Methodology Work in Statistics and Bioinformatics

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.

Biological Collaboration Work

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.

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 SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi, R., Kabbe R, Park PJ, Eils R, Schlesner M, PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, 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 JY#, Wu LJ, Wang XY, Ma JQ, Zhang Z, Shi Y, Ma LJ, Zhang S, Xi, R., Cao Y, Zhou J, Fan J*, Zhang XM*, Gao Q.* (2019) Activated and exhausted MAIT cells foster disease progression and indicate poor outcome in hepatocellular carcinoma. Clinical Cancer Research. 2019 Jun 1;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 YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi, R., Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. (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.