Academic Background
Ph.D. in Statistics (Harvard University)
M.S. in Pattern Recognition & Intelligent Systems (Tsinghua University)
B.E. in Automation (Tsinghua University)
Research Interest
Selected Publications
In Journals:
- Lijun Wang, Hongyu Zhao (joint corresponding author) and Xiaodan Fan (joint corresponding author) (2024+). Degrees of Freedom: Search Cost and Self-consistency. Journal of Computational and Graphical Statistics. Accepted.
- Lijun Wang, Zhuo Cao, Xiaodan Fan (joint corresponding author) and Hua-bai Li (joint corresponding author) (2024). Polarization Holes as an Indicator of Magnetic Field−Angular Momentum Alignment. I. Initial Tests. Astrophysical Journal, 966(2):237. DOI: 10.3847/1538-4357/ad3734.
- Julien Gheysens, Xiaodan Fan, Chaojie Wang and Nicolas Wicker (2024). Sampling from a Neural Network. Sankhya B. DOI: 10.1007/s13571-024-00329-9.
- Ran Liu, Ye-Fan Hu, Jin Du, Bao-Zhong Zhang, Thomas Yau, Xiaodan Fan (joint corresponding author) and Jian-Dong Huang (joint corresponding author) (2023). Family-Specific Training Improves Linear B Cell Epitope Prediction for Emerging Viruses. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 20(6):3669-3680. DOI: 10.1109/TCBB.2023.3311444.
- Vicki Wing-Ki Hui, Grace Lai-Hung Wong, Vincent Wai-Sun Wong, Henry Lik-Yuen Chan, Jimmy Che-To Lai, Yee-Kit Tse, Mandy Sze-Man Lai, Tsz-Fai Yam, Dongrong Li, Xiaodan Fan and Terry Cheuk-Fung Yip (2023). Baveno VII Criteria for Recompensation Predict Transplant-Free Survival in Patients with Hepatitis B-related Decompensated Cirrhosis. JHEP Reports. 5(9):100814. DOI: 10.1016/j.jhepr.2023.100814.
- Ying Zhao, Meigang Duan, Yao Ju, Zuogang Yang, Xin Deng, Haolan Huangfu, Xiaozhan Yang, Xiaodan Fan and Haoyi Zuo (2023). Low-Cost Wavefront Shaping via The Third-Order Correlation of Light Fields. Optics Letters. 48(19):4981-4984. DOI: 10.1364/OL.497293.
- Claudia HT Tam, Cadmon KP Lim, Andrea OY Luk, Mai Shi, Hoi Man Cheung, Alex CW Ng, Heung-man Lee, Eric SH Lau, Baoqi Fan, Guozhi Jiang, Alice PS Kong, Risa Ozaki, Elaine YK Chow, Ka Fai Lee, Shing Chung Siu, Grace Hui, Chiu Chi Tsang, Kam Piu Lau, Jenny YY Leung, Elaine YN Cheung, Man Wo Tsang, Grace Kam, Ip Tim Lau, June KY Li, Vincent TF Yeung, Emmy Lau, Stanley Lo, Samuel Fung, Yuk Lun Cheng, Chun Chung Chow, Xiaodan Fan, Ting Fung Chan, Kevin YL Yip, Si Lok, Weichuan Yu, Stephen KW Tsui, Hui-yao Lan, Cheuk Chun Szeto, Nelson LS Tang, Brian Tomlinson, Yu Huang, Alicia J Jenkins, Anthony Keech, Wing-yee So, Juliana CN Chan, Ronald CW Ma (2023). Identification of a Common Variant for Coronary Heart Disease at PDE1A Contributes to Individualized Treatment Goals and Risk Stratification of Cardiovascular Complications in Chinese Patients With Type 2 Diabetes. Diabetes Care, 46(6):1271 – 1281. DOI: 10.2337/dc22-2331.
- Guozhi Jiang, Andrea O Luk, Claudia HT Tam, Risa Ozaki, Cadmon KP Lim, Elaine YK Chow, Eric S Lau, Alice PS Kong, Baoqi Fan, Hong Kong Diabetes Register TRS Study Group, Ka Fai Lee, Shing Chung Siu, Grace Hui, Chiu Chi Tsang, Kam Piu Lau, Jenny Y Leung, Man-wo Tsang, Grace Kam, Ip Tim Lau, June K Li, Vincent T Yeung, Emmy Lau, Stanley Lo, Samuel Fung, Yuk Lun Cheng, Chun Chung Chow, Hong Kong Diabetes Biobank Study Group, Nelson LS Tang, Yu Huang, Hui-yao Lan, Richard A Oram, Cheuk Chun Szeto, Wing Yee So, Juliana CN Chan, Ronald CW Ma (2022). Clinical Predictors and Long-term Impact of Acute Kidney Injury on Progression of Diabetic Kidney Disease in Chinese Patients With Type 2 Diabetes. Diabetes, 71(3):520–529. DOI: 10.2337/db21-0694.
- Ran Liu, Ye-Fan Hu, Jian-Dong Huang (joint corresponding author) and Xiaodan Fan (joint corresponding author) (2023). A Bayesian Approach to Estimate MHC-peptide Binding Threshold. Briefings in Bioinformatics, 24(4):bbad208. DOI: 10.1093/bib/bbad208.
- Yetian Fan, April S Chan, Jun Zhu, Suet Yi Leung and Xiaodan Fan (corresponding author) (2023). A Bayesian Model for Identifying Cancer Subtypes from Paired Methylation Profiles. Briefings in Bioinformatics, 24(1):bbac568. DOI: 10.1093/bib/bbac568.
- Jin Du, Chaojie Wang, Lijun Wang, Shanjun Mao, Bencong Zhu, Zheng Li and Xiaodan Fan (corresponding author) (2023). Automatic Block-Wise Genotype-Phenotype Association Detection Based on Hidden Markov Model. BMC Bioinformatics, 24(1):138. DOI: 10.1186/s12859-023-05265-5.
- Chen Zhou, Shuaijian Dai, Yuanqiao Lin, Sheng Lian, Xiaodan Fan, Ning Li, Weichuan Yu (2023). Exhaustive Cross-Linking Search with Protein Feedback. Journal Proteome Research, 22(1):101-113. DOI: 10.1021/acs.jproteome.2c00500.
- Maolin Pan, Minggao Gu, Xianyi Wu and Xiaodan Fan (corresponding author) (2023). Globally and Symmetrically Identified Bayesian Multinomial Probit Model. Statistics and Computing, 33:68. DOI: 10.1007/s11222-023-10232-4.
- Hangjin Jiang, Han Li, Wing Hung Wong (joint corresponding author), Xiaodan Fan (joint corresponding author) (2023). Revealing Free Energy Landscape from MD Data via Conditional Angle Partition Tree. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(2):1384-1394. DOI: 10.1109/TCBB.2022.3172352.
- Jie Hu, Zirui Chen, Wenwei Lin and Xiaodan Fan (corresponding author) (2023). Bayesian Detection of Event Spreading Pattern from Multivariate Binary Time Series. Communications in Statistics-Simulation and Computation, 52(4):1225-1244. DOI: 10.1080/03610918.2021.1879138.
- Qiao Jin, Andrea O Luk, Eric SH Lau, Claudia HT Tam, Risa Ozaki, Cadmon KP Lim, Hongjiang Wu, Guozhi Jiang, Elaine YK Chow, Jack K Ng, Alice PS Kong, Baoqi Fan, Ka Fai Lee, Shing Chung Siu, Grace Hui, Chiu Chi Tsang, Kam Piu Lau, Jenny Y Leung, Man-wo Tsang, Grace Kam, Ip Tim Lau, June K Li, Vincent T Yeung, Emmy Lau, Stanley Lo, Samuel Fung, Yuk Lun Cheng, Chun Chung Chow, Yu Huang, Hui-yao Lan, Cheuk Chun Szeto, Wing Yee So, Juliana CN Chan, Ronald CW Ma, Cadmon King Poo Lim, Jenny YY Leung, Man Wo Tsang, Elaine Cheung, June Kam-yin Li, Vincent TF Yeung, Samuel KS Fung, Stephen Kwok-wing Tsui, Weichuan Yu, Brian Tomlinson, Si Lok, Ting Fung Chan, Kevin Yuk-lap Yip, Xiaodan Fan, Nelson LS Tang, Xiaoyu Tian, Shi Mai, Eric S Lau, Fei Xie, Sen Zhang, Pu Yu, Meng Wang, Heung Man Lee, Fangying Xie, Alex CW Ng, Grace Cheung, Ming Wai Yeung, Kitty KT Cheung, Rebecca YM Wong, So Hon Cheong, Katie KH Chan, Anthea Ka Yuen Lock, Ingrid Kwok Ying Tsang, Susanna Chi Pun Chan, Yin Wah Chan, Cherry Chiu, Chi Sang Hung, Cheuk Wah Ho, Ivy Hoi Yee Ng, Juliana Mun Chun Fok, Kai Man Lee, Hoi Sze Candy Leung, Ka Wah Lee, Hui Ming Chan, Winnie Wat, Tracy Lau, Rebecca Law, Ryan Chan, Candice Lau, Pearl Tsang, Vince Chan, Lap Ying Ho, Eva Wong, Josephine Chan, Sau Fung Lam, Jessy Pang and Yee Mui Lee (2022). Nonalbuminuric Diabetic Kidney Disease and Risk of All-Cause Mortality and Cardiovascular and Kidney Outcomes in Type 2 Diabetes: Findings From the Hong Kong Diabetes Biobank. American Journal of Kidney Diseases, 80(2):196-206.e1. DOI: 10.1053/j.ajkd.2021.11.011.
- Chaojie Wang, Jin Du and Xiaodan Fan (corresponding author) (2022). High-Dimensional Correlation Matrix Estimation for General Continuous Data with Bagging Technique. Machine Learning, 111:2905-2927. DOI: 10.1007/s10994-022-06138-3.
- Hangjin Jiang, Xingqiu Zhao, Ronald C.W. Ma and Xiaodan Fan (corresponding author) (2022). Consistent Screening Procedures in High-dimensional Binary Classification. Statistica Sinica, 32(1), 109-130. DOI: 10.5705/ss.202020.0088.
- Taobo Hu, Jingjing Li, Mengping Long, Jinbo Wu, Zhen Zhang, Fei Xie, Jin Zhao, Houpu Yang, Qianqian Song, Sheng Lian, Jiandong Shi, Xueyu Guo, Daoli Yuan, Dandan Lang, Guoliang Yu, Baosheng Liang, Xiaohua Zhou, Toyotaka Ishibashi, Xiaodan Fan, Weichuan Yu, Depeng Wang, Yang Wang, I-Feng Peng, Shu Wang (2022). Detection of Structural Variations and Fusion Genes in Breast Cancer Samples using Third-generation Sequencing. Frontiers in Cell and Developmental Biology, 10: 854640. DOI: 10.3389/fcell.2022.854640.
- Hangjin Jiang and Xiaodan Fan (corresponding author) (2021). The Two-step Clustering Approach for Metastable States Learning. International Journal of Molecular Sciences, 22(12), 6576. DOI: 10.3390/ijms22126576.
- Chaojie Wang and Xiaodan Fan (corresponding author) (2021). High-dimensional Correlation Matrix Estimation for Gaussian Data: a Bayesian Perspective. Statistics and Its Interface, 14(3), 351-358. DOI: 10.4310/20-SII655.
- Shanjun Mao, Xiaodan Fan (joint corresponding author) and Jie Hu (joint corresponding author) (2021). Correlation for Tree-Shaped Datasets and Its Bayesian Estimation. Computational Statistics & Data Analysis, 164, 107307. DOI: 10.1016/j.csda.2021.107307.
- Yingyu Chen, Chin Kiu Kwok (joint first author), Hangjin Jiang (joint corresponding author) and Xiaodan Fan (joint corresponding author) (2021). Detect differentially methylated regions using non-homogeneous hidden Markov model for bisulfite sequencing data. Methods, 189, 34-43. DOI: 10.1016/j.ymeth.2020.09.009. (R package: BSDMR)
- Wanxia Gai, Ze Zhou, Sean Agbor-Enoh, Xiaodan Fan, Sheng Lian, Peiyong Jiang, Suk Hang Cheng, John Wong, Stephen L Chan, Moon Kyoo Jang, Yanqin Yang, Raymond HS Liang, Wai Kong Chan, Edmond SK Ma, Tak Y Leung, Rossa WK Chiu, Hannah Valantine, KC Allen Chan, YM Dennis Lo (2021). Applications of Genetic-epigenetic Tissue Mapping for Plasma DNA in Prenatal Testing, Transplantation and Oncology. eLife, 10, e64356. DOI: 10.7554/eLife.64356.
- Yuanyuan Chen, Xiaodan Fan, Cong Pian (2021). Identifying Functional Modules Using Energy Minimization with Graph Cuts. Current Bioinformatics, 16(10), 1236-1243. DOI: 10.2174/2215083807666210702151919.
- Zutan Li, Hangjin Jiang, Lingpeng Kong, Yuanyuan Chen, Kun Lang, Xiaodan Fan, Liangyun Zhang, Cong Pian (2021). Deep6mA: a Deep Learning Framework for Exploring Similar Patterns in DNA N6-methyladenine Sites across Different Species. PLoS Computational Biology, 17(2), e1008767. DOI: 10.1371/journal.pcbi.1008767.
- Jiali Yang, Kun Lang, Guangle Zhang, Xiaodan Fan, Yuanyuan Chen, Cong Pian (2020). SOMM4mC: a second-order Markov model for DNA N4-methylcytosine site prediction in six species. Bioinformatics. 36(14), 4103-4105. DOI: 10.1093/bioinformatics/btaa507. (Web Server: SOMM4mC)
- Jie Hu, Huihui Qin and Xiaodan Fan (corresponding author) (2020). Can ODE Gene Regulatory Models Neglect Time Lag or Measurement Scaling? Bioinformatics. 36(13):4058-4064. DOI: 10.1093/bioinformatics/btaa268. (R Code: lagODE)
- Zhen Zhang, Jin Du, Qingchun Meng, Xiaoxia Rong (joint corresponding author) and Xiaodan Fan (joint corresponding author) (2020). The Spread of Information in Virtual Communities. Complexity, 2020, 6629318. DOI: 10.1155/2020/6629318.
- Hangjin Jiang, Hua-Bai Li (joint corresponding author) and Xiaodan Fan (joint corresponding author) (2020). Bayesian Revisit of the Relationship between the Total Field Strength and the Volume Density of Interstellar Clouds. The Astrophysical Journal. 890(2):153. DOI: 10.3847/1538-4357/ab672b.
- Hangjin Jiang and Xiaodan Fan (corresponding author) (2020). A Consistent Variable Screening Procedure with Family-wise Error Control. Journal of Statistical Computation and Simulation. 90(7):1267-1285. DOI: 10.1080/00949655.2020.1724291. (R Code: HHG-CIS)
- Cong Pian, Shanjun Mao, Guangle Zhang, Jin Du, Fei Li, Suet Yi Leung, Xiaodan Fan (corresponding author) (2020). Discovering Cancer-related miRNAs from miRNA-target Interactions by Support Vector Machines. Molecular Therapy: Nucleic Acids. 19:1423-1433. DOI: 10.1016/j.omtn.2020.01.019.
- Cong Pian, Guangle Zhang, Fei Li (joint corresponding author) and Xiaodan Fan (joint corresponding author) (2020). MM-6mAPred: Identifying DNA N6-methyladenine Sites Based on Markov Model. Bioinformatics, 36(2):388-392. DOI: 10.1093/bioinformatics/btz556. (Web Server: MM-6mAPred)
- Chaojie Wang, Linghao Shen, Han Li, Xiaodan Fan (corresponding author) (2020). Nonparametric Statistical Inference and Imputation for Incomplete Categorical Data. Statistics and Its Interface, 13(1):17-25. DOI: 10.4310/SII.2020.v13.n1.a2. (Software: R-package “MMDai“)
- Han Li, Minxuan Xu, Jun S. Liu and Xiaodan Fan (corresponding author) (2020). An Extended Mallows Model for Ranked Data Aggregation. Journal of the American Statistical Association, 115(530):730-746. DOI:10.1080/01621459.2019.1573733. (Software: R-package “ExtMallows“)
- Chun Li and Xiaodan Fan (corresponding author) (2019). On Nonparametric Conditional Independence Tests for Continuous Variables. WIREs Computational Statistics, 12(3):e1489. DOI: 10.1002/wics.1489.
- Cong Pian, Guangle Zhang, Libin Gao, Xiaodan Fan (joint corresponding author) and Fei Li (joint corresponding author) (2019). miR+Pathway: The Integration and Visualization of miRNA and KEGG Pathways. Briefings in Bioinformatics, 21(2):699-708. DOI:10.1093/bib/bby128. (Web Server: miR-pathway)
- Guozhi Jiang, Andrea On Yan Luk, Claudia Ha Ting Tam, Fangying Xie, Bendix Carstensen, Eric Siu Him Lau, Cadmon King Poo Lim, Heung Man Lee, Alex Chi Wai Ng, Maggie Chor Yin Ng, Risa Ozaki, Alice Pik Shan Kong, Chun Chung Chow, Xilin Yang, Hui-yao Lan, Stephen Kwok Wing Tsui, Xiaodan Fan, Cheuk Chun Szeto, Wing Yee So, Juliana C. N. Chan, Ronald C. W. Ma (2019). Progression of Diabetic Kidney Disease and Trajectory of Kidney Function Decline in Chinese Patients with Type 2 Diabetes. Kidney International, 95(1):178-187.
- Helen H.N. Yan, Hoi Cheong Siu, Simon Law, Siu Lun Ho, Sarah S.K. Yue, Wai Yin Tsui, Dessy Chan, April S. Chan, Stephanie Ma, Ka On Lam, Sina Bartfeld, Alice H.Y. Man, Bernard C.H. Lee, Annie S.Y. Chan, Jason W.H. Wong, Priscilla S.W. Cheng, Anthony K.W. Chan, Jiangwen Zhang, Jue Shi, Xiaodan Fan, Dora L.W. Kwong, Tak W. Mak, Siu Tsan Yuen, Hans Clevers, Suet Yi Leung (2018). A Comprehensive Human Gastric Cancer Organoid Biobank Captures Tumor Subtype Heterogeneity and Enables Therapeutic Screening. Cell Stem Cell, 23(6):882-897.e11.
- Wei Wang, Tong Liang, Fu Kit Sheong, Xiaodan Fan (joint corresponding author) and Xuhui Huang (joint corresponding author) (2018). An Efficient Bayesian Kinetic Lumping Algorithm to Identify Metastable Conformational States via Gibbs Sampling. The Journal of Chemical Physics, 149(7):072337.
- Linghao Shen, Jun Zhu, Shuo-Yen Robert Li and Xiaodan Fan (Corresponding Author) (2017). Detect Differentially Methylated Regions Using Non-homogeneous Hidden Markov Model for Methylation Array Data. Bioinformatics, 33(23):3701-3708. (Software: R-package “DMRMark“)
- Zengbing Lu, Man P. Ngan, Ge Lin, David T.W. Yew, Xiaodan Fan, Paul L.R. Andrews and John A. Rudd (2017). Gastric Myoelectric Activity during Cisplatin-Induced Acute and Delayed Emesis Reveals A Temporal Impairment of Slow Waves in Ferrets: Effects Not Reversed by The Glp-1 Receptor Antagonist, Exendin (9-39). Oncotarget, 8(58):98691-98707.
- Qing Zhang, Xiaodan Fan (joint first author), Yejun Wang, Ming-an Sun, Jianlin Shao and Dianjing Guo (2017). BPP: A Sequence-based Algorithm for Branch Point Prediction. Bioinformatics, 33(20):3166-3172.
- Qin Cao, Christine Anyansi, Xihao Hu, Liangliang Xu, Lei Xiong, Wenshu Tang, Myth T S Mok, Chao Cheng, Xiaodan Fan, Mark Gerstein, Alfred S L Cheng and Kevin Y Yip (2017). Reconstruction of Enhancer–Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines. Nature Genetics, 49(10):1428-1436.
- Guozhi Jiang, Claudia H.T. Tam, Andrea O.Y. Luk, Cadmon K. Lim, Xiaodan Fan, Nelson L. S. Tang, Stephen K.W. Tsui, Weichuan Yu, Brian Tomlinson, Yu Huang, Hui Yao Lan, Cheuk-Chun Szeto, Wing Yee So, Juliana C.N. Chan and Ronald C.W. Ma (2017). Estimation of Heritability for Diabetic Complications Based on Genome-wide Association Study in Chinese Population. Diabetologia, 60(1 supp):S174-S174.
- Hua-bai Li, Hangjin Jiang, Xiaodan Fan, Qilao Gu and Yapeng Zhang (2017). The Link between Magnetic-field Orientations and Star Formation Rates. Nature Astronomy, 1:0158.
- Alexandra M Davis, Xiaodan Fan, Linghao Shen, Paul Robinson, Christopher M Riggs (2017). Improved Radiological Diagnosis of Palmar Osteochondral Disease in The Thoroughbred Racehorse. Equine Veterinary Journal, 49(4):454-460.
- Timothy C.T. Ng, Chun Li (joint first author) and Xiaodan Fan (Corresponding Author) (2017). A Fast Algorithm for Reconstructing Multiple Sequence Alignment and Phylogeny Simultaneously. Current Bioinformatics, 12(4):329-348. (C++ Code: FAMAP for Windows/Linux)
- Guozhi Jiang, Cheng Hu, Claudia H.T. Tam, Eric S.H. Lau, Ying Wang, Andrea O.Y. Luk, Xilin Yang, Alice P.S. Kong, Janice S.K. Ho, Vincent K.L. Lam, Heung Man Lee, Jie Wang, Rong Zhang, Stephen K.W. Tsui, Maggie C.Y. Ng, Cheuk-Chun Szeto, Weiping Jia, Xiaodan Fan, Wing Yee So, Juliana C.N. Chan and Ronald C.W. Ma (2016). Genetic and Clinical Variables Identify Predictors for Chronic Kidney Disease in Type 2 Diabetes. Kidney International, 89(2):411-420.
- Han Li and Xiaodan Fan (Corresponding Author) (2016). A Pivotal Allocation-Based Algorithm for Solving the Label-Switching Problem in Bayesian Mixture Models. Journal of Computational and Graphical Statistics, 25(1):266-283. (R Code: PAR)
- Han Li, Chun Li, Jie Hu, Xiaodan Fan (Corresponding Author) (2015). A Resampling Based Clustering Algorithm for Replicated Gene Expression Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(6):1295-1303. (R Code: RC)
- Jie Hu, Zhongying Zhao, Hari Krishna Yalamanchili, Junwen Wang, Kenny Ye and Xiaodan Fan (Corresponding Author) (2015). Bayesian Detection of Embryonic Gene Expression Onset in C. elegans. Annals of Applied Statistics, 9(2):950-968.
- Shengtong Han, Raymond K.W. Wong, Thomas C.M. Lee, Shuo-Yen Robert Li and Xiaodan Fan (Corresponding Author) (2014). A Full Bayesian Approach for Boolean Genetic Network Inference. PLoS ONE, 9(12):e115806.
- Claudia H.T. Tam, Janice S.K. Ho, Ying Wang, Vincent K.L. Lam, Heung Man Lee, Guozhi Jiang, Eric S.H. Lau, Alice P.S. Kong, Xiaodan Fan, Jean L.F. Woo, Stephen K.W. Tsui, Maggie C.Y. Ng, Wing Yee So, Juliana C.N. Chan, Ronald C. W. Ma (2013). Use of Net Reclassification Improvement (NRI) Method Confirms The Utility of Combined Genetic Risk Score to Predict Type 2 Diabetes. PLoS ONE, 8(12):e83093.
- Baojun Chen, Enhao Zheng, Xiaodan Fan, Tong Liang, Qining Wang, Kunlin Wei, and Long Wang (2013). Locomotion Mode Classification Using A Wearable Capacitive Sensing System. IEEE Transactions on Neural Systems and Rehabilitation Engineering. 21(5), 744-755.
- Weiqiang Zhou, Hong Yan, Xiaodan Fan and Quan Hao (2013). Prediction of Protein-Protein Interactions Based on Molecular Interface Features and the Support Vector Machine. Current Bioinformatics, 8(1):3-8.
- Jin Xu, Qiwei Li, Victor O. K. Li, Shuo-Yen Robert Li and Xiaodan Fan (2013). Improved short adjacent repeat identification using three evolutionary Monte Carlo schemes. International Journal of Data Mining and Bioinformatics. 8(4):462-479.
- Tong Liang, Xiaodan Fan (Corresponding Author), Qiwei Li and Shuo-yen Robert Li (2012). Detection of Dispersed Short Tandem Repeats Using Reversible Jump Markov Chain Monte Carlo. Nucleic Acids Research, 40(19):e147. (Matlab Code: Pilot RJMCMC)
- Qing Zhang, Xiaodan Fan, Yejun Wang, Mingan Sun, Samuel S. M. Sun and Dianjing Guo (2012) A Model-Based Method for Gene Dependency Measurement. PLoS ONE, 7(7): e40918.
- Qiwei Li, Xiaodan Fan (Corresponding Author), Tong Liang, and Shuo-Yen Robert Li (2011). An MCMC Algorithm for Detecting Short Adjacent Repeats Shared by Multiple Sequences. Bioinformatics, 27(13):1772-1779. (C Code: BASARD)
- Heung Man Lee, Yi Sui, Hailu Zhao, Kwong Wai Choy, Xiaodan Fan, Wing Yee So, Juliana Chung Ngor Chan and Ronald Ching Wan Ma (2011). The Effects of Uninephrectomy and Accompanied ACEI Treatment on Myocardial Gene Expression. Diabetes, 60(Supp 1):A155.
- Xiaodan Fan, Yuan Yuan, and Jun S. Liu (2010). The EM Algorithm and the Rise of Computational Biology. Statistical Science, 25(4):476-491.
- Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Xiaodan Fan, Nelson L. S. Tang, and Weichuan Yu (2010). BOOST: A Fast Approach to Detecting Gene-Gene Interactions in Genome-wide Case-Control Studies. American Journal of Human Genetics, 87(3):325-40.
- Xiaodan Fan, Saumyadipta Pyne, and Jun S. Liu (2010). Bayesian Meta-Analysis for Identifying Periodically Expressed Genes in Fission Yeast Cell Cycle. The Annals of Applied Statistics, 4(2):988-1013.
- Xiaodan Fan and Jun S. Liu (2009). A Bayesian Model for Cross-Study Differential Gene Expression Comment. Journal of the American Statistical Association, 104(488):1314-1318.
- Xiaodan Fan, Jun Zhu, Eric E. Schadt, and Jun S. Liu (2007). Statistical Power of Phylo-HMM for Evolutionarily Conserved Element Detection. BMC Bioinformatics, 8(1), 374.
- Yingfei Sun, Xiaodan Fan (Joint First Authors), and Yanda Li (2003). Identifying Splicing Sites in Eukaryotic RNA: Support Vector Machine Approach. Computers in Biology and Medicine, 33(1):17-29.
- Xiaodan Fan, Yingfei Sun, and Yanda Li (2003). Rapid Development of Real-time Control Systems in C++ Based on RTW. Journal of Tsinghua University, 43(7):895-898.
- Yingfei Sun, Xiaodan Fan, and Yanda Li (2003). Secondary Structural Characteristic of Eukaryotic Gene Splicing Sites. Journal of Tsinghua University, 43(3):393-395.
In Conferences:
- Guozhi Jiang, Claudia H. T. Tam, Andrea O. Y. Luk, Alice P. S. Kong, Wing Yee So, Juliana C. N. Chan, Ronald C. W. Ma and Xiaodan Fan (corresponding author) (2016). Variable Selection and Prediction of Clinical Outcome with Multiply-Imputed Data via Bayesian Model Averaging. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), pages 727-730, Shenzhen, China.
- Guozhi Jiang, Claudia HT Tam, Andrea O Luk, Heung Man Lee, Cadmon K.P. Lim, Xiaodan Fan, Si Lok, Ting Fung Chan, Kevin Yuk-Lap Yip, Nelson Tang, Stephen KW Tsui, Weichuan Yu, Brian Tomlinson, Yu Huang, Huiyao Lan, Cheuk-Chun Szeto, Wing Yee So, Juliana C.N. Chan, Ronald C.W. Ma (2016). Genome-Wide Association Study in Chinese Identifies New Susceptibility Loci Associated with Chronic Kidney Disease in Type 2 Diabetes. Diabetes Research and Clinical Practice, 120(Supp 1):S49-S50.
- Guozhi Jiang, Eric S. Lau, Ying Wang, Andrea O. Y. Luk, Claudia H. Tam, Janice S. Ho, Vincent K. Lam, Heung M. Lee, Xiaodan Fan, Wing-Yee So, Juliana C. N. Chan, Ronald Ching Wan Ma (2013). Development of Prediction Models under Multiple Imputation for Coronary Heart Disease in Type 2 Diabetes Mellitus. DOI: 10.5220/0004244303120315. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2013), pages 312-315, Barcelona, Spain.
- Han Li and Xiaodan Fan (corresponding author) (2013). A coupled finite mixture model for transcriptional modules discovery. The 59th World Statistics Congress, Hong Kong.
- Jin Xu, Albert Y.S. Lam, Victor O. K. Li, Qiwei Li and Xiaodan Fan (corresponding author) (2012). Short Adjacent Repeat Identification Based on Chemical Reaction Optimization. In Proceedings of IEEE Congress on Evolutionary Computation (IEEE CEC 2012), Brisbane, Australia.
- Weiqiang Zhou, Hong Yan, Xiaodan Fan, Quan Hao (2011). Prediction of Protein-protein Interactions using Alpha Shape Modeling. In 2011 International Symposium on Computational Models for Life Sciences. AIP Conference Proceedings (CMLS-11), Volume 1371, pages 244-252, Toyama City, Japan.
- Qiwei Li, Tong Liang, Xiaodan Fan (corresponding author), Chunhui Xu, Weichang Yu, and Shuo-Yen Robert Li (2010). An Automatic Procedure to Search Highly Repetitive Sequences in Genome as Fluorescence in Situ Hybridization Probes and Its Application on Brachypodium Distachyon. In Proceedings of the 2010 IEEE International Conference on Bioinformatics & Biomedicine, Dec. 2010. pages 563-568, Hong Kong.
- Jin Xu, Qiwei Li, Xiaodan Fan, Victor O. K. Li, and Shuo-Yen Robert Li (2010). An Evolutionary Monte Carlo Algorithm for Identifying Short Adjacent Repeats in Multiple Sequences. In Proceedings of the 2010 IEEE International Conference on Bioinformatics & Biomedicine, Dec. 2010. pages 643-648, Hong Kong.
- Xiaodan Fan, Xinglai Ji, Rui Jiang (2018). Guest Editorial for Special Section on the Sixth National Conference on Bioinformatics and System Biology of China. IEEE-ACM Transactions On Computational Biology and Bioinformatics, 15(4):1092-1092.
Professional Services
- Associate Editor, Journal of Computational and Graphical Statistics (2012-07 to Present)
- Editorial Board Member, Frontiers in Genetics (2015-04 to Present)
- Guest Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics (2014-11 to 2018-04)
- Referee for Journals: Journal of the American Statistical Association, Annals of Applied Statistics, Journal of Computational and Graphical Statistics, Bioinformatics, PLoS Computational Biology, Psychometrika, Technometrics, etc.
- Organizing Committee Member of Conferences: the 12th ICSA International Conference, the 4th Institute of Mathematical Statistics Asia Pacific Rim Meeting, CUHK Symposium on Statistics, etc.
- Programme Committee Member of Conferences: ICBBB, BIBE, etc.
Teaching
- STAT 3003: Survey Methods (undergraduate course)
- STAT 3210: Statistical Techniques in Life Sciences (undergraduate course)
- STAT 6040: Studies on Selected Topics II (postgraduate course, focus on modelling and computing in Bioinformatics)
- STAT 6106: Applied Bayesian Methods (postgraduate course)
My Postgraduate Students
Ph.D. Students:
- Yu, Xinrui (Major: Statistics, 2024-present )
- Luo, Yongyi (Major: Statistics, 2024-present )
- Ji, Jie (Major: Statistics, 2021-present )
- Hui, Wing Ki (Major: Medical Sciences, co-supervised with Prof. Grace Lai-Hung Wong, 2021-2024)
- Li, Dongrong (Major: Statistics, 2020-2024 )
- Zhu, Bencong (Major: Statistics, 2020-2024 )
- Liu, Ran (Major: Statistics, 2019-2023 )
- Zhang, Zhen (Major: Statistics, 2019-2023 )
- Wang, Lijun (Major: Statistics, 2018-2022 )
- Lian, Sheng (Major: Statistics, 2017-2021 )
- Mao, Shanjun (Major: Statistics, 2017-2020)
- Zhu, Yulin (Major: Statistics, 2016-2020)
- Jiang, Hangjin (Major: Statistics, 2015-2018)
- Wang, Chaojie (Major: Statistics, 2014-2018)
- Shen, Linghao (Major: Information Engineering, 2013-2017)
- Hu, Jie (Major: Statistics, 2011-2015)
- Li, Chun (Major: Statistics, 2011-2014)
- Li, Han (Major: Statistics, 2010-2014)
- Jiang, Guozhi (Major: Medical Sciences, co-supervised with Prof. Ronald C.W. Ma, 2010-2013)
- Liang, Tong (Major: Information Engineering, co-supervised with Prof. Shuo-Yen Robert Li, 2008-2013)
- Han, Shengtong (Major: Statistics, 2009-2012)
M.Phil. Students:
- Kwok, Chin Kiu (Major: Statistics, 2016-2018)
- Tang, Sheung Ho (Major: Statistics, 2014-2016)
- Chen, Zirui (Major: Statistics, 2014-2016)
- Lau, Yuk Fai (Major: Statistics, 2013-2015)
- Chan, Kwun Cheung (Major: Statistics, 2012-2014)
- Lu, Jiayi (Major: Statistics, 2011-2013)
- Fung, Ling Hiu (Major: Statistics, 2010-2012)
- Li, Qiwei (Major: Information Engineering, co-supervised with Prof. Shuo-Yen Robert Li, 2008-2010)
My Research Staff
- Shi, Jiandong (Postdoc, 2024-present )
- Li, Mengyu (Exchange PhD student from RUC, 2023-2024 )
- Fan, Yetian (Postdoc, 2020-2022 )
- Du, Jin Yang (Postdoc, 2019-2021 )
- Chen, Yingyu (Postdoc, 2018-2019 )
- Pian, Cong (Postdoc, 2017-2019 )
- Pan, Maolin (Postdoc, 2015-2015 )
- Kong, Yunchuan (Research Assistant, 2013-2015 )
Major Research Grants
- RGC-GRF Grant; Capacity: Principal Investigator
Title: Spatially Constrained Anti-Community Model Motivated by 3D Chromatin Interactions
Period: 2024 – 2027
- UGC-CRF Grant; Capacity: Co-Principal Investigator
Title: A bioinformatics platform to decode causal effects of germline alterations in oral and oropharynx cancers
Period: 2024 – 2025
- FHB-HMRF Grant; Capacity: Co-Investigator
Title: Functional, Phenotypical, and Multimodal Analysis of the Tertiary Lymphoid Structure (TLS) and TLS B Cells as Potential Novel Biomarkers and Immunotherapeutic Targets for Lung Cancer
Period: 2022 – 2025
- Hong Kong ITC-mainland MOST Joint Funding Scheme; Capacity: Co-Investigator
Title: Detection and Functional Study of Genetic Structure Variations in Familial Breast Cancer Using the Third Generation Sequencing Technology
Period: 2022 – 2024
- UGC-CRF Grant; Capacity: Co-Principal Investigator
Title: Hong Kong’s Window on the Universe: Building a Pioneering Submillimetre Astronomical Camera
Period: 2021 – 2024
- RGC-GRF Grant; Capacity: Principal Investigator
Title: Consistent Model-free Ultra-high Dimensional Variable Selection for Binary Response
Period: 2020 – 2022
- RGC-GRF Grant; Capacity: Principal Investigator
Title: Detection of Differentially Methylated Regions Based on Array or Sequencing Data
Period: 2018 – 2020
- RGC-Theme-based Research Scheme; Capacity: Co-Principal Investigator
Title: Gastric Cancer Genomics and Beyond – Moving from Patient Samples to 3D Organoid Cultures for Integrative Genomics Analysis, Drug Sensitivity Assays, Cell Biological Studies and Animal Models
Period: 2016 – 2022
- RGC-GRF Grant; Capacity: Principal Investigator
Title: Bayesian Integrative Clustering for Combining Vectorial Data and Network Data
Period: 2016 – 2018
- RGC-Theme-based Research Scheme; Capacity: Co-Investigator
Title: An integrated trans-omics approach to diabetic cardio-renal complications: from novel discoveries to personalized medicine
Period: 2014 – 2018
- RGC-GRF Grant; Capacity: Principal Investigator
Title: Bayesian Model-based Clustering of the Conformational Space of Biomolecules
Period: 2013 – 2016
- UGC-AoE Grant; Capacity: Co-Investigator
Title: Institute of Network Coding
Period: 2010 – 2017
- RGC-GRF Grant; Capacity: Principal Investigator
Title: Bayesian Data Integration Approach for Cell-Cycle Gene Network Inference
Period: 2010 – 2012
- ITC-ITF; Capacity: Co-Investigator
Title: Developing a Platform to Deliver Personalized Healthcare Using Genotype-based Risk Algorithms to Predict Diabetes and Diabetic Complications
Period: 2010 – 2012