论文

方向1: 复杂生物组学数据处理与解析

基因多因素调控

(1) Zheng Wei; Wei Zhang; Huan Fang; Yanda Li; Xiaowo Wang, esATAC: An easy-to-use systematic pipeline for ATAC-seq data analysis, Bioinformatics, 2018, 34(15):2664-2665. https://doi.org/10.1093/bioinformatics/bty141
(2) 张祥林; 方欢; 汪小我, 三维基因组数据分析方法进展, 生物化学与生物物理进展, 2018, 45(11):1093-1105. https://doi.org/10.16476/j.pibb.2018.0101
(3) Shiming Ma; Tao Jiang; Rui Jiang, Constructing tissue-specific transcriptional regulatory networks via a Markov random field, BMC Genomics, 2018, 19:884. https://doi.org/10.1186/s12864-018-5277-6
(4) Wanwen Zeng; Mengmeng Wu; Rui Jiang, Prediction of enhancer-promoter interactions via natural language processing, BMC Genomics, 2018, 19:84. https://doi.org/10.1186/s12864-018-4459-6
(5) Qiao Liu; Fei Xia; Qijin Yin; Rui Jiang, Chromatin accessibility prediction via a hybrid deep convolutional neural network, Bioinformatics, 2018, 34(5):732-738. https://doi.org/10.1093/bioinformatics/btx679
(6) Mengmeng Wu; Wanwen Zeng; Wenqiang Liu; Yijia Zhang; Hairong Lv; Ting Chen; Rui Jiang; Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning, Methods, 2018, 145:41-50. https://doi.org/10.1016/j.ymeth.2018.06.002
(7) Zhiyi Qin; Peter Stoilov; Xuegong Zhang; Yi Xing, SEASTAR: systematic evaluation of alternative transcription start sites in RNA, Nucleic Acids Research, 2018, 46(8):e45. https://doi.org/10.1093/nar/gky053
(8) Aziz Khan; Xuegong Zhang, Making genome browsers portable and personal, Genome Biology, 2018, 19:93. https://doi.org/10.1186/s13059-018-1470-9
(9) Yuanyuan Li; Hui Zheng; Qiujun Wang; Chen Zhou; Lei Wei; Xuehui Liu; Wenhao Zhang; Yu Zhang; Zhenhai Du; Xiaowo Wang; Wei Xie, Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys, Genome Biology, 2018, 19(1):18. https://doi.org/10.1186/s13059-018-1390-8
(10) Aziz Khan; Anthony Mathelier; Xuegong Zhang, Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers, Epigenetics, 2018, 13:1559-2308. https://doi.org/10.1080/15592294.2018.1514231
(11) Wenran Li; Wing Hong Wong; Rui Jiang, DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning, Nucleic Acids Research, 2019, 47(10). https://doi.org/10.1093/nar/gkz167
(12) Qiao Liu; Hairong Lv; Rui Jiang, hicGAN infers super resolution Hi-C data with generative adversarial networks, Bioinformatics, 2019, 35: i99-i107. https://doi.org/10.1093/bioinformatics/btz317
(13) Qijin Yin; Mengmeng Wu; Qiao Liu; Hairong Lv; Rui Jiang, DeepHistone: a deep learning approach to predicting histone modifications, BMC Genomics, 2019, 20. https://doi.org/10.1186/s12864-019-5489-4
(14) Aziz Khan; Xuegong Zhang, Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers, Scientific Reports, 2019, 9. https://doi.org/10.1038/s41598-019-38979-9
(15) Wanwen Zeng; Yong Wang; Rui Jiang; Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network, Bioinformatics, 2020, 36(2):496-503. https://doi.org/10.1093/bioinformatics/btz562
(16) Wenran Li; Zhana Duren; Rui Jiang; Wing Hung Wong; A method for scoring the cell type-specific impacts of noncoding variants in personal genomes, Proc Natl Acad Sci, 2020, 117(35):21364-21372. https://doi.org/10.1073/pnas.1922703117
(17) Wanwen Zeng; Shengquan Chen; Xuejian Cui; Xiaoyang Chen; Zijiang Gao; Rui Jiang; SilencerDB: a comprehensive database of silencers, Nucleic Acids Research, 2021, 49: D221-D228. https://doi.org/10.1093/nar/gkaa839
(18) Wanwen Zeng; Jingxue Xin; Rui Jiang; Yong Wang; Reusability report: compressing regulatory networks to vectors for interpreting gene expression and genetic variants, Nature Machine Intelligence, 2021,(3):576-580. https://doi.org/10.1038/s42256-020-0205-2
(19) 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 in Bioinformatics, 2022, 23(1):1-11. https://doi.org/10.1093/bib/bbab362
(20) Qiao Liu; Wanwen Zeng; Wei Zhang; Sicheng Wang; Hongyang Chen; Rui Jiang; Mu Zhou; Shaoting Zhang; Deep generative modeling and clustering of single cell Hi-C data, Briefings in Bioinformatics, 2022,bbac494. https://doi.org/10.1093/bib/bbac494
(21) Lei Wei; Shuailin Li; Xiaowo Wang, In silico and in vitro protocols for quantifying gene expression noise modulated by microRNAs, STAR Protocols, 2022, 3(1):101205. https://doi.org/10.1016/j.xpro.2022.101205
(22) Xianglin Zhang; Xiaowo Wang; MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites, Bioinformatics, 2022, 38:i307-i315. https://doi.org/10.1093/bioinformatics/btac248
(23) Lekang Yuan; Zhen Xie; Ye Wang; Xiaowo Wang; DeSP: a systematic DNA storage error simulation pipeline, BMC Bioinformatics, 2022, 23(1). https://doi.org/10.1186/s12859-022-04723-w
(24) Qiao Liu; Kui Hua; Xuegong Zhang; Wing Hung Wong; Rui Jiang; DeepCAGE: Incorporating transcription factors in genome-wide prediction of chromatin accessibility, Genomics, Proteomics & Bioinformatics, 2022, 20:496-507. https://doi.org/10.1016/j.gpb.2021.08.015
(25) Guiying Wu; Xiangyu Li; Wenbo Guo; Zheng Wei; Tao Hu; Yiran Shan; Jin Gu; JEBIN: analyzing gene co-expressions across multiple datasets by joint network embedding, Briefings in Bioinformatics, 2022, 23(2):1-23. https://doi.org/10.1093/bib/bbab603

混合基因组测序

(26) Shansong Liu; Kui Hua; Sijie Chen; Xuegong Zhang, Comprehensive simulation of metagenomic sequencing data with non-uniform sampling distribution, Quantitative Biology, 2018, 6(2):175-185. https://doi.org/10.1007/s40484-018-0142-9
(27) Sijie Chen; Yixin Chen; Fengzhu Sun; Michael Waterman; Xuegong Zhang, A new statistic for efficient detection of repetitive sequences, Bioinformatics, 2019, 35(22):4596-4606. https://doi.org/10.1093/bioinformatics/btz262
(28) Kui Hua; Xuegong Zhang, Estimating the total genome length of a metagenomic sample using k-mers, BMC Genomics, 2019, 20. https://doi.org/10.1186/s12864-019-5467-x
(29) Zicheng Wang; Huazhe Lou; Ying Wang; Ron Shamir; Rui Jiang; Ting Chen, GePMI: A statistical model for personal intestinal microbiome identification, NPJ Biofilms and Microbiomes, 2018, 20. https://doi.org/10.1038/s41522-018-0065-2
(30) Cong-min Zhu; Jun-yi Zhang; Rui Guan; Lauren Hale; Ning Chen; Ming Li; Zu-hong Lu; Yun-feng Yang; Ji-Zhong Zhou; Ting Chen, Alternate succession of aggregate-forming cyanobacterial genera correlated with their attached bacteria by co-pathways, Science of the Total Environment, 2019, 688:867-879. https://doi.org/10.1016/j.scitotenv.2019.06.150
(31) Yuqing Yang; Xin Wang; Kaikun Xie; Congmin Zhu; Ning Chen; Ting Chen; kLDM: Inferring multiple metagenomic association networks based on the variation of environmental factors, Genomics, Proteomics & Bioinformatics, 2021, (21). https://doi.org/10.1016/j.gpb.2020.06.015

单细胞测序数据和空间转录组数据

(32) Miao Zhun; Deng Ke; Wang Xiaowo; Zhang Xuegong, DEsingle for detecting three types of differential expression in single-cell RNA-seq data, Bioinformatics, 2018, 34(18):3223-3224. https://doi.org/10.1093/bioinformatics/bty332
(33) Kui Hua; Xuegong Zhang, A case study on the detailed reproducibility of a human cell atlas project, Quantitative Biology, 2019, 7(2):162-169. https://doi.org/10.1007/s40484-018-0164-3
(34) Shengquan Chen; Kui Hua; Hongfei Cui; Rui Jiang, VPAC: Variational projection for accurate clustering of single-cell transcriptomic data, BMC Bioinformatics, 2019, 20. https://doi.org/10.1186/s12859-019-2742-4
(35) Wanwen Zeng; Xi Chen; Zhana Duren; Yong Wang; Rui Jiang; Wing Hung Wong, DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data, Nature Communications, 2019, 10. https://doi.org/10.1038/s41467-019-12547-1
(36) Yue Hu; Xi Xi; Qian Yang; Xuegong Zhang; SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data, BMC Bioinformatics, 2020, 21:184. https://doi.org/10.1186/s12859-020-3534-6
(37) Wendao Liu; Xuegong Zhang; Single-cell alternative splicing analysis reveals dominance of single transcript variant, Genomics, 2020, 112(3):2418-2425. https://doi.org/10.1016/j.ygeno.2020.01.014
(38) Najeebullah Shah; Jiaqi Li; Fanhong Li; Wenchang Chen; Haoxiang Gao; Sijie Chen; Kui Hua; Xuegong Zhang; An Experiment on Ab Initio Discovery of Biological Knowledge from scRNA-Seq Data Using Machine Learning, Patterns, 2020, 1(100071). https://doi.org/10.1016/j.patter.2020.100071
(39) Kaikun Xie; Yu Huang; Feng Zeng; Zehua Liu; Ting Chen; scAIDE: clustering of large-scale single-cell RNA-seq data reveals putative and rare cell types, NAR Genomics and Bioinformatics, 2020, 2(4). https://doi.org/10.1093/nargab/lqaa082
(40) Qiuyu Lian; Hongyi Xin; Jianzhu Ma; Liza Konnikova; Wei Chen; Jin Gu; Kong Chen; Artificial-cell-type aware cell type classification in CITE-seq, Bioinformatics, 2020,36(S1):i542-i550. https://doi.org/10.1093/bioinformatics/btaa467
(41) Xiaoyang Chen; Shengquan Chen; Rui Jiang; EnClaSC: A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes, BMC Bioinformatics, 2020, 21:392. https://doi.org/10.1186/s12859-020-03679-z
(42) Minsheng Hao; Kui Hua; Xuegong Zhang; SOMDE: a scalable method for identifying spatially variable genes with self-organizing map, Bioinformatics, 2021, 37(23):4392-4398. https://doi.org/10.1093/bioinformatics/btab471
(43) Ziheng Zou; Kui Hua; Xuegong Zhang; HGC: fast hierarchical clustering for large-scale single-cell data, Bioinformatics, 2021, 37(12):3964-3965. https://doi.org/10.1093/bioinformatics/btab420
(44) Shengquan Chen; Boheng Zhang; Xiaoyang Chen; Xuegong Zhang; Rui Jiang; stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics, Bioinformatics, 2021, 37:299-307. https://doi.org/10.1093/bioinformatics/btab298
(45) 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 Research, 2021, 49:W483-490. https://doi.org/10.1093/nar/gkab337
(46) Shengquan Chen; Guanao Yan; Wenyu Zhang; Jinzhao Li; Rui Jiang; Zhixiang Lin; RA3 is a reference-guided approach for epigenetic characterization of single cells, Nature Communications, 2021, 12:2177. https://doi.org/10.1038/s41467-021-22495-4
(47) Qiao Liu; Shengquan Chen; Rui Jiang; Wing Wung Wong; Simultaneous deep generative modelling and clustering of single-cell genomic data, Nature Machine Intelligence, 2021, 3:536-544. https://doi.org/10.1038/s42256-021-00333-y
(48) 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, Bioinformatics, 2021,37(2):285-287. https://doi.org/10.1093/bioinformatics/btaa1106
(49) 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, Nature Machine Intelligence, 2022, 4(2):116-126. https://doi.org/10.1038/s42256-021-00432-w
(50) 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 in Bioinformatics, 2022, 23(1):1-11. https://doi.org/10.1093/bib/bbab362
(51) Yanhong Wu; Qifan Hu; Shicheng Wang; Changyi Liu; Yiran Shan; Wenbo Guo; Rui Jiang; Xiaowo Wang; Jin Gu; Highly Regional Genes: graph-based gene selection for single-cell RNA-seq data, Journal of Genetics and Genomics, 2022, 49:891-899. https://doi.org/10.1016/j.jgg.2022.01.004
(52) Tianxing Ma; Haochen Li; Xuegong Zhang; Discovering single-cell eQTLs from scRNA-seq data only, Gene, 2022, 829:146520. https://doi.org/10.1016/j.gene.2022.146520
(53) Keyi Li; Xiaoyang Chen; Shuang Song; Lin Hou; Shengquan Chen; Rui Jiang; Cofea: correlation-based feature selection for single-cell chromatin accessibility data, Briefings in Bioinformatics, in press, 2023. https://doi.org/10.1093/bib/bbad458
(54) Zijing Gao; Xiaoyang Chen; Zhen Li; Xuejian Cui; Shengquan Chen; Rui Jiang, scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data, Journal of Genetics and Genomics, in press, 2023. https://doi.org/10.1016/j.jgg.2023.09.011
(55) Qiao Liu; Wanwen Zeng; Wei Zheng; Sicheng Wang; Hongyang Chen; Rui Jiang; Mu Zhou; Shaoting Zhang, Deep generative modeling and clustering of single cell Hi-C data, Briefings in Bioinformatics, bbac494, 2023. https://doi.org/10.1093/bib/bbac494
(56) Shengquan Chen; Rongxiang Wang; Wenxin Long; Rui Jiang, ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data, Bioinformatics, 39(1): btac842, 2023. https://doi.org/10.1093/bioinformatics/btac842
(57) Rui Jiang; Zhen Li; Yuhang Jia; Siyu Li; Shengquan Chen, SINFONIA: Scalable identification of spatially variable genes for deciphering spatial domains, Cells, 12(4): 604, 2023. https://doi.org/10.3390/cells12040604
(58) 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 in Bioinformatics, 2023, 24(6): bbad359. https://doi.org/10.1093/bib/bbad359

方向2: 重大疾病的生物和医学数据整合分析

(59) Yaru Liang; Chang Liu; Maoyang Lu; Qiongye Dong; Zimu Wang; Zhuoran Wang; Wenxiang Xiong; Nannan Zhang; Jiawei Zhou; Qingfei Liu; Xiaowo Wang; Zhao Wang, Calorie restriction is the most reasonable anti-ageing intervention: a meta-analysis of survival curves, Scientific Reports, 2018.04.10, 8. https://doi.org/10.1038/s41598-018-24146-z
(60) Qiuyu Lian; Shicheng Wang; Guchao Zhang; Dongfang Wang; Guijuan Luo; Jing Tang; Lei Chen; Jin Gu, HCCDB: a database of hepatocellular carcinoma expression atlas, Genomics Proteomics Bioinformatics, 2018, 16(4):269-275. https://doi.org/10.1016/j.gpb.2018.07.003
(61) Huijuan Feng; Tingting Li; Xuegong Zhang, Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data, BMC Genomics, 2018, 19:564. https://doi.org/10.1186/s12864-018-4925-1
(62) Jiaxing Cui; Hongfei Cui; Mingran Yang; Shiyu Du; Junfeng Li; Yingxue Li; Liyang Liu; Xuegong Zhang; Shao Li, Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade, Protein Cell, 2019, 10(7):496-509. https://doi.org/10.1007/s13238-018-0596-6
(63) Yuqing Yang; Xin Wang; Yu Huang; Ning Chen; Juhong Shi; Ting Chen, Ontology-based venous thromboembolism risk assessment model developing from medical records, BMC Medical Informatics and Decision Making, 2019, 19(Suppl 4). https://doi.org/10.1186/s12911-019-0856-2
(64) Dongfang Wang; Yanjing Zhu; Jing Tang; Qiuyu Lian; Guijuan Luo; Wen Wen; Michael Zhang; Hongyang Wang; Lei Chen; Jin Gu, Integrative molecular analysis of metastatic hepatocellular carcinoma, BMC Medical Genomics, 2019, 12. https://doi.org/10.1186/s12920-019-0586-4
(65) Wanwen Zeng; Xu Min; Rui Jiang, EnDisease: a manually curated database for enhancer-disease associations, Database, 2019, baz020. https://doi.org/10.1093/database/baz020
(66) Kang Zhang; Xiaohong Liu; Jun Shen; Zhihuan Li; Ye Sang; Xingwang Wu; Yunfei Zha; Wenhua Liang; Chengdi Wang; Ke Wang; Linsen Ye; Ming Gao; Zhongguo Zhou; Liang Li; Jin Wang; Zehong Yang; Huimin Cai; Jie Xu; Lei Yang; Wenjia Cai; Wenqin Xu; Shaoxu Wu; Wei Zhang; Shanping Jiang; Lianghong Zheng; Xuan Zhang; Li Wang; Liu Lu; Jiaming Li; Haiping Yin; Winston Wang; Oulan Li; Charlotte Zhang; Liang Liang; Tao Wu; Ruiyun Deng; Kang Wei; Yong Zhou; Ting Chen; Johnson Yiu-Nam Lau; Manson Fok; Jianxing He; Tianxin Lin; Weimin Li; Guangyu Wang, Clinically Applicable AI System for Accurate Diagnosis, Quantitative Measurements, and Prognosis of COVID-19 Pneumonia Using Computed Tomography, Cell, 2020, 181:1423-1433. https://doi.org/10.1016/j.cell.2020.08.029
(67) Pengshuai Yang; Yupeng Zhai; Lin Li; Hairong Lv; Jigang Wang; Chengzhan Zhu; Rui Jiang, A deep metric learning approach for histopathological image retrieval, Methods, 2020, 179(1):14-25. https://doi.org/10.1016/j.ymeth.2020.05.015
(68) Jiangshao Gu; Ying Shi; Yifang Zhu; Ning Chen; Haibo Wang; Zongjiu Zhang; Ting Chen, Ambient air pollution and cause-specific risk of hospital admission in China: A nationwide time-series study, PLoS Medicine, 2020, 17(8):e1003188. https://doi.org/10.1371/journal.pmed.1003188
(69) Jiangshao Gu; Ying Shi; Ning Chen; Haibo Wang; Ting Chen, Ambient fine particulate matter and hospital admissions for ischemic and hemorrhagic strokes and transient ischemic attack in 248 Chinese cities, Science of the Total Environment, 2020, 715. https://doi.org/10.1016/j.scitotenv.2020.136896
(70) Bo Zheng; Dongfang Wang; Xinyao Qiu; Guijuan Luo; Tong Wu; Shuai Yang; Zhixuan Li; Yanjing Zhu; Xuan Wu; Shan Wang; Ziqi Gu; Siyun Shen; Seogsong Jeong; Rui Wu; Yang Ge; Jin Gu; Hongyang Wang; Lei Chen, Trajectory and Functional Analysis of PD-1 high CD4+ CD8+ T Cells in Hepatocellular Carcinoma by Single-Cell Cytometry and Transcriptome Sequencing, Advanced Science, 2020, 7(13):2000224. https://doi.org/10.1002/advs.202000224
(71) Jing Tang; Cheng-Jun Sui; Dong-Fang Wang; Xin-Yuan Lu; Gui-Juan Luo; Qing Zhao; Qiuyu Lian; Seogsong Jeong; Xi-Meng Lin; Yan-Jing Zhu; Bo Zheng; Rui Wu; Qing Wang; Xiao-Long Liu; Jing-Feng Liu; Qiang Xia; Gang Wu; Jin Gu; Hong-Yang Wang; Lei Chen, Targeted sequencing reveals the mutational landscape responsible for sorafenib therapy in advanced hepatocellular carcinoma, Theranostics, 2020, 10(12):5384-5397. https://doi.org/10.7150/thno.41616
(72) Hanqing He; Panglian Xu; Xiaofei Zhang; Min Liao; Qiongye Dong; Tingting Cong; Baixue Tang; Xiuxiu Yang; Maoqing Ye; Yingjun Chang; Weihua Liu; Xiaowo Wang; Zhenyu Ju; Jianwei Wang, Aging-induced IL27Ra signaling impairs hematopoietic stem cells, Blood, 2020, 136(2):183-198. https://doi.org/10.1182/blood.2019003910
(73) Jiaqi Guan; Runzhe Li; Sheng Yu; Xuegong Zhang, A method for generating synthetic electronic medical record text, IEEE TCBB, 2021, 18(1):173-182. https://doi.org/10.1109/TCBB.2019.2948985
(74) Tong Wu; Guijuan Luo; Qiuyu Lian; Chengjun Sui; Jing Tang; Yanjing Zhu; Bo Zheng; Zhixuan Li; Yani Zhang; Yangqianwen Zhang; Jinxia Bao; Ji Hu; Siyun Shen; Zhao Yang; Jianmin Wu; Kaiting Wang; Yan Zhao; Shuai Yang; Shan Wang; Xinyao Qiu; Wenwen Wang; Xuan Wu; Hongyang Wang; Jin Gu; Lei Chen, Discovery of a carbamoyl phosphate synthetase 1–deficient HCC subtype with therapeutic potential through integrative genomic and experimental analysis, Hepatology, 2021, 6(74):3249-3268. https://doi.org/10.1002/hep.32088
(75) Gang Yang; Wenfang Guan; Zhe Cao; Wenbo Guo; Guangbing Xiong; Fangyu Zhao; Mengyu Feng; Jiangdong Qiu; Yueze Liu; Michael Q Zhang; Lei You; Taiping Zhang; Yupei Zhao; Jin Gu, Integrative genomic analysis of gemcitabine resistance in pancreatic cancer by patient-derived xenograft models, Clinical Cancer Research, 2021, (27):3383-3396. https://doi.org/10.1158/1078-0432.CCR-19-3975
(76) Rui Wu; Wenbo Guo; Xinyao Qiu; Shicheng Wang; Chengjun Sui; Qiuyu Lian; Jianmin Wu; Yiran Shan; Zhao Yang; Shuai Yang; Tong Wu; Kaiting Wang; Yanjing Zhu; Shan Wang; Changyi Liu; Yangqianwen Zhang; Bo Zheng; Zhixuan Li; Yani Zhang; Siyun Shen; Yan Zhao; Wenwen Wang; Jinxia Bao; Ji Hu; Xuan Wu; Xiaoqing Jiang; Hongyang Wang; Jin Gu; Lei Chen, Comprehensive analysis of spatial architecture in primary liver cancer, Science Advances, 2021, 7:eabg3750. https://doi.org/10.1126/sciadv.abg3750
(77) Yu Yu; Minzhen Tao; Libin Xu; Lei Cao; Baoyu Le; Na An; Jilin Dong; Yajie Xu; Baoxing Yang; Wei Li; Bing Liu; Qiong Wu; Yinying Lu; Zhen Xie; Xiaohua Lian, Systematic screening reveals synergistic interactions that overcome MAPK inhibitor resistance in cancer cells, Cancer Biology & Medicine, 2021, 10. https://doi.org/10.20892/j.issn.2095-3941.2020.0560
(78) Yiming Xu; Xiaohong Liu; Liyan Pan; Xiaojian Mao; Huiying Liang; Guangyu Wang; Ting Chen, Explainable dynamic multimodal variational autoencoder for the prediction of patients with suspected central precocious puberty, IEEE Journal of Biomedical and Health Informatics, 2022, 3103271. https://doi.org/10.1109/JBHI.2021.3103271
(79) Kang Zhang; Xiaohong Liu; Jie Xu; Jin Yuan; Wenjia Cai; Ting Chen; Kai Wang; Yuanxu Gao; Sheng Nie; Xiaodong Xu; Xiaoqi Qin; Yuandong Su; Wenqin Xu; Andrea Olvera; Kanmin Xue; Zhihuan Li; Meixia Zhang; Xiaoxi Zeng; Charlotte L. Zhang; Oulan Li; Edward E. Zhang; Jie Zhu; Yiming Xu; Daniel Kermany; Kaixin Zhou; Ying Pan; Shaoyun Li; Iat Fan Lai; Ying Chi; Changuang Wang; Michelle Pei; Guangxi Zang; Qi Zhang; Johnson Lau; Dennis Lam; Xiaoguang Zou; Aizezi Wumaier; Jianquan Wang; J. Yin Shen; Fan Fan Hou; Ping Zhang; Tao Xu; Tao Xu; Yong Zhou; Guangyu Wang, Deep learning models for the detection and incidence prediction of chronic kidney disease and type-2 diabetes from retinal fundus images, Nature Biomedical Engineering, 2021, 6(5):533-545. https://doi.org/10.1038/s41551-021-00745-6
(80) Guangyu Wang; Xiaohong Liu; Jun Shen; Chengdi Wang; Zhihuan Li; Linsen Ye; Xingwang Wu; Ting Chen; Kai Wang; Xuan Zhang; Zhongguo Zhou; Jian Yang; Ye Sang; Ruiyun Deng; Wenhua Liang; Tao Yu; Ming Gao; Jin Wang; Zehong Yang; Huimin Cai; Guangming Lu; Lingyan Zhang; Lei Yang; Wenqin Xu; Winston Wang; Andrea Olvera; Ian Ziyar; Charlotte Zhang; Oulan Li; Weihua Liao; Jun Liu; Wen Chen; Wei Chen; Jichan Shi; Lianghong Zheng; Longjiang Zhang; Zhihan Yan; Xiaoguang Zou; Guiping Lin; Guiqun Cao; Laurance L. Lau; Long Mo; Yong Liang; Michael Roberts; Evis Sala; Carola-Bibiane Schonlieb; Manson Fok; Johnson Yiu-Nam Lau; Tao Xu; Jianxing He; Kang Zhang; Weimin Li; Tianxin Lin, A deep-learning pipeline for the diagnosis and discrimination of viral, non-viral and COVID-19 pneumonia from chest X-ray images, Nature Biomedical Engineering, 2021 Jun, 6(5):509-521. https://doi.org/10.1038/s41551-021-00704-1
(81) Kaikun Xie; Zehua Liu; Ning Chen; Ting Chen, redPATH: Reconstructing the pseudo development time of cell lineages in single-cell RNA-seq data and applications in cancer genomics, Genomics, Proteomics & Bioinformatics, 2021, (19):292-305. https://doi.org/10.1016/j.gpb.2020.06.014
(82) Pengshuai Yang; Zhiwei Hong; Xiaoxu Yin; Chengzhan Zhu; Rui Jiang, Self-supervised visual representation learning for histopathological images, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2021), Lecture Notes in Computer Science, vol 12902. Springer, Cham. https://doi.org/10.1007/978-3-030-87196-3_5
(83) Ke Wang; Guangyu Wang; Kang Zhang; Ting Chen, An adversarial collaborative-learning approach for corneal scar segmentation with ocular anterior segment photography, IEEE International Conference on Image Processing (ICIP 2021). https://doi.org/10.1109/ICIP42928.2021.9506621
(84) Xiaohong Liu; Kai Wang; Ting Chen, Deep active learning for fibrosis segmentation of chest CT scans from COVID-19 patients, IEEE International Conference on Image Processing (ICIP), 2021. https://doi.org/10.1109/ICIP42928.2021.9506413
(85) Liang Chen; Kui Hua; Ningning Zhang; Jingyu Wang; Jian Meng; Zhenliang Hu; Haoxiang Gao; Fanhong Li; Yang Chen; Jie Ren; Liyang Liu; Qiming Zhou; Jin Gu; Jiangping Song; Xuegong Zhang; Shengshou Hu, Multifaceted Spatial and Functional Zonation of Cardiac Cells in Adult Human Heart, Circulation, 2022, 145(4):315-318. https://doi.org/10.1161/CIRCULATIONAHA.121.055690
(86) Weili Fu; Sijie Chen; Runze Yang; Chen Li; Haoxiang Gao; Jian Li; Xuegong Zhang, Cellular features of localized microenvironments in human meniscal degeneration: a single-cell transcriptomic study, eLife, 2022, 11. https://doi.org/10.7554/eLife.79585
(87) Xiaofei Zhang; Tingting Cong; Lei Wei; Bixi Zhong; Xiaowo Wang; Jin Sun; Shuxia Wang; Meng Michelle Xu; Ping Zhu; Hong Jiang; Jianwei Wang, YTHDF3 modulates hematopoietic stem cells by recognizing RNA m6A modification on Ccnd1, Haematologica, 2022, 107(10):2290-2291. https://doi.org/10.3324/haematol.2021.279739
(88) Xianglin Zhang; Xiaodong Jia; Bixi Zhong; Lei Wei; Jiaqi Li; Wei Zhang; Huan Fang; Yanda Li; Yinying Lu; Xiaowo Wang, Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA, Briefings in Bioinformatics, 2022, 23(4):1-11. https://doi.org/10.1093/bib/bbac278
(89) Yingchi Zhang; Shicheng Wang; Jingliao Zhang; Chao Liu; Xinqi Li; Wenbo Guo; Yongjuan Duan; Xiaoyan Chen; Suyu Zong; Jiarui Zheng; Yixuan Wu; Xiaoli Chen; Xuelian Cheng; Yanxia Chang; Yue Wang; Feng Ding; Wenyu Yang; Xiaojuan Chen; Ye Guo; Li Zhang; Yumei Chen; Yao Zou; Xiaofan Zhu; Jin Gu; Tao Cheng, Elucidating minimal residual disease of paediatric B-cell acute lymphoblastic leukaemia by single-cell analysis, Nature Cell Biology, 2022, 24(2):242-252. https://doi.org/10.1038/s41556-021-00814-7
(90) Xi Xi; Haochen Li; Shengquan Chen; Tingting Lv; Tianxing Ma; Rui Jiang; Ping Zhang; Wing Hung Wong; Xuegong Zhang, Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling, iScience, 2022, 25(8):104790-104790. https://doi.org/10.1016/j.isci.2022.104790
(91) Xi Xi; Haochen Li; Lei Wei; Xuegong Zhang, Protocol for using GRPath to identify putative gene regulation paths in complex human diseases, Star Protocols, 2022, 3(4):101831. https://doi.org/10.1016/j.xpro.2022.101831
(92) Nan Yan; Weiyan Xie; Dongfang Wang; Qiuyue Fang; Guo Jing; Yiyuan Chen; Xinqi Li; Lei Gong; Jialin Wang; Wenbo Guo; Xuegong Zhang; Yazhuo Zhang; Jin Gu; Chuzhong Li, Single cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors, Genome Medicine 2024, 16:2. https://doi.org/10.1186/s13073-023-01267-3
(93) Yiran Shan; Qian Zhang; Wenbo Guo; Yanhong Wu; Yuxin Miao; Hongyi Xin; Qiuyu Lian; Jin Gu, TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics, Genomics Proteomics & Bioinformatics, 2022, 20(5):974-988. https://doi.org/10.1016/j.gpb.2022.11.012
(94) Qijin Yin; Rui Fan; Xusheng Cao; Qiao Liu; Rui Jiang; Wanwen Zeng, DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction, Quantitative Biology, 2023, 11(3): 260-274. https://doi.org/10.15302/J-QB-022-0320
(95) Linlin Guo; Linying Guo; Jiao Li; Yaowen Gu; Jiayang Wang; Ying Cui; Qing Qian; Ting Chen; Rui Jiang; Si Zheng, Characteristics and Admission Preferences of Pediatric Emergency Patients and Their Waiting Time Prediction Using Electronic Medical Record Data: Retrospective Comparative Analysis, J Med Internet Res, 2023, 25:e49605. https://doi.org/10.2196/49605
(96) Yuze Gao; Jiangshao Gu; Ying Shi; Haibo Wang; Ting Chen; Qian Di, Association of short-term exposure to ambient fine particle matter with hospital admission risks and costs in China, a case-crossover study, Global Transitions, 2023, 5, 40-49. https://doi.org/10.1016/j.glt.2023.04.00
(97) Shangzhi Gu; Lixue Wang; Rong Han; Xiaohong Liu; Yizhe Wang; Ting Chen; Zhuozhao Zheng, Detection of sarcopenia using deep learning-based Artificial Intelligence Body Part Measure System (AIBMS), Frontiers in Physiology, 2023, 1092352. https://doi.org/10.3389/fphys.2023
(98) Yiming Xu; Bowen Zheng; Xiaohong Liu; Tao Wu; Jinxiu Ju; Shijie Wang; Yufan Lian; Hongjun Zhang; Tong Liang; Ye Sang; Rui Jiang; Guangyu Wang; Jie Ren; Ting Chen, Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames, Briefings in Bioinformatics, 2023, 24(1):1–13. https://doi.org/10.1093/bib/bbac569
(99) Zhan Wang; Haiyang Bian; Jiaqi Li; Jin Xu; Haining Fan; Xinze Wu; Yuntai Cao; Bin Guo; Xiaolei Xu; Haijiu Wang; Lingqiang Zhang; Hu Zhou; Jianfeng Fan; Youyou Ren; Yunping Geng; Xiaobin Feng; Luming Li; Lei Wei; Xuegong Zhang, Detection and subtyping of hepatic echinococcosis from plain CT images with deep learning: a retrospective, multicentre study, The Lancet Digital Health, 2023, 5(11):e754-e762. https://doi.org/10.1016/S2589-7500(23)00136-X
(100) Jiaqi Li; Zhenbin Qiu; Chao Zhang; Sijie Chen; Mengmin Wang; Qiuchen Meng; Haiming Lu; Lei Wei; Hairong Lv; Wenzhao Zhong; Xuegong Zhang; ITHscore: comprehensive quantification of intra-tumor heterogeneity in NSCLC by multi-scale radiomic features, European Radiology, 2023, 33(2): 893-903. https://doi.org/10.1007/s00330-022-09055-0
(101) Yang Zhang; Gan Liu; Minzhen Tao; Hui Ning; Wei Guo; Gaofei Yin; Wen Gao; Lifei Feng; Jin Gu; Zhen Xie; Zhigang Huang, Integrated transcriptome study of the tumor microenvironment for treatment response prediction in male predominant hypopharyngeal carcinoma, Nature Communications, 14(1), 1466. https://doi.org/10.1038/s41467-023-37159-8
(102) Gan Liu; Qifan Hu; Shuguang Peng; Hui Ning; Jiajia Mai; Xi Chen; Minzhen Tao; Qiang Liu; Huiya Huang; Yun Jiang; Yanhua Ding; Xuegong Zhang; Jin Gu; Zhen Xie, The spatial and single-cell analysis reveals remodeled immune microenvironment induced by synthetic oncolytic adenovirus treatment, Cancer Letters, 581, 216485. https://doi.org/10.1016/j.canlet.2023.216485
(103) Jiaqi Li; Zhuofeng Li, Lei Wei, Xuegong Zhang, Machine Learning in Lung Cancer Radiomics, Machine Intelligence Research, 2023: 1-30. https://doi.org/10.1007/s11633-022-1364-x

方向3: 生物分子系统及其人工调控的信息理论

复杂分子系统的调控模型

(104) Qiongye Dong; Lei Wei; Michael Q. Zhang; Xiaowo Wang, Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence, Aging-US, 2018.06, 10(6):1489~1505. https://doi.org/10.18632/aging.101485
(105) Xuehui Liu; Lei Wei; Qiongye Dong; Liyang Liu; Michael Zhang; Zhen Xie; Xiaowo Wang, A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass, Aging, 2019, 11(12):4011~4031. https://doi.org/10.18632/aging.102034
(106) Lei Wei; Ye Yuan; Tao Hu; Shuailin Li; Tianrun Cheng; Jinzhi Lei; Zhen Xie; Michael Zhang; Xiaowo Wang, Regulation by competition: a hidden layer of gene regulatory network, Quantitative Biology, 2019, 7(2):110~121. https://doi.org/10.1007/s40484-018-0162-5
(107) Shining Ma; Tao Jiang; Rui Jiang, Constructing tissue-specific transcriptional regulatory networks via a Markov random field, BMC Genomics, 2019, 19. https://doi.org/10.1186/s12864-018-5277-6
(108) Zhen Zhao; Qiongye Dong; Xuehui Liu; Lei Wei; Liyang Liu; Yanda Li; Xiaowo Wang, Dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest, Genomics, 2020, 112(2):1309-1317. https://doi.org/10.1016/j.ygeno.2019.07.020
(109) Wanwen Zeng; Shengquan Chen; Xuejian Cui; Xiaoyang Chen; Zijing Gao; Rui Jiang, SilencerDB: a comprehensive database of silencers, Nucleic Acids Research, 2020, gkaa839. https://doi.org/10.1093/nar/gkaa839
(110) Lei Wei; Shuailin Li; Pengcheng Zhang; Tao Hu; Michael Q. Zhang; Zhen Xie; Xiaowo Wang, Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits, Cell Reports, 2021, (36):109573. https://doi.org/10.1016/j.celrep.2021.109573
(111) Tao Hu; Lei Wei; Shuailin Li; Tianrun Cheng; Xuegong Zhang; Xiaowo Wang, Single-cell transcriptomes reveal characteristics of microRNA in gene expression noise reduction, Genomics Proteomics & Bioinformatics, 2021, 5. https://doi.org/10.1016/j.gpb.2021.05.002
(112) Xianglin Zhang; Xuehui Liu; Zhenhai Du; Lei Wei; Huan Fang; Qiongye Dong; Jing Niu; Yanda Li; Juntao Gao; Michael Q. Zhang; Wei Xie; Xiaowo Wang, The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence, Genome Research, 2021, (31):1-15. https://doi.org/10.1101/gr.275235.121
(113) Congmin Zhu; Junyi Zhang; Xin Wang; Yuqing Yang; Ning Chen; Zuhong Lu; Qinyu Ge; Rui Jiang; Xuegong Zhang; Yunfeng Yang; Ting Chen, Responses of cyanobacterial aggregate microbial communities to algal blooms, Water Research, 2021, 117014:196. https://doi.org/10.1016/j.watres.2021.117014
(114) Wanwen Zeng; Qiao Liu; Qijin Yin; Rui Jiang; Wing Hung Wong, HiChIPdb: a comprehensive database of HiChIP regulatory interactions, Nucleic Acids Research, 2022, gkac859. https://doi.org/10.1093/nar/gkac859
(115) Zheng Wei; Kui Hua; Lei Wei; Shining Ma; Rui Jiang; Xuegong Zhang; Yanda Li; Wing H. Wong; Xiaowo Wang, NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks, PNAS 120, 15 (2023). https://doi.org/10.1073/pnas.2216698120
(116) Minsheng Hao; Erpai Luo; Yinxin Chen; Yanhong Wu; Chen Li; Sijie Chen; Haoxiang Gao; Haiyang Bian; Jin Gu; Lei Wei; Xuegong Zhang; STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning, Communications Biology [accepted]. https://doi.org/10.1038/s42003-023-05640-1

合成生物学人工调控

(117) 胡冠华; 王也; 魏磊; 汪小我, 通过合成基因线路实现细胞分类, 生命科学, 2018.08.25, (08):799~809. https://doi.org/10.13376/j.cbls/2018095
(118) Huiya Huang; Yiqi Liu; Weixi Liao; Yubing Cao; Qiang Liu; Yakun Gao; Yinqing Lu; Zhen Xie, Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy, Nature Communications, 2019, 10(1). https://doi.org/10.1038/s41467-019-12794-2
(119) Dacheng Ma; Zhimeng Xu; Zhaoyu Zhang; Yi Chen; Xiangzhi Zeng; Yiyang Zhang; Tingyue Deng; Mengfei Ren; Zheng Sun; Rui Jiang; Zhen Xie, Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information, Nature Communications, 2019, 10(1). https://doi.org/10.1038/s41467-019-08395-8
(120) Ye Wang; Haochen Wang; Lei Wei; Shuailin Li; Liyang Liu; Xiaowo Wang, Synthetic promoter design in Escherichia coli based on a deep generative network, Nucleic Acids Research, 2020, 48(12):6403-6412. https://doi.org/10.1093/nar/gkaa325
(121) Yang Liu; Filipe Pinto; Xinyi Wan; Zhugen Yang; Shuguang Peng; Mengxi Li; Jonathan M Cooper; Zhen Xie; Christopher E French; Baojun Wang, Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors, Nature Communications, 11;13(1):1937. https://doi.org/10.1038/s41467-022-29604-x
(122) Pengcheng Zhang, Haochen, Hanwen Xu, Lei Wei, Liyang Liu, Zhirui Hu, Xiaowo Wang, Deep flanking sequence engineering for efficient promoter design using DeepSEED, Nature Communications, 2023, 14, 6309. https://doi.org/10.1038/s41467-023-41899-y
(123) Zhimeng Xu; Dacheng Ma; Houzhen Su; Xiaodong Jia; Yinqing Li; Yinying Lu; Zhen Xie, Explore the dominant factor in prime editing via a view of DNA processing, Synthetic and Systems Biotechnology, 2023, 8(3):371-377. https://doi.org/10.1016/j.synbio.2023.05.007
(124) Gan Liu; Qifan Hu; Shuguang Peng; Hui Ning; Jiajia Mai; Xi Chen; Minzhen Tao; Qiang Liu; Huiya Huang; Yun Jiang; Yanhua Ding; Xuegong Zhang; Jin Gu; Zhen Xie; Hui Ning; Gan Liu; Lei Li; Qiang Liu; Huiya Huang; Zhen Xie, Nature Communications, 2023, 14(1), 7193. https://doi.org/10.1038/s41467-023-43065-w

数基生命系统与集成细胞图谱

(125) Chen Sijie; Luo Yanting; Gao Haoxiang; Li Fanhong; Li Jiaqi; Chen Yixin; You Renke; Lv Hairong; Hua Kui; Jiang Rui; Zhang Xuegong, Toward a unified information framework for cell atlas assembly, National Science Review, 2022, 9(3). https://doi.org/10.1093/nsr/nwab179
(126) Sijie Chen; Yanting Luo; Haoxiang Gao; Fanhong Li; Yang Chen; Jiaqi Li; Renke You; Minsheng Hao; Haiyang Bian; Xi Xi; Wenrui Li; Weiyu Li; Mingli Ye; Qiuchen Meng; Ziheng Zou; Chen Li; Haochen Li; Yangyuan Zhang; Yanfei Cui; Lei Wei; Fufeng Chen; Xiaowo Wang; Hairong Lv; Kui Hua; Rui Jiang; Xuegong Zhang, hECA: The cell-centric assembly of a cell atlas, iScience, 2022, 25(5):104318-104318. https://doi.org/10.1016/j.isci.2022.104318
(127) Yixin Chen; Minsheng Hao; Haoxiang Gao; Jiaqi Li; Sijie Chen; Fanhong Li; Lei Wei; Xuegong Zhang, Protocol for profiling cell-centric assembled single-cell human transcriptome data in hECA, Star Protocols, 2022, 3(3):101589-101589. https://doi.org/10.1016/j.xpro.2022.101589
(128) Zhang X, Wei L, Jiang R, et al. Building digital life systems for future biology and medicine, Quantitative Biology, 2023, 11(3): 207-213. https://doi.org/10.15302/J-QB-023-0331

专利

（1）张学工; 陈文昌; 闾海荣, 基于病历文本的病人相似性度量装置及方法，2020-11-20至2040-11-20，中国，ZL 2018 1 0697392.X
（2）张学工；关嘉麒；闾海荣，一种仿真文本病历的生成方法及系统，2021-04-30至2041-04-30，中国，ZL 2018 1 0600640.4
（3）张学工；李季；闾海荣；陈文昌，一种中文电子病历文本分析方法与系统，2021-01-15至2041-01-15，中国，ZL 2018 1 0635258.7
（4）张学工；林子坤；闾海荣，病历数据结构化分析处理方法，2021-11-05至2041-11-05，中国，ZL 2018 1 0594098.6
（5）闾海荣; 李猛; 江瑞; 张学工; 李林, 基于随机森林的股骨头头像分割装置及分割方法，2020-9-29至2040-9-29，中国，ZL 2018 1 0550215.9
（6）张学工；方翔；路海明；陈斯杰，基于CT影像的肿瘤异质性分析系统，2021-02-26至2041-02-26，中国，ZL 2018 1 1237087.9
（7）闾海荣; 耿照旭; 江瑞; 张学工; 李林, 医用图像处理装置及医用图像处理方法，2020-11-20至2040-11-20，中国，ZL 2018 1 0548920.5
（8）张学工; 李想之; 方翔; 陆海明, 融合CT影像和个性化信息的分析系统、方法、装置及介质，2022-3-18至2042-3-18，中国, ZL 2019 1 0404688.2
（9）闾海荣; 周容辰; 张学工; 江瑞; 李林, 医疗数据系统的权限管理方法，2022-5-20至2042-5-20，中国，ZL2019 1 1199645.1
（10）闾海荣；周容辰；江瑞；张学工，一种病理切片图片显示方法及系统，2022-09-23至2042-09-23，中国，ZL 2018 1 0581501.1