scholarly_work.md

layout	page
title	Publications

[//]:# Selected Publications [//]:# ---

Tumor Clonal Dynamics

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

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

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

{:.paper} Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy{:.papertitle}
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{:.authors}
Nature Communications, vol. 10, no. 1, pp. 657, Dec. 2019{:.journal}
☕DOI: 10.1038/s41467-019-08593-4{:.doi}

{:.paper} Quantitative evidence for early metastatic seeding in colorectal cancer{:.papertitle}
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{:.authors}
Nature Genetics, vol. 51, no. 7, pp. 1113--1122, Jul. 2019{:.journal}
☕DOI: 10.1038/s41588-019-0423-x{:.doi}

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

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

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

Analytics in Cancer Genomics

{:.paper} Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors{:.papertitle}
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{:.authors}
Nature Communications, vol. 9, no. 1, pp. 1048, Dec. 2018{:.journal}
☕DOI: 10.1038/s41467-018-03099-x{:.doi}

{:.paper} Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element{:.papertitle}
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{:.authors}
Cell, May 2018{:.journal}
☕DOI: 10.1016/j.cell.2018.03.068{:.doi}

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data{:.papertitle}
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{:.authors}
Genome Biology, vol. 16, no. 1, pp. 7, Jan. 2015{:.journal}
☕DOI: 10.1186/s13059-014-0558-0{:.doi}

{:.paper} Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids{:.papertitle}
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{:.authors}
Nature Communications, vol. 5, pp. 3518, Jan. 2014{:.journal}
☕DOI: 10.1038/ncomms4518{:.doi}

{:.paper} CD74-NRG1 fusions in lung adenocarcinoma{:.papertitle}
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{:.authors}
Cancer Discovery, vol. 4, pp. 415--422, Jan. 2014{:.journal}
☕DOI: 10.1158/2159-8290.CD-13-0633{:.doi}

{:.paper} Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.{:.papertitle}
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{:.authors}
Nature genetics, vol. 44, no. 10, pp. 1104--1110, Oct. 2012{:.journal}
☕DOI: [doi: 10.1038/ng.2396](https://dx.doi.org/doi: 10.1038/ng.2396){:.doi}

{:.paper} Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours.{:.papertitle}
R. Sun, X. Fu, Y. Li, Y. Xie, and Y. Mao{:.authors}
BMC genomics, vol. 10, no. 1, pp. 93, Feb. 2009{:.journal}
☕DOI: [doi: 10.1186/1471-2164-10-93](https://dx.doi.org/doi: 10.1186/1471-2164-10-93){:.doi}

{:.paper} Simultaneously detection of genomic and expression alterations in prostate cancer using cDNA microarray.{:.papertitle}
M. Jiang, M. Li, X. Fu, Y. Huang, H. Qian, R. Sun, Y. Mao, Y. Xie, and Y. Li{:.authors}
The Prostate, vol. 68, no. 14, pp. 1496--1509, Oct. 2008{:.journal}
☕DOI: [doi: 10.1002/pros.20756](https://dx.doi.org/doi: 10.1002/pros.20756){:.doi}

Algorithms for genomic sequence analysis

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

{:.paper} Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS{:.papertitle}
A.K. Emde, M. Schulz, D. Weese, R. Sun, M. Vingron, V. Kalscheuer, S. Haas, and K. Reinert{:.authors}
Bioinformatics, vol. 28, no. 5, pp. 619--627, Mar. 2012{:.journal}
☕DOI: [doi: 10.1093/bioinformatics/bts019](https://dx.doi.org/doi: 10.1093/bioinformatics/bts019){:.doi}

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