Xuegong Zhang

According to our database, Xuegong Zhang authored at least 98 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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., January, 2024

NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data.

Tianxing Ma, Zetong Zhao, Haochen Li, Lei Wei, Xuegong Zhang

Quant. Biol., 2024

Current opinions on large cellular models.

Minsheng Hao, Lei Wei, Fan Yang, Jianhua Yao, Christina V. Theodoris, Bo Wang, Xin Li, Ge Yang, Xuegong Zhang

Quant. Biol., 2024

A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas.

Rui Jiang, Xiaoxu Yin, Pengshuai Yang, Lingchao Cheng, Juan Hu, Jiao Yang, Ying Wang, Xiaodan Fu, Li Shang, Liling Li, Wei Lin, Huan Zhou, Fufeng Chen, Xuegong Zhang, Zhongliang Hu, Hairong Lv

Nat. Mac. Intell., 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, Qiuyu Lian, Lei Chen, Xuegong Zhang, Yongchang Zheng, Jin Gu

Genom. Proteom. Bioinform., 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

Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models.

Tianyu Zhang, Yuxiang Ren, Chengbin Hou, Hairong Lv, Xuegong Zhang

CoRR, 2024

Weakly-supervised causal discovery based on fuzzy knowledge and complex data complementarity.

Wenrui Li, Wei Zhang, Qinghao Zhang, Xuegong Zhang, Xiaowo Wang

CoRR, 2024

Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs.

Tianyu Zhang, Chengbin Hou, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv

CoRR, 2024

scDiffusion: conditional generation of high-quality single-cell data using diffusion model.

Erpai Luo, Minsheng Hao, Lei Wei, Xuegong Zhang

CoRR, 2024

MMA-RNN: A multi-level multi-task attention-based recurrent neural network for discrimination and localization of atrial fibrillation.

Yifan Sun, Jingyan Shen, Yunfan Jiang, Zhaohui Huang, Minsheng Hao, Xuegong Zhang

Biomed. Signal Process. Control., 2024

scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis.

Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei, Xuegong Zhang

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Machine Learning in Lung Cancer Radiomics.

Jiaqi Li, Zhuofeng Li, Lei Wei, Xuegong Zhang

Mach. Intell. Res., December, 2023

Building digital life systems for future biology and medicine.

Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv

Quant. Biol., September, 2023

Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics.

Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Xuegong Zhang, Lei Wei

Briefings Bioinform., September, 2023

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data.

Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang

Bioinform., August, 2023

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

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022

AggEnhance: Aggregation Enhancement by Class Interior Points in Federated Learning with Non-IID Data.

Jinxiang Ou, Yunheng Shen, Feng Wang, Qiao Liu, Xuegong Zhang, Hairong Lv

ACM Trans. Intell. Syst. Technol., 2022

Yanda Li: A never-stopping pioneer, investigator and founder.

Xuegong Zhang, Jin Gu

Quant. Biol., 2022

Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding.

Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang

Nat. Mach. Intell., 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, Hairong Lv

Medical Image Anal., 2022

Network traffic characteristics of hyperscale data centers in the era of cloud applications.

Fulong Yan, Chongjin Xie, Jie Zhang, Yongqing Xi, Zhiping Yao, Yang Liu, Xingming Lin, Jianbo Huang, Yu Ce, Xuegong Zhang, Nicola Calabretta

JOCN, 2022

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility.

Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang

Genom. Proteom. Bioinform., 2022

DualGCN: a dual graph convolutional network model to predict cancer drug response.

Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang, Xuegong Zhang

BMC Bioinform., 2022

scGraph: a graph neural network-based approach to automatically identify cell types.

Qijin Yin, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv

Bioinform., 2022

ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data.

Wei Zhang, Hanwen Xu, Rong Qiao, Bixi Zhong, Xianglin Zhang, Jin Gu, Xuegong Zhang, Lei Wei, Xiaowo Wang

Briefings Bioinform., 2022

2021

A Method for Generating Synthetic Electronic Medical Record Text.

Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Featured articles dedicated to the 20th anniversary of the human genome.

Xuegong Zhang

Quant. Biol., 2021

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.

Shengquan Chen, Qiao Liu, Xuejian Cui, Zhan-Ying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang

Nucleic Acids Res., 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

HGC: fast hierarchical clustering for large-scale single-cell data.

Ziheng Zou, 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

SOMDE: a scalable method for identifying spatially variable genes with self-organizing map.

Minsheng Hao, Kui Hua, Xuegong Zhang

Bioinform., 2021

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics.

Shengquan Chen, Boheng Zhang, Xiaoyang Chen, Xuegong Zhang, Rui Jiang

Bioinform., 2021

2020

An Experiment on <i>Ab Initio</i> 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

SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data.

Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang

BMC Bioinform., 2020

2019

QB: Embracing the future of quantitative understanding and engineering of life.

Xuegong Zhang

Quant. Biol., 2019

A case study on the detailed reproducibility of a Human Cell Atlas project.

Kui Hua, Xuegong Zhang

Quant. Biol., 2019

Estimating the total genome length of a metagenomic sample using k-mers.

Kui Hua, Xuegong Zhang

BMC Genom., 2019

A new statistic for efficient detection of repetitive sequences.

Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang

Bioinform., 2019

Pixel-Level Clustering Reveals Intra-Tumor Heterogeneity in Non-Small Cell Lung Cancer.

Jiaqi Li, Haiming Lu, Xiang Fang, Sijie Chen, Xuegong Zhang

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution.

Shansong Liu, Kui Hua, Sijie Chen, Xuegong Zhang

Quant. Biol., 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

An Overview of Bioinformatics Challenges for Human Cell Atlas.

Xuegong Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Generation of Synthetic Electronic Medical Record Text.

Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017

The 7th National Conference on Bioinformatics and Systems Biology of China.

Zhirong Sun, Kui Hua, Xuegong Zhang, Feng-Biao Guo, Jian Huang

Quant. Biol., 2017

Reading the Underlying Information From Massive Metagenomic Sequencing Data.

Xuegong Zhang, Shansong Liu, Hongfei Cui, Ting Chen

Proc. IEEE, 2017

2016

Special collection of recent advances in next-generation bioinformatics, part II.

Xuegong Zhang

Quant. Biol., 2016

Special collection of recent advances in next-generation bioinformatics.

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

An overview of major metagenomic studies on human microbiomes in health and disease.

Hongfei Cui, Yingxue Li, Xuegong Zhang

Quant. Biol., 2016

dbSUPER: a database of super-enhancers in mouse and human genome.

Aziz Khan, Xuegong Zhang

Nucleic Acids Res., 2016

Precision Medicine: What Challenges Are We Facing?

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

Genom. Proteom. Bioinform., 2016

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

2015

dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis.

Chao Ye, Bo Jiang, Xuegong Zhang, Jun S. Liu

Bioinform., 2015

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

RNAseqViewer: visualization tool for RNA-Seq data.

Xavier Rogé, Xuegong Zhang

Bioinform., 2014

Multiclass feature selection algorithms base on R-SVM.

Qifeng Xu, Xuegong Zhang

Proceedings of the IEEE China Summit & International Conference on Signal and Information Processing, 2014

2013

Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology).

Xuegong Zhang, Fengzhu Sun

Quant. Biol., 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

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

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

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data.

Xinyun Ma, Xuegong Zhang

BMC Bioinform., 2013

2012

Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes.

Chao Wu, Jun Zhu, Xuegong Zhang

BMC Bioinform., 2012

2011

Sequence Alignment as Hypothesis Testing.

Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman

J. Comput. Biol., 2011

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.

Xi Wang, Xuegong Zhang

BMC Syst. Biol., 2011

Network-based group variable selection for detecting expression quantitative trait loci (eQTL).

Weichen Wang, Xuegong Zhang

BMC Bioinform., 2011

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.

Zhengpeng Wu, Xi Wang, Xuegong Zhang

Bioinform., 2011

2010

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang

Bioinform., 2010

2009

The Seventh Asia Pacific Bioinformatics Conference (APBC2009).

Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang

BMC Bioinform., 2009

A Comparative Study of Ensemble Learning Approaches in the Classification of Breast Cancer Metastasis.

Wangshu Zhang, Feng Zeng, Xuebing Wu, Xuegong Zhang, Rui Jiang

Proceedings of the International Joint Conferences on Bioinformatics, 2009

2008

Estimating the Confidence Interval for Prediction Errors of Support Vector Machine Classifiers.

Bo Jiang, Xuegong Zhang, Tianxi Cai

J. Mach. Learn. Res., 2008

Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure.

Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Michael Q. Zhang, Xuegong Zhang

Proceedings of the IEEE Congress on Evolutionary Computation, 2008

2007

Neighbor number, valley seeking and clustering.

Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li

Pattern Recognit. Lett., 2007

Identifications of conserved 7-mers in 3'-UTRs and microRNAs in <i>Drosophila</i>.

Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li

BMC Bioinform., 2007

Computing exact <i>P</i>-values for DNA motifs.

Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, Michael Q. Zhang

Bioinform., 2007

OSCAR: One-class SVM for accurate recognition of <i>cis</i>-elements.

Bo Jiang, Michael Q. Zhang, Xuegong Zhang

Bioinform., 2007

Integrative data mining in systems biology: from text to network mining.

Yonghong Peng, Xuegong Zhang

Artif. Intell. Medicine, 2007

Pattern Recognition in Mining High-Throughput Genomics/Proteomics Data: The New Challenges in Old Questions.

Xuegong Zhang

Proceedings of the 2007 International Conference on Computing: Theory and Applications (ICCTA 2007), 2007

Prediction of Kinase-Specific Phosphorylation Sites by One-Class SVMs.

Tingting Li, Hu Fu, Xuegong Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007

2006

Significance of Gene Ranking for Classification of Microarray Samples.

Chaolin Zhang, Xuesong Lu, Xuegong Zhang

IEEE ACM Trans. Comput. Biol. 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

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

Predicting methylation status of CpG islands in the human brain.

Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang

Bioinform., 2006

Embryonics: A Path to Artificial Life?

Xuegong Zhang, Gabriel Dragffy, Anthony G. Pipe

Artif. Life, 2006

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, Yanda Li, Xuegong Zhang

BMC Bioinform., 2005

htSNPer1.0: software for haplotype block partition and htSNPs selection.

Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang

BMC Bioinform., 2005

MicroRNA identification based on sequence and structure alignment.

Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li

Bioinform., 2005

A Novel Chamber Scheduling Method in Etching Tools Using Adaptive Neural Networks.

Hua Xu, Peifa Jia, Xuegong Zhang

Proceedings of the Advances in Neural Networks - ISNN 2005, Second International Symposium on Neural Networks, Chongqing, China, May 30, 2005

A Neural Network Based Method for Shape Measurement in Steel Plate Forming Robot.

Hua Xu, Peifa Jia, Xuegong Zhang

Proceedings of the Advances in Neural Networks - ISNN 2005, Second International Symposium on Neural Networks, Chongqing, China, May 30, 2005

2004

The RTOC Open System for Controlling Fictitious Roaming Platform.

Hua Xu, Yiming Cao, Zehong Yang, Peifa Jia, Xuegong Zhang

Proceedings of the 2004 IEEE International Conference on Robotics and Biomimetics, 2004

A Learning Algorithm with Gaussian Regularizer for Kernel Neuron.

Jianhua Xu, Xuegong Zhang

Proceedings of the Advances in Neural Networks, 2004

Parallelization of Bayesian Network based SNPs Pattern Analysis and Performance Characterization on SMP/HT.

Justin J. Song, Eric Q. Li, Wei Hu, Steven Ge, Chunrong Lai, Yimin Zhang, Xuegong Zhang, Wenguang Chen, Weimin Zheng

Proceedings of the 10th International Conference on Parallel and Distributed Systems, 2004

Discovering possible context dependences around SNP sites in human genes with Bayesian network learning.

Xi Ma, Jun Cai, Wei Hu, Yimin Zhang, Yanda Li, Xuegong Zhang

Proceedings of the 8th International Conference on Control, 2004

A simple strategy for detecting outlier samples in microarray data.

Xuesong Lu, Yanda Li, Xuegong Zhang

Proceedings of the 8th International Conference on Control, 2004

2002

Kernel Nearest Neighbor Algorithm.

Kai Yu, Liang Ji, Xuegong Zhang

Neural Process. Lett., 2002

2000

The signal reconstruction of speech by KPCA.

Hui Yan, Xuegong Zhang, Yanda Li, Liqin Shen, Weibin Zhu

Proceedings of the Sixth International Conference on Spoken Language Processing, 2000

Joint speech signal enhancement based on spectral subtraction and SVD filter.

Wenkai Lu, Xuegong Zhang, Yanda Li, Liqin Shen, Weibin Zhu

Proceedings of the Sixth International Conference on Spoken Language Processing, 2000