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.