| Circular ecDNA promotes accessible chromatin and high oncogene expression S Wu, KM Turner, N Nguyen, R Raviram, M Erb, J Santini, J Luebeck, ... Nature 575 (7784), 699-703, 2019 | 383 | 2019 |
| Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions JP Shen, D Zhao, R Sasik, J Luebeck, A Birmingham, ... Nature methods 14 (6), 573-576, 2017 | 360 | 2017 |
| Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers H Kim, NP Nguyen, K Turner, S Wu, AD Gujar, J Luebeck, J Liu, ... Nature Genetics 52 (9), 891-897, 2020 | 294 | 2020 |
| Exploring the landscape of focal amplifications in cancer using AmpliconArchitect V Deshpande, J Luebeck, NPD Nguyen, M Bakhtiari, KM Turner, ... Nature communications 10 (1), 392, 2019 | 195 | 2019 |
| Quantitative missense variant effect prediction using large-scale mutagenesis data VE Gray, RJ Hause, J Luebeck, J Shendure, DM Fowler Cell systems 6 (1), 116-124. e3, 2018 | 183 | 2018 |
| EcDNA hubs drive cooperative intermolecular oncogene expression KL Hung, KE Yost, L Xie, Q Shi, K Helmsauer, J Luebeck, R Schöpflin, ... Nature 600 (7890), 731-736, 2021 | 140 | 2021 |
| Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis D Zhao, MG Badur, J Luebeck, JH Magaña, A Birmingham, R Sasik, ... Molecular cell 69 (4), 699-708. e7, 2018 | 93 | 2018 |
| Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA EN Bergstrom, J Luebeck, M Petljak, A Khandekar, M Barnes, T Zhang, ... Nature 602 (7897), 510-517, 2022 | 80 | 2022 |
| AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications J Luebeck, C Coruh, SR Dehkordi, JT Lange, KM Turner, V Deshpande, ... Nature Communications 11 (1), 1-14, 2020 | 60 | 2020 |
| ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer ND Nguyen, V Deshpande, J Luebeck, PS Mischel, V Bafna Nucleic acids research 46 (7), 3309-3325, 2018 | 54 | 2018 |
| Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH KL Hung, J Luebeck, SR Dehkordi, CI Colón, R Li, ITL Wong, C Coruh, ... Nature Genetics, 1-9, 2022 | 48 | 2022 |
| Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges K Song, JK Minami, A Huang, SR Dehkordi, SH Lomeli, J Luebeck, ... Cancer discovery 12 (4), 1046-1069, 2022 | 37 | 2022 |
| Epigenetic dysregulation from chromosomal transit in micronuclei AS Agustinus, D Al-Rawi, B Dameracharla, R Raviram, BSCL Jones, ... Nature 619 (7968), 176-183, 2023 | 36 | 2023 |
| EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA U Rajkumar, K Turner, J Luebeck, V Deshpande, M Chandraker, ... iScience 21, 428-435, 2019 | 30 | 2019 |
| Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus J Luebeck, AWT Ng, PC Galipeau, X Li, CA Sanchez, ... Nature, 1-8, 2023 | 27 | 2023 |
| CRISPR-Cas9 gene editing of hematopoietic stem cells from patients with Friedreich’s ataxia CJ Rocca, JN Rainaldi, J Sharma, Y Shi, JH Haquang, J Luebeck, P Mali, ... Molecular Therapy-Methods & Clinical Development 17, 1026-1036, 2020 | 24 | 2020 |
| Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription J Pang, N Nguyen, J Luebeck, L Ball, A Finegersh, S Ren, T Nakagawa, ... Clinical Cancer Research 27 (24), 6772-6786, 2021 | 22 | 2021 |
| FaNDOM: Fast nested distance-based seeding of optical maps SR Dehkordi, J Luebeck, V Bafna Patterns 2 (5), 2021 | 15 | 2021 |
| Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma OS Chapman, J Luebeck, S Sridhar, ITL Wong, D Dixit, S Wang, G Prasad, ... Nature Genetics, 1-11, 2023 | 12* | 2023 |
| Immortalization and transformation of primary cells mediated by engineered ecDNAs D Pradella, M Zhang, R Gao, YA Melissa, KM Gluchowska, ... bioRxiv, 2023.06. 25.546239, 2023 | 4 | 2023 |
Vineet BafnaProfessor, Computer Science & Engineering, University of California, San DiegoVerified email at cs.ucsd.edu
