Search Results - "Sun, Ruping"

Characterizing the ecological and evolutionary dynamics of cancer by Zahir, Nastaran, Sun, Ruping, Gallahan, Daniel, Gatenby, Robert A., Curtis, Christina

“…Tumor initiation and progression are somatic evolutionary processes driven by the accumulation of genetic alterations, some of which confer selective fitness…”
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Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element by Cho, Seung Woo, Xu, Jin, Sun, Ruping, Mumbach, Maxwell R., Carter, Ava C., Chen, Y. Grace, Yost, Kathryn E., Kim, Jeewon, He, Jing, Nevins, Stephanie A., Chin, Suet-Feung, Caldas, Carlos, Liu, S. John, Horlbeck, Max A., Lim, Daniel A., Weissman, Jonathan S., Curtis, Christina, Chang, Howard Y.

“…Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions…”
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The deubiquitinase USP11 ameliorates intervertebral disc degeneration by regulating oxidative stress-induced ferroptosis via deubiquitinating and stabilizing Sirt3 by Zhu, Jian, Sun, Ruping, Sun, Kaiqiang, Yan, Chen, Jiang, Jialin, Kong, Fanqi, Shi, Jiangang

“…Increasing studies have reported that intervertebral disc degeneration (IVDD) is the main contributor and independent risk factor for low back pain (LBP), it…”
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Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy by Caswell-Jin, Jennifer L., McNamara, Katherine, Reiter, Johannes G., Sun, Ruping, Hu, Zheng, Ma, Zhicheng, Ding, Jie, Suarez, Carlos J., Tilk, Susanne, Raghavendra, Akshara, Forte, Victoria, Chin, Suet-Feung, Bardwell, Helen, Provenzano, Elena, Caldas, Carlos, Lang, Julie, West, Robert, Tripathy, Debu, Press, Michael F., Curtis, Christina

“…Genomic changes observed across treatment may result from either clonal evolution or geographically disparate sampling of heterogeneous tumors. Here we use…”
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Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors by Sun, Ruping, Nikolakopoulos, Athanasios N

“…Can metastatic-primary (M-P) genomic divergence measured from next generation sequencing reveal the natural history of metastatic dissemination? This remains…”
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Evolving copy number gains promote tumor expansion and bolster mutational diversification by Wang, Zicheng, Xia, Yunong, Mills, Lauren, Nikolakopoulos, Athanasios N., Maeser, Nicole, Dehm, Scott M., Sheltzer, Jason M., Sun, Ruping

“…The timing and fitness effect of somatic copy number alterations (SCNA) in cancer evolution remains poorly understood. Here we present a framework to determine…”
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Somatic variant detection from multi-sampled genomic sequencing data of tumor specimens using the ith.Variant pipeline by Maeser, Nicole, Khan, Aziz, Sun, Ruping

“…A common technique for uncovering intra-tumor genomic heterogeneity (ITH) is variant detection. However, it can be challenging to reliably characterize ITH…”
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Quantitative evidence for early metastatic seeding in colorectal cancer by Hu, Zheng, Ding, Jie, Ma, Zhicheng, Sun, Ruping, Seoane, Jose A., Scott Shaffer, J., Suarez, Carlos J., Berghoff, Anna S., Cremolini, Chiara, Falcone, Alfredo, Loupakis, Fotios, Birner, Peter, Preusser, Matthias, Lenz, Heinz-Josef, Curtis, Christina

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Centrosomal Protein 55 (CEP55) Drives Immune Exclusion and Resistance to Immune Checkpoint Inhibitors in Colorectal Cancer by Wangmo, Dechen, Gates, Travis J, Zhao, Xianda, Sun, Ruping, Subramanian, Subbaya

“…Colorectal cancer (CRC) currently ranks as the third most common cancer in the United States, and its incidence is on the rise, especially among younger…”
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Publisher Correction: Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy by Caswell-Jin, Jennifer L., McNamara, Katherine, Reiter, Johannes G., Sun, Ruping, Hu, Zheng, Ma, Zhicheng, Ding, Jie, Suarez, Carlos J., Tilk, Susanne, Raghavendra, Akshara, Forte, Victoria, Chin, Suet-Feung, Bardwell, Helen, Provenzano, Elena, Caldas, Carlos, Lang, Julie, West, Robert, Tripathy, Debu, Press, Michael F., Curtis, Christina

“…The original version of this Article omitted from the Author Contributions statement that ‘R.S. and J.G.R contributed equally to this work.’ This has been…”
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Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS by EMDE, Anne-Katrin, SCHULZ, Marcel H, WEESE, David, RUPING SUN, VINGRON, Martin, KALSCHEUER, Vera M, HAAS, Stefan A, REINERT, Knut

“…The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing…”
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Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours by Sun, Ruping, Fu, Xuping, Li, Yao, Xie, Yi, Mao, Yumin

“…Recently, microRNAs (miRNAs) have taken centre stage in the field of human molecular oncology. Several studies have shown that miRNA profiling analyses offer…”
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Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads by RUPING SUN, LOVE, Michael I, ZEMOJTEL, Tomasz, EMDE, Anne-Katrin, CHUNG, Ho-Ryun, VINGRON, Martin, HAAS, Stefan A

“…We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing. By…”
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Simultaneously detection of genomic and expression alterations in prostate cancer using cDNA microarray by Jiang, Mei, Li, Ming, Fu, Xuping, Huang, Yan, Qian, Hui, Sun, Ruping, Mao, Yumin, Xie, Yi, Li, Yao

“…BACKGROUND Prostate cancer is a common disease among men but the knowledge of the prostate carcinogenesis is still limited. METHODS cDNA microarray‐based…”
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A population genetics perspective on the determinants of intra-tumor heterogeneity by Hu, Zheng, Sun, Ruping, Curtis, Christina

“…Cancer results from the acquisition of somatic alterations in a microevolutionary process that typically occurs over many years, much of which is occult…”
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Big Bang Tumor Growth and Clonal Evolution by Sun, Ruping, Hu, Zheng, Curtis, Christina

“…The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although…”
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Parameter estimation from single patient, single time-point sequencing data of recurrent tumors by Leder, Kevin, Sun, Ruping, Wang, Zicheng, Zhang, Xuanming

“…In this study, we develop consistent estimators for key parameters that govern the dynamics of tumor cell populations when subjected to pharmacological…”
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Quantitative evidence for early metastatic seeding in colorectal cancer by Hu, Zheng, Ding, Jie, Ma, Zhicheng, Sun, Ruping, Seoane, Jose A., Scott Shaffer, J., Suarez, Carlos J., Berghoff, Anna S., Cremolini, Chiara, Falcone, Alfredo, Loupakis, Fotios, Birner, Peter, Preusser, Matthias, Lenz, Heinz-Josef, Curtis, Christina

“…Both the timing and molecular determinants of metastasis are unknown, hindering treatment and prevention efforts. Here we characterize the evolutionary…”
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Hesperidin mitigates oxidative stress-induced ferroptosis in nucleus pulposus cells via Nrf2/NF-κB axis to protect intervertebral disc from degeneration by Zhu, Jian, Sun, Ruping, Yan, Chen, Sun, Kaiqiang, Gao, Lu, Zheng, Bing, Shi, Jiangang

“…Intervertebral disc degeneration (IVDD), a widely known contributor to low back pain (LBP), has been proved to be a global health challenging conundrum…”
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Between-region genetic divergence reflects the mode and tempo of tumor evolution by Sun, Ruping, Hu, Zheng, Sottoriva, Andrea, Graham, Trevor A, Harpak, Arbel, Ma, Zhicheng, Fischer, Jared M, Shibata, Darryl, Curtis, Christina

“…Christina Curtis and colleagues simulate spatial tumor growth under different evolutionary models and compare their results to multiregion sequencing data…”
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