R/qtl: QTL Mapping in Experimental Crosses. - Karl W. Broman; Hao Wu 003; Saunak Sen; Gary A. Churchill (Bioinform., 2003)

R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. - Brian S. Yandell; Tapan Mehta; Samprit Banerjee; Daniel Shriner; Ramprasad Venkataraman; Jee Young Moon; W. Whipple Neely; Hao Wu 003; Randy von Smith; Nengjun Yi (Bioinform., 2007)

JAMIE: joint analysis of multiple ChIP-chip experiments. - Hao Wu 003; Hongkai Ji (Bioinform., 2010)

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. - Li Chen 029; Chi Wang 003; Zhaohui S. Qin; Hao Wu 003 (Bioinform., 2015)

PROPER: comprehensive power evaluation for differential expression using RNA-seq. - Hao Wu 003; Chi Wang 003; Zhijin Wu (Bioinform., 2015)

Predicting tumor purity from methylation microarray data. - Naiqian Zhang; Hua-Jun Wu; Weiwei Zhang; Jun Wang; Hao Wu 003; Xiaoqi Zheng (Bioinform., 2015)

Experimental Design and Power Calculation for RNA-seq Experiments. - Zhijin Wu; Hao Wu 003 (Statistical Genomics, 2016)

Differential methylation analysis for BS-seq data under general experimental design. - Yongseok Park; Hao Wu 003 (Bioinform., 2016)

Measuring the spatial correlations of protein binding sites. - Yingying Wei; Hao Wu 003 (Bioinform., 2016)

Accounting for tumor purity improves cancer subtype classification from DNA methylation data. - Weiwei Zhang; Hao Feng 005; Hao Wu 003; Xiaoqi Zheng (Bioinform., 2017)

Two-phase differential expression analysis for single cell RNA-seq. - Zhijin Wu; Yi Zhang; Michael L. Stitzel; Hao Wu 003 (Bioinform., 2018)

Disease prediction by cell-free DNA methylation. - Hao Feng 005; Peng Jin; Hao Wu 003 (Briefings Bioinform., 2019)

Dissecting differential signals in high-throughput data from complex tissues. - Ziyi Li 001; Zhijin Wu; Peng Jin; Hao Wu 003 (Bioinform., 2019)

Differential methylation analysis for bisulfite sequencing using DSS. - Hao Feng 005; Hao Wu 003 (Quant. Biol., 2019)

A comprehensive review of computational prediction of genome-wide features. - Tianlei Xu; Xiaoqi Zheng; Ben Li; Peng Jin; Zhaohui S. Qin; Hao Wu 003 (Briefings Bioinform., 2020)

Robust partial reference-free cell composition estimation from tissue expression. - Ziyi Li 001; Zhenxing Guo; Ying Cheng; Peng Jin; Hao Wu 003 (Bioinform., 2020)

Simulation, power evaluation and sample size recommendation for single-cell RNA-seq. - Kenong Su; Zhijin Wu; Hao Wu 003 (Bioinform., 2020)

A novel virtual drug screening pipeline with deep-leaning as core component identifies inhibitor of pancreatic alpha-amylase. - Haiping Zhang; Tingting Zhang; Konda Mani Saravanan; Linbu Liao; Hao Wu 003; Haishan Zhang; Huiling Zhang; Yi Pan 001; Xuli Wu; Yanjie Wei (BIBM, 2021)

Accurate feature selection improves single-cell RNA-seq cell clustering. - Kenong Su; Tianwei Yu; Hao Wu 003 (Briefings Bioinform., 2021)

Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing. - Zhenxing Guo; Andrew M. Shafik; Peng Jin; Zhijin Wu; Hao Wu 003 (Bioinform., 2021)

Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. - Weiwei Zhang; Hao Wu 003; Ziyi Li 001 (Bioinform., 2021)

A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq. - Xiaobo Sun; Xiaochu Lin; Ziyi Li 001; Hao Wu 003 (Briefings Bioinform., 2022)

EDClust: an EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing. - Xin Wei; Ziyi Li 001; Hongkai Ji; Hao Wu 003 (Bioinform., 2022)

Differential RNA methylation analysis for MeRIP-seq data under general experimental design. - Zhenxing Guo; Andrew M. Shafik; Peng Jin; Hao Wu 003 (Bioinform., 2022)

A cofunctional grouping-based approach for non-redundant feature gene selection in unannotated single-cell RNA-seq analysis. - Tao Deng; Siyu Chen; Ying Zhang; Yuanbin Xu; Da Feng; Hao Wu 003; Xiaobo Sun (Briefings Bioinform., 2023)

MIXER: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data. - Tao Deng; Mengqian Huang; Kaichen Xu; Yan Lu 010; Siyu Chen; Yucheng Xu; Nina Xie; Hao Wu 003; Xiaobo Sun (BCB, 2024)

Spatiotemporal attention boosts calling of complicated variations from long reads' alignment data. - Ying Shi 004; Shifu Luo; Yi Pan 001; Hao Wu 003; Wenjian Wang; Jinyan Li (BCB, 2024)

Detecting and Subtyping Anomalous Single Cells with M2ASDA. - Kaichen Xu; Kainan Liu; Linjie Wang; Yueyang Ding; Yan Lu 010; Hao Wu 003; Xiaobo Sun (BCB, 2024)

Target-oriented Reference Construction for supervised cell type identification in scRNA-seq. - Xin Wei; Wenjing Ma; Zhijin Wu; Hao Wu 003 (BIBM, 2024)

SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric. - Yue Lyu; Steven H. Lin; Hao Wu 003; Ziyi Li 001 (Bioinform., 2024)