Jens-christian Luebeck

Title(s)Postdoctoral Scholar, Computer Science and Engineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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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. 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:
    2. 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: 2     Fields:    Translation:HumansCells
    3. 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: 5     Fields:    Translation:Humans
    4. 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: 12     Fields:    Translation:HumansCells
    5. 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: 3     Fields:    Translation:HumansCells
    6. 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: 4  
    7. 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: 12     Fields:    Translation:HumansCells
    8. 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: 54     Fields:    Translation:HumansCells
    9. 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: 3  
    10. 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: 94     Fields:    Translation:HumansCells
    11. 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: 11  
    12. 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: 47     Fields:    Translation:HumansCells
    13. 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: 16     Fields:    Translation:HumansCells
    14. 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: 37     Fields:    Translation:HumansCells
    15. 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: 55     Fields:    Translation:HumansAnimals
    16. 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: 138     Fields:    Translation:HumansCells
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