On Relationship Inference Using Gamete Identity by Descent Data. - Hongyu Zhao 003; Feng Liang (J. Comput. Biol., 2001)

YMD: a microarray database for large-scale gene expression analysis. - Kei-Hoi Cheung; Kevin P. White; Janet Hager; Mark Gerstein; Valerie Reinke; Kenneth Nelson; Peter Masiar; Ranjana Srivastava; Yuli Li; Ju Li; Hongyu Zhao 003; Jinming Li; et al. (AMIA, 2002)

Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. - Baolin Wu; Tom Abbott; David Fishman; Walter McMurray; Gil Mor; Kathryn L. Stone; David Ward; Kenneth R. Williams; Hongyu Zhao 003 (Bioinform., 2003)

PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. - Deyun Pan; Ning Sun; Kei-Hoi Cheung; Zhong Guan; Ligeng Ma; Matthew Holford; Xingwang Deng; Hongyu Zhao 003 (BMC Bioinform., 2003)

A statistical method for identifying differential gene-gene co-expression patterns. - Yinglei Lai; Baolin Wu; Liang Chen; Hongyu Zhao 003 (Bioinform., 2004)

Information assessment on predicting protein-protein interactions. - Nan Lin; Baolin Wu; Ronald Jansen; Mark Gerstein; Hongyu Zhao 003 (BMC Bioinform., 2004)

A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. - Yin Liu; Hongyu Zhao 003 (BMC Bioinform., 2004)

Handling multiple testing while interpreting microarrays with the Gene Ontology Database. - Michael V. Osier; Hongyu Zhao 003; Kei-Hoi Cheung (BMC Bioinform., 2004)

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. - Wenming Zhao; Jing Wang 003; Ximiao He; Xiaobing Huang; Yongzhi Jiao; Mingtao Dai; Shulin Wei; Jian Fu; Ye Chen; Xiaoyu Ren; Yong Zhang 036; Peixiang Ni; et al. (Nucleic Acids Res., 2004)

Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach. - Weichuan Yu; Xiaoye Li; Hongyu Zhao 003 (CSB Workshops, 2005)

Negative correlation between compositional symmetries and local recombination rates. - Liang Chen; Hongyu Zhao 003 (Bioinform., 2005)

A semiparametric approach for marker gene selection based on gene expression data. - Zhong Guan; Hongyu Zhao 003 (Bioinform., 2005)

VitaPad: visualization tools for the analysis of pathway data. - Matthew Holford; Naixin Li; Prakash M. Nadkarni; Hongyu Zhao 003 (Bioinform., 2005)

Detection of DNA copy number alterations using penalized least squares regression. - Tao Huang; Baolin Wu; Paul Lizardi; Hongyu Zhao 003 (Bioinform., 2005)

Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. - Yin Liu; Nianjun Liu; Hongyu Zhao 003 (Bioinform., 2005)

HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. - Kui Zhang; Fengzhu Sun; Hongyu Zhao 003 (Bioinform., 2005)

Are scale-free networks robust to measurement errors? - Nan Lin; Hongyu Zhao 003 (BMC Bioinform., 2005)

A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data. - Yinglei Lai; Hongyu Zhao 003 (Comput. Biol. Chem., 2005)

Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. - Nicholas Carriero; Michael V. Osier; Kei-Hoi Cheung; Perry L. Miller; Mark Gerstein; Hongyu Zhao 003; Baolin Wu; Scott Rifkin; Joseph T. Chang; Heping Zhang; Kevin P. White; Kenneth R. Williams; et al. (J. Am. Medical Informatics Assoc., 2005)

Integrating mRNA Decay Information into Co-Regulation Study. - Liang Chen; Hongyu Zhao 003 (J. Comput. Sci. Technol., 2005)

Pathway analysis using random forests classification and regression. - Herbert Pang; Aiping Lin; Matthew Holford; Bradley E. Enerson; Bin Lu; Michael P. Lawton; Eugenia Floyd; Hongyu Zhao 003 (Bioinform., 2006)

PSMIX: an R package for population structure inference via maximum likelihood method. - Baolin Wu; Nianjun Liu; Hongyu Zhao 003 (BMC Bioinform., 2006)

Detecting and aligning peaks in mass spectrometry data with applications to MALDI. - Weichuan Yu; Baolin Wu; Ning Lin; Kathy Stone; Kenneth R. Williams; Hongyu Zhao 003 (Comput. Biol. Chem., 2006)

Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space-Based Approach. - Weichuan Yu; Xiaoye Li; Junfeng Liu; Baolin Wu; Kenneth R. Williams; Hongyu Zhao 003 (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry. - Weichuan Yu; Junfeng Liu; Chris Colangelo; Erol E. Gulcicek; Hongyu Zhao 003 (Comput. Biol. Chem., 2007)

Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis. - Valentin Dinu; Hongyu Zhao 003; Perry L. Miller (J. Biomed. Informatics, 2007)

Estimating dynamic models for gene regulation networks. - Jiguo Cao; Hongyu Zhao 003 (Bioinform., 2008)

Considering dependence among genes and markers for false discovery control in eQTL mapping. - Liang Chen; Tiejun Tong; Hongyu Zhao 003 (Bioinform., 2008)

Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. - Debayan Datta; Hongyu Zhao 003 (Bioinform., 2008)

Building pathway clusters from Random Forests classification using class votes. - Herbert Pang; Hongyu Zhao 003 (BMC Bioinform., 2008)

Is Subcellular Localization Informative for Modeling Protein-Protein Interaction Signal? - Junfeng Liu; Hongyu Zhao 003; Jun Tan; Dajie Luo; Weichuan Yu; E. James Harner; Weichung Joe Shih (J. Electr. Comput. Eng., 2008)

Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data. - Debayan Datta; Hongyu Zhao 003 (BMC Bioinform., 2009)

Genotyping and inflated type I error rate in genome-wide association case/control studies. - Joshua N. Sampson; Hongyu Zhao 003 (BMC Bioinform., 2009)

Pathway analysis using random forests with bivariate node-split for survival outcomes. - Herbert Pang; Debayan Datta; Hongyu Zhao 003 (Bioinform., 2010)

Reverse Engineering of Gene Regulation Networks with an Application to the DREAM4 in silico Network Challenge. - Hyonho Chun; Jia Kang; Xianghua Zhang; Minghua Deng; Haisu Ma; Hongyu Zhao 003 (Handbook of Statistical Bioinformatics, 2011)

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. - Haisu Ma; Eric E. Schadt; Lee M. Kaplan; Hongyu Zhao 003 (Bioinform., 2011)

Score regularization for peptide identification. - Zengyou He; Hongyu Zhao 003; Weichuan Yu (BMC Bioinform., 2011)

Bias Detection and Correction in RNA-Sequencing Data. - Wei Zheng; Lisa M. Chung; Hongyu Zhao 003 (BMC Bioinform., 2011)

Some theoretical properties of Silverman's method for Smoothed functional principal component analysis. - Xin Qi 014; Hongyu Zhao 003 (J. Multivar. Anal., 2011)

M3: an improved SNP calling algorithm for Illumina BeadArray data. - Gengxin Li; Joel Gelernter; Henry R. Kranzler; Hongyu Zhao 003 (Bioinform., 2012)

iFad: an integrative factor analysis model for drug-pathway association inference. - Haisu Ma; Hongyu Zhao 003 (Bioinform., 2012)

FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. - Haisu Ma; Hongyu Zhao 003 (Bioinform., 2012)

Improved mean estimation and its application to diagonal discriminant analysis. - Tiejun Tong; Liang Chen; Hongyu Zhao 003 (Bioinform., 2012)

Joint analysis of expression profiles from multiple cancers improves the identification of microRNA-gene interactions. - Xiaowei Chen; Frank J. Slack; Hongyu Zhao 003 (Bioinform., 2013)

Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. - Can Yang 002; Lin Wang; Shuqin Zhang; Hongyu Zhao 003 (Bioinform., 2013)

Differential expression analysis for paired RNA-seq data. - Lisa M. Chung; John P. Ferguson; Wei Zheng; Feng Qian; Vincent Bruno; Ruth R. Montgomery; Hongyu Zhao 003 (BMC Bioinform., 2013)

Utilizing protein structure to identify non-random somatic mutations. - Gregory A. Ryslik; Yuwei Cheng; Kei-Hoi Cheung; Yorgo Modis; Hongyu Zhao 003 (BMC Bioinform., 2013)

Sparse principal component analysis by choice of norm. - Xin Qi 014; Ruiyan Luo; Hongyu Zhao 003 (J. Multivar. Anal., 2013)

HapBoost: A Fast Approach to Boosting Haplotype Association Analyses in Genome-Wide Association Studies. - Xiang Wan; Can Yang 002; Qiang Yang 001; Hongyu Zhao 003; Weichuan Yu (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Multisample aCGH Data Analysis via Total Variation and Spectral Regularization. - Xiaowei Zhou 001; Can Yang 002; Xiang Wan; Hongyu Zhao 003; Weichuan Yu (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

A spatial simulation approach to account for protein structure when identifying non-random somatic mutations. - Gregory A. Ryslik; Yuwei Cheng; Kei-Hoi Cheung; Robert D. Bjornson; Daniel Zelterman; Yorgo Modis; Hongyu Zhao 003 (BMC Bioinform., 2014)

A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations. - Gregory A. Ryslik; Yuwei Cheng; Kei-Hoi Cheung; Yorgo Modis; Hongyu Zhao 003 (BMC Bioinform., 2014)

Ttn as a likely causal gene for QTL of alcohol preference on mouse chromosome 2. - Lishi Wang; Yan Jiao; Yue Huang; Beth Bennett; Robert W. Williams; Dawei Li; Hongyu Zhao 003; Joel Gelernter; Henry R. Kranzler; Lindsay A. Farrer; Weikuan Gu (BMC Bioinform., 2014)

Low-Rank Modeling and Its Applications in Image Analysis. - Xiaowei Zhou 001; Can Yang 002; Hongyu Zhao 003; Weichuan Yu (ACM Comput. Surv., 2014)

CCLasso: correlation inference for compositional data through Lasso. - Huaying Fang; Chengcheng Huang; Hongyu Zhao 003; Minghua Deng (Bioinform., 2015)

M3-S: a genotype calling method incorporating information from samples with known genotypes. - Gengxin Li; Hongyu Zhao 003 (BMC Bioinform., 2015)

The application of sparse estimation of covariance matrix to quadratic discriminant analysis. - Jiehuan Sun; Hongyu Zhao 003 (BMC Bioinform., 2015)

Functional Module Analysis for Gene Coexpression Networks with Network Integration. - Shuqin Zhang; Hongyu Zhao 003; Michael K. Ng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes. - Yiyi Liu; Hongyu Zhao 003 (Bioinform., 2016)

GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation. - Qiongshi Lu; Xinwei Yao 002; Yiming Hu; Hongyu Zhao 003 (Bioinform., 2016)

NBLDA: negative binomial linear discriminant analysis for RNA-Seq data. - Kai Dong; Hongyu Zhao 003; Tiejun Tong; Xiang Wan (BMC Bioinform., 2016)

Leveraging protein quaternary structure to identify oncogenic driver mutations. - Gregory A. Ryslik; Yuwei Cheng; Yorgo Modis; Hongyu Zhao 003 (BMC Bioinform., 2016)

Efficient Drug-Pathway Association Analysis via Integrative Penalized Matrix Decomposition. - Cong Li; Can Yang 002; Greg Hather; Ray Liu; Hongyu Zhao 003 (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles. - Michael I. Klein; David F. Stern; Hongyu Zhao 003 (BMC Bioinform., 2017)

A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits. - Kang K. Yan; Hongyu Zhao 003; Herbert Pang (BMC Bioinform., 2017)

gCoda: Conditional Dependence Network Inference for Compositional Data. - Huaying Fang; Chengcheng Huang; Hongyu Zhao 003; Minghua Deng (J. Comput. Biol., 2017)

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture. - Dongjun Chung; Hang J. Kim; Hongyu Zhao 003 (PLoS Comput. Biol., 2017)

Leveraging functional annotations in genetic risk prediction for human complex diseases. - Yiming Hu; Qiongshi Lu; Ryan Powles; Xinwei Yao 002; Can Yang 002; Fang Fang; Xinran Xu; Hongyu Zhao 003 (PLoS Comput. Biol., 2017)

Variable importance-weighted random forests. - Yiyi Liu; Hongyu Zhao 003 (Quant. Biol., 2017)

Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA. - Hang J. Kim; Zhenning Yu; Andrew Lawson; Hongyu Zhao 003; Dongjun Chung (Bioinform., 2018)

Spectral clustering based on learning similarity matrix. - Seyoung Park; Hongyu Zhao 003 (Bioinform., 2018)

Estimating a sparse reduction for general regression in high dimensions. - Tao Wang 067; Mengjie Chen; Hongyu Zhao 003; Lixing Zhu (Stat. Comput., 2018)

Pivotal variable detection of the covariance matrix and its application to high-dimensional factor models. - Junlong Zhao; Hongyu Zhao 003; Lixing Zhu (Stat. Comput., 2018)

An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies. - Boyang Li 011; Qiongshi Lu; Hongyu Zhao 003 (Briefings Bioinform., 2019)

ProteomicsBrowser: MS/proteomics data visualization and investigation. - Gang Peng 004; Rashaun Wilson; Yishuo Tang; TuKiet T. Lam; Angus C. Nairn; Kenneth R. Williams; Hongyu Zhao 003 (Bioinform., 2019)

Network Clustering Analysis Using Mixture Exponential-Family Random Graph Models and Its Application in Genetic Interaction Data. - Yishu Wang 003; Huaying Fang; Dejie Yang; Hongyu Zhao 003; Minghua Deng (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Inference of Dynamic Graph Changes for Functional Connectome. - Dingjue Ji; Junwei Lu; Yiliang Zhang; Siyuan Gao; Hongyu Zhao 003 (AISTATS, 2020)

NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution. - Daiwei Tang; Seyoung Park; Hongyu Zhao 003 (Bioinform., 2020)

Predicting viral exposure response from modeling the changes of co-expression networks using time series gene expression data. - Fangli Dong; Yong He; Tao Wang 067; Dong Han; Hui Lu 004; Hongyu Zhao 003 (BMC Bioinform., 2020)

An empirical Bayes approach to normalization and differential abundance testing for microbiome data. - Tiantian Liu; Hongyu Zhao 003; Tao Wang 067 (BMC Bioinform., 2020)

Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies. - Shuang Song 006; Wei Jiang 019; Lin Hou; Hongyu Zhao 003 (PLoS Comput. Biol., 2020)

Leveraging functional annotation to identify genes associated with complex diseases. - Wei Liu; Mo Li; Wenfeng Zhang; Geyu Zhou; Xing Wu; Jiawei Wang; Qiongshi Lu; Hongyu Zhao 003 (PLoS Comput. Biol., 2020)

Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics. - Yiliang Zhang; Youshu Cheng; Wei Jiang 019; Yixuan Ye; Qiongshi Lu; Hongyu Zhao 003 (Briefings Bioinform., 2021)

Transformation and differential abundance analysis of microbiome data incorporating phylogeny. - Chao Zhou; Hongyu Zhao 003; Tao Wang 067 (Bioinform., 2021)

A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. - Hongyu Li; Biqing Zhu; Zhichao Xu; Taylor Adams; Naftali Kaminski; Hongyu Zhao 003 (BMC Bioinform., 2021)

RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators. - Xujun Wang; Zhengtao Zhang; Wenyi Qin; Shiyi Liu; Cong Liu 020; Georgi Z. Genchev; Lijian Hui; Hongyu Zhao 003; Hui Lu 004 (Genom. Proteom. Bioinform., 2021)

Calculating Orthologous Protein-Coding Sequence Set Probability Using the Poisson Process. - Junfeng Liu; Yi Wang; Hongyu Zhao 003 (J. Comput. Biol., 2021)

Model-Based Microbiome Data Ordination: A Variational Approximation Approach. - Yanyan Zeng; Hongyu Zhao 003; Tao Wang 067 (J. Comput. Graph. Stat., 2021)

Special issue on genome wide association study. - Lin Hou; Qiongshi Lu; Can Yang 002; Hongyu Zhao 003 (Quant. Biol., 2021)

Integrative modeling of transmitted and de novo variants identifies novel risk genes for congenital heart disease. - Mo Li; Xue Zeng; Chentian Jin; Sheng Chih Jin; Weilai Dong; Martina Brueckner; Richard Lifton; Qiongshi Lu; Hongyu Zhao 003 (Quant. Biol., 2021)

Transcriptome wide association studies: general framework and methods. - Yuhan Xie; Nayang Shan; Hongyu Zhao 003; Lin Hou (Quant. Biol., 2021)

Roles of statistical modeling in characterizing the genetic basis of human diseases and traits. - Hongyu Zhao 003 (Quant. Biol., 2021)

A general kernel boosting framework integrating pathways for predictive modeling based on genomic data. - Li Zeng; Zhaolong Yu; Yiliang Zhang; Hongyu Zhao 003 (BCB, 2022)

MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys. - Tiantian Liu; Peirong Xu; Yueyao Du; Hui Lu 004; Hongyu Zhao 003; Tao Wang 067 (Briefings Bioinform., 2022)

A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data. - Biqing Zhu; Hongyu Li; Le Zhang 013; Sreeganga S. Chandra; Hongyu Zhao 003 (Briefings Bioinform., 2022)

ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks. - Yuge Wang; Tianyu Liu 005; Hongyu Zhao 003 (Bioinform., 2022)

fastANCOM: a fast method for analysis of compositions of microbiomes. - Chao Zhou; Huimin Wang; Hongyu Zhao 003; Tao Wang 067 (Bioinform., 2022)

An unbiased kinship estimation method for genetic data analysis. - Wei Jiang 019; Xiangyu Zhang; Siting Li; Shuang Song 006; Hongyu Zhao 003 (BMC Bioinform., 2022)

Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders. - Yuge Wang; Hongyu Zhao 003 (PLoS Comput. Biol., 2022)

A Manifold Proximal Linear Method for Sparse Spectral Clustering with Application to Single-Cell RNA Sequencing Data Analysis. - Zhongruo Wang; Bingyuan Liu; Shixiang Chen; Shiqian Ma; Lingzhou Xue; Hongyu Zhao 003 (INFORMS J. Optim., 2022)

phyloMDA: an R package for phylogeny-aware microbiome data analysis. - Tiantian Liu; Chao Zhou; Huimin Wang; Hongyu Zhao 003; Tao Wang 067 (BMC Bioinform., 2022)

MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data. - Tianyu Liu 005; Yuge Wang; Rex Ying; Hongyu Zhao 003 (NeurIPS, 2023)

Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective. - Jianlei Gu; Jiawei Dai; Hui Lu 004; Hongyu Zhao 003 (Genom. Proteom. Bioinform., 2023)

CARE as a wearable derived feature linking circadian amplitude to human cognitive functions. - Shuya Cui; Qingmin Lin; Yuanyuan Gui; Yunting Zhang; Hui Lu 004; Hongyu Zhao 003; Xiaolei Wang; Xinyue Li; Fan Jiang (npj Digit. Medicine, 2023)

A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. - Wenxuan Deng; Bolun Li; Jiawei Wang; Wei Jiang 019; Xiting Yan; Ningshan Li; Milica Vukmirovic; Naftali Kaminski; Jing Wang 003; Hongyu Zhao 003 (Briefings Bioinform., 2023)

HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol. - Zhiwei Cheng; Leijie Li; Yuening Zhang; Yongyong Ren; Jianlei Gu; Xinbo Wang; Hongyu Zhao 003; Hui Lu 004 (Briefings Bioinform., 2023)

Genomic risk prediction of cardiovascular diseases among type 2 diabetes patients in the UK Biobank. - Yixuan Ye; Jiaqi Hu; Fuyuan Pang; Can Cui; Hongyu Zhao 003 (Frontiers Bioinform., 2023)

Benchmarking of local genetic correlation estimation methods using summary statistics from genome-wide association studies. - Chi Zhang; Yiliang Zhang; Yunxuan Zhang; Hongyu Zhao 003 (Briefings Bioinform., 2023)

Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research. - Tianyu Liu 001; Yijia Xiao; Xiao Luo 001; Hua Xu 001; Wenjin Jim Zheng; Hongyu Zhao 003 (EMNLP (Findings), 2024)

Semi-supervised Knowledge Transfer Across Multi-omic Single-cell Data. - Fan Zhang 111; Tianyu Liu 001; Zihao Chen; Xiaojiang Peng; Chong Chen 002; Xian-Sheng Hua 001; Xiao Luo 001; Hongyu Zhao 003 (NeurIPS, 2024)

LDER-GE estimates phenotypic variance component of gene-environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information. - Zihan Dong; Wei Jiang 019; Hongyu Li; Andrew T. Dewan; Hongyu Zhao 003 (Briefings Bioinform., 2024)

CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis. - Tianyu Liu 005; Wenxin Long; Zhiyuan Cao; Yuge Wang; Chuan Hua He; Le Zhang 013; Stephen M. Strittmatter; Hongyu Zhao 003 (Briefings Bioinform., 2024)

Joint modeling of human cortical structure: Genetic correlation network and composite-trait genetic correlation. - Jiangnan Shen; Yiliang Zhang; Zhaohan Zhu; Youshu Cheng; Biao Cai; Yize Zhao; Hongyu Zhao 003 (NeuroImage, 2024)

StrokeClassifier: ischemic stroke etiology classification by ensemble consensus modeling using electronic health records. - Ho-Joon Lee; Lee H. Schwamm; Lauren H. Sansing; Hooman Kamel; Adam DeHavenon; Ashby C. Turner; Kevin N. Sheth; Smita Krishnaswamy; Cynthia Brandt; Hongyu Zhao 003; Harlan M. Krumholz; Richa Sharma (npj Digit. Medicine, 2024)

A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics. - Zhiwei Cheng; Yongyong Ren; Xinbo Wang; Yuening Zhang; Yingqi Hua; Hongyu Zhao 003; Hui Lu 004 (Briefings Bioinform., 2025)

Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations. - Youshu Cheng; Geyu Zhou; Hongyu Li; Xinyu Zhang; Amy Justice; Claudia Martinez; Bradley E. Aouizerat; Ke Xu; Hongyu Zhao 003 (Briefings Bioinform., 2025)

Degrees of Freedom: Search Cost and Self-Consistency. - Lijun Wang; Hongyu Zhao 003; Xiaodan Fan (J. Comput. Graph. Stat., 2025)

Towards Artificial Intelligence Research Assistant for Expert-Involved Learning. - Tianyu Liu 001; Simeng Han; Xiao Luo 001; Hanchen Wang 002; Pan Lu; Biqing Zhu; Yuge Wang; Keyi Li; Jiapeng Chen; Rihao Qu; Yufeng Liu; Xinyue Cui; et al. (CoRR, 2025)