Xuegong Zhang

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 53

Top Topics

Differential Expression

Feature Selection Algorithms

Electronic Medical Record

Top Venues

Genom. Proteom. Bioinform.

Publications

Yifan Sun, Jingyan Shen, Yunfan Jiang, Zhaohui Huang, Minsheng Hao, Xuegong Zhang
MMA-RNN: A multi-level multi-task attention-based recurrent neural network for discrimination and localization of atrial fibrillation. Biomed. Signal Process. Control. 89 (2024)
Tianxing Ma, Zetong Zhao, Haochen Li, Lei Wei, Xuegong Zhang
NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data. Quant. Biol. 12 (1) (2024)
Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei, Xuegong Zhang
scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis. RECOMB (2024)
Tianyu Zhang, Chengbin Hou, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv
Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs. CoRR (2024)
Wenrui Li, Wei Zhang, Qinghao Zhang, Xuegong Zhang, Xiaowo Wang
Weakly-supervised causal discovery based on fuzzy knowledge and complex data complementarity. CoRR (2024)
Erpai Luo, Minsheng Hao, Lei Wei, Xuegong Zhang
scDiffusion: conditional generation of high-quality single-cell data using diffusion model. CoRR (2024)
Ziming Jiang, Yanhong Wu, Yuxin Miao, Kaige Deng, Fan Yang, Shuhuan Xu, Yupeng Wang, Renke You, Lei Zhang, Yuhan Fan, Wenbo Guo, Qiuyu Lian, Lei Chen, Xuegong Zhang, Yongchang Zheng, Jin Gu
HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC. Genom. Proteom. Bioinform. 22 (1) (2024)
Qiuchen Meng, Lei Wei, Kun Ma, Ming Shi, Xinyi Lin, Joshua W. K. Ho, Yinqing Li, Xuegong Zhang
scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. Briefings Bioinform. 25 (2) (2024)
Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Xuegong Zhang, Lei Wei
Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. Briefings Bioinform. 24 (6) (2023)
Jiaqi Li, Zhuofeng Li, Lei Wei, Xuegong Zhang
Machine Learning in Lung Cancer Radiomics. Mach. Intell. Res. 20 (6) (2023)
Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. CoRR (2023)
Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv
Building digital life systems for future biology and medicine. Quant. Biol. 11 (3) (2023)
Jing Gong, Minsheng Hao, Xingyi Cheng, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. NeurIPS (2023)
Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. Bioinform. 39 (8) (2023)
Yifan Sun, Jingyan Shen, Yunfan Jiang, Zhaohui Huang, Minsheng Hao, Xuegong Zhang
MMA-RNN: A Multi-level Multi-task Attention-based Recurrent Neural Network for Discrimination and Localization of Atrial Fibrillation. CoRR (2023)
Fulong Yan, Chongjin Xie, Jie Zhang, Yongqing Xi, Zhiping Yao, Yang Liu, Xingming Lin, Jianbo Huang, Yu Ce, Xuegong Zhang, Nicola Calabretta
Network traffic characteristics of hyperscale data centers in the era of cloud applications. JOCN 15 (10) (2022)
Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang
DualGCN: a dual graph convolutional network model to predict cancer drug response. BMC Bioinform. (4) (2022)
Jinxiang Ou, Yunheng Shen, Feng Wang, Qiao Liu, Xuegong Zhang, Hairong Lv
AggEnhance: Aggregation Enhancement by Class Interior Points in Federated Learning with Non-IID Data. ACM Trans. Intell. Syst. Technol. 13 (6) (2022)
Pengshuai Yang, Xiaoxu Yin, Haiming Lu, Zhongliang Hu, Xuegong Zhang, Rui Jiang, Hairong Lv
CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological Images. Medical Image Anal. 81 (2022)
Wei Zhang, Hanwen Xu, Rong Qiao, Bixi Zhong, Xianglin Zhang, Jin Gu, Xuegong Zhang, Lei Wei, Xiaowo Wang
ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data. Briefings Bioinform. 23 (1) (2022)
Xuegong Zhang, Jin Gu
Yanda Li: A never-stopping pioneer, investigator and founder. Quant. Biol. 10 (1) (2022)
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang
DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility. Genom. Proteom. Bioinform. 20 (3) (2022)
Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang
Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. Nat. Mach. Intell. 4 (2) (2022)
Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv
scGraph: a graph neural network-based approach to automatically identify cell types. Bioinform. 38 (11) (2022)
Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. Bioinform. 37 (Supplement) (2021)
Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang
Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction. Genom. Proteom. Bioinform. 19 (3) (2021)
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
A Method for Generating Synthetic Electronic Medical Record Text. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Minsheng Hao, Kui Hua, Xuegong Zhang
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map. Bioinform. 37 (23) (2021)
Xuegong Zhang
Featured articles dedicated to the 20th anniversary of the human genome. Quant. Biol. 9 (1) (2021)
Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang, Xiaowo Wang
CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images. Bioinform. 37 (2) (2021)
Ziheng Zou, Kui Hua, Xuegong Zhang
HGC: fast hierarchical clustering for large-scale single-cell data. Bioinform. 37 (21) (2021)
Najeebullah Shah, Jiaqi Li, Fanhong Li, Wenchang Chen, Haoxiang Gao, Sijie Chen, Kui Hua, Xuegong Zhang
Discovery of Biological Knowledge from scRNA-Seq Data Using Machine Learning. Patterns 1 (5) (2020)
Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang
SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data. BMC Bioinform. 21 (1) (2020)
Xuegong Zhang
QB: Embracing the future of quantitative understanding and engineering of life. Quant. Biol. 7 (1) (2019)
Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang
A new statistic for efficient detection of repetitive sequences. Bioinform. 35 (22) (2019)
Kui Hua, Xuegong Zhang
Estimating the total genome length of a metagenomic sample using k-mers. BMC Genom. 20 (S2) (2019)
Jiaqi Li, Haiming Lu, Xiang Fang, Sijie Chen, Xuegong Zhang
Pixel-Level Clustering Reveals Intra-Tumor Heterogeneity in Non-Small Cell Lung Cancer. BIBM (2019)
Kui Hua, Xuegong Zhang
A case study on the detailed reproducibility of a Human Cell Atlas project. Quant. Biol. 7 (2) (2019)
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
Generation of Synthetic Electronic Medical Record Text. CoRR (2018)
Shansong Liu, Kui Hua, Sijie Chen, Xuegong Zhang
Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution. Quant. Biol. 6 (2) (2018)
Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang
DEsingle for detecting three types of differential expression in single-cell RNA-seq data. Bioinform. 34 (18) (2018)
Xuegong Zhang
An Overview of Bioinformatics Challenges for Human Cell Atlas. BIBM (2018)
Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang
Generation of Synthetic Electronic Medical Record Text. BIBM (2018)
Xuegong Zhang, Shansong Liu, Hongfei Cui, Ting Chen
Reading the Underlying Information From Massive Metagenomic Sequencing Data. Proc. IEEE 105 (3) (2017)
Zhirong Sun, Kui Hua, Xuegong Zhang, Feng-Biao Guo, Jian Huang
The 7th National Conference on Bioinformatics and Systems Biology of China. Quant. Biol. 5 (2) (2017)
Aziz Khan, Xuegong Zhang
dbSUPER: a database of super-enhancers in mouse and human genome. Nucleic Acids Res. 44 (Database-Issue) (2016)
Hongfei Cui, Yingxue Li, Xuegong Zhang
An overview of major metagenomic studies on human microbiomes in health and disease. Quant. Biol. 4 (3) (2016)
Zhun Miao, Xuegong Zhang
Differential expression analyses for single-cell RNA-Seq: old questions on new data. Quant. Biol. 4 (4) (2016)
Xuegong Zhang
Special collection of recent advances in next-generation bioinformatics, part II. Quant. Biol. 4 (2) (2016)
Xuegong Zhang
Special collection of recent advances in next-generation bioinformatics. Quant. Biol. 4 (1) (2016)
Tatiana C. Mangericao, Zhanhao Peng, Xuegong Zhang
Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls. BMC Syst. Biol. 10 (S-1) (2016)
Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jing-Fa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu
Precision Medicine: What Challenges Are We Facing? Genom. Proteom. Bioinform. 14 (5) (2016)
Chao Ye, Bo Jiang, Xuegong Zhang, Jun S. Liu
dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis. Bioinform. 31 (11) (2015)
Leying Guan, Qian Yang, Mengting Gu, Liang Chen, Xuegong Zhang
Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation. Quant. Biol. 2 (2) (2014)
Qifeng Xu, Xuegong Zhang
Multiclass feature selection algorithms base on R-SVM. ChinaSIP (2014)
Xavier Rogé, Xuegong Zhang
RNAseqViewer: visualization tool for RNA-Seq data. Bioinform. 30 (6) (2014)
Hongshan Jiang, Ying Zhao, Wenguang Chen, Weimin Zheng, Xuegong Zhang
Improving cis-regulatory elements modeling by consensus scaffolded mixture models. Sci. China Inf. Sci. 56 (1) (2013)
Chao Wu, Jun Zhu, Xuegong Zhang
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. BMC Bioinform. 14 (2013)
Xuegong Zhang, Fengzhu Sun
Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology). Quant. Biol. 1 (2) (2013)
Xinyun Ma, Xuegong Zhang
NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. BMC Bioinform. 14 (2013)
Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric Schadt
Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic. PLoS Comput. Biol. 9 (3) (2013)
Chao Wu, Jun Zhu, Xuegong Zhang
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. BMC Bioinform. 13 (2012)
Zhengpeng Wu, Xi Wang, Xuegong Zhang
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinform. 27 (4) (2011)
Weichen Wang, Xuegong Zhang
Network-based group variable selection for detecting expression quantitative trait loci (eQTL). BMC Bioinform. 12 (2011)
Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman
Sequence Alignment as Hypothesis Testing. J. Comput. Biol. 18 (5) (2011)
Xi Wang, Xuegong Zhang
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. BMC Syst. Biol. 5 (S-2) (2011)
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinform. 26 (1) (2010)
Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, Rui Jiang
A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer Metastasis. IJCBS (2009)
Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang
The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinform. 10 (S-1) (2009)
Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Michael Q. Zhang, Xuegong Zhang
Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure. IEEE Congress on Evolutionary Computation (2008)
Bo Jiang, Xuegong Zhang, Tianxi Cai
Estimating the Confidence Interval for Prediction Errors of Support Vector Machine Classifiers. J. Mach. Learn. Res. 9 (2008)
Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li
Neighbor number, valley seeking and clustering. Pattern Recognit. Lett. 28 (2) (2007)
Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li
. BMC Bioinform. 8 (2007)
Xuegong Zhang
Pattern Recognition in Mining High-Throughput Genomics/Proteomics Data: The New Challenges in Old Questions. ICCTA (2007)
Tingting Li, Hu Fu, Xuegong Zhang
Prediction of Kinase-Specific Phosphorylation Sites by One-Class SVMs. BIBM (2007)
Bo Jiang, Michael Q. Zhang, Xuegong Zhang
-elements. Bioinform. 23 (21) (2007)
Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, Michael Q. Zhang
-values for DNA motifs. Bioinform. 23 (5) (2007)
Yonghong Peng, Xuegong Zhang
Integrative data mining in systems biology: from text to network mining. Artif. Intell. Medicine 41 (2) (2007)
Chaolin Zhang, Xuesong Lu, Xuegong Zhang
Significance of Gene Ranking for Classification of Microarray Samples. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (3) (2006)
Jianhua Xu, Xuegong Zhang, Suqin Sun
Tuning SVM Parameters for Classifying Geographical Origins of Chinese Medical Herbs. Int. J. Wavelets Multiresolution Inf. Process. 4 (4) (2006)
Xuegong Zhang, Gabriel Dragffy, Anthony G. Pipe
Embryonics: A Path to Artificial Life? Artif. Life 12 (3) (2006)
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
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinform. 7 (2006)
Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang
Predicting methylation status of CpG islands in the human brain. Bioinform. 22 (18) (2006)
Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li
MicroRNA identification based on sequence and structure alignment. Bioinform. 21 (18) (2005)
Hua Xu, Peifa Jia, Xuegong Zhang
A Novel Chamber Scheduling Method in Etching Tools Using Adaptive Neural Networks. ISNN (3) (2005)
Hua Xu, Peifa Jia, Xuegong Zhang
A Neural Network Based Method for Shape Measurement in Steel Plate Forming Robot. ISNN (3) (2005)
Chenghai Xue, Fei Li, Tao He, Guo-Ping Liu, Yanda Li, Xuegong Zhang
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinform. 6 (2005)
Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang
htSNPer1.0: software for haplotype block partition and htSNPs selection. BMC Bioinform. 6 (2005)
Xuesong Lu, Yanda Li, Xuegong Zhang
A simple strategy for detecting outlier samples in microarray data. ICARCV (2004)
Jianhua Xu, Xuegong Zhang
A Learning Algorithm with Gaussian Regularizer for Kernel Neuron. ISNN (1) (2004)
Xi Ma, Jun Cai, Wei Hu, Yimin Zhang, Yanda Li, Xuegong Zhang
Discovering possible context dependences around SNP sites in human genes with Bayesian network learning. ICARCV (2004)
Hua Xu, Yiming Cao, Zehong Yang, Peifa Jia, Xuegong Zhang
The RTOC Open System for Controlling Fictitious Roaming Platform. ROBIO (2004)
Justin J. Song, Eric Q. Li, Wei Hu, Steven Ge, Chunrong Lai, Yimin Zhang, Xuegong Zhang, Wenguang Chen, Weimin Zheng
Parallelization of Bayesian Network based SNPs Pattern Analysis and Performance Characterization on SMP/HT. ICPADS (2004)
Kai Yu, Liang Ji, Xuegong Zhang
Kernel Nearest Neighbor Algorithm. Neural Process. Lett. 15 (2) (2002)
Hui Yan, Xuegong Zhang, Yanda Li, Liqin Shen, Weibin Zhu
The signal reconstruction of speech by KPCA. INTERSPEECH (2000)
Wenkai Lu, Xuegong Zhang, Yanda Li, Liqin Shen, Weibin Zhu
Joint speech signal enhancement based on spectral subtraction and SVD filter. INTERSPEECH (2000)