Biological Statistics and Computational Genomics

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Selected Publications

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+) Tracking the evolution history of intrahepatic cholangiocarcinoma by multiregional whole exome sequencing, Journal of Hepatology, In Press.

Chen, C., Xi, R. * and Lin, N. (2018) Community detection by L0-penalized graph Laplacian. Electronic Journal of Statistics, 12:1867–1900.
/Code

Xia, Y., Liu, Y., Deng, M. and Xi, R.* (2017) SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms, Bioinformatics, 1;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.

Chang, J.#, Tan, W.#, Ling, Z.#, Xi, R.#, Shao, M. #, …, 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.

Xi, R.*, Lee, S., Xia, Y., Kim, T. and Park, P.*  (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):6274-86./package

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., Daley, G.Q.* (2015) Hallmarks of pluripotency, Nature, 525 (7570), 469-478.

The Cancer Genome Atlas Research Network (Including Xi, R.) (2015) Comprehensive Molecular Characterization of Cutaneous Melanoma. Cell, 161(7):1681-96.
/ShatterSeek Package

Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh C, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ.* (2013) Diverse mechanisms of somatic structural variations in human cancer genomes. Cell, 153:919-29, 2013.


Kim, T.M., Xi R., Luquette L.J, Park R.W., Johnson M.D., Park P.J.* (2013) Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Research, 23(2):217-27.

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.* (2011). Copy number alteration detection in sequencing data using the Bayesian information criterion, Proceedings of the National Academy of Sciences, USA, 108(46):E1128-36. /Package

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

Kharchenko, P.V., Xi, R.,and Park, P.* (2011). Evidence for dosage compensation between the X and autosomes in mammals, Nature Genetics, 43(12):1167-9.

Lin, N. and Xi, R. (2010). Aggregated Estimating Equation Estimation, Statistics and Its Interface 4:73-84. /Commented By Hajirahimova and Aliyeva (2015) and Wang et al. (2015)

Li, Q., Xi, R.* and Lin, N.* (2010). Bayesian Regularized Quantile Regression, Bayesian Analysis 5, 533-556. /Code

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.


Full Publication List

Statistics and Bioinformatics Methodology


Xia,Y., Liu, Y., Deng, M. and Xi, R.* (2018+) Detecting virus integration sites based on multiple related sequencing data by VirTect, BMC Genomics, Accepted.


Chen, C., Xi, R. * and Lin, N. (2018) Community detection by L0-penalized graph Laplacian. Electronic Journal of Statistics, 12:1867–1900/Code

Xia, Y., Liu, Y., Deng, M. and Xi, R.* (2017) SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms, Bioinformatics, 1;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, BCM Bioinformatics, 18(Suppl 3):53.

Xi, R.*, Li, Y. and Hu, Y. (2016) Bayesian Quantile Regression Based on the Empirical Likelihood with spike and slab priors, Bayesian Analysis, 11(3): 821-855. /code for multiple quantile regresion/R Package

Xi, R.
*, Lee, S., Xia, Y., Kim, T. and Park, P.*  (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):6274-86./package

Xi, R. and Lin, N.* (2016) Direct Regression Modelling of High-order Moments in Big Data, Statistics and Its Interface,  9(4), 445-452.

Xi, R., Lin, N., Chen, Y.* and Kim (2012), Y. Compression and Aggregation of Bayesian Estimates for Data Intensive Computing; Knowledge and Information Systems, 33(1), 191-212.

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.* (2011). Copy number alteration detection in sequencing data using the Bayesian information criterion, Proceedings of the National Academy of Sciences, USA, 108(46):E1128-36. /Package

Lin, N. and Xi, R. (2010). Aggregated Estimating Equation Estimation, Statistics and Its Interface 4:73-84. /Commented By Hajirahimova and Aliyeva (2015) and Wang et al. (2015)

Xi, R., Kim, T. M. and Park, P.J.* (2010) Detecting Structural Variation Using Next-generation Sequencing, Briefings in Functional Genomics, 9(5-6):405-15.

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. /Code

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.


Biology Collaboration Work


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+) Tracking the evolution history of intrahepatic cholangiocarcinoma by multiregional whole exome sequencing, Journal of Hepatology, In Press.

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, pages 359–373.

Chang, J.#, Tan, W.#, Ling, Z.#, Xi, R.#, Shao, M. #, …, 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. C.#, Duan, M.,# Lin, Y. H., Zhou, X. Y., Worthley, D. L., ...  Xi R., Shi YY*, Fan J.* (2017). Cell Culture System for Analysis of Genetic Heterogeneity Within Hepatocellular Carcinomas and Response to Pharmacologic Agents. Gastroenterology, 152 (1), 232-242. e4.

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.

Shi, J.#, Xing, Q.#, Duan, M.#, Wang, Z., Yang, L., Zhao, Y., Wang, Xiao, Liu, Y., Deng, M., Ding, Z., Ke, A., Zhou, J., Fan, J., Cao, Y., Wang, J.,*, Xi, R.,*, and Gao, Q.* (2016) Inferring the progression of multifocal liver cancer from spatial and temporal genomic heterogeneity, Oncotarget, 7(3):2867-77.

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., Daley, G.Q.* (2015) Hallmarks of pluripotency, Nature, 525 (7570), 469-478.

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

The Cancer Genome Atlas Research Network (Including Xi, R.) (2015) Comprehensive Molecular Characterization of Cutaneous Melanoma. Cell, 161(7):1681-96.
/ShatterSeek Package

The Cancer Genome Atlas Research Network (Including Xi, R.) (2014), Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513:202-209

Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh C, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ.* (2013) Diverse mechanisms of somatic structural variations in human cancer genomes. Cell, 153:919-29, 2013.


Kim, T.M., Xi R., Luquette L.J, Park R.W., Johnson M.D., Park P.J.* (2013) Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Research, 23(2):217-27.

Xi, R., Lee, S., Park, P. *(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.

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

The Cancer Genome Atlas Research Network (Including Xi, R.) (2012).  Comprehensive genomic characterization of squamous cell lung cancers, Nature, 489:519-525.

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

Kharchenko, P.V., Xi, R.,and Park, P.* (2011). Evidence for dosage compensation between the X and autosomes in mammals, Nature Genetics, 43(12):1167-9.

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.* (2011). Comprehensive analysis of the chromatin landscape in Drosophila melanogaster, Nature 471(7339):480-5.