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J. Z. Sanborn, Ph.D. - Publications

Affiliations: 
Biomolecular Engineering and Bioinformatics University of California, Santa Cruz, Santa Cruz, CA, United States 
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Reimann H, Nguyen A, Sanborn JZ, Vaske CJ, Benz SC, Niazi K, Rabizadeh S, Spilman P, Mackensen A, Ruebner M, Hein A, Beckmann MW, van der Meijden ED, Bausenwein J, Kretschmann S, et al. Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy. Journal For Immunotherapy of Cancer. 9. PMID 34172517 DOI: 10.1136/jitc-2021-002605  0.635
2021 Denkert C, Untch M, Benz S, Schneeweiss A, Weber KE, Schmatloch S, Jackisch C, Sinn HP, Golovato J, Karn T, Marmé F, Link T, Budczies J, Nekljudova V, Schmitt WD, ... ... Sanborn JZ, et al. Reconstructing tumor history in breast cancer: signatures of mutational processes and response to neoadjuvant chemotherapy. Annals of Oncology : Official Journal of the European Society For Medical Oncology. 32: 500-511. PMID 33418062 DOI: 10.1016/j.annonc.2020.12.016  0.36
2020 Newton Y, Sedgewick AJ, Cisneros L, Golovato J, Johnson M, Szeto CW, Rabizadeh S, Sanborn JZ, Benz SC, Vaske C. Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples. Scientific Reports. 10: 17597. PMID 33077815 DOI: 10.1038/s41598-020-74483-1  0.681
2020 Kang T, Yau C, Wong CK, Sanborn JZ, Newton Y, Vaske C, Benz SC, Krings G, Camarda R, Henry JE, Stuart J, Powell M, Benz CC. A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population. Breast Cancer Research : Bcr. 22: 81. PMID 32736587 DOI: 10.1186/S13058-020-01322-6  0.589
2020 Adashek JJ, Kato S, Parulkar R, Szeto CW, Sanborn JZ, Vaske CJ, Benz SC, Reddy SK, Kurzrock R. Transcriptomic silencing as a potential mechanism of treatment resistance. Jci Insight. 5. PMID 32493840 DOI: 10.1172/Jci.Insight.134824  0.75
2020 Heskett MB, Sanborn JZ, Boniface C, Goode B, Chapman J, Garg K, Rabban JT, Zaloudek C, Benz SC, Spellman PT, Solomon DA, Cho RJ. Multiregion exome sequencing of ovarian immature teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. PMID 31911616 DOI: 10.1038/S41379-019-0446-Y  0.671
2019 Lee KL, Benz SC, Hicks KC, Nguyen A, Gameiro SR, Palena C, Sanborn JZ, Su Z, Ordentlich P, Rohlin L, Lee JH, Rabizadeh S, Soon-Shiong P, Niazi K, Schlom J, et al. Efficient tumor clearance and diversified immunity through neoepitope vaccines and combinatorial immunotherapy. Cancer Immunology Research. PMID 31292145 DOI: 10.1158/2326-6066.Cir-18-0620  0.604
2019 Newton Y, Golovato J, Tan IB, Lam JYC, Yu G, Koo S, Chua C, Yeong JPS, Ping C, Skanderup A, Göke J, Johnson M, Rabizadeh S, Sanborn JZ, Benz SC, et al. Genomic and immune infiltration differences between MSI and MSS GI tumors. Journal of Clinical Oncology. 37: 528-528. DOI: 10.1200/Jco.2019.37.4_Suppl.528  0.738
2018 North JP, Golovato J, Vaske CJ, Sanborn JZ, Nguyen A, Wu W, Goode B, Stevers M, McMullen K, Perez White BE, Collisson EA, Bloomer M, Solomon DA, Benz SC, Cho RJ. Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma. Nature Communications. 9: 1894. PMID 29760388 DOI: 10.1038/S41467-018-04008-Y  0.597
2018 Rabizadeh S, Garner C, Sanborn JZ, Benz SC, Reddy S, Soon-Shiong P. Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer. Oncotarget. 9: 19223-19232. PMID 29721196 DOI: 10.18632/oncotarget.24973  0.709
2018 Garner C, Reddy S, Sanborn JZ, Benz SC, Soon-Shiong P, Rabizadeh S. Tumor-normal sequencing to reveal frequency of false positive error rates with tumor-only sequencing in GI cancers and with RNA sequencing as a new standard of precision molecular profiling. Journal of Clinical Oncology. 36: 224-224. DOI: 10.1200/Jco.2018.36.4_Suppl.224  0.718
2018 Nguyen A, Sanborn JZ, Vaske CJ, Rabizadeh S, Tan IB, Benz SC. Validation of omics based MSI calling to improve upon traditional methods of MSI detection. Journal of Clinical Oncology. 36: e15663-e15663. DOI: 10.1200/Jco.2018.36.15_Suppl.E15663  0.544
2018 Thyparambil SP, Kim YJ, Chambers A, Yan D, SELLAPPAN S, Gong C, Sedgewick A, Newton Y, Sanborn JZ, Vaske CJ, Benz SC, Cecchi F, Kang H, Hembrough TA. Comprehensive proteomic and genomic profiling to identify therapeutic targets in adenoid cystic carcinoma. Journal of Clinical Oncology. 36: 6053-6053. DOI: 10.1200/Jco.2018.36.15_Suppl.6053  0.618
2018 Denkert C, Untch M, Benz SC, Weber K, Golovato J, Budczies J, Nekljudova V, Stickeler E, Parulkar R, Schneeweiss A, Jackisch C, Sanborn JZ, Conrad B, Wiebringhaus H, Huober JB, et al. Signatures of mutational processes and response to neoadjuvant chemotherapy in breast cancer: A genome-based investigation in the neoadjuvant GeparSepto trial. Journal of Clinical Oncology. 36: 574-574. DOI: 10.1200/Jco.2018.36.15_Suppl.574  0.631
2018 Schwartz C, Little J, Vaske CJ, Benz SC, Soon-Shiong P, Rabizadeh S, Sanborn JZ. The NantOmics Pharmacogenomics Test: An integrative panomic approach to pharmacogenomics screening. Journal of Clinical Oncology. 36: 2575-2575. DOI: 10.1200/Jco.2018.36.15_Suppl.2575  0.527
2018 Nguyen A, Garner C, Reddy SK, Sanborn JZ, Benz SC, Seery TE, Rabizadeh S. Three-fold overestimation of tumor mutation burden using 248 gene panel versus whole exome. Journal of Clinical Oncology. 36: 12117-12117. DOI: 10.1200/Jco.2018.36.15_Suppl.12117  0.656
2018 Pal SK, Vanderwalde AM, Szeto C, Benz SC, Sanborn JZ, Vaske CJ, Reddy SK, Hamid O. Co-expression patterns of immune checkpoint molecules in relation to PD-L1 expression. Journal of Clinical Oncology. 36: 12113-12113. DOI: 10.1200/Jco.2018.36.15_Suppl.12113  0.661
2016 Nguyen A, Sanborn JZ, Vaske CJ, Rabizadeh S, Niazi K, Soon-Shiong P, Benz SC. Identifying patient-specific neoepitopes for cell-based and vaccine immunotherapy targets in breast cancer patients by HLA typing and predicting MHC presentation from whole genome and RNA sequencing data. Journal of Clinical Oncology. 34: 11606-11606. DOI: 10.1200/Jco.2016.34.15_Suppl.11606  0.625
2015 Favero F, McGranahan N, Salm M, Birkbak NJ, Sanborn JZ, Benz SC, Becq J, Peden JF, Kingsbury Z, Grocok RJ, Humphray S, Bentley D, Spencer-Dene B, Gutteridge A, Brada M, et al. Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome. Annals of Oncology : Official Journal of the European Society For Medical Oncology / Esmo. 26: 880-7. PMID 25732040 DOI: 10.1093/Annonc/Mdv127  0.603
2015 Rabizadeh S, Benz SC, Burrows J, Hembrough TA, Sanborn JZ, Vaske CJ, Soon-Shiong P. Genomics, transcriptomics, and proteomics in the clinical setting: Integrating whole genome and RNA sequencing with quantitative proteomics to better inform clinical treatment selection. Journal of Clinical Oncology. 33: 11093-11093. DOI: 10.1200/Jco.2015.33.15_Suppl.11093  0.694
2015 Benz SC, Rabizadeh S, Sanborn JZ, Vaske CJ, Palmer GA, Soon-Shiong P. Protein expression by genetic mutations identified in gene panels (hotspots) and efficacy of targeted treatments. Journal of Clinical Oncology. 33: 11005-11005. DOI: 10.1200/Jco.2015.33.15_Suppl.11005  0.68
2014 Zheng CL, Wang NJ, Chung J, Moslehi H, Sanborn JZ, Hur JS, Collisson EA, Vemula SS, Naujokas A, Chiotti KE, Cheng JB, Fassihi H, Blumberg AJ, Bailey CV, Fudem GM, et al. Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes. Cell Reports. 9: 1228-34. PMID 25456125 DOI: 10.1016/J.Celrep.2014.10.031  0.311
2014 Rabizadeh S, Benz SC, Sanborn JZ, Vaske CJ, Soon-Shiong P. A comprehensive analysis of molecular profiles across over 10,000 tumor and germ-line exomes across more than 20 tumor types: Novel mechanisms and targets for clinical treatment. Journal of Clinical Oncology. 32: 11031-11031. DOI: 10.1200/Jco.2014.32.15_Suppl.11031  0.715
2013 Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, et al. The somatic genomic landscape of glioblastoma. Cell. 155: 462-77. PMID 24120142 DOI: 10.1016/J.Cell.2013.09.034  0.604
2013 Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Research. 73: 6036-45. PMID 23940299 DOI: 10.1158/0008-5472.Can-13-0186  0.717
2013 Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM. The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Research. 41: W218-24. PMID 23748957 DOI: 10.1093/Nar/Gkt473  0.674
2011 Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Research. 39: D951-9. PMID 21059681 DOI: 10.1093/Nar/Gkq1113  0.768
2010 Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (Oxford, England). 26: i237-45. PMID 20529912 DOI: 10.1093/Bioinformatics/Btq182  0.761
2009 Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, Karolchik D, Archie J, Lenburg ME, Esserman LJ, Kent WJ, Haussler D, Wang T. The UCSC Cancer Genomics Browser. Nature Methods. 6: 239-40. PMID 19333237 DOI: 10.1038/Nmeth0409-239  0.756
2007 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. Plos Computational Biology. 3: e247. PMID 18085818 DOI: 10.1371/Journal.Pcbi.0030247  0.74
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