Publications

You can also find these articles on my Google Scholar profile.

* indicates shared first-authorship.

• Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. “FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.” NAR Genomics and Bioinformatics. 2022.

• Bergstrom E, Luebeck J, et al. “Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA.” Nature. 2022.

• Song K, Minami JK, Huang A, Dehkordi SR, Lomeli SH, Luebeck J, et al. “Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in overcoming targeted therapy dosage challenges.” Cancer Discovery. 2021.

• Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, et al. “ecDNA hubs drive cooperative intermolecular oncogene expression.” Nature. 2021.

• Pang J*, Nguyen NP*, Luebeck J*, et al. “Extrachromosomal DNA in HPV mediated oropharyngeal cancer drives diverse oncogene transcription.” Clinical Cancer Research. 2021.

• Dehkordi SR*, Luebeck J*, Bafna V. “FaNDOM: Fast Nested Distance-Based Seeding of Optical Maps.” Cell Patterns. 2021.

Luebeck J, Coruh C, Dehkordi SR, et al. “Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancer.” Nature Communications. 2020.

• Kim H, Nguyen N, Turner K, Wu S, Gujar A, Luebeck J, et al. “Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.” Nature Genetics. 2020.

• Rocca C, Rainaldi J, Sharma J, Shi Y, Haquang J, Luebeck J, Mali P, Cherqui S. “CRISPR/Cas9 gene editing of hematopoietic stem cells from patients with Friedreich’s ataxia.” Molecular Therapy – Methods & Clinical Development. 2020.

• Rajkumar U, Turner K, Luebeck J, et al. “EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA.” iScience. 2019.

• Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, et al. “Circular ecDNA promotes accessible chromatin and high oncogene expression.” Nature. 2019. (Publication subsequently featured in a New York Times article by Carl Zimmer).

• Deshpande V, Luebeck J, Nguyen ND, et al. “Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.” Nature Communications. 2019.

• Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V. “ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.” Nucleic Acids Research. 2018.

• Zhao D, Badur MG, Luebeck J, et al. “Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis.” Molecular Cell. 2018.

• Gray VE, Hause RJ, Luebeck J, Shendure J, Fowler DM. “Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data.” Cell Systems. 2018.

• Shen JP, Zhao D, Sasik R, Luebeck J, et al. “Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.” Nature Methods. 2017.