Joint speech signal enhancement based on spectral subtraction and SVD filter. - Wenkai Lu; Xuegong Zhang; Yanda Li; Liqin Shen; Weibin Zhu (INTERSPEECH, 2000)

The signal reconstruction of speech by KPCA. - Hui Yan; Xuegong Zhang; Yanda Li; Liqin Shen; Weibin Zhu (INTERSPEECH, 2000)

Kernel Nearest Neighbor Algorithm. - Kai Yu; Liang Ji; Xuegong Zhang (Neural Process. Lett., 2002)

A simple strategy for detecting outlier samples in microarray data. - Xuesong Lu; Yanda Li; Xuegong Zhang (ICARCV, 2004)

Discovering possible context dependences around SNP sites in human genes with Bayesian network learning. - Xi Ma; Jun Cai; Wei Hu 002; Yimin Zhang 002; Yanda Li; Xuegong Zhang (ICARCV, 2004)

Parallelization of Bayesian Network based SNPs Pattern Analysis and Performance Characterization on SMP/HT. - Justin J. Song; Eric Q. Li; Wei Hu 002; Steven Ge; Chunrong Lai; Yimin Zhang 002; Xuegong Zhang; Wenguang Chen; Weimin Zheng (ICPADS, 2004)

Kernels based on weighted Levenshtein distance. - Jianhua Xu; Xuegong Zhang (IJCNN, 2004)

A Learning Algorithm with Gaussian Regularizer for Kernel Neuron. - Jianhua Xu; Xuegong Zhang (ISNN (1), 2004)

The RTOC Open System for Controlling Fictitious Roaming Platform. - Hua Xu; Yiming Cao; Zehong Yang; Peifa Jia; Xuegong Zhang (ROBIO, 2004)

A Neural Network Based Method for Shape Measurement in Steel Plate Forming Robot. - Hua Xu; Peifa Jia; Xuegong Zhang (ISNN (3), 2005)

A Novel Chamber Scheduling Method in Etching Tools Using Adaptive Neural Networks. - Hua Xu; Peifa Jia; Xuegong Zhang (ISNN (3), 2005)

MicroRNA identification based on sequence and structure alignment. - Xiaowo Wang; Jing Zhang 010; Fei Li; Jin Gu; Tao He; Xuegong Zhang; Yanda Li (Bioinform., 2005)

htSNPer1.0: software for haplotype block partition and htSNPs selection. - Keyue Ding; Jing Zhang 010; Kaixin Zhou; Yan Shen; Xuegong Zhang (BMC Bioinform., 2005)

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. - Chenghai Xue; Fei Li; Tao He; Guo-Ping Liu 003; Yanda Li; Xuegong Zhang (BMC Bioinform., 2005)

Embryonics: A Path to Artificial Life? - Xuegong Zhang; Gabriel Dragffy; Anthony G. Pipe (Artif. Life, 2006)

Predicting methylation status of CpG islands in the human brain. - Fang Fang; Shicai Fan; Xuegong Zhang; Michael Q. Zhang (Bioinform., 2006)

Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. - Xuegong Zhang; Xin Lu; Qian Shi; Xiu-qin Xu; Hon-chiu E. Leung; Lyndsay N. Harris; James D. Iglehart; Alexander Miron; Jun S. Liu; Wing Hung Wong (BMC Bioinform., 2006)

Tuning SVM Parameters for Classifying Geographical Origins of Chinese Medical Herbs. - Jianhua Xu; Xuegong Zhang; Suqin Sun (Int. J. Wavelets Multiresolution Inf. Process., 2006)

Significance of Gene Ranking for Classification of Microarray Samples. - Chaolin Zhang; Xuesong Lu; Xuegong Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Prediction of Kinase-Specific Phosphorylation Sites by One-Class SVMs. - Tingting Li; Hu Fu; Xuegong Zhang (BIBM, 2007)

Pattern Recognition in Mining High-Throughput Genomics/Proteomics Data: The New Challenges in Old Questions. - Xuegong Zhang (ICCTA, 2007)

Integrative data mining in systems biology: from text to network mining. - Yonghong Peng; Xuegong Zhang (Artif. Intell. Medicine, 2007)

OSCAR: One-class SVM for accurate recognition of cis-elements. - Bo Jiang 005; Michael Q. Zhang; Xuegong Zhang (Bioinform., 2007)

Computing exact P-values for DNA motifs. - Jing Zhang 012; Bo Jiang 005; Ming Li 001; John Tromp; Xuegong Zhang; Michael Q. Zhang (Bioinform., 2007)

Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. - Jin Gu; Hu Fu 001; Xuegong Zhang; Yanda Li (BMC Bioinform., 2007)

Neighbor number, valley seeking and clustering. - Chaolin Zhang; Xuegong Zhang; Michael Q. Zhang; Yanda Li (Pattern Recognit. Lett., 2007)

Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure. - Ujjwal Maulik; Anirban Mukhopadhyay 001; Sanghamitra Bandyopadhyay; Michael Q. Zhang; Xuegong Zhang (IEEE Congress on Evolutionary Computation, 2008)

Estimating the Confidence Interval for Prediction Errors of Support Vector Machine Classifiers. - Bo Jiang 005; Xuegong Zhang; Tianxi Cai (J. Mach. Learn. Res., 2008)

A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer Metastasis. - Wangshu Zhang; Feng Zeng; Xuebing Wu; Xuegong Zhang; Rui Jiang 001 (IJCBS, 2009)

The Seventh Asia Pacific Bioinformatics Conference (APBC2009). - Michael Q. Zhang; Michael S. Waterman; Xuegong Zhang (BMC Bioinform., 2009)

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. - Likun Wang 003; Zhixing Feng; Xi Wang 002; Xiaowo Wang; Xuegong Zhang (Bioinform., 2010)

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. - Zhengpeng Wu; Xi Wang 002; Xuegong Zhang (Bioinform., 2011)

Network-based group variable selection for detecting expression quantitative trait loci (eQTL). - Weichen Wang; Xuegong Zhang (BMC Bioinform., 2011)

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. - Xi Wang 002; Xuegong Zhang (BMC Syst. Biol., 2011)

Sequence Alignment as Hypothesis Testing. - Lu Meng; Fengzhu Sun; Xuegong Zhang; Michael S. Waterman (J. Comput. Biol., 2011)

Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. - Chao Wu; Jun Zhu; Xuegong Zhang (BMC Bioinform., 2012)

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. - Xinyun Ma; Xuegong Zhang (BMC Bioinform., 2013)

Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma. - Chao Wu; Jun Zhu; Xuegong Zhang (BMC Bioinform., 2013)

Improving cis-regulatory elements modeling by consensus scaffolded mixture models. - Hongshan Jiang; Ying Zhao; Wenguang Chen; Weimin Zheng; Xuegong Zhang (Sci. China Inf. Sci., 2013)

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic. - Zhixing Feng; Gang Fang; Jonas Korlach; Tyson Clark; Khai Luong; Xuegong Zhang; Wing Wong; Eric E. Schadt (PLoS Comput. Biol., 2013)

Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology). - Xuegong Zhang; Fengzhu Sun (Quant. Biol., 2013)

Multiclass feature selection algorithms base on R-SVM. - Qifeng Xu; Xuegong Zhang (ChinaSIP, 2014)

RNAseqViewer: visualization tool for RNA-Seq data. - Xavier Rogé; Xuegong Zhang (Bioinform., 2014)

Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation. - Leying Guan; Qian Yang; Mengting Gu; Liang Chen; Xuegong Zhang (Quant. Biol., 2014)

dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis. - Chao Ye; Bo Jiang 005; Xuegong Zhang; Jun S. Liu (Bioinform., 2015)

Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls. - Tatiana C. Mangericao; Zhanhao Peng; Xuegong Zhang (BMC Syst. Biol., 2016)

Precision Medicine: What Challenges Are We Facing? - Yu Xue 001; Eric-Wubbo Lameijer; Kai Ye 001; Kunlin Zhang; Suhua Chang; Xiaoyue Wang; Jianmin Wu; Ge Gao; Fangqing Zhao; Jian Li; Chunsheng Han; Shuhua Xu; et al. (Genom. Proteom. Bioinform., 2016)

dbSUPER: a database of super-enhancers in mouse and human genome. - Aziz Khan 001; Xuegong Zhang (Nucleic Acids Res., 2016)

An overview of major metagenomic studies on human microbiomes in health and disease. - Hongfei Cui; Yingxue Li; Xuegong Zhang (Quant. Biol., 2016)

Differential expression analyses for single-cell RNA-Seq: old questions on new data. - Zhun Miao; Xuegong Zhang (Quant. Biol., 2016)

Special collection of recent advances in next-generation bioinformatics. - Xuegong Zhang (Quant. Biol., 2016)

Special collection of recent advances in next-generation bioinformatics, part II. - Xuegong Zhang (Quant. Biol., 2016)

Reading the Underlying Information From Massive Metagenomic Sequencing Data. - Xuegong Zhang; Shansong Liu; Hongfei Cui; Ting Chen 006 (Proc. IEEE, 2017)

The 7th National Conference on Bioinformatics and Systems Biology of China. - Zhirong Sun; Kui Hua; Xuegong Zhang; Feng-Biao Guo; Jian Huang 004 (Quant. Biol., 2017)

Generation of Synthetic Electronic Medical Record Text. - Jiaqi Guan; Runzhe Li; Sheng Yu 002; Xuegong Zhang (BIBM, 2018)

An Overview of Bioinformatics Challenges for Human Cell Atlas. - Xuegong Zhang (BIBM, 2018)

DEsingle for detecting three types of differential expression in single-cell RNA-seq data. - Zhun Miao; Ke Deng; Xiaowo Wang; Xuegong Zhang (Bioinform., 2018)

Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution. - Shansong Liu; Kui Hua; Sijie Chen; Xuegong Zhang (Quant. Biol., 2018)

Pixel-Level Clustering Reveals Intra-Tumor Heterogeneity in Non-Small Cell Lung Cancer. - Jiaqi Li; Haiming Lu; Xiang Fang; Sijie Chen; Xuegong Zhang (BIBM, 2019)

A new statistic for efficient detection of repetitive sequences. - Sijie Chen; Yixin Chen; Fengzhu Sun; Michael S. Waterman; Xuegong Zhang (Bioinform., 2019)

Estimating the total genome length of a metagenomic sample using k-mers. - Kui Hua; Xuegong Zhang (BMC Genom., 2019)

A case study on the detailed reproducibility of a Human Cell Atlas project. - Kui Hua; Xuegong Zhang (Quant. Biol., 2019)

QB: Embracing the future of quantitative understanding and engineering of life. - Xuegong Zhang (Quant. Biol., 2019)

SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data. - Yue Hu; Xi Xi; Qian Yang; Xuegong Zhang (BMC Bioinform., 2020)

An Experiment on Ab Initio Discovery of Biological Knowledge from scRNA-Seq Data Using Machine Learning. - Najeebullah Shah; Jiaqi Li; Fanhong Li; Wenchang Chen; Haoxiang Gao; Sijie Chen; Kui Hua; Xuegong Zhang (Patterns, 2020)

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. - Shengquan Chen; Boheng Zhang; Xiaoyang Chen; Xuegong Zhang; Rui Jiang 001 (Bioinform., 2021)

SOMDE: a scalable method for identifying spatially variable genes with self-organizing map. - Minsheng Hao; Kui Hua; Xuegong Zhang (Bioinform., 2021)

CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images. - Tao Hu; Shixiong Xu; Lei Wei; Xuegong Zhang; Xiaowo Wang (Bioinform., 2021)

HGC: fast hierarchical clustering for large-scale single-cell data. - Ziheng Zou; Kui Hua; Xuegong Zhang (Bioinform., 2021)

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction. - Tao Hu; Lei Wei; Shuailin Li; Tianrun Cheng; Xuegong Zhang; Xiaowo Wang (Genom. Proteom. Bioinform., 2021)

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. - Shengquan Chen; Qiao Liu 008; Xuejian Cui; Zhan-Ying Feng; Chunquan Li; Xiaowo Wang; Xuegong Zhang; Yong Wang; Rui Jiang 001 (Nucleic Acids Res., 2021)

Featured articles dedicated to the 20th anniversary of the human genome. - Xuegong Zhang (Quant. Biol., 2021)

A Method for Generating Synthetic Electronic Medical Record Text. - Jiaqi Guan; Runzhe Li; Sheng Yu 002; Xuegong Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data. - Wei Zhang 241; Hanwen Xu; Rong Qiao; Bixi Zhong; Xianglin Zhang; Jin Gu; Xuegong Zhang; Lei Wei; Xiaowo Wang (Briefings Bioinform., 2022)

scGraph: a graph neural network-based approach to automatically identify cell types. - Qijin Yin; Qiao Liu 008; Zhuoran Fu; Wanwen Zeng; Boheng Zhang; Xuegong Zhang; Rui Jiang 001; Hairong Lv (Bioinform., 2022)

DualGCN: a dual graph convolutional network model to predict cancer drug response. - Tianxing Ma; Qiao Liu 008; Haochen Li 003; Mu Zhou; Rui Jiang 001; Xuegong Zhang (BMC Bioinform., 2022)

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility. - Qiao Liu 008; Kui Hua; Xuegong Zhang; Wing Hung Wong; Rui Jiang 001 (Genom. Proteom. Bioinform., 2022)

Network traffic characteristics of hyperscale data centers in the era of cloud applications. - Fulong Yan; Chongjin Xie; Jie Zhang 006; Yongqing Xi; Zhiping Yao; Yang Liu; Xingming Lin; Jianbo Huang; Yu Ce; Xuegong Zhang; Nicola Calabretta (JOCN, 2022)

CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological Images. - Pengshuai Yang; Xiaoxu Yin; Haiming Lu; Zhongliang Hu; Xuegong Zhang; Rui Jiang 001; Hairong Lv (Medical Image Anal., 2022)

Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. - Xiaoyang Chen; Shengquan Chen; Shuang Song 006; Zijing Gao; Lin Hou; Xuegong Zhang; Hairong Lv; Rui Jiang 001 (Nat. Mach. Intell., 2022)

Yanda Li: A never-stopping pioneer, investigator and founder. - Xuegong Zhang; Jin Gu (Quant. Biol., 2022)

AggEnhance: Aggregation Enhancement by Class Interior Points in Federated Learning with Non-IID Data. - Jinxiang Ou; Yunheng Shen; Feng Wang 047; Qiao Liu 008; Xuegong Zhang; Hairong Lv (ACM Trans. Intell. Syst. Technol., 2022)

xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. - Jing Gong; Minsheng Hao; Xingyi Cheng; Xin Zeng; Chiming Liu; Jianzhu Ma; Xuegong Zhang; Taifeng Wang; Le Song (NeurIPS, 2023)

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. - Chen Li; Xiaoyang Chen; Shengquan Chen; Rui Jiang 001; Xuegong Zhang (Bioinform., 2023)

Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. - Haochen Li 003; Tianxing Ma; Minsheng Hao; Wenbo Guo 010; Jin Gu; Xuegong Zhang; Lei Wei (Briefings Bioinform., 2023)

Building digital life systems for future biology and medicine. - Xuegong Zhang; Lei Wei; Rui Jiang 001; Xiaowo Wang; Jin Gu; Zhen Xie; Hairong Lv (Quant. Biol., 2023)

Machine Learning in Lung Cancer Radiomics. - Jiaqi Li; Zhuofeng Li; Lei Wei; Xuegong Zhang (Mach. Intell. Res., 2023)

Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models. - Tianyu Zhang; Yuxiang Ren; Chengbin Hou; Hairong Lv; Xuegong Zhang (BIBM, 2024)

scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis. - Haiyang Bian; Yixin Chen; Xiaomin Dong; Chen Li 001; Minsheng Hao; Sijie Chen; Jinyi Hu; Maosong Sun 001; Lei Wei; Xuegong Zhang (RECOMB, 2024)

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data. - Chuxi Xiao; Yixin Chen; Qiuchen Meng; Lei Wei; Xuegong Zhang (Briefings Bioinform., 2024)

MMA-RNN: A multi-level multi-task attention-based recurrent neural network for discrimination and localization of atrial fibrillation. - Yifan Sun 010; Jingyan Shen; Yunfan Jiang 002; Zhaohui Huang; Minsheng Hao; Xuegong Zhang (Biomed. Signal Process. Control., 2024)

scDiffusion: conditional generation of high-quality single-cell data using diffusion model. - Erpai Luo; Minsheng Hao; Lei Wei; Xuegong Zhang (CoRR, 2024)

QueST: Querying Functional and Structural Niches on Spatial Transcriptomics Data via Contrastive Subgraph Embedding. - Mo Chen; Minsheng Hao; Xuegong Zhang; Lei Wei (CoRR, 2024)

HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC. - Ziming Jiang; Yanhong Wu; Yuxin Miao; Kaige Deng; Fan Yang; Shuhuan Xu; Yupeng Wang; Renke You; Lei Zhang; Yuhan Fan; Wenbo Guo 010; Qiuyu Lian; et al. (Genom. Proteom. Bioinform., 2024)

A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas. - Rui Jiang 001; Xiaoxu Yin; Pengshuai Yang; Lingchao Cheng; Juan Hu; Jiao Yang; Ying Wang; Xiaodan Fu; Li Shang; Liling Li; Wei Lin; Huan Zhou; et al. (Nat. Mac. Intell., 2024)

Current opinions on large cellular models. - Minsheng Hao; Lei Wei; Fan Yang 081; Jianhua Yao 001; Christina V. Theodoris; Bo Wang 044; Xin Li; Ge Yang 002; Xuegong Zhang (Quant. Biol., 2024)

NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data. - Tianxing Ma; Zetong Zhao; Haochen Li 003; Lei Wei; Xuegong Zhang (Quant. Biol., 2024)

scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. - Qiuchen Meng; Lei Wei; Kun Ma; Ming Shi; Xinyi Lin; Joshua W. K. Ho; Yinqing Li; Xuegong Zhang (Briefings Bioinform., 2024)

Weakly Supervised Causal Discovery Based on Fuzzy Knowledge and Complex Data Complementarity. - Wenrui Li; Wei Zhang 241; Qinghao Zhang; Xuegong Zhang; Xiaowo Wang (IEEE Trans. Fuzzy Syst., 2024)

Computational methods and data resources for predicting tumor neoantigens. - Xiaofei Zhao; Lei Wei; Xuegong Zhang (Briefings Bioinform., 2025)

A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs. - Xiaohao Mao; Yu Huang; Ye Jin; Lun Wang; Xuanzhong Chen; Honghong Liu; Xinglin Yang; Haopeng Xu; Xiaodong Luan; Ying Xiao; Siqin Feng; Jiahao Zhu; et al. (npj Digit. Medicine, 2025)

Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs. - Tianyu Zhang; Chengbin Hou; Rui Jiang 001; Xuegong Zhang; Chenghu Zhou; Ke Tang 001; Hairong Lv (IEEE Trans. Neural Networks Learn. Syst., 2025)

Benchmarking AI scientists in omics data-driven biological research. - Erpai Luo; Jinmeng Jia; Yifan Xiong; Xiangyu Li; Xiaobo Guo; Baoqi Yu; Lei Wei; Xuegong Zhang (CoRR, 2025)

DrVD-Bench: Do Vision-Language Models Reason Like Human Doctors in Medical Image Diagnosis? - Tianhong Zhou; Yin Xu; Yingtao Zhu; Chuxi Xiao; Haiyang Bian; Lei Wei; Xuegong Zhang (CoRR, 2025)