Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
8 papers
Recent·Most cited
K. Zhu, M. G. Jones, J. Luebeck, X. Bu, H. Yi, K. L. Hung, I. T.-L. Wong, S. Zhang, P. S. Mischel, H. Y. Chang, V. Bafna
CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.
bioRxiv · Feb 15, 2024Cancer Biology
S. R. Dehkordi, I. T.-L. Wong, J. Ni, J. Luebeck, K. Zhu, G. Prasad, L. Krockenberger, G. Xu, B. Chowdhury, U. Rajkumar, A. Caplin, D. Muliaditan, C. Coruh, Q. Jin, K. Turner, , V. Bafna
The paper introduces OM2BFB, an algorithm detecting BFB amplifications using OGMs, showing high precision and recall, and finds BFB events are common in certain cancers but not linked to intratumoral heterogeneity or rapid genome change.
bioRxiv · Dec 12, 2023 · PreprintCancer Biology
K. L. Hung, M. G. Jones, I. T.-L. Wong, J. T. Lange, J. Luebeck, E. Scanu, B. J. He, L. Brückner, R. Li, R. C. Gonzalez, R. Schmargon, J. R. Dörr, J. A. Belk, V. Bafna, B. Werner, , H. Y. Chang
This study shows that multiple extrachromosomal DNA species are coordinately inherited in cancer cells through mitotic co-segregation, enabling oncogene cooperation and guiding therapeutic strategies.
bioRxiv · Jul 18, 2023 · PreprintCancer Biology
D. Pradella, M. Zhang, R. Gao, Y. A. Melissa, K. M. Gluchowska, Y. Cendon Florez, T. Mishra, G. La Rocca, M. Weigl, Z. Jiao, H. H. M. Nguyen, F. Grimm, M. Lisi, C. Mastroleo, K. Chen, , A. Ventura
This paper describes a method to engineer large focal amplifications in primary cells using ecDNAs, showing they promote proliferation and transformation.
bioRxiv · Jun 25, 2023 · PreprintCancer Biology
M. S. Lin, S.-Y. Jo, J. Luebeck, H. Y. Chang, S. Wu, P. S. Mischel, V. Bafna
The paper identifies transcriptional correlates of ecDNA in tumors, showing upregulation of DNA repair and downregulation of immune pathways.
bioRxiv · Apr 24, 2023Cancer Biology
A. Agustinus, R. Raviram, B. Dameracharla, J. Luebeck, S. Stransky, L. Scipioni, R. Myers, M. DiBona, M. Duran, B. Weigelt, S. Yomtoubian, E. Toufektchan, P. Mischel, V. Mittal, S. Shah, , S. F. Bakhoum
This study shows that chromosomal transit through micronuclei causes epigenetic dysregulation in cancer cells, leading to long-term chromatin accessibility abnormalities.
bioRxiv · Jan 12, 2022Cancer Biology
K. L. Hung, J. Luebeck, S. R. Dehkordi, C. Coruh, J. A. Law, W. J. Greenleaf, P. S. Mischel, V. Bafna, H. Y. Chang
This study introduces CRISPR-CATCH, a method to purify and analyze extrachromosomal DNA, revealing hypomethylation and structural details of ecDNA in cancer cells.
bioRxiv · Nov 28, 2021Cancer Biology
O. S. Chapman, J. Luebeck, S. Wani, A. Tiwari, M. Pagadala, S. Wang, J. D. Larson, J. T. Lange, I. T.-L. Wong, S. R. Dehkordi, S. Chandran, M. Adam, Y. Lin, E. Juarez, J. T. Robinson, , L. Chavez
This study identifies ecDNA in 18% of medulloblastoma patients, linking it to higher relapse and mortality rates and suggesting enhancer rewiring as an oncogenic mechanism.
bioRxiv · Oct 18, 2021 · PreprintCancer Biology