Hongyu Zhao

127 papers A* 2A 1Misc 1Journal 119Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
A novel two-sample Mendelian randomization framework integrating common and rare variants: application to assess the effect of HDL-C on preeclampsia risk.
Briefings Bioinform.
Yu Zhang, Ming Li, David M. Haas, C. Noel Bairey Merz, Tsegaselassie Workalemahu, Kelli Ryckman, Janet M. Catov, Lisa D. Levine, Alexa Freedman, George R. Saade, Jiaqi Hu, Hongyu Zhao, Xihao Li, Nianjun Liu, Qi Yan
2026 J jnl
Embeddings from language models are good learners for single-cell data analysis.
Patterns
Tianyu Liu, Tianqi Chen, Wangjie Zheng, Xiao Luo, Yiqun Chen, Hongyu Zhao
2026 J jnl
UBD: incorporating uncertainty in cell type proportion estimates from bulk samples to infer cell-type-specific profiles.
Briefings Bioinform.
Youshu Cheng, Chen Lin, Hongyu Li, Ke Xu, Hongyu Zhao
2025 J jnl
A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics.
Briefings Bioinform.
Zhiwei Cheng, Yongyong Ren, Xinbo Wang, Yuening Zhang, Yingqi Hua, Hongyu Zhao, Hui Lu
2025 J jnl
A perspective on developing foundation models for analyzing spatial transcriptomic data.
Quant. Biol.
Tianyu Liu, Minsheng Hao, Xinhao Liu, Hongyu Zhao
2025 J jnl
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis.
Briefings Bioinform.
Tianyu Liu, Wenxin Long, Zhiyuan Cao, Yuge Wang, Chuan Hua He, Le Zhang, Stephen M. Strittmatter, Hongyu Zhao
2025 J jnl
Degrees of Freedom: Search Cost and Self-Consistency.
J. Comput. Graph. Stat.
Lijun Wang, Hongyu Zhao, Xiaodan Fan
2025 J jnl
Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations.
Briefings Bioinform.
Youshu Cheng, Geyu Zhou, Hongyu Li, Xinyu Zhang, Amy Justice, Claudia Martinez, Bradley E. Aouizerat, Ke Xu, Hongyu Zhao
2025 J jnl
Robust pleiotropy-decomposed polygenic scores identify distinct contributions to elevated coronary artery disease polygenic risk.
PLoS Comput. Biol.
Jiaqi Hu, Yixuan Ye, Chi Zhang, Yunfeng Ruan, Pradeep Natarajan, Hongyu Zhao
2025 J jnl
Towards Artificial Intelligence Research Assistant for Expert-Involved Learning.
CoRR
Tianyu Liu, Simeng Han, Xiao Luo, Hanchen Wang, Pan Lu, Biqing Zhu, Yuge Wang, Keyi Li, Jiapeng Chen, Rihao Qu, Yufeng Liu, Xinyue Cui, Aviv Yaish, Yuhang Chen, Minsheng Hao, Chuhan Li, Kexing Li, Arman Cohan, Hua Xu, Mark Gerstein, James Zou, Hongyu Zhao
2024 — conf
Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.
EMNLP (Findings)
Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, Wenjin Jim Zheng, Hongyu Zhao
2024 J jnl
Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research.
CoRR
Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, W. Jim Zheng, Hongyu Zhao
2024 J jnl
Joint modeling of human cortical structure: Genetic correlation network and composite-trait genetic correlation.
NeuroImage
Jiangnan Shen, Yiliang Zhang, Zhaohan Zhu, Youshu Cheng, Biao Cai, Yize Zhao, Hongyu Zhao
2024 J jnl
LDER-GE estimates phenotypic variance component of gene-environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information.
Briefings Bioinform.
Zihan Dong, Wei Jiang, Hongyu Li, Andrew T. Dewan, Hongyu Zhao
2024 A* conf
Semi-supervised Knowledge Transfer Across Multi-omic Single-cell Data.
NeurIPS
Fan Zhang, Tianyu Liu, Zihao Chen, Xiaojiang Peng, Chong Chen, Xian-Sheng Hua, Xiao Luo, Hongyu Zhao
2024 J jnl
StrokeClassifier: ischemic stroke etiology classification by ensemble consensus modeling using electronic health records.
npj Digit. Medicine
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, Harlan M. Krumholz, Richa Sharma
2023 J jnl
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy.
Briefings Bioinform.
Wenxuan Deng, Bolun Li, Jiawei Wang, Wei Jiang, Xiting Yan, Ningshan Li, Milica Vukmirovic, Naftali Kaminski, Jing Wang, Hongyu Zhao
2023 J jnl
Benchmarking of local genetic correlation estimation methods using summary statistics from genome-wide association studies.
Briefings Bioinform.
Chi Zhang, Yiliang Zhang, Yunxuan Zhang, Hongyu Zhao
2023 J jnl
CARE as a wearable derived feature linking circadian amplitude to human cognitive functions.
npj Digit. Medicine
Shuya Cui, Qingmin Lin, Yuanyuan Gui, Yunting Zhang, Hui Lu, Hongyu Zhao, Xiaolei Wang, Xinyue Li, Fan Jiang
2023 J jnl
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective.
Genom. Proteom. Bioinform.
Jianlei Gu, Jiawei Dai, Hui Lu, Hongyu Zhao
2023 J jnl
Genomic risk prediction of cardiovascular diseases among type 2 diabetes patients in the UK Biobank.
Frontiers Bioinform.
Yixuan Ye, Jiaqi Hu, Fuyuan Pang, Can Cui, Hongyu Zhao
2023 J jnl
HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol.
Briefings Bioinform.
Zhiwei Cheng, Leijie Li, Yuening Zhang, Yongyong Ren, Jianlei Gu, Xinbo Wang, Hongyu Zhao, Hui Lu
2023 A* conf
MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data.
NeurIPS
Tianyu Liu, Yuge Wang, Rex Ying, Hongyu Zhao
2023 J jnl
MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data.
CoRR
Tianyu Liu, Yuge Wang, Rex Ying, Hongyu Zhao
2022 J jnl
A Manifold Proximal Linear Method for Sparse Spectral Clustering with Application to Single-Cell RNA Sequencing Data Analysis.
INFORMS J. Optim.
Zhongruo Wang, Bingyuan Liu, Shixiang Chen, Shiqian Ma, Lingzhou Xue, Hongyu Zhao
2022 J jnl
A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data.
Briefings Bioinform.
Biqing Zhu, Hongyu Li, Le Zhang, Sreeganga S. Chandra, Hongyu Zhao
2022 — conf
A general kernel boosting framework integrating pathways for predictive modeling based on genomic data.
BCB
Li Zeng, Zhaolong Yu, Yiliang Zhang, Hongyu Zhao
2022 J jnl
An unbiased kinship estimation method for genetic data analysis.
BMC Bioinform.
Wei Jiang, Xiangyu Zhang, Siting Li, Shuang Song, Hongyu Zhao
2022 J jnl
MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys.
Briefings Bioinform.
Tiantian Liu, Peirong Xu, Yueyao Du, Hui Lu, Hongyu Zhao, Tao Wang
2022 J jnl
Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders.
PLoS Comput. Biol.
Yuge Wang, Hongyu Zhao
2022 J jnl
ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks.
Bioinform.
Yuge Wang, Tianyu Liu, Hongyu Zhao
2022 J jnl
fastANCOM: a fast method for analysis of compositions of microbiomes.
Bioinform.
Chao Zhou, Huimin Wang, Hongyu Zhao, Tao Wang
2022 J jnl
phyloMDA: an R package for phylogeny-aware microbiome data analysis.
BMC Bioinform.
Tiantian Liu, Chao Zhou, Huimin Wang, Hongyu Zhao, Tao Wang
2021 J jnl
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data.
BMC Bioinform.
Hongyu Li, Biqing Zhu, Zhichao Xu, Taylor Adams, Naftali Kaminski, Hongyu Zhao
2021 J jnl
Calculating Orthologous Protein-Coding Sequence Set Probability Using the Poisson Process.
J. Comput. Biol.
Junfeng Liu, Yi Wang, Hongyu Zhao
2021 J jnl
Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics.
Briefings Bioinform.
Yiliang Zhang, Youshu Cheng, Wei Jiang, Yixuan Ye, Qiongshi Lu, Hongyu Zhao
2021 J jnl
Integrative modeling of transmitted and
Quant. Biol.
Mo Li, Xue Zeng, Chentian Jin, Sheng Chih Jin, Weilai Dong, Martina Brueckner, Richard Lifton, Qiongshi Lu, Hongyu Zhao
2021 J jnl
Model-Based Microbiome Data Ordination: A Variational Approximation Approach.
J. Comput. Graph. Stat.
Yanyan Zeng, Hongyu Zhao, Tao Wang
2021 J jnl
Roles of statistical modeling in characterizing the genetic basis of human diseases and traits.
Quant. Biol.
Hongyu Zhao
2021 J jnl
Special issue on genome wide association study.
Quant. Biol.
Lin Hou, Qiongshi Lu, Can Yang, Hongyu Zhao
2021 J jnl
Transcriptome wide association studies: general framework and methods.
Quant. Biol.
Yuhan Xie, Nayang Shan, Hongyu Zhao, Lin Hou
2021 J jnl
Transformation and differential abundance analysis of microbiome data incorporating phylogeny.
Bioinform.
Chao Zhou, Hongyu Zhao, Tao Wang
2020 J jnl
A Manifold Proximal Linear Method for Sparse Spectral Clustering with Application to Single-Cell RNA Sequencing Data Analysis.
CoRR
Zhongruo Wang, Bingyuan Liu, Shixiang Chen, Shiqian Ma, Lingzhou Xue, Hongyu Zhao
2020 J jnl
A general kernel boosting framework integrating pathways for predictive modeling based on genomic data.
CoRR
Li Zeng, Zhaolong Yu, Yiliang Zhang, Hongyu Zhao
2020 J jnl
An empirical Bayes approach to normalization and differential abundance testing for microbiome data.
BMC Bioinform.
Tiantian Liu, Hongyu Zhao, Tao Wang
2020 A conf
Inference of Dynamic Graph Changes for Functional Connectome.
AISTATS
Dingjue Ji, Junwei Lu, Yiliang Zhang, Siyuan Gao, Hongyu Zhao
2020 J jnl
Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies.
PLoS Comput. Biol.
Shuang Song, Wei Jiang, Lin Hou, Hongyu Zhao
2020 J jnl
Leveraging functional annotation to identify genes associated with complex diseases.
PLoS Comput. Biol.
Wei Liu, Mo Li, Wenfeng Zhang, Geyu Zhou, Xing Wu, Jiawei Wang, Qiongshi Lu, Hongyu Zhao
2020 J jnl
NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution.
Bioinform.
Daiwei Tang, Seyoung Park, Hongyu Zhao
2020 J jnl
Predicting viral exposure response from modeling the changes of co-expression networks using time series gene expression data.
BMC Bioinform.
Fangli Dong, Yong He, Tao Wang, Dong Han, Hui Lu, Hongyu Zhao
2019 J jnl
An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies.
Briefings Bioinform.
Boyang Li, Qiongshi Lu, Hongyu Zhao
2019 J jnl
Network Clustering Analysis Using Mixture Exponential-Family Random Graph Models and Its Application in Genetic Interaction Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yishu Wang, Huaying Fang, Dejie Yang, Hongyu Zhao, Minghua Deng
2019 J jnl
ProteomicsBrowser: MS/proteomics data visualization and investigation.
Bioinform.
Gang Peng, Rashaun Wilson, Yishuo Tang, TuKiet T. Lam, Angus C. Nairn, Kenneth R. Williams, Hongyu Zhao
2018 J jnl
Estimating a sparse reduction for general regression in high dimensions.
Stat. Comput.
Tao Wang, Mengjie Chen, Hongyu Zhao, Lixing Zhu
2018 J jnl
Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA.
Bioinform.
Hang Joon Kim, Zhenning Yu, Andrew Lawson, Hongyu Zhao, Dongjun Chung
2018 J jnl
Pivotal variable detection of the covariance matrix and its application to high-dimensional factor models.
Stat. Comput.
Junlong Zhao, Hongyu Zhao, Lixing Zhu
2018 J jnl
Spectral clustering based on learning similarity matrix.
Bioinform.
Seyoung Park, Hongyu Zhao
2017 J jnl
A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits.
BMC Bioinform.
Kang K. Yan, Hongyu Zhao, Herbert Pang
2017 J jnl
GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles.
BMC Bioinform.
Michael I. Klein, David F. Stern, Hongyu Zhao
2017 J jnl
Leveraging functional annotations in genetic risk prediction for human complex diseases.
PLoS Comput. Biol.
Yiming Hu, Qiongshi Lu, Ryan Powles, Xinwei Yao, Can Yang, Fang Fang, Xinran Xu, Hongyu Zhao
2017 J jnl
Variable importance-weighted random forests.
Quant. Biol.
Yiyi Liu, Hongyu Zhao
2017 J jnl
gCoda: Conditional Dependence Network Inference for Compositional Data.
J. Comput. Biol.
Huaying Fang, Chengcheng Huang, Hongyu Zhao, Minghua Deng
2017 J jnl
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture.
PLoS Comput. Biol.
Dongjun Chung, Hang Joon Kim, Hongyu Zhao
2016 J jnl
Efficient Drug-Pathway Association Analysis via Integrative Penalized Matrix Decomposition.
IEEE ACM Trans. Comput. Biol. Bioinform.
Cong Li, Can Yang, Greg Hather, Ray Liu, Hongyu Zhao
2016 J jnl
GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation.
Bioinform.
Qiongshi Lu, Xinwei Yao, Yiming Hu, Hongyu Zhao
2016 J jnl
Leveraging protein quaternary structure to identify oncogenic driver mutations.
BMC Bioinform.
Gregory A. Ryslik, Yuwei Cheng, Yorgo Modis, Hongyu Zhao
2016 J jnl
NBLDA: negative binomial linear discriminant analysis for RNA-Seq data.
BMC Bioinform.
Kai Dong, Hongyu Zhao, Tiejun Tong, Xiang Wan
2016 J jnl
Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes.
Bioinform.
Yiyi Liu, Hongyu Zhao
2015 J jnl
CCLasso: correlation inference for compositional data through Lasso.
Bioinform.
Huaying Fang, Chengcheng Huang, Hongyu Zhao, Minghua Deng
2015 J jnl
Functional Module Analysis for Gene Coexpression Networks with Network Integration.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuqin Zhang, Hongyu Zhao, Michael K. Ng
2015 J jnl
M
BMC Bioinform.
Gengxin Li, Hongyu Zhao
2015 J jnl
The application of sparse estimation of covariance matrix to quadratic discriminant analysis.
BMC Bioinform.
Jiehuan Sun, Hongyu Zhao
2014 J jnl
A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations.
BMC Bioinform.
Gregory A. Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Yorgo Modis, Hongyu Zhao
2014 J jnl
A spatial simulation approach to account for protein structure when identifying non-random somatic mutations.
BMC Bioinform.
Gregory A. Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Robert D. Bjornson, Daniel Zelterman, Yorgo Modis, Hongyu Zhao
2014 J jnl
Low-Rank Modeling and Its Applications in Image Analysis.
CoRR
Xiaowei Zhou, Can Yang, Hongyu Zhao, Weichuan Yu
2014 J jnl
Low-Rank Modeling and Its Applications in Image Analysis.
ACM Comput. Surv.
Xiaowei Zhou, Can Yang, Hongyu Zhao, Weichuan Yu
2014 J jnl
Ttn as a likely causal gene for QTL of alcohol preference on mouse chromosome 2.
BMC Bioinform.
Lishi Wang, Yan Jiao, Yue Huang, Beth Bennett, Robert W. Williams, Dawei Li, Hongyu Zhao, Joel Gelernter, Henry R. Kranzler, Lindsay A. Farrer, Weikuan Gu
2013 J jnl
Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping.
Bioinform.
Can Yang, Lin Wang, Shuqin Zhang, Hongyu Zhao
2013 J jnl
Differential expression analysis for paired RNA-seq data.
BMC Bioinform.
Lisa M. Chung, John P. Ferguson, Wei Zheng, Feng Qian, Vincent Bruno, Ruth R. Montgomery, Hongyu Zhao
2013 J jnl
HapBoost: A Fast Approach to Boosting Haplotype Association Analyses in Genome-Wide Association Studies.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiang Wan, Can Yang, Qiang Yang, Hongyu Zhao, Weichuan Yu
2013 J jnl
Joint analysis of expression profiles from multiple cancers improves the identification of microRNA-gene interactions.
Bioinform.
Xiaowei Chen, Frank J. Slack, Hongyu Zhao
2013 J jnl
Multisample aCGH Data Analysis via Total Variation and Spectral Regularization.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiaowei Zhou, Can Yang, Xiang Wan, Hongyu Zhao, Weichuan Yu
2013 J jnl
Sparse principal component analysis by choice of norm.
J. Multivar. Anal.
Xin Qi, Ruiyan Luo, Hongyu Zhao
2013 J jnl
Utilizing protein structure to identify non-random somatic mutations.
BMC Bioinform.
Gregory A. Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Yorgo Modis, Hongyu Zhao
2012 J jnl
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment.
Bioinform.
Haisu Ma, Hongyu Zhao
2012 J jnl
Improved mean estimation and its application to diagonal discriminant analysis.
Bioinform.
Tiejun Tong, Liang Chen, Hongyu Zhao
2012 J jnl
M
Bioinform.
Gengxin Li, Joel Gelernter, Henry R. Kranzler, Hongyu Zhao
2012 J jnl
iFad: an integrative factor analysis model for drug-pathway association inference.
Bioinform.
Haisu Ma, Hongyu Zhao
2011 J jnl
Bias Detection and Correction in RNA-Sequencing Data.
BMC Bioinform.
Wei Zheng, Lisa M. Chung, Hongyu Zhao
2011 J jnl
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.
Bioinform.
Haisu Ma, Eric E. Schadt, Lee M. Kaplan, Hongyu Zhao
2011 — ch.
Reverse Engineering of Gene Regulation Networks with an Application to the DREAM4
Handbook of Statistical Bioinformatics
Hyonho Chun, Jia Kang, Xianghua Zhang, Minghua Deng, Haisu Ma, Hongyu Zhao
2011 J jnl
Score regularization for peptide identification.
BMC Bioinform.
Zengyou He, Hongyu Zhao, Weichuan Yu
2011 J jnl
Some theoretical properties of Silverman's method for Smoothed functional principal component analysis.
J. Multivar. Anal.
Xin Qi, Hongyu Zhao
2010 J jnl
Pathway analysis using random forests with bivariate node-split for survival outcomes.
Bioinform.
Herbert Pang, Debayan Datta, Hongyu Zhao
2009 J jnl
Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data.
BMC Bioinform.
Debayan Datta, Hongyu Zhao
2009 J jnl
Genotyping and inflated type I error rate in genome-wide association case/control studies.
BMC Bioinform.
Joshua N. Sampson, Hongyu Zhao
2008 J jnl
Building pathway clusters from Random Forests classification using class votes.
BMC Bioinform.
Herbert Pang, Hongyu Zhao
2008 J jnl
Considering dependence among genes and markers for false discovery control in eQTL mapping.
Bioinform.
Liang Chen, Tiejun Tong, Hongyu Zhao
2008 J jnl
Estimating dynamic models for gene regulation networks.
Bioinform.
Jiguo Cao, Hongyu Zhao
2008 J jnl
Is Subcellular Localization Informative for Modeling Protein-Protein Interaction Signal?
J. Electr. Comput. Eng.
Junfeng Liu, Hongyu Zhao, Jun Tan, Dajie Luo, Weichuan Yu, E. James Harner, Weichung Joe Shih
2008 J jnl
Statistical methods to infer cooperative binding among transcription factors in
Bioinform.
Debayan Datta, Hongyu Zhao
2007 J jnl
A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry.
Comput. Biol. Chem.
Weichuan Yu, Junfeng Liu, Chris Colangelo, Erol E. Gulcicek, Hongyu Zhao
2007 J jnl
Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis.
J. Biomed. Informatics
Valentin Dinu, Hongyu Zhao, Perry L. Miller
2006 J jnl
Detecting and aligning peaks in mass spectrometry data with applications to MALDI.
Comput. Biol. Chem.
Weichuan Yu, Baolin Wu, Ning Lin, Kathy Stone, Kenneth R. Williams, Hongyu Zhao
2006 J jnl
Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space-Based Approach.
IEEE ACM Trans. Comput. Biol. Bioinform.
Weichuan Yu, Xiaoye Li, Junfeng Liu, Baolin Wu, Kenneth R. Williams, Hongyu Zhao
2006 J jnl
PSMIX: an R package for population structure inference via maximum likelihood method.
BMC Bioinform.
Baolin Wu, Nianjun Liu, Hongyu Zhao
2006 J jnl
Pathway analysis using random forests classification and regression.
Bioinform.
Herbert Pang, Aiping Lin, Matthew Holford, Bradley E. Enerson, Bin Lu, Michael P. Lawton, Eugenia Floyd, Hongyu Zhao
2005 J jnl
A semiparametric approach for marker gene selection based on gene expression data.
Bioinform.
Zhong Guan, Hongyu Zhao
2005 J jnl
A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data.
Comput. Biol. Chem.
Yinglei Lai, Hongyu Zhao
2005 — conf
Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach.
CSB Workshops
Weichuan Yu, Xiaoye Li, Hongyu Zhao
2005 J jnl
Are scale-free networks robust to measurement errors?
BMC Bioinform.
Nan Lin, Hongyu Zhao
2005 J jnl
Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies.
J. Am. Medical Informatics Assoc.
Nicholas Carriero, Michael V. Osier, Kei-Hoi Cheung, Perry L. Miller, Mark Gerstein, Hongyu Zhao, Baolin Wu, Scott Rifkin, Joseph T. Chang, Heping Zhang, Kevin P. White, Kenneth R. Williams, Martin H. Schultz
2005 J jnl
Detection of DNA copy number alterations using penalized least squares regression.
Bioinform.
Tao Huang, Baolin Wu, Paul Lizardi, Hongyu Zhao
2005 J jnl
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination.
Bioinform.
Kui Zhang, Fengzhu Sun, Hongyu Zhao
2005 J jnl
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms.
Bioinform.
Yin Liu, Nianjun Liu, Hongyu Zhao
2005 J jnl
Integrating mRNA Decay Information into Co-Regulation Study.
J. Comput. Sci. Technol.
Liang Chen, Hongyu Zhao
2005 J jnl
Negative correlation between compositional symmetries and local recombination rates.
Bioinform.
Liang Chen, Hongyu Zhao
2005 J jnl
VitaPad: visualization tools for the analysis of pathway data.
Bioinform.
Matthew Holford, Naixin Li, Prakash M. Nadkarni, Hongyu Zhao
2004 J jnl
A computational approach for ordering signal transduction pathway components from genomics and proteomics Data.
BMC Bioinform.
Yin Liu, Hongyu Zhao
2004 J jnl
A statistical method for identifying differential gene-gene co-expression patterns.
Bioinform.
Yinglei Lai, Baolin Wu, Liang Chen, Hongyu Zhao
2004 J jnl
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
Nucleic Acids Res.
Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, Jun Wang
2004 J jnl
Handling multiple testing while interpreting microarrays with the Gene Ontology Database.
BMC Bioinform.
Michael V. Osier, Hongyu Zhao, Kei-Hoi Cheung
2004 J jnl
Information assessment on predicting protein-protein interactions.
BMC Bioinform.
Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao
2003 J jnl
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data.
Bioinform.
Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn L. Stone, David Ward, Kenneth R. Williams, Hongyu Zhao
2003 J jnl
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for
BMC Bioinform.
Deyun Pan, Ning Sun, Kei-Hoi Cheung, Zhong Guan, Ligeng Ma, Matthew Holford, Xingwang Deng, Hongyu Zhao
2002 Misc conf
YMD: a microarray database for large-scale gene expression analysis.
AMIA
Kei-Hoi Cheung, Kevin P. White, Janet Hager, Mark Gerstein, Valerie Reinke, Kenneth Nelson, Peter Masiar, Ranjana Srivastava, Yuli Li, Ju Li, Hongyu Zhao, Jinming Li, David B. Allison, Michael Snyder, Perry L. Miller, Kenneth R. Williams
2001 J jnl
On Relationship Inference Using Gamete Identity by Descent Data.
J. Comput. Biol.
Hongyu Zhao, Feng Liang