Wang, C., Chen, Z., and Xi, R.* (2025) Feature screening for clustering analysis of count data with an application to single-cell RNA-sequencing, Annals of Applied Statistics, In Press

Tang, J., Chen, Z., Qian, K., Huang, S., He, Y., Yin, S., He, X., Ye, B., Zhuang, Y., Meng, H.*, Xi, J.* and Xi, R.* (2025) An interpretable multi-modal dimension reduction framework SpaHDmap enhances resolution in spatial transcriptomics, Nature Cell Biology, In Press

Huang, Y., Wang, C., Tang, J., Wu, W.* and Xi, R.* (2025) A Generic Family of Graphical Models: Diversity, Efficiency, and Heterogeneity, Proceedings of the Forty-second International Conference on Machine Learning (ICML 2025)

Zhao, Y., Luquette, L. J., Veit, A. D., Wang, X., Xi, R., Viswanadham, V. V., and Park, P. J.* (2025) High-resolution detection of copy number alterations in single cells with HiScanner, Nature Communications, 16(1), 5477

Chen, X., Ran, Q., Tang, J., Chen, Z., Huang, S., Shi, X.* and Xi, R.* (2025) Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics, Bioinformatics, 41(4), btaf131

Chen, Z., Wang, C., and Xi, R.* (2025) Protocol for directly selecting cell type marker genes for single-cell clustering analyses by Festem, STAR Protocols, 6(1), 103514

Wang, X., Jin, Z., Shi, Y., and Xi, R.* (2025) Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA, Cell Reports Methods, 5(1)

Chen, Z., Wang, C., Huang, S., Shi, Y., and Xi, R.* (2024) Directly selecting cell-type marker genes for single-cell clustering analyses, Cell Reports Methods, 4(7)

Tang, J., Wang, C., Xiao, F., and Xi, R.* (2024) Single-cell gene regulatory network analysis for mixed cell populations, Quantitative Biology

Zhang, T., Jia, H., Song, T., Lv, L., Gulhan, D. C., Wang, H., Guo, W., Xi, R., Guo, H., and Shen, N.* (2023) De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data, Genome Medicine, 15(1), 115

Xia, Y.#, Jin, Z.#, Zhang, C.#, Ouyang, L.#, Dong, Y., Li, J., Guo, L., Jing, B., Shi, Y., Miao, S. and Xi, R.* (2023) TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing, Nature Communications, 5935

Shi, Y.#, Jing, B.# and Xi, R.* (2023) Comprehensive analysis of neoantigens derived from structural variation across whole genomes from 2528 tumors, Genome Biology, 24, 169

Xiao, F.#, Tang, J.#, Fang, H. and Xi, R.* (2022) Estimating graphical models for count data with applications to single-cell gene network, NeurIPS 2022

Jin, Z., Huang, W., Shen, N., Li, J., Wang, X., Dong, J., Park, P. and Xi, R.* (2022) Single cell gene fusion detection by scFusion, Nature Communications, 13, 1084.

Liu, X., Yang, X., Ouyang, L., Guo, G., Su, J., Xi, R.*, Yuan, K.* and Yuan, F.* (2022) Protein Language Model Predicts Mutation Pathogenicity and Clinical Prognosis, NeurIPS 2022 Workshop on Learning Meaningful Representations of Life

Wu, L., Wang, H., Xia, Y. and Xi, R.* (2020) CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome, Bioinformatics, 36(12), 3890-3891.

Corts-Ciriano, I., Lee, J., Xi, R., Jain, D., Jung, Y.L., Yang, L., Gordenin, D., Klimczak, L.J., Zhang, C.Z., Pellman, D.S., PCAWG Structural Variation Working Group, Park, P.J.* and PCAWG Consortium (2020) Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing, Nature Genetics, 52(3):331-341.

Chen, C., Wu, C., Wu, L. Wang, X., Deng, M. and Xi, R.* (2020) scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition, Bioinformatics, 36(10), 3156-3161.

Xia,Y.#, Liu, Y.#, Deng, M. and Xi, R.* (2019) Detecting virus integration sites based on multiple related sequencing data by VirTect, BMC Medical Genomics, 12(1), 19.

Chen, C., Xi, R.* and Lin, N. (2018) Community detection by L0-penalized graph Laplacian, Electronic Journal of Statistics, 12(1), 1842-1866.

Xia, Y., Liu, Y., Deng, M. and Xi, R.* (2017) SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms, Bioinformatics, 33(21):3348-3354.

Yuan, H., Xi, R.*, Chen, C. and Deng, M.* (2017) Differential network analysis via lasso penalized D-trace loss, Biometrika, 104 (4): 755-770.

Xia, Y., Liu Y., Deng, M. and Xi, R.* (2017) Pysim-sv: a package for simulating structural variation data with GC-biases, BMC Bioinformatics, 18(Suppl 3):53.

Xi, R.*, Lee, S., Xia, Y., Kim, T. and Park, P. J.* (2016) Copy number analysis of whole genome data using BIC-seq2 and its application to detection of cancer susceptibility variants, Nucleic Acids Research, 44(13):6274-6286.

Nam, J.Y., Kim, N.K., Kim, S.C., Joung, J.G., Xi, R., Lee, S. Park, P.J.* and Park, W.Y.* (2015) Evaluation of somatic copy number estimation tools for whole-exome sequencing data, Briefings in Bioinformatics, bbv055.

Xi, R.*, Li, Y. and Hu, Y. (2015) Bayesian quantile regression based on the empirical likelihood with spike and slab priors, Bayesian Analysis, 11(3): 821-855.

Xi, R. and Lin, N.* (2015) Direct regression modelling of high-order moments in big data, Statistics and Its Interface, 9(4):445-452.

Yang, L., Luquette, L.J., , Gehlenborg, N., Xi, R., Haseley, P.S., Hsieh, C.H., Zhang, C., Ren, X., Protopopov, A., Chin, L., Kucherlapati, R., Lee, C. and Park, P.J.* (2013) Diverse mechanisms of somatic structural variations in human cancer genomes, Cell, 153(4):919-929.

Xi, R., Lin, N., Chen, Y.* and Kim, Y. (2012) Compression and aggregation of Bayesian estimates for data intensive computing, Knowledge and Information Systems, 33(1):191-212.

Xi, R., Lee, S. and Park, P.J.* (2012) A Survey of copy number variation detection tools based on high-throughput sequencing data, Current Protocols in Human Genetics, Chapter 7:Unit7.19, John Wiley & Sons, Inc.

Xi, R., Hadjipanayis, A.G., Luquette, L.J., Kim, T.M., Lee, E., Zhang, J.H., Johnson, M.D., Muzny, D.M., Wheeler, D.A., Kucherlapati, R., and Park, P.J.* (2011) Copy number alteration detection in sequencing data using the Bayesian information criterion, Proceedings of the National Academy of Sciences, USA, 108(46):E1128-1136.

Xi, R., Kim, T. M. and Park, P.J.* (2010) Detecting structural variation using next-generation sequencing, Briefings in Functional Genomics, 9(5-6):405-415.

Lin, N.* and Xi, R. (2010) Aggregated estimating equation estimation, Statistics and Its Interface, 4:73-84.

Kim, T.M., Luquette, L.J., Xi, R. and Park, P.J.* (2010) rSW-seq: algorithm for detection of copy number alterations in deep sequencing data, BMC Bioinformatics, 11:423.

Li, Q., Xi, R.* and Lin, N.* (2010) Bayesian regularized quantile regression, Bayesian Analysis, 5:533-556.

Lin, N.* and Xi, R. (2010) Fast surrogates of U-statistics, Computational Statistics and Data Analysis, 54:16-24.

Xi, R., Lin, N., and Chen, Y.* (2009) Compression and aggregation for logistic regression analysis in data cubes, IEEE Transactions on Knowledge and Data Engineering, 21(4):479-492.

Huang, S., Ouyang, L., Tang, J., Qian, K., Chen, X., Xu, Z., Ming, J.* and Xi, R.* (2024) Spatial transcriptomics: a new frontier in cancer research, Clinical Cancer Bulletin, 3(1), 13

Han, D. J., Kim, S., Lee, S. Y., …, Xi, R., and Kim, J.* (2024) Evolutionary dependency of cancer mutations in gene pairs inferred by nonsynonymous-synonymous mutation ratios, Genome Medicine, 16(1), 103

Rao, D., Li, J., Zhang, M., Huang, S., …, Jia, F.*, Zhang, X.*, Xi, R.*, and Gao, Q.* (2024) Multi-model analysis of gallbladder cancer reveals the role of OxLDL-absorbing neutrophils in promoting liver invasion, Experimental Hematology & Oncology, 13(1), 58

Xu, Z., Huang, S., Song, Y., Xu, C., Yan, H., Linkun, O., Lv, B., Yuan, F., Xu, B., Wang, H., Xi, R.* and Yu, J.* (2024) Identification of eight genes associated with recurrent patellar dislocation, iScience, 27(5)

Yin, S.#, Yu, Y.#, Wu, N.#, Zhuo, M., …, Xi, R., Ye, B.*, Jiang, L.* and Xi, J. J.* (2024) Patient-derived tumor-like cell clusters for personalized chemo- and immunotherapies in non-small cell lung cancer, Cell Stem Cell, 31(5), 717–733

Kong, D.#, Huang, S.#, Miao, X.#, Li, J., Wu, Z., Shi, Y., Liu, H., Jiang, Y., Yu, X., Xie, M., Shen, Z., Cai, J., Xi, R.* and Gong, W.* (2023) The dynamic cellular landscape of grafts with acute rejection after heart transplantation, Journal of Heart and Lung Transplant, 42(2):160-172.

Lee, S.#, Wang, H.#, Cho, H.J., Xi, R.* and Kim, T.M.* (2022) The shaping of cancer genomes with the regional impact of mutation processes, Experimental & Molecular Medicine, 54, 1049–1060

Song, G.#, Shi, Y.#, Meng, L.#, Ma, J.#, Huang, S., Zhang, J., Wu, Y., Li, J., Yang, S., Rao, D., Cheng, Y., Lin, J., Ji, S., Liu, Y., Shan, J., Wang, X., Shu, Z., Ke, A., Wang, X., Cao, Y., Yuan, J., Jian, Z., Jia, F.*, Zhang, X.*, Xi, R.*, Gao, Q.* (2022) Single-cell transcriptomic analysis suggests two molecularly subtypes of intrahepatic cholangiocarcinoma, Nature Communications, 13, 1642.

Wu, Y., Yang, S., Ma, J., Chen, Z., …, Xi, R., Bai, F., Zhou, J., Fan, J., Zhang, X.*, Gao, Q.* (2022) Spatiotemporal immune landscape of colorectal cancer liver metastasis at single-cell level, Cancer Discovery, 12(1), 134-153.

Zhao, J.#, Wu, L.#, Li, W., Wang, Y., Zheng, H., Sun, T., Zhang, H., Xi, R., Liu, W.*, Sun, Z.* (2021) Genomics landscape of 185 Streptococcus thermophilus and identification of fermentation biomarkers, Food Research International, 150 Part A:110711.

Song, G.#; Shi, Y.#; Zhang, M.#; Goswami, Sh.#; Afridi, S., Meng, L., Ma, J., Chen, Y., Lin, Y., Zhang, J., Liu, Y., Jin, Z., Yang, S., Rao, D., Zhang, S., Ke, A., Wang, X., Cao, Y., Zhou, J., Fan, J., Zhang, X.*, Xi, R.*, Gao, Q.* (2020) Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression, Cell Discovery, 6(90).

Cui, Y.#, Chen, H.#, Xi, R.#, Cui, H.#, Zhao, Y.#, Xu, E.#, Yan, T., Lu, X., Huang, F., Kong, P., Li, Y., Zhu, X., Wang, J., Zhu, W., Wang, J., Ma, Y., Zhou, Y., Guo, S., Zhang, L., Liu, Y., Wang, B., Xi, Y., Sun, R., Yu, X., Zhai, Y., Wang, F., Yang, J., Wang, B., Cheng, C., Liu, J., Song, B., Li, H., Wang, Y., Zhang, Y., Cheng, X., Zhan, Q.*, Li, Y.* and Liu, Z.* (2020) Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma, Cell Research, 30(10):902-913.

Yin, S.#, Xi, R.#, Wu, A.#, Wang, S.#, Li, Y., Wang, C., Tang, L., Xia, Y., Yang, D., Li, J., Ye, B., Yu, Y., Wang, J., Zhang, H., Ren, F., Zhang, Y., Shen, D., Wang, L., Ying, X., Li, Z., Bu, Z., Ji, Xin, Gao, X., Jia, Y., Jia, Z., Li, N., Li, Z., Ji, J.* and Xi, J.Z.* (2020) Patient-derived tumor-like cell clusters for drug testing in cancer therapy, Science Translational Medicine, 12(549), eaaz1723.

Sieverling, L., Hong, C., Koser, S. D., Ginsbach, P, Kleinheinz, K., Hutter, B., Braun, D. M., Cortés-Ciriano, I., Xi, R., Kabbe, R., Park, P. J., Eils, R., Schlesner, M., PCAWG-Structural Variation Working Group, Brors, B., Rippe, K., Jones, D. T. W., Feuerbach, L.#, PCAWG Consortium (2020) Genomic footprints of activated telomere maintenance mechanisms in cancer, Nature Communications, 11(1):733.

Zhang, Y.#, Yang, L.#, Kucherlapati, M., Hadjipanayis, A., Pantazi, A., Bristow, C. A., Lee, E. A., Mahadeshwar, H. S., Tang, J., Zhang, J., Seth, S., Lee, S., Ren, X., Song, X., Sun, H., Seidman, J., Luquette, L. J., Xi, R., Chin, L., Protopopov, A., Park, P. J., Kucherlapati, R., Creighton, C. J.* (2019) Global impact of somatic structural variation on the DNA methylome of human cancers, Genome Biology, 20(1):209.

Duan, M.#, Goswami, S.#, Shi, J. Y.#, Wu, L. J., Wang, X. Y., Ma, J. Q., Zhang, Z., Shi, Y., Ma, L. J., Zhang, S., Xi, R., Cao, Y., Zhou, J., Fan, J.*, Zhang, X. M.*, Gao, Q.* (2019) Activated and exhausted MAIT cells foster disease progression and indicate poor outcome in hepatocellular carcinoma, Clinical Cancer Research, 25(11):3304-3316.

Dong, L. Q.#, Shi, Y.#, Ma, L.#, Gao, D., Yang, L., Wang, X., Zhang, S., Ding, Z., Zhang, Z., Wang, Z., Liu, L., Zheng, B., Yuan, K., Ke, A., Zhou, J., Fan, J.*, Xi, R.* and Gao, Q.* (2018) Spatial and temporal clonal evolution of intrahepatic cholangiocarcinoma, Journal of Hepatology, 69(1), 89-98.

Duan, M., Hao, J., Cui, S., Worthley, D., Zhang, S., Wang, Z., Shi, J., Liu, L., Wang, X., Ke, A., Cao, Y., Xi, R., Zhang, X., Zhou, J., Fan, J.*, Li, C.* and Gao, Q.* (2018) Diverse modes of clonal evolution in HBV-related hepatocellular carcinoma revealed by single-cell genome sequencing, Cell Research, 28(3), 359-373.

Chang, J.#, Tan, W.#, Ling, Z.#, Xi, R.#, Shao, M.#, Chen, M., Luo, Y., Zhao, Y., Liu, Y., Huang, X., Xia, Y., Hu, J., Parker, J., Marron, D., Cui, Q., Peng, L., Chu, J., Li, H., Du, Z., Han, Y., Tan, W., Liu, Z., Zhan, Q., Li, Y., Mao, W.*, Wu, C.* and Lin, D. (2017) Comprehensive analysis of esophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and novel genomic alterations, Nature Communications, 8:15290.

Gao, Q., Wang, Z., Duan, M., Lin, Y., Zhou, X., Worthley, D. L., Xi, R., Shi, Y.* and Fan, J.* (2017) Cell culture system for analysis of genetic heterogeneity within hepatocellular carcinomas and response to pharmacologic agents, Gastroenterology, 152(1):232-242.

Zhang, Y., Kwok-Shing Ng, P., Kucherlapati, M., Chen, F., Liu, Y., Tsang, Y. H., de Velasco, G., Jeong, K. J., Akbani, R., Hadjipanayis, A., Pantazi, A., Bristow, C. A., Lee, E., Mahadeshwar, H. S., Tang, J., Zhang, J., Yang, L., Seth, S., Lee, S., Ren, X., Song, X., Sun, H, Seidman, J., Luquette, L. J., Xi, R., Chin, L., Protopopov, A., Westbrook, T. F., Shelley, C. S., Choueiri, T. K., Ittmann, M., Van Waes, C., Weinstein, J. N., Liang, H., Henske, E. P., Godwin, A. K., Park, P. J., Kucherlapati, R., Scott, K. L., Mills, G. B., Kwiatkowski, D. J., Creighton, C. J. (2017) A pan-cancer proteogenomic atlas of PI3K/AKT/mTOR pathway alterations, Cancer Cell, 31(6):820-832.e3.

Ping, Z., Xia, Y., Shen, T., Parekh, V., Siegal, G. P., Eltoum, I. E., He, J., Chen, D., Deng, M., Xi, R., and Shen, D.* (2016) A microscopic landscape of the invasive breast cancer genome, Scientific Reports, 6, 27545.

Cancer Genome Atlas Research Network (Including Xi, R.) (2015) Comprehensive molecular characterization of cutaneous melanoma, Cell, 161(7):1681-1696.

Shi, J.#, Xing, Q.#, Duan, M.#, Wang, Z., Yang, L., Zhao, Y., Wang, X., Liu, Y., Deng, M., Ding, Z., Ke, A., Zhou, J., Fan, J., Cao, Y., Wang, J.*, Xi, R.*, and Gao, Q.* (2015) Inferring the progression of multifocal liver cancer from spatial and temporal genomic heterogeneity, Oncotarget, 7(3):2867-2877.

De Los Angeles, A.#, Ferrari, F.#, Xi, R., Fujiwara, Y., Benvenisty, N., Deng, H., Hochedlinger, K., Jaenisch, R., Lee, S., Leitch, H. G., Lensch, M. W., Lujan, E., Pei, D., Rossant, J., Wernig, M., Park, P. J. and Daley, G. Q.* (2015) Hallmarks of pluripotency, Nature, 525(7570):469-478.

Kim, T. M., Xi, R., Luquette, L. J., Park, R. W., Johnson, M. D. and Park, P. J.* (2013) Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes, Genome Research, 23(2):217-227.

Cancer Genome Atlas Research Network (including Xi, R.) (2012) Comprehensive molecular characterization of human colon and rectal cancer, Nature, 487:330-337.

Tan, X., Hu, L., Luquette, L. J., Gao, G., Liu, Y., Qu, H., Xi, R., Lu, Z. J., Park, P. J.* and Elledge, S. J.* (2012) Systematic identification of synergistic drug pairs targeting HIV, Nature Biotechnology, 30:1125-1130

Cancer Genome Atlas Research Network (Including Xi, R.) (2012) Comprehensive genomic characterization of squamous cell lung cancers, Nature, 489(7417):519-25.

Kharchenko, P. V., Alekseyenko, A. A., Schwartz, Y. B., Minoda, A., Riddle, N. C., Ernst, J., Sabo, P. J., Larschan, E., Gorchakov, A. A., Gu, T., Linder-Basso, D., Plachetka, A., Shanower, G., Tolstorukov, M. Y., Luquette, L. J., Xi, R., Jung, Y. L., Park, R. W., Bishop, E. P., Canfield, T. P., Sandstrom, R., Thurman, R. E., MacAlpine, D. M., Stamatoyannopoulos, J. A., Kellis, M., Elgin, S. C. R., Kuroda, M. I., Pirrotta, V., Karpen, G. H. and Park, P. J.* (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster, Nature, 471(7339):480-485.

Kharchenko, P. V., Xi, R., and Park, P. J.* (2011) Evidence for dosage compensation between the X and autosomes in mammals, Nature Genetics, 43(12):1167-1169.

Gan, S., Xi, R., Yang, J., and Zheng, R. (2026) Generic properties of vector fields identical on a compact set and codimension one partially hyperbolic dynamics, Journal of Differential Equations, 453(Part 3), 113870

Xi, R., Lee, S., and Park, P.* (2012) A survey of copy number variation detection tools based on high-throughput sequencing data, Current Protocols in Human Genetics, Chapter 7: Unit 7.19, John Wiley & Sons, Inc.