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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.
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