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Xue-Gong Zhang · SciRah

Researcher profile · Semantic Scholar

Xue-Gong Zhang

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Xue-Gong Zhang — researcher profile on SciRah

h-index: 48
Works: 237
Citations: 16K

Most-cited papers

A survey of best practices for RNA-seq data analysis
A. Conesa, Pedro Madrigal, Sonia Tarazona, D. Gómez-Cabrero +7 more
2016Genome Biology2,648 citations Open access
Semantic Scholar
Large Scale Foundation Model on Single-cell Transcriptomics
Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu +6 more
2023bioRxiv725 citations Open access
Semantic Scholar
dbSUPER: a database of super-enhancers in mouse and human genome
Aziz Khan, Xue-Gong Zhang
2015bioRxiv394 citations Open access
Semantic Scholar
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Zhun Miao, Ke Deng, Xiaowo Wang, Xue-Gong Zhang
2017bioRxiv233 citations Open access
Semantic Scholar
Precise temporal regulation of alternative splicing during neural development
Sebastien M. Weyn-Vanhentenryck, Hui-Juan Feng, Dmytro Ustianenko, Rachel Duffié +9 more
2018bioRxiv213 citations Open access
Semantic Scholar
Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae
Jing Li, Jing-Wen Li, Zhixing Feng, Juanjuan Wang +11 more
2016PLoS Pathogens120 citations Open access
Semantic Scholar
Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade
Jiaxing Cui, Hongfei Cui, Mingran Yang, Shi-Yu Du +5 more
2018Protein & Cell112 citations Open access
Semantic Scholar
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics
Shengquan Chen, Bo-Heng Zhang, Xiao-Yang Chen, Xue-Gong Zhang +1 more
2021bioRxiv111 citations Open access
Semantic Scholar
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
E. Schadt, O. Banerjee, G. Fang, Zhixing Feng +12 more
2013Genome Research100 citations Open access
Semantic Scholar
Erratum to: A survey of best practices for RNA-seq data analysis
A. Conesa, Pedro Madrigal, Sonia Tarazona, D. Gómez-Cabrero +7 more
2016Genome Biology99 citations Open access
Semantic Scholar
SOMDE: A scalable method for identifying spatially variable genes with self-organizing map
Minsheng Hao, Kui Hua, Xue-Gong Zhang
2020bioRxiv97 citations Open access
Semantic Scholar
Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630
Yong Chen, Yunfeng Ding, Li Yang, Jin-Hai Yu +32 more
2013Nucleic Acids Research93 citations Open access
Semantic Scholar
Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding
Xiao-Yang Chen, Shengquan Chen, Shuang Song, Zijing Gao +4 more
2022Nature Machine Intelligence87 citations
Semantic Scholar
Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu
Junfeng Li, Jun-Yi Zhang, Liyang Liu, Yucai Fan +4 more
2015Scientific Reports83 citations Open access
Semantic Scholar
Generation of Synthetic Electronic Medical Record Text
Jiaqi Guan, Run-Zhe Li, Sheng Yu, Xue-Gong Zhang
2018IEEE International Conference on Bioinformatics and Biomedicine61 citations Open access
Semantic Scholar
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data
Hui-Juan Feng, Xue-Gong Zhang, Chao-Lin Zhang
2015Nature Communications60 citations Open access
Semantic Scholar
CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological Images
Pengshuai Yang, Xiaoxu Yin, Haiming Lu, Zhongliang Hu +3 more
2022Medical Image Anal.59 citations
Semantic Scholar
Responses of cyanobacterial aggregate microbial communities to algal blooms.
Cong-Min Zhu, Jun-Yi Zhang, Xin Wang, Yu-Qing Yang +7 more
2020Water Research59 citations Open access
Semantic Scholar
Network embedding-based representation learning for single cell RNA-seq data
Xiangyu Li, Weizheng Chen, Yang Chen, Xue-Gong Zhang +2 more
2017Nucleic Acids Research51 citations Open access
Semantic Scholar
TRANSCRIPTOME ANALYSIS USING NEXT-GENERATION SEQUENCING
J. Li, Haiyan Huang, M. Qian, Xue-Gong Zhang
201550 citations
Semantic Scholar
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data
Jing Gong, Minsheng Hao, Xin Zeng, Chiming Liu +5 more
2023bioRxiv48 citations Open access
Semantic Scholar
Super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers
Aziz Khan, Anthony Mathelier, Xue-Gong Zhang
2018bioRxiv45 citations Open access
Semantic Scholar
hECA: The cell-centric assembly of a cell atlas
Sijie Chen, Yanting Luo, Haoxiang Gao, Fan-Hong Li +22 more
2021bioRxiv44 citations Open access
Semantic Scholar
A Method for Generating Synthetic Electronic Medical Record Text
Jiaqi Guan, Run-Zhe Li, Sheng Yu, Xue-Gong Zhang
2019IEEE/ACM Transactions on Computational Biology & Bioinformatics41 citations
Semantic Scholar
DualGCN: a dual graph convolutional network model to predict cancer drug response
Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou +2 more
2022BMC Bioinformatics40 citations Open access
Semantic Scholar
Abstract 5545: Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration
Yi-Fan Zhou, Yusra B. Medik, B. Patel, D. Zamler +35 more
2022Cancer Research40 citations
Semantic Scholar
scGraph: a graph neural network-based approach to automatically identify cell types
Qi-Jin Yin, Qiao Liu, Zhuoran Fu, Wan-Wen Zeng +4 more
2022Bioinform.36 citations
Semantic Scholar
Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets
Lu Zhang, Xiao-Qiao Liu, Xue-Gong Zhang, Ronghua Chen
2015Zeitschrift für Induktive Abstammungs- und Vererbungslehre36 citations
Semantic Scholar
qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data
Zhixing Feng, Jing Li, Jing-Ren Zhang, Xue-Gong Zhang
2014Nucleic Acids Research32 citations Open access
Semantic Scholar
Cellular features of localized microenvironments in human meniscal degeneration: a single-cell transcriptomic study
Wei-Li Fu, Sijie Chen, Runze Yang, Chen Li +3 more
2022eLife31 citations Open access
Semantic Scholar
Systematic identification of cancer-related long noncoding RNAs and aberrant alternative splicing of quintuple-negative lung adenocarcinoma through RNA-Seq.
Lu Zhang, Shi-Yong Li, Yoon-La Choi, Jinseon Lee +9 more
2017Lung Cancer31 citations
Semantic Scholar
Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers
Aziz Khan, Xue-Gong Zhang
2019Scientific Reports30 citations Open access
Semantic Scholar
Differential expression analyses for single-cell RNA-Seq: old questions on new data
Zhun Miao, Xue-Gong Zhang
2016Quantitative Biology29 citations Open access
Semantic Scholar
HGC: fast hierarchical clustering for large-scale single-cell data
Ziheng Zou, Kui Hua, Xue-Gong Zhang
2021bioRxiv26 citations Open access
Semantic Scholar
SEASTAR: systematic evaluation of alternative transcription start sites in RNA
Zhiyi Qin, P. Stoilov, Xue-Gong Zhang, Yi Xing
2018Nucleic Acids Research26 citations Open access
Semantic Scholar
Computational operon prediction in whole-genomes and metagenomes.
S. A. J. Zaidi, Xue-Gong Zhang
2016Briefings in Functional Genomics24 citations
Semantic Scholar
CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images
Tao Hu, Shixiong Xu, Lei Wei, Xue-Gong Zhang +1 more
2021Bioinform.23 citations
Semantic Scholar
Single-cell alternative splicing analysis reveals dominance of single transcript variant.
Wendao Liu, Xue-Gong Zhang
2020Genomics23 citations Open access
Semantic Scholar
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
Shengquan Chen, Qiao Liu, Xue-Jian Cui, Zhanying Feng +5 more
2021Nucleic Acids Res.21 citations Open access
Semantic Scholar
CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens
Binbin Wang, Tao-Yun Ji, Xue-Ya Zhou, Jing Wang +8 more
2016Scientific Reports21 citations Open access
Semantic Scholar
scRecover: Discriminating true and false zeros in single-cell RNA-seq data for imputation
Zhun Miao, Jiaqi Li, Xue-Gong Zhang
2019bioRxiv20 citations Open access
Semantic Scholar
Precision Medicine: What Challenges Are We Facing?
Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang +17 more
2016Genomics, Proteomics & Bioinformatics19 citations Open access
Semantic Scholar
SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data
Yue Hu, Xi Xi, Qian-Min Yang, Xue-Gong Zhang
2018BMC Bioinformatics18 citations Open access
Semantic Scholar
Resolving the genetic heterogeneity of prelingual hearing loss within one family: Performance comparison and application of two targeted next generation sequencing approaches
Yu Lu, Xue-Ya Zhou, Zhanguo Jin, Jing Cheng +9 more
2014Journal of Human Genetics17 citations Open access
Semantic Scholar
Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction
Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng +2 more
2021Genomics, Proteomics & Bioinformatics16 citations Open access
Semantic Scholar
Reading the Underlying Information From Massive Metagenomic Sequencing Data
Xue-Gong Zhang, Shansong Liu, Hongfei Cui, Ting Chen
2017Proceedings of the IEEE16 citations Open access
Semantic Scholar
Multiple domains of bacterial and human Lon proteases define substrate selectivity
Li-Hong He, Dongyang Luo, Fan Yang, Chun-Hao Li +3 more
2018Emerging Microbes and Infections15 citations Open access
Semantic Scholar
Identification and functional analysis of a novel LHX1 mutation associated with congenital absence of the uterus and vagina
Wei Zhang, Xue-Ya Zhou, Liyang Liu, Ying Zhu +8 more
2017OncoTarget15 citations Open access
Semantic Scholar
Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia
Xinmiao Fan, L. Ping, Hao Sun, Yushan Chen +5 more
2020Frontiers in Genetics14 citations Open access
Semantic Scholar
ulfasQTL: an ultra-fast method of composite splicing QTL analysis
Qian-Min Yang, Yue Hu, Jun Yu Li, Xue-Gong Zhang
2017BMC Genomics14 citations Open access
Semantic Scholar

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Rui Jiang×5
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Minsheng Hao×4
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Zhun Miao×4
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Liyang Liu — researcher profile on SciRah

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