Publications

Tumor Clonal Dynamics

Evolving copy number gains promote tumor expansion and bolster mutational diversification
Z Wang, Y Xia, L Mills, A.N. Nikolakopoulos, N Maeser, JM Sheltzer, R. Sun
Nature Communications, 15, 2025, Mar. 2024
☕DOI: 10.1038/s41467-024-46414-5

Elements and Evolutionary Determinants of Genomic Divergence Between Paired Primary and Metastatic Tumors
R. Sun and A.N. Nikolakopoulos
PLoS Computational Biology, 17(3):e1008838, Mar. 2021
☕DOI: 10.1371/journal.pcbi.1008838

Characterizing the ecological and evolutionary dynamics of cancer
N. Zahir, R. Sun, D. Gallahan, R.A. Gatenby, and C. Curtis
Nature Genetics, vol. 52, no. 8, pp. 759–767, Jul. 2020
☕DOI: 10.1038/s41588-020-0668-4

Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy
J.L. Caswell-Jin, K. McNamara, J.G. Reiter, R. Sun, Z. Hu, Z. Ma, J. Ding, C.J. Suarez, S. Tilk, A. Raghavendra, V. Forte, S.F. Chin, H. Bardwell, E. Provenzano, C. Caldas, J. Lang, R. West, D. Tripathy, M.F. Press, and C. Curtis
Nature Communications, vol. 10, no. 1, pp. 657, Dec. 2019
☕DOI: 10.1038/s41467-019-08593-4

Quantitative evidence for early metastatic seeding in colorectal cancer
Z. Hu, J. Ding, Z. Ma, R. Sun, J.A. Seoane, J. Scott Shaffer, C.J. Suarez, A.S. Berghoff, C. Cremolini, A. Falcone, F. Loupakis, P. Birner, M. Preusser, H.J. Lenz, and C. Curtis
Nature Genetics, vol. 51, no. 7, pp. 1113–1122, Jul. 2019
☕DOI: 10.1038/s41588-019-0423-x

Big Bang Tumor Growth and Clonal Evolution
R. Sun, Z. Hu, and C. Curtis
Cold Spring Harbor Perspectives in Medicine, pp. a028381, Jul. 2017
☕DOI: 10.1101/cshperspect.a028381

Between-region genetic divergence reflects the mode and tempo of tumor evolution
R. Sun, Z. Hu, A. Sottoriva, T.A. Graham, A. Harpak, Z. Ma, J.M. Fischer, D. Shibata, and C. Curtis
Nature Genetics, vol. 49, no. 7, pp. 1015–1024, Jun. 2017
☕DOI: 10.1038/ng.3891

A population genetics perspective on the determinants of intra-tumor heterogeneity
Z. Hu, R. Sun, and C. Curtis
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, vol. 1867, no. 2, pp. 109–126, Apr. 2017
☕DOI: 10.1016/j.bbcan.2017.03.001

Analytics in Cancer Genomics

Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors
J. George, V. Walter, M. Peifer, L.B. Alexandrov, D. Seidel, F. Leenders, L. Maas, C. M{ü}ller, I. Dahmen, T.M. Delhomme, M. Ardin, N. Leblay, G. Byrnes, R. Sun, A. De Reynies, A. McLeer-Florin, G. Bosco, F. Malchers, R. Menon, J. Altm{ü}ller, C. Becker, et. al., and R.K. Thomas
Nature Communications, vol. 9, no. 1, pp. 1048, Dec. 2018
☕DOI: 10.1038/s41467-018-03099-x

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element
S.W. Cho, J. Xu, R. Sun, M.R. Mumbach, A.C. Carter, Y.G. Chen, K.E. Yost, J. Kim, J. He, S.A. Nevins, S.F. Chin, C. Caldas, S.J. Liu, M.A. Horlbeck, D.A. Lim, J.S. Weissman, C. Curtis, and H.Y. Chang
Cell, May 2018
☕DOI: 10.1016/j.cell.2018.03.068

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data
L. Fernandez-Cuesta, R. Sun, R. Menon, J. George, S. Lorenz, L. Meza-Zepeda, M. Peifer, et. al., S.A. Haas, and R.K. Thomas
Genome Biology, vol. 16, no. 1, pp. 7, Jan. 2015
☕DOI: 10.1186/s13059-014-0558-0

Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids
L. Fernandez-Cuesta, M. Peifer, X. Lu, R. Sun, L. Ozretic, D. Seidel, T. Zander, F. Leenders, J. George, C. M{ü}ller, I. Dahmen, B. Pinther, G. Bosco, K. Konrad, J. Altm{ü}ller, P. N{ü}rnberg, V. Achter, U. Lang, P.M. Schneider, M. Bogus, et. al., and R.K. Thomas
Nature Communications, vol. 5, pp. 3518, Jan. 2014
☕DOI: 10.1038/ncomms4518

CD74-NRG1 fusions in lung adenocarcinoma
L. Fernandez-Cuesta, D. Plenker, H. Osada, R. Sun, R. Menon, F. Leenders, S. Ortiz-Cuaran, M. Peifer, M. Bos, et. al., and R.K. Thomas
Cancer Discovery, vol. 4, pp. 415–422, Jan. 2014
☕DOI: 10.1158/2159-8290.CD-13-0633

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.
M. Peifer, L. Fern{á}ndez-Cuesta, M. Sos, J. George, D. Seidel, L. Kasper, D. Plenker, F. Leenders, R. Sun, T. Zander, R. Menon, M. Koker, I. Dahmen, C. M{ü}ller, V. Di Cerbo, H.U. Schildhaus, J. Altm{ü}ller, I. Baessmann, C. Becker, B. de Wilde, et. al., S. Haas, and R. Thomas
Nature genetics, vol. 44, no. 10, pp. 1104–1110, Oct. 2012
☕DOI: doi: 10.1038/ng.2396

Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours.
R. Sun, X. Fu, Y. Li, Y. Xie, and Y. Mao
BMC genomics, vol. 10, no. 1, pp. 93, Feb. 2009
☕DOI: doi: 10.1186/1471-2164-10-93

Simultaneously detection of genomic and expression alterations in prostate cancer using cDNA microarray.
M. Jiang, M. Li, X. Fu, Y. Huang, H. Qian, R. Sun, Y. Mao, Y. Xie, and Y. Li
The Prostate, vol. 68, no. 14, pp. 1496–1509, Oct. 2008
☕DOI: doi: 10.1002/pros.20756

Algorithms for genomic sequence analysis

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
R. Sun, M. Love, T. Zemojtel, A.K. Emde, H.R. Chung, M. Vingron, and S. Haas
Bioinformatics (Oxford, England), vol. 28, no. 7, pp. 1024–1025, Apr. 2012
☕DOI: doi: 10.1093/bioinformatics/bts064

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
A.K. Emde, M. Schulz, D. Weese, R. Sun, M. Vingron, V. Kalscheuer, S. Haas, and K. Reinert
Bioinformatics, vol. 28, no. 5, pp. 619–627, Mar. 2012
☕DOI: doi: 10.1093/bioinformatics/bts019

Modeling read counts for CNV detection in exome sequencing data.
M. Love, A. My{š}i{č}kov{á}, R. Sun, V. Kalscheuer, M. Vingron, and S. Haas
Statistical applications in genetics and molecular biology, vol. 10, no. 1, Nov. 2011
☕DOI: doi: 10.2202/1544-6115.1732