Xuegong Zhang

Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, 2008, 2008 IEEE Congress on Evolutionary Computation (IEEE World Congress on Computational Intelligence).

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

Gang Fang, Xuegong Zhang, Wing Wong, 2013, PLoS Comput. Biol..

Complicated evolutionary patterns of microRNAs in vertebrates

Xuegong Zhang, Yanda Li, Xiaowo Wang, 2008, Science in China Series C: Life Sciences.

Bioinformatics study indicates possible microRNA-regulated pathways in the differentiation of breast cancer

Xuegong Zhang, Z. Shao, Wei Huang, 2010 .

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

Tyson A. Clark, A. Kasarskis, J. Korlach, 2013, Genome research.

Systematic identification of cancer-related long noncoding RNAs and aberrant alternative splicing of quintuple-negative lung adenocarcinoma through RNA-Seq.

Xuegong Zhang, Zhuolin Gong, Shiyong Li, 2017, Lung cancer.

Prediction of kinase‐specific phosphorylation sites with sequence features by a log‐odds ratio approach

Xuegong Zhang, Tingting Li, Xuegong Zhang, 2007, Proteins.

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

Aziz Khan, Xuegong Zhang, Xuegong Zhang, 2015, bioRxiv.

From big biological data to big discovery: The past decade and the future

Xuegong Zhang, Rui Jiang, Jin Gu, 2016 .

Comparison of gene expression in hepatocellular carcinoma, liver development, and liver regeneration

Xuegong Zhang, Tingting Li, Jian Huang, 2010, Molecular Genetics and Genomics.

Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae

Xuegong Zhang, Xiaowo Wang, Yingxue Li, 2013, Science China Life Sciences.

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development.

Michael Q. Zhang, Fuchu He, Ying Jiang, 2009, Genomics.

Different patterns and functional importance of correlation between adjacent alternative exons in human and mouse

Xuegong Zhang, Chenghai Xue, Yanda Li, 2008 .

Prediction of transcription start sites based on feature selection using AMOSA.

Sanghamitra Bandyopadhyay, Michael Q. Zhang, Xuegong Zhang, 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

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

Xuegong Zhang, 2021, Quant. Biol..

Exome Sequencing Identifies a Novel Frameshift Mutation of MYO6 as the Cause of Autosomal Dominant Nonsyndromic Hearing Loss in a Chinese Family

Xuegong Zhang, P. Sham, J. Chen, 2014, Annals of human genetics.

Resolving the genetic heterogeneity of prelingual hearing loss within one family: Performance comparison and application of two targeted next generation sequencing approaches

Xuegong Zhang, K. Choy, Xueya Zhou, 2014, Journal of Human Genetics.

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

Sijie Chen, Xuegong Zhang, Kui Hua, 2018, Quantitative Biology.

Reading the Underlying Information From Massive Metagenomic Sequencing Data

Xuegong Zhang, Hongfei Cui, Shansong Liu, 2017, Proceedings of the IEEE.

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse

Yanda Li, Xiaowo Wang, Jianning Bi, 2008, BMC Genomics.

Analysis and prediction of super-enhancers using sequence and chromatin signatures

Xuegong Zhang, Aziz Khan, Xuegong Zhang, 2017, bioRxiv.

Single-cell alternative splicing analysis reveals dominance of single transcript variant.

Xuegong Zhang, Wendao Liu, 2020, Genomics.

The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data

Xuegong Zhang, Zhiyi Qin, 2017, PloS one.

Improving cis-regulatory elements modeling by consensus scaffolded mixture models

Wenguang Chen, Weimin Zheng, Ying Zhao, 2011, Science China Information Sciences.

hECA: The cell-centric assembly of a cell atlas

Xuegong Zhang, R. Jiang, Lei Wei, 2021, bioRxiv.

A human ensemble cell atlas (hECA) enables in data cell sorting

Xuegong Zhang, Rui Jiang, Lei Wei, 2021 .

Multiple domains of bacterial and human Lon proteases define substrate selectivity

Xuegong Zhang, Chunhao Li, Lihong He, 2018, Emerging Microbes & Infections.

Using class-center vectors to build support vector machines

Xuegong Zhang, Xuegong Zhang, 1999, Neural Networks for Signal Processing IX: Proceedings of the 1999 IEEE Signal Processing Society Workshop (Cat. No.98TH8468).

Erratum to: A survey of best practices for RNA-seq data analysis

Daniel J. Gaffney, A. Mortazavi, Xuegong Zhang, 2016, Genome Biology.

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

Xuegong Zhang, Kui Hua, Xuegong Zhang, 2018, bioRxiv.

Identifying differentially spliced genes from two groups of RNA-seq samples.

Xuegong Zhang, Zhixing Feng, Xuegong Zhang, 2013, Gene.

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

Xuegong Zhang, Xi Wang, Zhengpeng Wu, 2011, Bioinform..

A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data.

Michael Q. Zhang, Jun Li, Xuegong Zhang, 2006, American journal of human genetics.

Alignment-free supervised classification of metagenomes by recursive SVM

Hongfei Cui, Xuegong Zhang, Xuegong Zhang, 2013, BMC Genomics.

Pattern recognition methods in microarray based oncology study

Xuesong Lu, Xuegong Zhang, Xuegong Zhang, 2009 .

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

Xuegong Zhang, W. Wong, R. Jiang, 2022, Genom. Proteom. Bioinform..

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

Weichen Wang, Xuegong Zhang, Xuegong Zhang, 2011, BMC Bioinformatics.

Discovering single-cell eQTLs from scRNA-seq data only

Xuegong Zhang, Haochen Li, Tianxing Ma, 2021, bioRxiv.

Symptom combinations associated with outcome and therapeutic effects in a cohort of cases with SARS.

A Joseph Layon, Yanda Li, Shao Li, 2006, The American journal of Chinese medicine.

Abstract 5545: Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration

Xuegong Zhang, N. Ajami, J. Wargo, 2022, Cancer Research.

Computational operon prediction in whole-genomes and metagenomes.

Xuegong Zhang, Xuegong Zhang, Syed Shujaat Ali Zaidi, 2016, Briefings in functional genomics.

Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia

Xuegong Zhang, Rui Jiang, Hao Sun, 2020, Frontiers in Genetics.

Kernel Nearest-Neighbor Algorithm

Xuegong Zhang, Liang Ji, Kai Yu, 2002, Neural Processing Letters.

Improvement of Dscam homophilic binding affinity throughout Drosophila evolution

Xuegong Zhang, Qiang Yang, Guang-Zhong Wang, 2014, BMC Evolutionary Biology.

Precise temporal regulation of alternative splicing during neural development

Sebastien M. Weyn-Vanhentenryck, Xuegong Zhang, Chaolin Zhang, 2018, bioRxiv.

Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics

Xin Lu, Arndt Asperger, Xuegong Zhang, 2004, Proteomics.

A multiclass kernel perceptron algorithm

Jianhua Xu, Xuegong Zhang, Xuegong Zhang, 2005, 2005 International Conference on Neural Networks and Brain.

Generation of Synthetic Electronic Medical Record Text

Sheng Yu, Xuegong Zhang, Jiaqi Guan, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Large Scale Foundation Model on Single-cell Transcriptomics

Xuegong Zhang, Jianzhu Ma, Yucheng Guo, 2023, bioRxiv.

xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data

Xuegong Zhang, Jianzhu Ma, Taifeng Wang, 2023, bioRxiv.

Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade

Xuegong Zhang, Shao Li, Liyang Liu, 2018, Protein & Cell.

Significance of Gene Ranking for Classification of Microarray Samples

Xuesong Lu, Xuegong Zhang, Chaolin Zhang, 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data

Xuegong Zhang, Tingting Li, Huijuan Feng, 2016, bioRxiv.

Large Scale Foundation Model on Single-cell Transcriptomics

Xuegong Zhang, Jianzhu Ma, Yucheng Guo, 2023, bioRxiv.

Interaction between variants of two glycosyltransferase genes in IgA nephropathy.

Xuegong Zhang, Yanda Li, Lei Yu, 2009, Kidney international.

Identification and functional analysis of a novel LHX1 mutation associated with congenital absence of the uterus and vagina

Xuegong Zhang, Xueya Zhou, Binbin Wang, 2017, Oncotarget.

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, 2013, BMC Bioinformatics.

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

Tianxi Cai, Xuegong Zhang, Bo Jiang, 2008, J. Mach. Learn. Res..

Embryonics: A Path to Artificial Life?

Anthony G. Pipe, Gabriel Dragffy, Xuegong Zhang, 2006, Artificial Life.

Methodology Research on Refraction Stack Imaging of Refractive Seismic Recording

Xuegong Zhang, Yan-Da Li, Xiuxiu Lu, 2001 .

Multi-locus association study of schizophrenia susceptibility genes with a posterior probability method

Xuegong Zhang, Yan Shen, Qi Xu, 2005, Science in China Series C: Life Sciences.

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btl662 Sequence analysis Computing exact P-values for DNA motifs

Michael Q. Zhang, Ming Li, Xuegong Zhang, 2022 .

A simulation study on gene expression regulation via stochastic model

Xuegong Zhang, Chao Ye, 2014, CCC 2014.

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

Xuegong Zhang, Ziheng Zou, Kui Hua, 2021, bioRxiv.

OSCAR: One-class SVM for accurate recognition of cis-elements

Michael Ruogu Zhang, Xuegong Zhang, B. Jiang, 2007, Bioinform..

Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers

Xuegong Zhang, Aziz Khan, 2019, Scientific Reports.

BIOINFORMATICS ORIGINAL PAPER Sequence analysis

Xuegong Zhang, Yanda Li, Jin Gu, 2005 .

The effect of U1 snRNA binding free energy on the selection of 5' splice sites.

Xuegong Zhang, Yanda Li, Huiyu Xia, 2005, Biochemical and biophysical research communications.

Finding distinct biclusters from background in gene expression matrices

Xuegong Zhang, D. Burger, Zhengpeng Wu, 2007, Bioinformation.

Multiclass feature selection algorithms base on R-SVM

Xuegong Zhang, Qifeng Xu, Xuegong Zhang, 2014, 2014 IEEE China Summit & International Conference on Signal and Information Processing (ChinaSIP).

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.

Xiaofeng Zhu, Todd L Edwards, Wei Guo, 2013, American journal of human genetics.

Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population

Xuegong Zhang, Xueya Zhou, Dingliang Zhu, 2013, Molecular Biology Reports.

Karyotyping of comparative genomic hybridization human metaphases by using support vector machines.

Liang Ji, Zhenzhen Kou, Xuegong Zhang, 2002, Cytometry.

Predicting Microvascular Invasion of Hepatocellular Carcinoma by texture analysis of multi-phase MR image

Xuegong Zhang, Xiaolong Liu, Geng Chen, 2020 .

Self-organizing map as a new method for clustering and data analysis

Yanda Li, Xuegong Zhang, Xuegong Zhang, 1993, Proceedings of 1993 International Conference on Neural Networks (IJCNN-93-Nagoya, Japan).

Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network.

Xuegong Zhang, Shao Li, Yanda Li, 2007, IET systems biology.

Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model

Xuegong Zhang, R. Jiang, Qijin Yin, 2021, bioRxiv.

A Method for Generating Synthetic Electronic Medical Record Text

Xuegong Zhang, Sheng Yu, Jiaqi Guan, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

Xuegong Zhang, Rui Jiang, Qiao Liu, 2022, Bioinform..

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

Yan Shen, Xuegong Zhang, Jing Zhang, 2005, BMC Bioinformatics.

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

Xuegong Zhang, Xinyun Ma, 2013, BMC Bioinformatics.

RNAseqViewer: visualization tool for RNA-Seq data

Xuegong Zhang, Xavier Rogé, Xuegong Zhang, 2014, Bioinform..

Short read mapping for exome sequencing.

Xuegong Zhang, Binbin Wang, You-Qiang Song, 2013, Methods in molecular biology.

Observations on potential novel transcripts from RNA-Seq data

Xuegong Zhang, Xuegong Zhang, Xi Wang, 2011 .

Isoform reconstruction using short RNA-Seq reads by maximum likelihood is NP-hard

Xuegong Zhang, Rui Jiang, Xuegong Zhang, 2013, 1305.0916.

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

Hu Fu, Tingting Li, Xuegong Zhang, 2007, 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007).

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Todd H. Stokes, Kevin C. Dorff, Aaron M. Smalter, 2010, Nature Biotechnology.

scMetric: An R package of metric learning and visualization for single-cell RNA-seq data

Xuegong Zhang, Wenchang Chen, 2018, bioRxiv.

Multi-Locus Penetrance Variance Analysis Method for Association Study in Complex Diseases

Yanda Li, Zhongqi Zhang, Xuegong Zhang, 2006, Human Heredity.

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.

Andrew D. Johnson, Jeanette S. Andrews, M. Fornage, 2013, American journal of human genetics.

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

Xuegong Zhang, Xiaowo Wang, Zhixing Feng, 2010, Bioinform..

Opportunities and methods for studying alternative splicing in cancer with RNA-Seq.

Xuegong Zhang, Huijuan Feng, Zhiyi Qin, 2013, Cancer letters.

Predicting the fate of microRNA target genes based on sequence features.

Xuegong Zhang, Xi Wang, Yunfei Pei, 2009, Journal of theoretical biology.

Responses of cyanobacterial aggregate microbial communities to algal blooms.

Xuegong Zhang, Ting Chen, Rui Jiang, 2020, Water research.

A Learning Algorithm with Gaussian Regularizer for Kernel Neuron

Jianhua Xu, Xuegong Zhang, Xuegong Zhang, 2004, ISNN.

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

Xuegong Zhang, Jun Zhu, Chao Wu, 2013, BMC Bioinformatics.

The prognostic value of intraoperative HRV during anesthesia in patients presenting for non-cardiac surgery

Xuegong Zhang, Yajun Xue, Ping Zhang, 2023, BMC Anesthesiology.

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

Xuegong Zhang, Weichen Wang, 2011, BMC Bioinformatics.

Computational operon prediction in whole-genomes and metagenomes.

Xuegong Zhang, S. S. Zaidi, 2016, Briefings in functional genomics.

Computing exact p-values for DNA motifs ( Part I )

Michael Q. Zhang, Xuegong Zhang, Ming Li, 2006 .

Bioinformatics Original Paper Predicting Methylation Status of Cpg Islands in the Human Brain

Michael Q. Zhang, Xuegong Zhang, Shicai Fan, 2022 .

Incorporating Gene Expression in Genome-wide Prediction of Chromatin Accessibility via Deep Learning

Wing Hong Wong, Xuegong Zhang, R. Jiang, 2019, bioRxiv.

A simple strategy for detecting outlier samples in microarray data

Xuesong Lu, Yanda Li, Xuegong Zhang, 2004, ICARCV 2004 8th Control, Automation, Robotics and Vision Conference, 2004..

CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images

Xiaowo Wang, Xuegong Zhang, Tao Hu, 2021, Bioinform..

Precision Medicine: What Challenges Are We Facing?

Kai Ye, Jun Yu, Yu Xue, 2016, Genom. Proteom. Bioinform..