Courtney Onodera, PhD
Bioinformatics Scientist Supvr
EVP - Physician Serv
Chancellor/EVC/FAS

Publications (41)

Top publication keywords:
GliomaTumor Necrosis Factor Receptor-Associated Peptides and ProteinsReceptor, Platelet-Derived Growth Factor alphaMutationGerm-Line MutationDEAD-box RNA HelicasesGATA3 Transcription FactorNeoplasms, NeuroepithelialBiomarkers, TumorRNA, AntisenseEnhancer Elements, GeneticBrain NeoplasmsMesotheliomaLateral VentriclesProtein Kinase C-alpha

• HER2 overexpression in urothelial carcinoma with GATA3 and PPARG copy number gains.
  The oncologist 2024 Zhu X, Chan E, Turski ML, Mendez CE, Hsu SC, Kumar V, Shipp C, Jindal T, Chang K, Onodera C, Devine WP, Grenert JP, Stohr BA, Ding CC, Stachler MD, Quigley DA, Feng FY, Chu CE, Porten SP, Chou J, …
• Copy Number Loss at Chromosome 14q11.2 Correlates With the Proportion of T Cells in Biopsies and Helps Identify T-Cell Neoplasms.
  Archives of pathology & laboratory medicine 2023 Saglam A, Singh K, Kumar J, Gollapudi S, Mukherjee S, Singh A, Butzmann A, Kaplan L, Andreadis C, Ai WZ, Fakhri B, Rajkovic A, Wen KW, Onodera C, Van Ziffle J, Devine PW, Ohgami RS
• APOBEC Mutational Signature and Tumor Mutational Burden as Predictors of Clinical Outcomes and Treatment Response in Patients With Advanced Urothelial Cancer.
  Frontiers in oncology 2022 Natesan D, Zhang L, Martell HJ, Jindal T, Devine P, Stohr B, Espinosa-Mendez C, Grenert J, Van Ziffle J, Joseph N, Umetsu S, Onodera C, Turski M, Chan E, Desai A, Aggarwal R, Wong A, Porten S, Chou J,…
• Phase II Trial of the Combination of Temsirolimus and Sorafenib in Advanced Hepatocellular Carcinoma with Tumor Mutation Profiling.
  Liver cancer 2021 Kelley RK, Joseph NM, Nimeiri HS, Hwang J, Kulik LM, Ngo Z, Behr SC, Onodera C, Zhang K, Bocobo AG, Benson AB, Venook AP, Gordan JD
• APOBEC signatures and high tumour mutational burden as predictors of clinical outcomes and response to therapy in patients with urothelial carcinoma.
  Annals of Oncology 2020 D. Natesan, L. Zhang, H. Martell, P. Devine, B. Stohr, J. Grenert, J. Van Ziffle, N. Joseph, B.C. Bastian, S. Umetsu, C. Onodera, E. Chan, A. Desai, S. Porten, J. Chou, T. Friedlander, L. Fong, E.J. …

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• Correlation of tumor mutational burden (TMB) with molecular profiling and clinical characteristics in patients with bladder cancer.
  Journal of Clinical Oncology 2020 Divya Natesan, Henry Martell, Patrick Devine, Bradley A. Stohr, James P. Grenert, Jessica Van Ziffle, Nancy M. Joseph, Boris C. Bastian, Sarah E Umetsu, Courtney Onodera, Emily Chan, Arpita Desai, …
• Pediatric bithalamic gliomas have a distinct epigenetic signature and frequent EGFR exon 20 insertions resulting in potential sensitivity to targeted kinase inhibition.
  Acta neuropathologica 2020 Mondal G, Lee JC, Ravindranathan A, Villanueva-Meyer JE, Tran QT, Allen SJ, Barreto J, Gupta R, Doo P, Van Ziffle J, Onodera C, Devine P, Grenert JP, Samuel D, Li R, Metrock LK, Jin LW, Antony R, …
• Gliomas arising in the setting of Li-Fraumeni syndrome stratify into two molecular subgroups with divergent clinicopathologic features.
  Acta neuropathologica 2020 Sloan EA, Hilz S, Gupta R, Cadwell C, Ramani B, Hofmann J, Kline CN, Banerjee A, Reddy A, Oberheim Bush NA, Chang S, Braunstein S, Chang EF, Raffel C, Gupta N, Sun PP, Kim JYH, Moes G, Alva E, Li R, …
• Clinicopathologic and molecular features of intracranial desmoplastic small round cell tumors.
  Brain pathology (Zurich, Switzerland) 2019 Lee JC, Villanueva-Meyer JE, Ferris SP, Cham EM, Zucker J, Cooney T, Gilani A, Kleinschmidt-DeMasters BK, Trembath D, Mafra M, Chiang J, Ellison DW, Cho SJ, Horvai AE, Van Ziffle J, Onodera C, Devine …
• Next-Generation Sequencing of Retinoblastoma Identifies Pathogenic Alterations beyond RB1 Inactivation That Correlate with Aggressive Histopathologic Features.
  Ophthalmology 2019 Afshar AR, Pekmezci M, Bloomer MM, Cadenas NJ, Stevers M, Banerjee A, Roy R, Olshen AB, Van Ziffle J, Onodera C, Devine WP, Grenert JP, Bastian BC, Solomon DA, Damato BE
• Complete Response and Immune-Mediated Adverse Effects With Checkpoint Blockade: Treatment of Mismatch Repair-Deficient Colorectal Neuroendocrine Carcinoma.
  JCO precision oncology 2019 Whitman J, Kardosh A, Diaz L, Fong L, Hope T, Onodera C, Joseph N, Le D, Fisher G, Bergsland E
• PATH-38. ROSETTE-FORMING GLIONEURONAL TUMOR IS DEFINED BY FGFR1 ACTIVATING ALTERATIONS WITH FREQUENT ACCOMPANYING PI3K AND MAPK PATHWAY MUTATIONS.
  Neuro-Oncology 2019 Lucas Calixto-Hope, Julieann Lee, Emily Sloan, Jeffrey Hofmann, Jessica Van Ziffle, Courtney Onodera, James Grenert, Patrick Devine, Cassie Kline, Anu Banerjee, Jennifer Clarke, Jennie Taylor, Nancy …
• PATH-66. THE GENOMIC LANDSCAPE OF SPINAL CORD EPENDYMOMA.
  Neuro-Oncology 2019 Biswarathan Ramani, Javier Villanueva-Meyer, Christine Glastonbury, Ece Meram, Kyle Walsh, Jennie Taylor, Jessica van Ziffle, Courtney Onodera, James Grenert, Andrew Bollen, Arie Perry, Tarik Tihan, …
• Myxoid glioneuronal tumor, PDGFRA p.K385-mutant: clinical, radiologic, and histopathologic features.
  Brain pathology (Zurich, Switzerland) 2019 Lucas CG, Villanueva-Meyer JE, Whipple N, Oberheim Bush NA, Cooney T, Chang S, McDermott M, Berger M, Cham E, Sun PP, Putnam A, Zhou H, Bollo R, Cheshier S, Poppe MM, Fung KM, Sung S, Glenn C, Fan X, …
• Recurrent non-canonical histone H3 mutations in spinal cord diffuse gliomas.
  Acta neuropathologica 2019 Sloan EA, Cooney T, Oberheim Bush NA, Buerki R, Taylor J, Clarke JL, Torkildson J, Kline C, Reddy A, Mueller S, Banerjee A, Butowski N, Chang S, Mummaneni PV, Chou D, Tan L, Theodosopoulos P, …
• High-grade neuroepithelial tumor with BCOR exon 15 internal tandem duplication-a comprehensive clinical, radiographic, pathologic, and genomic analysis.
  Brain pathology (Zurich, Switzerland) 2019 Ferris SP, Velazquez Vega J, Aboian M, Lee JC, Van Ziffle J, Onodera C, Grenert JP, Saunders T, Chen YY, Banerjee A, Kline CN, Gupta N, Raffel C, Samuel D, Ruiz-Diaz I, Magaki S, Wilson D, Neltner J, …
• Genomic profiling of combined hepatocellular-cholangiocarcinoma reveals similar genetics to hepatocellular carcinoma.
  The Journal of pathology 2019 Joseph NM, Tsokos CG, Umetsu SE, Shain AH, Kelley RK, Onodera C, Bowman S, Talevich E, Ferrell LD, Kakar S, Krings G
• Primary intracranial sarcomas with DICER1 mutation often contain prominent eosinophilic cytoplasmic globules and can occur in the setting of neurofibromatosis type 1.
  Acta neuropathologica 2019 Lee JC, Villanueva-Meyer JE, Ferris SP, Sloan EA, Hofmann JW, Hattab EM, Williams BJ, Guo H, Torkildson J, Florez A, Van Ziffle J, Onodera C, Grenert JP, Cho SJ, Horvai AE, Jones DTW, Pfister SM, …
• Oligodendrogliomas, IDH-mutant and 1p/19q-codeleted, arising during teenage years often lack TERT promoter mutation that is typical of their adult counterparts.
  Acta neuropathologica communications 2018 Lee J, Putnam AR, Chesier SH, Banerjee A, Raffel C, Van Ziffle J, Onodera C, Grenert JP, Bastian BC, Perry A, Solomon DA
• The genetic landscape of gliomas arising after therapeutic radiation.
  Acta neuropathologica 2018 López GY, Van Ziffle J, Onodera C, Grenert JP, Yeh I, Bastian BC, Clarke J, Oberheim Bush NA, Taylor J, Chang S, Butowski N, Banerjee A, Mueller S, Kline C, Torkildson J, Samuel D, Siongco A, Raffel C…
• Well-differentiated papillary mesothelioma of the peritoneum is genetically defined by mutually exclusive mutations in TRAF7 and CDC42.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2018 Stevers M, Rabban JT, Garg K, Van Ziffle J, Onodera C, Grenert JP, Yeh I, Bastian BC, Zaloudek C, Solomon DA
• Myxoid glioneuronal tumor of the septum pellucidum and lateral ventricle is defined by a recurrent PDGFRA p.K385 mutation and DNT-like methylation profile.
  Acta neuropathologica 2018 Solomon DA, Korshunov A, Sill M, Jones DTW, Kool M, Pfister SM, Fan X, Bannykh S, Hu J, Danielpour M, Li R, Johnston J, Cham E, Cooney T, Sun PP, Oberheim Bush NA, McDermott M, Van Ziffle J, Onodera C…
• The genetic landscape of ganglioglioma.
  Acta neuropathologica communications 2018 Pekmezci M, Villanueva-Meyer JE, Goode B, Van Ziffle J, Onodera C, Grenert JP, Bastian BC, Chamyan G, Maher OM, Khatib Z, Kleinschmidt-DeMasters BK, Samuel D, Mueller S, Banerjee A, Clarke JL, Cooney …
• A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle.
  Nature communications 2018 Goode B, Mondal G, Hyun M, Ruiz DG, Lin YH, Van Ziffle J, Joseph NM, Onodera C, Talevich E, Grenert JP, Hewedi IH, Snuderl M, Brat DJ, Kleinschmidt-DeMasters BK, Rodriguez FJ, Louis DN, Yong WH, Lopes…
• Adenomatoid tumors of the male and female genital tract are defined by TRAF7 mutations that drive aberrant NF-kB pathway activation.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2017 Goode B, Joseph NM, Stevers M, Van Ziffle J, Onodera C, Talevich E, Grenert JP, Yeh I, Bastian BC, Phillips JJ, Garg K, Rabban JT, Zaloudek C, Solomon DA
• Genomic Analysis of Pigmented Epithelioid Melanocytomas Reveals Recurrent Alterations in PRKAR1A, and PRKCA Genes.
  The American journal of surgical pathology 2017 Cohen JN, Joseph NM, North JP, Onodera C, Zembowicz A, LeBoit PE
• Genomic profiling of breast secretory carcinomas reveals distinct genetics from other breast cancers and similarity to mammary analog secretory carcinomas.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2017 Krings G, Joseph NM, Bean GR, Solomon D, Onodera C, Talevich E, Yeh I, Grenert JP, Hosfield E, Crawford ED, Jordan RC, van Zante A, Zaloudek C, Shin SJ, Chen YY
• Targeted next-generation DNA sequencing of paired tumor and normal DNA to reveal frequent actionable germline alterations.
  Journal of Clinical Oncology 2017 Wolfgang Michael Korn, Iwei Yey, Jessica Van Ziffle, James P Grenert, Nancy Joseph, David A. Solomon, Megan Laurance, Eric Talevich, Courtney Onodera, Gregor Krings, Bradley A. Stohr, Amie Blanco, …
• Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy.
  Neuro-oncology 2017 Kline CN, Joseph NM, Grenert JP, van Ziffle J, Talevich E, Onodera C, Aboian M, Cha S, Raleigh DR, Braunstein S, Torkildson J, Samuel D, Bloomer M, Campomanes AGA, Banerjee A, Butowski N, Raffel C, …
• Genomic profiling of malignant peritoneal mesothelioma reveals recurrent alterations in epigenetic regulatory genes BAP1, SETD2, and DDX3X.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2016 Joseph NM, Chen YY, Nasr A, Yeh I, Talevich E, Onodera C, Bastian BC, Rabban JT, Garg K, Zaloudek C, Solomon DA
• Genomic profiling of malignant phyllodes tumors reveals aberrations in FGFR1 and PI-3 kinase/RAS signaling pathways and provides insights into intratumoral heterogeneity.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2016 Liu SY, Joseph NM, Ravindranathan A, Stohr BA, Greenland NY, Vohra P, Hosfield E, Yeh I, Talevich E, Onodera C, Van Ziffle JA, Grenert JP, Bastian BC, Chen YY, Krings G
• The Cancer Genome Atlas Analysis Predicts MicroRNA for Targeting Cancer Growth and Vascularization in Glioblastoma.
  Molecular therapy : the journal of the American Society of Gene Therapy 2015 Wong HA, Fatimy RE, Onodera C, Wei Z, Yi M, Mohan A, Gowrisankaran S, Karmali P, Marcusson E, Wakimoto H, Stephens R, Uhlmann EJ, Song JS, Tannous B, Krichevsky AM
• Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast.
  Development (Cambridge, England) 2014 Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M
• Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes.
  Nature cell biology 2013 Chen J, Torcia S, Xie F, Lin CJ, Cakmak H, Franciosi F, Horner K, Onodera C, Song JS, Cedars MI, Ramalho-Santos M, Conti M
• Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo.
  Cell reports 2013 Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M
• Gene isoform specificity through enhancer-associated antisense transcription.
  PloS one 2012 Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D
• FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
  Nature methods 2010 Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D
• An RNA gene expressed during cortical development evolved rapidly in humans.
  Nature 2006 Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, Haussler D
• Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana.
  The Plant cell 2005 Overvoorde PJ, Okushima Y, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Liu A, Onodera C, Quach H, Smith A, Yu G, Theologis A
• Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19.
  The Plant cell 2005 Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A
• Empirical analysis of transcriptional activity in the Arabidopsis genome.
  Science (New York, N.Y.) 2003 Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH…