Publications
* denotes equal contribution. Also on Google Scholar.
2026
- AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomesLuebeck J*, Liefeld T*, Wong ITL*, Huang E*, et al. Nature Methods
- A living multi-omics PDX biobank of high-risk sarcomas reveals ecDNA-driven oncogene amplification in osteosarcomaZhao W, Cheng Z, Tian K, … Luebeck J, … Hua Y. Advanced Science
- scAmp analyzes focal gene amplifications at single-cell resolutionJones MG, Weiser NE, Hung KL, … Luebeck J, … Chang HY. Nature Communications
- Examining the role of extrachromosomal DNA in lung cancerKhandekar A, Hoang PH, Luebeck J, et al. J Natl Cancer Inst
- Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitectLi C, Dehkordi SR, Muliaditan D, DasGupta R, Luebeck J, et al. Bioinformatics
- Preservation and clonal behavior of extrachromosomal DNA in patient-derived xenograft models of childhood cancersKenkre R, Chapman OS, Chow EYC, Luebeck J, et al. Genome Medicine
- High-depth whole genome sequencing of premalignant breast lesions reveals rearrangement hotspotsChmelova L, Davies HR, Degasperi A, … Luebeck J, … Nik-Zainal S. Nature Communications
- EcDNA-borne structural variants drive oncogenic fusion transcript amplificationYi H, Zhang S, Swinderman J, … Luebeck J, … Chang HY. Cell
2025
- Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3DChowdhury B, Zhu K, Li C, Alsing J, Luebeck J, et al. Nature Communications
- Enhancer activation from transposable elements in extrachromosomal DNAKraft K, Murphy SE, Jones MG, … Luebeck J, … Chang HY. Nature Cell Biology
- Extrachromosomal DNA-driven oncogene spatial heterogeneity and evolution in glioblastomaNoorani I, Haughey M, Luebeck J, et al. Cancer Discovery
- Spatial-temporal diversity of extrachromosomal DNA shapes urothelial carcinoma evolution and tumor-immune microenvironmentLv W, Zeng Y, Li C, … Luebeck J, … Han P. Cancer Discovery
- Three-dimensional genome landscape of primary human cancersYost KE, Zhao Y, Hung KL, … Luebeck J, … Chang HY. Nature Genetics
- Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancerNakagawa T, Luebeck J, Zhu K, et al. Nature Communications
- Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneityDehkordi SR, Wong ITL, Ni J, Luebeck J, et al. Nature Communications
- Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repairRose JC, Belk JA, Wong ITL, Luebeck J, et al. Cancer Discovery
2024
- Engineered extrachromosomal oncogene amplifications promote tumorigenesisPradella D, Zhang M, Gao R, … Luebeck J, … Ventura A. Nature
- Origins and impact of extrachromosomal DNABailey C, Pich O, Thol K, Watkins TBK, Luebeck J, et al. Nature
- Coordinated inheritance of extrachromosomal DNAs in cancer cellsHung KL, Jones MG, Wong ITL, … Luebeck J, et al. Nature
- Enhancing transcription–replication conflict targets ecDNA-positive cancersTang J, Weiser NE, Wang G, … Luebeck J, … Chang HY. Nature
- Mapping extrachromosomal DNA amplifications during cancer progressionKim H, Kim S, Wade T, … Luebeck J, Verhaak RGW. Nature Genetics
- CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencingZhu K, Jones MG, Luebeck J, et al. Genome Research
- Transcriptional immune suppression and upregulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumorsLin MS, Jo SY, Luebeck J, et al. eLife
- Oncogenic extrachromosomal DNA identification using whole-genome sequencing from formalin-fixed glioblastomasNoorani I*, Luebeck J*, Rowan A, et al. Annals of Oncology
2023
- Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastomaChapman OS, Luebeck J, Sridhar S, et al. Nature Genetics
- Epigenetic dysregulation from chromosomal transit in micronucleiAgustinus A, Al-Rawi D, Dameracharla B, … Luebeck J, et al. Nature
- Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneityRaviram R, Raman A, Preissl S, … Luebeck J, et al. PNAS
- Extrachromosomal DNA in the cancerous transformation of Barrett's esophagusLuebeck J, Ng AWT, Galipeau PC, et al. Nature
2022
- Targeted profiling of human extrachromosomal DNA by CRISPR-CATCHHung KL, Luebeck J, Dehkordi SR, et al. Nature Genetics
- FastViFi: fast and accurate detection of (hybrid) viral DNA and RNAJavadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. NAR Genomics and Bioinformatics
- Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNABergstrom EN, Luebeck J, Petljak M, et al. Nature
2021
- Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in overcoming targeted therapy dosage challengesSong K, Minami JK, Huang A, Dehkordi SR, Lomeli SH, Luebeck J, et al. Cancer Discovery
- ecDNA hubs drive cooperative intermolecular oncogene expressionHung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, et al. Nature
- Extrachromosomal DNA in HPV-mediated oropharyngeal cancer drives diverse oncogene transcriptionPang J*, Nguyen N*, Luebeck J*, et al. Clinical Cancer Research
- FaNDOM: fast nested distance-based seeding of optical mapsDehkordi SR*, Luebeck J*, Bafna V. Patterns
2020
- Integrated analysis of NGS and optical mapping resolves the complex structures of focal amplifications in cancerLuebeck J, Coruh C, Dehkordi SR, et al. Nature Communications
- Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancersKim H, Nguyen N, Turner K, Wu S, Gujar A, Luebeck J, et al. Nature Genetics
- CRISPR/Cas9 gene editing of hematopoietic stem cells from patients with Friedreich's ataxiaRocca C, Rainaldi J, Sharma J, … Luebeck J, Mali P, Cherqui S. Mol Ther Methods Clin Dev
2019
- EcSeg: semantic segmentation of metaphase images containing extrachromosomal DNARajkumar U, Turner K, Luebeck J, et al. iScience
- Circular ecDNA promotes accessible chromatin and high oncogene expressionWu S, Turner KM, Nguyen N, … Luebeck J, et al. Nature
- Exploring the landscape of focal amplifications in cancer using AmpliconArchitectDeshpande V, Luebeck J, Nguyen ND, et al. Nature Communications
2018
- ViFi: accurate detection of viral integration and mRNA fusionNguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V. Nucleic Acids Research
- Combinatorial CRISPR-Cas9 metabolic screens reveal critical redox control points dependent on the KEAP1-NRF2 regulatory axisZhao D, Badur MG, Luebeck J, et al. Molecular Cell
- Quantitative missense variant effect prediction using large-scale mutagenesis dataGray VE, Hause RJ, Luebeck J, Shendure J, Fowler DM. Cell Systems
2017
- Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactionsShen JP, Zhao D, Sasik R, Luebeck J, et al. Nature Methods
2026 · preprints
- Inferring ecDNA evolution from allele frequency spectraDameracharla B, Prasad G, Luebeck J, … Bafna V. bioRxiv
- Endogenous mutational mechanisms and metabolic context shape endometrial cancerSang J, Zhang M, Chavez S, … Luebeck J, … Zhang T. bioRxiv
- Fast and accurate resolution of ecDNA sequence using Cycle-ExtractorFaizrahnemoon M, Luebeck J, Hung KL, et al. bioRxiv
2025 · preprints
- Extrachromosomal DNA associates with poor survival across a broad spectrum of childhood solid tumorsChapman OS, Sridhar S, Chow EYC, … Luebeck J, … Chavez L. medRxiv
Other writing
- AmpliconSuite and AmpliconRepository: enabling ecDNA research at scaleSpringer Nature Research Communities
- Closing the gap between tool development and biology to decode extrachromosomal DNA in cancerCancer Grand Challenges
- AmpliconReconstructor: revealing focally amplified rearrangements in cancerNature Research Cancer Community