Jens-christian Luebeck

Title(s)Assistant Project Scientist, Computer Science and Engineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0003-4391-979X Additional info
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    University of Washington, SeattleBS06/2015Applied Computational & Mathematical Sciences
    UC San Diego, La JollaMS03/2019Computer Science
    UC San Diego, La JollaPhD12/2021Bioinformatics & Systems Biology

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity. Nat Commun. 2025 Feb 10; 16(1):1497. Raeisi Dehkordi S, Wong IT, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Gnanasekar A, Coruh C, Jin Q, Turner K, Teo SX, Pang AWC, Alexandrov LB, Chua CEL, Furnari FB, Maciejowski J, Paulson TG, Law JA, Chang HY, Yue F, DasGupta R, Zhao J, Mischel PS, Bafna V. PMID: 39929823; PMCID: PMC11811125.
      View in: PubMed   Mentions:    Fields:    
    2. Disparate Pathways for Extrachromosomal DNA Biogenesis and Genomic DNA Repair. Cancer Discov. 2025 Jan 13; 15(1):69-82. Rose JC, Belk JA, Wong IT, Luebeck J, Horn HT, Daniel B, Jones MG, Yost KE, Hung KL, Kolahi KS, Curtis EJ, Kuo CJ, Bafna V, Mischel PS, Chang HY. PMID: 39109936; PMCID: PMC11726015.
      View in: PubMed   Mentions:    Fields:    
    3. Engineered extrachromosomal oncogene amplifications promote tumorigenesis. Nature. 2025 Jan; 637(8047):955-964. Pradella D, Zhang M, Gao R, Yao MA, Gluchowska KM, Cendon-Florez Y, Mishra T, La Rocca G, Weigl M, Jiao Z, Nguyen HHM, Lisi M, Ozimek MM, Mastroleo C, Chen K, Grimm F, Luebeck J, Zhang S, Zolli AA, Sun EG, Dameracharla B, Zhao Z, Pritykin Y, Sigel C, Chang HY, Mischel PS, Bafna V, Antonescu CR, Ventura A. PMID: 39695225; PMCID: PMC11754114.
      View in: PubMed   Mentions:    Fields:    
    4. Origins and impact of extrachromosomal DNA. Nature. 2024 Nov; 635(8037):193-200. Bailey C, Pich O, Thol K, Watkins TBK, Luebeck J, Rowan A, Stavrou G, Weiser NE, Dameracharla B, Bentham R, Lu WT, Kittel J, Yang SYC, Howitt BE, Sharma N, Litovchenko M, Salgado R, Hung KL, Cornish AJ, Moore DA, Houlston RS, Bafna V, Chang HY, Nik-Zainal S, Kanu N, McGranahan N, Genomics England Consortium, Flanagan AM, Mischel PS, Jamal-Hanjani M, Swanton C. PMID: 39506150; PMCID: PMC11540846.
      View in: PubMed   Mentions: 1     Fields:    
    5. Coordinated inheritance of extrachromosomal DNAs in cancer cells. Nature. 2024 Nov; 635(8037):201-209. Hung KL, Jones MG, Wong IT, Curtis EJ, Lange JT, He BJ, Luebeck J, Schmargon R, Scanu E, Brückner L, Yan X, Li R, Gnanasekar A, Chamorro González R, Belk JA, Liu Z, Melillo B, Bafna V, Dörr JR, Werner B, Huang W, Cravatt BF, Henssen AG, Mischel PS, Chang HY. PMID: 39506152; PMCID: PMC11541006.
      View in: PubMed   Mentions: 1     Fields:    
    6. Enhancing transcription-replication conflict targets ecDNA-positive cancers. Nature. 2024 Nov; 635(8037):210-218. Tang J, Weiser NE, Wang G, Chowdhry S, Curtis EJ, Zhao Y, Wong IT, Marinov GK, Li R, Hanoian P, Tse E, Mojica SG, Hansen R, Plum J, Steffy A, Milutinovic S, Meyer ST, Luebeck J, Wang Y, Zhang S, Altemose N, Curtis C, Greenleaf WJ, Bafna V, Benkovic SJ, Pinkerton AB, Kasibhatla S, Hassig CA, Mischel PS, Chang HY. PMID: 39506153; PMCID: PMC11540844.
      View in: PubMed   Mentions: 2     Fields:    
    7. Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma. bioRxiv. 2024 Oct 25. Noorani I, Haughey M, Luebeck J, Rowan A, Grönroos E, Terenzi F, Wong IT, Kittel J, Bailey C, Weeden C, Bell D, Joo E, Barbe V, Jones MG, Nye E, Green M, Meader L, Norton EJ, Fabian M, Kanu N, Jamal-Hanjani M, Santarius T, Nicoll J, Boche D, Chang HY, Bafna V, Huang W, Mischel PS, Swanton C, Werner B. PMID: 39484416; PMCID: PMC11526901.
      View in: PubMed   Mentions:
    8. Mapping extrachromosomal DNA amplifications during cancer progression. Nat Genet. 2024 Nov; 56(11):2447-2454. Kim H, Kim S, Wade T, Yeo E, Lipsa A, Golebiewska A, Johnson KC, An S, Ko J, Nam Y, Lee HY, Kang S, Chung H, Niclou SP, Moon HE, Paek SH, Bafna V, Luebeck J, Verhaak RGW. PMID: 39402156; PMCID: PMC11549044.
      View in: PubMed   Mentions: 2     Fields:    
    9. CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. Genome Res. 2024 Oct 11; 34(9):1344-1354. Zhu K, Jones MG, Luebeck J, Bu X, Yi H, Hung KL, Wong IT, Zhang S, Mischel PS, Chang HY, Bafna V. PMID: 38981681; PMCID: PMC11529860.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    10. Enhancer activation from transposable elements in extrachromosomal DNA. bioRxiv. 2024 Sep 08. Kraft K, Murphy SE, Jones MG, Shi Q, Bhargava-Shah A, Luong C, Hung KL, He BJ, Li R, Park SK, Weiser NE, Luebeck J, Bafna V, Boeke JD, Mischel PS, Boettiger AN, Chang HY. PMID: 39282372; PMCID: PMC11398463.
      View in: PubMed   Mentions:
    11. Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer. Res Sq. 2024 Sep 05. Nakagawa T, Luebeck J, Zhu K, Lange JT, Sasik R, Phillips C, Sadat S, Javadzadeh S, Yang Q, Wang A, Pestonjamasp K, Rosenthal B, Fisch KM, Mischel P, Bafna V, Califano JA. PMID: 39281879; PMCID: PMC11398563.
      View in: PubMed   Mentions:
    12. Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors. Elife. 2024 Jun 19; 12. Lin MS, Jo SY, Luebeck J, Chang HY, Wu S, Mischel PS, Bafna V. PMID: 38896472; PMCID: PMC11186631.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    13. CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. bioRxiv. 2024 May 18. Zhu K, Jones MG, Luebeck J, Bu X, Yi H, Hung KL, Wong IT, Zhang S, Mischel PS, Chang HY, Bafna V. PMID: 38405779; PMCID: PMC10888815.
      View in: PubMed   Mentions:
    14. Oncogenic extrachromosomal DNA identification using whole-genome sequencing from formalin-fixed glioblastomas. Ann Oncol. 2024 Jun; 35(6):570-573. Noorani I, Luebeck J, Rowan A, Grönroos E, Barbe V, Fabian M, Nicoll JAR, Boche D, Bafna V, Mischel PS, Swanton C. PMID: 38555024.
      View in: PubMed   Mentions:    Fields:    
    15. Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change. bioRxiv. 2023 Dec 13. Dehkordi SR, Wong IT, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Coruh C, Jin Q, Turner K, Teo SX, Pang AWC, Alexandrov LB, Chua CEL, Furnari FB, Paulson TG, Law JA, Chang HY, Yue F, DasGupta R, Zhao J, Mischel PS, Bafna V. PMID: 38168210; PMCID: PMC10760206.
      View in: PubMed   Mentions:
    16. Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors. bioRxiv. 2023 Nov 28. Lin MS, Jo SY, Luebeck J, Chang HY, Wu S, Mischel PS, Bafna V. PMID: 37162993; PMCID: PMC10168239.
      View in: PubMed   Mentions:
    17. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet. 2023 Dec; 55(12):2189-2199. Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. PMID: 37945900; PMCID: PMC10703696.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    18. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. bioRxiv. 2023 Jul 19. Hung KL, Jones MG, Wong IT, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, Huang W, Henssen AG, Mischel PS, Chang HY. PMID: 37503111; PMCID: PMC10371175.
      View in: PubMed   Mentions:
    19. Immortalization and transformation of primary cells mediated by engineered ecDNAs. bioRxiv. 2023 Jun 26. Pradella D, Zhang M, Gao R, Yao MA, Gluchowska KM, Florez YC, Mishra T, Rocca G, Weigl M, Jiao Z, Nguyen HHM, Grimm F, Lisi M, Mastroleo C, Chen K, Luebeck J, Bafna V, Antonescu CR, Ventura A. PMID: 37425909; PMCID: PMC10327150.
      View in: PubMed   Mentions:
    20. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature. 2023 Jul; 619(7968):176-183. Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. PMID: 37286593; PMCID: PMC10322720.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    21. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proc Natl Acad Sci U S A. 2023 05 16; 120(20):e2210991120. Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, Li YE, Fang R, Baback T, Mugford J, Han CZ, Glass CK, Barr CL, Mischel PS, Bafna V, Escoubet L, Ren B, Chen CC. PMID: 37155843; PMCID: PMC10194019.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    22. Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus. Nature. 2023 04; 616(7958):798-805. Luebeck J, Ng AWT, Galipeau PC, Li X, Sanchez CA, Katz-Summercorn AC, Kim H, Jammula S, He Y, Lippman SM, Verhaak RGW, Maley CC, Alexandrov LB, Reid BJ, Fitzgerald RC, Paulson TG, Chang HY, Wu S, Bafna V, Mischel PS. PMID: 37046089; PMCID: PMC10132967.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    23. Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Nat Genet. 2022 11; 54(11):1746-1754. Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong IT, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, González RC, Swanton C, Curtis C, Jamal-Hanjani M, Henssen AG, Law JA, Greenleaf WJ, Lo RS, Mischel PS, Bafna V, Chang HY. PMID: 36253572; PMCID: PMC9649439.
      View in: PubMed   Mentions: 37     Fields:    Translation:Humans
    24. FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA. NAR Genom Bioinform. 2022 Jun; 4(2):lqac032. Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. PMID: 35493723; PMCID: PMC9041341.
      View in: PubMed   Mentions:
    25. Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges. Cancer Discov. 2022 04 01; 12(4):1046-1069. Song K, Minami JK, Huang A, Dehkordi SR, Lomeli SH, Luebeck J, Goodman MH, Moriceau G, Krijgsman O, Dharanipragada P, Ridgley T, Crosson WP, Salazar J, Pazol E, Karin G, Jayaraman R, Balanis NG, Alhani S, Sheu K, Ten Hoeve J, Palermo A, Motika SE, Senaratne TN, Paraiso KH, Hergenrother PJ, Rao PN, Multani AS, Peeper DS, Bafna V, Lo RS, Graeber TG. PMID: 34930786; PMCID: PMC9192483.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    26. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature. 2022 02; 602(7897):510-517. Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. PMID: 35140399; PMCID: PMC8850194.
      View in: PubMed   Mentions: 51     Fields:    
    27. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature. 2021 12; 600(7890):731-736. Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong IT, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. PMID: 34819668; PMCID: PMC9126690.
      View in: PubMed   Mentions: 94     Fields:    Translation:HumansCells
    28. Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription. Clin Cancer Res. 2021 12 15; 27(24):6772-6786. Pang J, Nguyen N, Luebeck J, Ball L, Finegersh A, Ren S, Nakagawa T, Flagg M, Sadat S, Mischel PS, Xu G, Fisch K, Guo T, Cahill G, Panuganti B, Bafna V, Califano J. PMID: 34548317; PMCID: PMC8710294.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    29. FaNDOM: Fast nested distance-based seeding of optical maps. Patterns (N Y). 2021 May 14; 2(5):100248. Raeisi Dehkordi S, Luebeck J, Bafna V. PMID: 34027500; PMCID: PMC8134938.
      View in: PubMed   Mentions: 9  
    30. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nat Commun. 2020 09 01; 11(1):4374. Luebeck J, Coruh C, Dehkordi SR, Lange JT, Turner KM, Deshpande V, Pai DA, Zhang C, Rajkumar U, Law JA, Mischel PS, Bafna V. PMID: 32873787; PMCID: PMC7463033.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    31. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat Genet. 2020 09; 52(9):891-897. Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, Chang HY, Beck CR, Mischel PS, Bafna V, Verhaak RGW. PMID: 32807987; PMCID: PMC7484012.
      View in: PubMed   Mentions: 185     Fields:    Translation:HumansCells
    32. CRISPR-Cas9 Gene Editing of Hematopoietic Stem Cells from Patients with Friedreich's Ataxia. Mol Ther Methods Clin Dev. 2020 Jun 12; 17:1026-1036. Rocca CJ, Rainaldi JN, Sharma J, Shi Y, Haquang JH, Luebeck J, Mali P, Cherqui S. PMID: 32462051; PMCID: PMC7240056.
      View in: PubMed   Mentions: 13  
    33. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019 11; 575(7784):699-703. Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. PMID: 31748743; PMCID: PMC7094777.
      View in: PubMed   Mentions: 225     Fields:    Translation:HumansCells
    34. EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA. iScience. 2019 Nov 22; 21:428-435. Rajkumar U, Turner K, Luebeck J, Deshpande V, Chandraker M, Mischel P, Bafna V. PMID: 31706138; PMCID: PMC6849072.
      View in: PubMed   Mentions: 27  
    35. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat Commun. 2019 01 23; 10(1):392. Deshpande V, Luebeck J, Nguyen ND, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V. PMID: 30674876; PMCID: PMC6344493.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansCells
    36. ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res. 2018 04 20; 46(7):3309-3325. Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V. PMID: 29579309; PMCID: PMC6283451.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    37. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Mol Cell. 2018 02 15; 69(4):699-708.e7. Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. PMID: 29452643; PMCID: PMC5819357.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    38. Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data. Cell Syst. 2018 Jan 24; 6(1):116-124.e3. Gray VE, Hause RJ, Luebeck J, Shendure J, Fowler DM. PMID: 29226803; PMCID: PMC5799033.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansAnimals
    39. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. PMID: 28319113; PMCID: PMC5449203.
      View in: PubMed   Mentions: 174     Fields:    Translation:HumansCells
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