SUN Lab

Publication

2024 | 2023 |2022 | 2021 | 2020 | 2019 | 2012-2018

2024

Zhen Miao, Tian Tian, Wei Chen, Qianwen Wang, Liang Ma, Dan Zhang, Min Xie, Zijin Yu, Xiya Guo, Genxiang Bai, Shaoli Zhao, Xi Chen, Wenyi Wang, Yizhou Gao, Shicheng Guo✉, Ming Luo✉, Ling Yuan✉, Caihuan Tian✉, Liang Wu✉, Guangchuang Yu✉, Dake Zhang✉, and Shiquan Sun✉. Spatial resolved transcriptomics: Computational insights into gene transcription across tissue and organ architecture in diverse applications. The Innovation Life. 2024, 2: 100097.

Yue Fan, Lei Li, and Shiquan Sun✉. Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq. Genome Biology. 2024, 24: 96. [Reproducibility Code] [Web Server] [R/Rcpp package]

Yue Fan, Xuzhao Bian, Xiaogao Meng, Lei Li, Laiyi Fu, Yanan Zhang, Long Wang, Yan Zhang, Dalong Gao, Xiong Guo, Mikko J. Lammi, Guangdun Peng✉, and Shiquan Sun✉. Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration. Annals of the Rheumatic Diseases. 2024, 83: 926-944. [Reproducibility Code] [ scRNA-seq and Spatial Data]

Xiya Guo, Jin Ning, Yuanze Chen, Guoliang Liu, Liyan Zhao, Yue Fan, and Shiquan Sun✉. Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies. Briefings in Functional Genomics. 2024, 23: 95-109.

2022

Jianfei Zhu, Yue Fan, Yanlu Xiong, Wenchen Wang, Jiakuan Chen, Yanmin Xia, Jie Lei✉, Li Gong✉, Shiquan Sun✉, and Tao Jiang✉. Delineating the dynamic evolution from preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics. Experimental & Molecular Medicine. 2022, 54: 2060–2076. [ Spatial Data ] [ scRNA-seq Data ]

Ling Zhou, Shiquan Sun, Haoda Fu, and Peter X.K. Song✉. Subgroup-effects models for the analysis of personal treatment effects. Annals of Applied Statistics. 2022, 16:80-103.

2021

Jiaqiang Zhu, Shiquan Sun, and Xiang Zhou. Non-parametric test enables scalable and robust detection of spatial expression patterns in large spatial transcriptomics studies. Genome Biology. 2021, 22:184.

Yue Fan, Dalong Gao, Yingang Zhang, Jiaqiang Zhu, Feng Zhang, Lu Wang, Yan Wen, Xiong Guo and Shiquan Sun. Genome-Wide Differentially Methylated Region Analysis to Reveal Epigenetic Differences of Articular Cartilage in Kashin–Beck Disease and Osteoarthritis. Frontiers in Cell and Developmental Biology. 2021, 9: 241. [pdf]

Jing Ye, Yan Wen, Xifang Sun, Xiaomeng Chu, Ping Li, Bolun Cheng, Shiqiang Cheng, Li Liu, Lu Zhang, Mei Ma, Xin Qi, Chujun Liang, Om Prakash Kafle, Yumeng Jia, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Shiquan Sun and Feng Zhang. Socioeconomic deprivation index is associated with psychiatric disorders: an observational and genome-wide gene-environment interaction analysis in the UK Biobank cohort. Biological Psychiatry. 2021, 89(9): 888-895.

2020

Zhongshang Yuan, Huanhuan Zhu, Ping Zeng, Sheng Yang, Shiquan Sun, Can Yang, Jin Liu, and Xiang Zhou. Testing and controlling for horizontal pleiotropy with the probabilistic Mendelian randomization in transcriptome-wide association studies. Nature Communications. 2020, 11: 3861.

Shiquan Sun*, Jiaqiang Zhu*, and Xiang Zhou. Statistical analysis of spatial expression pattern for spatially resolved transcriptomic studies. Nature Methods. 2020, 17: 193-200. [pdf] [R/Rcpp package]

Ying Ma*, Shiquan Sun*, Xuequn Shang, Evan T. Keller, Mengjie Chen, and Xiang Zhou. Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies. Nature Communications. 2020, 11: 1585. [pdf] [R/Rcpp package]

2019

Shiquan Sun, Jiaqiang Zhu, Ying Ma, and Xiang Zhou. Accuracy, Robustness and Scalability of Dimensionality Reduction Methods for Single Cell RNAseq Analysis. Genome Biology. 2019, 20: 269. [pdf]

Shiquan Sun*, Jiaqiang Zhu*, Sahar Mozaffari, Carole Ober, Mengjie Chen, and Xiang Zhou. Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies. Bioinformatics. 2019, 35: 487-496. [pdf] [R/Rcpp package]

Shiquan Sun, Yabo Chen, Yang Liu, and Xuequn Shang. A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data. BMC Systems Biology. 2019, 13: 28. [pdf]

Shiquan Sun, Yang Liu, and Xuequn Shang. Deep generative autoencoder for low-dimensional embeding extraction from single-cell RNAseq data. IEEE International Conference on Bioinformatics and Biomedicine(BIBM), San Diego, CA, USA, Nov 2019, p.19351647. [pdf]

Yue Fan, Tauras P Vilgalys, Shiquan Sun, Qinke Peng, Jenny Tung, and Xiang Zhou. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. Genome Biology. 2019, 20: 220. [pdf] [R/Rcpp package]

Xifang Sun, Shiquan Sun, and Sheng Yang. An efficient and flexible method for deconvoluting bulk RNA-Seq data with single-cell RNA-Seq data. Cells. 2019, 8: 1161. [pdf]

2012-2018

Shiquan Sun*, Xifang Sun*, and Yan Zheng. Higher-order partial least squares for predicting gene expression levels from chromatin states. BMC Bioinformatics, 2018, 19: 113. [pdf]

Shiquan Sun, Michelle Hood, Laura Scott, Qinke Peng, Sayan Mukherjee, Jenny Tung, and Xiang Zhou. Differential expression analysis for RNAseq using Poisson mixed models. Nucleic Acids Research. 2017, 45: e106. [pdf] [C/C++ and R/Rcpp packages]

Shiquan Sun, Xiongpan Zhang, and Qinke Peng. A high-order representation and classification method for transcription factor binding sites recognition in Escherichia coli. Artificial Intelligence in Medicine. 2017, 75: 16–23. [pdf]

Shiquan Sun, Qinke Peng, and Xiaokang Zhang. Global feature selection from microarray data using Lagrange multipliers. Knowledge-Based Systems. 2016, 110: 267–274. [pdf]

Shiquan Sun, Qinke Peng, and Adnan Shakoor. A kernel-based multivariate feature selection method for microarray data classification. PLoS One. 2014, 9: e102541. [pdf]

Shiquan Sun, and Qinke Peng. A hybrid PSO-GSA strategy for high-dimensional optimization and microarray data clustering. IEEE International Conference on Information and Automation (ICIA), IEEE, Hulun Buir Inner Mongolia, 2014, p.41-46. [pdf]

Jing Zhang, Qinke Peng, and Shiquan Sun. Collaborative filtering recommendation algorithm based on user preference derived from item domain features. Physica A: Statistical Mechanics and its Applications 2014, 396: 66-76. [pdf]

Shiquan Sun, Shuping Gao, Yuan Liang, and Jiang Bian. Method of multiple attributive group decision making based on data fusion. Systems Engineering and Electronics (Chinese Version) 2012, 34: 2094-2097. [pdf]

Jibin Lan, Mingming Hu, Xinmiao Ye, and Shiquan Sun. Deriving interval weights from an interval multiplicative consistent fuzzy preference relation. Knowledge-Based Systems. 2012, 26: 128-134. [pdf]