing reveal Acebutolol and Amiloride for osteoporosis treatment

H. Deng, L. Tan, Yue Zhang, 2022, bioRxiv.

Gene Expression and Profiling

Ji-Gang Zhang, H. Deng, Chao Xu, 2016 .

Applied Computational Genomics

J. Beckmann, H. Deng, C. Baumgartner, 2018, Translational Bioinformatics.

Network-Based Transcriptome-Wide Expression Study for Postmenopausal Osteoporosis.

H. Deng, Yu Zhou, Xiang-He Meng, 2020, The Journal of clinical endocrinology and metabolism.

Long Noncoding RNA Analyses for Osteoporosis Risk in Caucasian Women

H. Deng, Chao Xu, Q. Tian, 2019 .

Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women

T. Niu, Yu-ping Wang, H. Deng, 2016, PloS one.

Epigenetically Silenced Candidate Tumor Suppressor Genes in Prostate Cancer: Identified by Modeling Methylation Stratification and Applied to Progression Prediction

H. Deng, E. Flemington, Kun Zhang, 2018, Cancer Epidemiology, Biomarkers & Prevention.

Fast and Accurate Detection of Complex Imaging Genetics Associations Based on Greedy Projected Distance Correlation

Vince D. Calhoun, Hong-Wen Deng, Yu-Ping Wang, 2018, IEEE Transactions on Medical Imaging.

Quantitative proteomics and integrative network analysis identified novel genes and pathways related to osteoporosis.

Ji-Gang Zhang, H. Deng, Chao Xu, 2016, Journal of proteomics.

RNA-sequencing study of peripheral blood monocytes in chronic periodontitis.

Yu-ping Wang, H. Deng, Yao-Zhong Liu, 2016, Gene.

NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning

Md. Ashad Alam, Balachandran Manavalan, H. Kurata, 2021, Briefings Bioinform..

Identification of genetic loci shared between Alzheimer’s disease and hypertension

H. Deng, J. Greenbaum, Megan Sullivan, 2022, Molecular Genetics and Genomics.

GigaAssay – An adaptable high-throughput saturation mutagenesis assay platform

Mira V. Han, M. Schiller, Zhi Wei, 2022, Genomics.

Simultaneous detection of novel genes and SNPs by adaptive p-value combination

H. Deng, Zheyang Wu, Hong Zhang, 2022, Frontiers in Genetics.

Identify gene expression pattern change at transcriptional and post-transcriptional levels

Ji-Gang Zhang, H. Deng, Chao Xu, 2019, Transcription.

Long Noncoding RNA Analyses for Osteoporosis Risk in Caucasian Women

H. Deng, Chao Xu, Q. Tian, 2019, Calcified Tissue International.

Application of Clinical Bioinformatics

J. Beckmann, H. Deng, C. Baumgartner, 2016, Translational Bioinformatics.

Biostatistics, Data Mining and Computational Modeling

Hao He, Dongdong Lin, Hong-Wen Deng, 2016 .

A Sparse Regression Method for Group-Wise Feature Selection with False Discovery Rate Control

Hong-Wen Deng, Alexej Gossmann, Shaolong Cao, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A generalized kernel machine approach to identify higher-order composite effects in multi-view datasets pdf

Hui Shen, Yu-Ping Wang, Hong-Wen Deng, 2020, ArXiv.

A kernel machine method for detecting higher order interactions in multimodal datasets: Application to schizophrenia

Vince D. Calhoun, Hong-Wen Deng, Yu-Ping Wang, 2018, Journal of Neuroscience Methods.

Segmentation of M-FISH Images for Improved Classification of Chromosomes With an Adaptive Fuzzy C-means Clustering Algorithm

Yu-Ping Wang, H. Deng, Hyohoon Cao, 2012, IEEE Transactions on Fuzzy Systems.

MicroRNA–mRNA interaction analysis to detect potential dysregulation in complex diseases

Yu-ping Wang, Ji-Gang Zhang, H. Deng, 2015, Network Modeling Analysis in Health Informatics and Bioinformatics.

Drug Repurposing for COVID-19 Treatment by Integrating Network Pharmacology and Transcriptomics

H. Deng, L. Tan, Xiang-He Meng, 2021, Pharmaceutics.

Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants

Xiang-He Meng, Hong-Mei Xiao, Hong-Wen Deng, 2020, Bioinform..

A Review of Integrative Imputation for Multi-Omics Datasets

Chaoyang Zhang, Joseph Luttrell, Chong Wu, 2020, Frontiers in Genetics.

Integrated Analysis of Gene Expression and Copy Number Data on Gene Shaving Using Independent Component Analysis

Vince D. Calhoun, Jinhua Sheng, Yu-Ping Wang, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Characterization of Human Chromosomal Material Exchange with Regard to the Chromosome Translocations Using Next-Generation Sequencing Data

Yu-ping Wang, Ji-Gang Zhang, H. Deng, 2014, Genome biology and evolution.

The Next Generation Sequencing and Applications in Clinical Research

Junbo Duan, Hong-Wen Deng, Yu-Ping Wang, 2016 .

Association of rare PTP4A1-PHF3-EYS variants with alcohol dependence

H. Deng, Xingguang Luo, L. Zuo, 2013, Journal of Human Genetics.

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

Tao Yang, Hong-Wen Deng, Tianhua Niu, 2014, BMC Bioinformatics.

Inferring causal relationships between phenotypes using summary statistics from genome-wide association studies

H. Deng, Hui Shen, Xiangding Chen, 2018, Human Genetics.

On Combining Reference Data to Improve Imputation Accuracy

Jun Chen, Ji-Gang Zhang, Yu-Fang Pei, 2013, PloS one.

Network-Based Approach to Repurpose Approved Drugs for COVID-19 by Integrating GWAS and Text Mining Data

H. Deng, Hui Shen, Sheng Wang, 2022, Processes.

Joint Detection of Associations Between DNA Methylation and Gene Expression From Multiple Cancers

Hong-Wen Deng, Yu-Ping Wang, Ji-Gang Zhang, 2018, IEEE Journal of Biomedical and Health Informatics.

Zp4 is completely dispensable for fertility in female rats†

H. Deng, Hongmei Xiao, R. Quan, 2021, Biology of Reproduction.

Mutant Zp1 impedes incorporation of ZP3 and ZP4 in the zona pellucida, resulting in zona absence and female infertility in rats†

H. Deng, Hongmei Xiao, R. Quan, 2021, Biology of Reproduction.

A new permutation strategy of pathway-based approach for genome-wide association study

Yuan Chen, Hong-Wen Deng, Yan-Fang Guo, 2009, BMC Bioinformatics.

Novel strategy for disease risk prediction incorporating predicted gene expression and DNA methylation data: a multi‐phased study of prostate cancer

W. Pan, T. Rebbeck, C. Haiman, 2021, Cancer communications.

Cell‐specific network analysis of human folliculogenesis reveals network rewiring in antral stage oocytes

H. Deng, Hongmei Xiao, J. Greenbaum, 2021, Journal of cellular and molecular medicine.

Integrative analysis of GWASs, human protein interaction, and gene expression identified gene modules associated with BMDs.

Jian Li, Yu-Ping Wang, Yan-Fang Guo, 2014, The Journal of clinical endocrinology and metabolism.

Genome partitioning of genetic variation for height from 11,214 sibling pairs.

W. G. Hill, P. Visscher, N. Martin, 2007, American journal of human genetics.

GWA-based pleiotropic analysis identified potential SNPs and genes related to type 2 diabetes and obesity

H. Deng, Hui Shen, Hao He, 2020, Journal of Human Genetics.

Population clustering based on copy number variations detected from next generation sequencing data

Yu-Ping Wang, Junbo Duan, Hong-Wen Deng, 2014, J. Bioinform. Comput. Biol..

Common Copy Number Variation Detection From Multiple Sequenced Samples

Yu-Ping Wang, Junbo Duan, Hong-Wen Deng, 2014, IEEE Transactions on Biomedical Engineering.

Detection of common copy number variation with application to population clustering from next generation sequencing data

Yu-Ping Wang, Junbo Duan, Hong-Wen Deng, 2012, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Proteomic Profiling: Data Mining and Analyses

Wei Zhu, Yong Zeng, Hong-Wen Deng, 2016 .

An adaptive strategy for association analysis of common or rare variants using entropy theory

H. Deng, Chao Xu, Yu-mei Li, 2017, Journal of Human Genetics.

SNPP: automating large-scale SNP genotype data management

Hong-Wen Deng, Lan-Juan Zhao, Miao-Xin Li, 2005, Bioinform..

The Impact of Imputation on Meta-Analysis of Genome-Wide Association Studies

H. Deng, Jian Li, Yu-Fang Pei, 2012, PloS one.

BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches

H. Kurata, H. Deng, M. Hasan, 2022, Briefings Bioinform..

Epigenetics of Mitochondria-Associated Genes in Striated Muscle

H. Deng, M. Ehrlich, K. Ehrlich, 2021, Epigenomes.

Single-cell RNA sequencing of human femoral head in vivo

Y. Liu, H. Deng, Hui Shen, 2021, Aging.

Identifying Gene Interaction Enrichment for Gene Expression Data

Jian Li, Hong-Wen Deng, Ji-Gang Zhang, 2009, PloS one.

Network‐based proteomic analysis for postmenopausal osteoporosis in Caucasian females

Ji-Gang Zhang, H. Deng, Hui Shen, 2016, Proteomics.

Replication of 6 Obesity Genes in a Meta-Analysis of Genome-Wide Association Studies from Diverse Ancestries

C. Bouchard, Ji-Gang Zhang, H. Deng, 2014, PloS one.

Network-based investigation of genetic modules associated with functional brain networks in schizophrenia

Hao He, Vince D. Calhoun, Dongdong Lin, 2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine.

Novel PMM2 missense mutation in a Chinese family with non-syndromic premature ovarian insufficiency

H. Deng, Hongmei Xiao, Jiafeng Huang, 2020, Journal of Assisted Reproduction and Genetics.

Gene selection for classification of microarray data based on the Bayes error

Hong-Wen Deng, Ji-Gang Zhang, Ji-Gang Zhang, 2007, BMC Bioinformatics.

A systematic dissection of human primary osteoblasts in vivo at single-cell resolution

Yu-ping Wang, H. Deng, Hui Shen, 2020, bioRxiv.

CNV-TV: A robust method to discover copy number variation from short sequencing reads

Yu-Ping Wang, Junbo Duan, Hong-Wen Deng, 2013, BMC Bioinformatics.

Influence of mouse defective zona pellucida in folliculogenesis on apoptosis of granulosa cells and developmental competence of oocytes†

H. Deng, Hongmei Xiao, Chao Lv, 2019, Biology of Reproduction.

Mutation of rat Zp2 causes ROS-mediated oocyte apoptosis.

Ying Sun, H. Deng, Hongmei Xiao, 2020, Reproduction.

Mutant Zp1 results in Zona Pellucida Lacking and Female Infertility in Rats and Humans

H. Deng, Hongmei Xiao, R. Quan, 2019, bioRxiv.

Identification of PDXDC1 as a novel pleiotropic susceptibility locus shared between lumbar spine bone mineral density and birth weight

H. Deng, Xiang-He Meng, J. Greenbaum, 2022, Journal of Molecular Medicine.

Causal Analysis of Health Interventions and Environments for Influencing the Spread of COVID-19 in the United States of America

E. Boerwinkle, M. Xiong, H. Deng, 2020, Frontiers in Applied Mathematics and Statistics.

Bayesian robust analysis for genetic architecture of quantitative traits

Xin Wang, Hong-Wen Deng, Runqing Yang, 2008, Bioinform..

Integrative lncRNA–mRNA co‐expression network analysis identifies novel lncRNA E2F3‐IT1 for rheumatoid arthritis

H. Deng, S. Lei, F. Deng, 2021, Clinical and translational medicine.

Gene shaving using a sensitivity analysis of kernel based machine learning approach, with applications to cancer data

Hong-Wen Deng, Md. Ashad Alam, Md Ashad Alam, 2019, PloS one.

Identification of Genes for Complex Diseases Using Integrated Analysis of Multiple Types of Genomic Data

Yu-Ping Wang, Hongbao Cao, Hong-Wen Deng, 2012, PloS one.

Attenuated Monocyte Apoptosis, a New Mechanism for Osteoporosis Suggested by a Transcriptome-Wide Expression Study of Monocytes

Ji-Gang Zhang, H. Deng, Yao-Zhong Liu, 2015, PloS one.

Integrative analysis of multiple diverse omics datasets by sparse group multitask regression

Hao He, Dongdong Lin, Yu-Ping Wang, 2014, Front. Cell Dev. Biol..

Geographical differences in osteoporosis, obesity, and sarcopenia related traits in white American cohorts

Ji-Gang Zhang, H. Deng, Hui Shen, 2019, Scientific Reports.

Most synonymous allelic variants in HIV tat are not silent

J. Rotter, M. Schiller, H. Deng, 2023, Genomics.

Group sparse canonical correlation analysis for genomic data integration

V. Calhoun, Yu-ping Wang, D. Lin, 2013, BMC Bioinformatics.

Classification of Multicolor Fluorescence In Situ Hybridization (M-FISH) Images With Sparse Representation

Yu-ping Wang, Hongbao Cao, H. Deng, 2012, IEEE Transactions on NanoBioscience.

Alteration of circulating microbiome and its associated regulation role in rheumatoid arthritis: Evidence from integration of multiomics data

H. Deng, S. Lei, F. Deng, 2020, Clinical and translational medicine.

GigaAssay – a high-throughput assay system for molecular functions and cell processes

Mira V. Han, M. Schiller, Zhi Wei, 2021 .

Group sparse canonical correlation analysis for genomic data integration

Vince D. Calhoun, Dongdong Lin, Yu-Ping Wang, 2013, BMC Bioinformatics.

Potential Molecular Mechanisms of Alzheimer’s Disease from Genetic Studies

H. Deng, Hui Shen, M. Nwadiugwu, 2023, Biology.

An integrative imputation method based on multi-omics datasets

Yu-ping Wang, D. Lin, Jingyao Li, 2016, BMC Bioinformatics.

Unified tests for fine scale mapping and identifying sparse high-dimensional sequence associations

Yu-Ping Wang, Hong-Wen Deng, Alexej Gossmann, 2015, Bioinform..

Unified tests for fine scale mapping and identifying sparse high-dimensional sequence associations

Yu-Ping Wang, Hong-Wen Deng, Alexej Gossmann, 2015, BCB.

Scaled sparse high-dimensional tests for localizing sequence variants

Yu-Ping Wang, Hong-Wen Deng, Huaizhen Qin, 2014, BCB.

Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for BMD Variation

Yu Zhou, Ji-Gang Zhang, Chuan Qiu, 2015, PloS one.

PhD: a web database application for phenotype data management

Hong-Wen Deng, Miao-Xin Li, Jin-Long Li, 2005, Bioinform..

A Statistical Test for Differential Network Analysis Based on Inference of Gaussian Graphical Model

Yu-ping Wang, Ji-Gang Zhang, H. Deng, 2019, Scientific Reports.

Gene-based GWAS analysis for consecutive studies of GEFOS

Ji-Gang Zhang, H. Deng, Chao Xu, 2018, Osteoporosis International.

Data supporting a saturation mutagenesis assay for Tat-driven transcription with the GigaAssay

Mira V. Han, M. Schiller, H. Deng, 2022, Data in Brief.

Transcriptomic Data Identified Key Transcription Factors for Osteoporosis in Caucasian Women

H. Deng, Chao Xu, Q. Tian, 2018, Calcified Tissue International.