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Courtney Onodera, PhD

Title(s)Bioinformatics Scientist Supvr, EVP - Physician Serv
SchoolChancellor/EVC/FAS
Address2340 Sutter Street
San Francisco CA 94115
Phone--
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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. Correlation of tumor mutational burden (TMB) with molecular profiling and clinical characteristics in patients with bladder cancer. Journal of Clinical Oncology. 2020 May 20; 38(15_suppl):e17025-e17025. 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, Anthony C. Wong, Sima P. Porten, Jonathan Chou, Terence W. Friedlander, Eric Jay Small, Lawrence Fong, Eric Alejandro Sweet-Cordero, Vadim S Koshkin. .
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    2. Pediatric bithalamic gliomas have a distinct epigenetic signature and frequent EGFR exon 20 insertions resulting in potential sensitivity to targeted kinase inhibition. Acta Neuropathol. 2020 06; 139(6):1071-1088. 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, Alashari M, Cheshier S, Whipple NS, Bruggers C, Raffel C, Gupta N, Kline CN, Reddy A, Banerjee A, Hall MD, Mehta MP, Khatib Z, Maher OM, Brathwaite C, Pekmezci M, Phillips JJ, Bollen AW, Tihan T, Lucas JT, Broniscer A, Berger MS, Perry A, Orr BA, Solomon DA. PMID: 32303840.
      View in: PubMed   Mentions: 1     Fields:    
    3. Gliomas arising in the setting of Li-Fraumeni syndrome stratify into two molecular subgroups with divergent clinicopathologic features. Acta Neuropathol. 2020 May; 139(5):953-957. 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, Bruggers CS, Alashari M, Wetmore C, Garg S, Dishop M, Van Ziffle J, Onodera C, Devine P, Grenert JP, Lee JC, Phillips JJ, Pekmezci M, Tihan T, Bollen AW, Berger MS, Costello JF, Perry A, Solomon DA. PMID: 32157385.
      View in: PubMed   Mentions:    Fields:    
    4. Clinicopathologic and molecular features of intracranial desmoplastic small round cell tumors. Brain Pathol. 2020 03; 30(2):213-225. 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 P, Grenert JP, de Voijs CMA, van Blokland WTM, de Leng WWJ, Ploegmakers MJ, Flucke U, Pekmezci M, Bollen AW, Tihan T, Koelsche C, von Deimling A, Wesseling P, Solomon DA, Perry A. PMID: 31837177.
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    5. Next-Generation Sequencing of Retinoblastoma Identifies Pathogenic Alterations beyond RB1 Inactivation That Correlate with Aggressive Histopathologic Features. Ophthalmology. 2020 Jun; 127(6):804-813. 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. PMID: 32139107.
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    6. PATH-66. THE GENOMIC LANDSCAPE OF SPINAL CORD EPENDYMOMA. Neuro-Oncology. 2019 Nov 11; 21(Supplement_6):vi158-vi158. 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, David Solomon, Melike Pekmezci. .
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    7. PATH-38. ROSETTE-FORMING GLIONEURONAL TUMOR IS DEFINED BY FGFR1 ACTIVATING ALTERATIONS WITH FREQUENT ACCOMPANYING PI3K AND MAPK PATHWAY MUTATIONS. Neuro-Oncology. 2019 Nov 11; 21(Supplement_6):vi151-vi152. 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 Ann Oberheim-Bush, Robin Buerki, Nicholas Butowski, Susan Chang, Mike McDermott, Manish Aghi, Philip Theodosopoulos, Shawn Hervey-Jumper, Mitchel Berger, Corey Raffel, Nalin Gupta, Bette Kleinschmidt-DeMasters, Matthew Wood, Marjorie Grafe, Hua Guo, Peter Sun, Joseph Torkildson, Tabitha Cooney, Cynthia Fata, David Scharnhorst, David Samuel, Serguei Bannykh, Ziad Khatib, Ossama Maher, Gabriel Chamyan, Liset Pelaez, Carole Brathwaite, Lee-way Jin, Mirna Lechpammer, Donald Born, Hannes Vogel, Han Lee, Joanna Phillips, Melike Pekmezci, Andrew Bollen, Tarik Tihan, Arie Perry, David Solomon. .
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    8. Myxoid glioneuronal tumor, PDGFRA p.K385-mutant: clinical, radiologic, and histopathologic features. Brain Pathol. 2020 May; 30(3):479-494. 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, Bannykh S, Hu J, Danielpour M, Li R, Alva E, Johnston J, Van Ziffle J, Onodera C, Devine P, Grenert JP, Lee JC, Pekmezci M, Tihan T, Bollen AW, Perry A, Solomon DA. PMID: 31609499.
      View in: PubMed   Mentions:    Fields:    
    9. Complete Response and Immune-Mediated Adverse Effects With Checkpoint Blockade: Treatment of Mismatch Repair–Deficient Colorectal Neuroendocrine Carcinoma. JCO Precision Oncology. 2019 Nov 1; (3):1-7. Julia Whitman, Adel Kardosh, Luis Diaz, Lawrence Fong, Thomas Hope, Courtney Onodera, Nancy Joseph, Dung Le, George Fisher, Emily Bergsland. .
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    10. Recurrent non-canonical histone H3 mutations in spinal cord diffuse gliomas. Acta Neuropathol. 2019 11; 138(5):877-881. 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, McDermott M, Berger M, Raffel C, Gupta N, Sun PP, Li Y, Shah V, Cha S, Braunstein S, Raleigh DR, Samuel D, Scharnhorst D, Fata C, Guo H, Moes G, Kim JYH, Koschmann C, Van Ziffle J, Onodera C, Devine P, Grenert JP, Lee JC, Pekmezci M, Phillips JJ, Tihan T, Bollen AW, Perry A, Solomon DA. PMID: 31515627.
      View in: PubMed   Mentions: 1     Fields:    
    11. High-grade neuroepithelial tumor with BCOR exon 15 internal tandem duplication-a comprehensive clinical, radiographic, pathologic, and genomic analysis. Brain Pathol. 2020 01; 30(1):46-62. 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, Al-Hajri Z, Phillips JJ, Pekmezci M, Bollen AW, Tihan T, Schniederjan M, Cha S, Perry A, Solomon DA. PMID: 31104347.
      View in: PubMed   Mentions: 1     Fields:    
    12. Genomic profiling of combined hepatocellular-cholangiocarcinoma reveals similar genetics to hepatocellular carcinoma. J Pathol. 2019 06; 248(2):164-178. Joseph NM, Tsokos CG, Umetsu SE, Shain AH, Kelley RK, Onodera C, Bowman S, Talevich E, Ferrell LD, Kakar S, Krings G. PMID: 30690729.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    13. Primary intracranial sarcomas with DICER1 mutation often contain prominent eosinophilic cytoplasmic globules and can occur in the setting of neurofibromatosis type 1. Acta Neuropathol. 2019 03; 137(3):521-525. 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, Koelsche C, von Deimling A, Korshunov A, Perry A, Solomon DA. PMID: 30649606.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    14. Oligodendrogliomas, IDH-mutant and 1p/19q-codeleted, arising during teenage years often lack TERT promoter mutation that is typical of their adult counterparts. Acta Neuropathol Commun. 2018 09 19; 6(1):95. Lee J, Putnam AR, Chesier SH, Banerjee A, Raffel C, Van Ziffle J, Onodera C, Grenert JP, Bastian BC, Perry A, Solomon DA. PMID: 30231927.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    15. The genetic landscape of gliomas arising after therapeutic radiation. Acta Neuropathol. 2019 01; 137(1):139-150. 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, Gupta N, Kunwar S, Mummaneni P, Aghi M, Theodosopoulos P, Berger M, Phillips JJ, Pekmezci M, Tihan T, Bollen AW, Perry A, Solomon DA. PMID: 30196423.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    16. Well-differentiated papillary mesothelioma of the peritoneum is genetically defined by mutually exclusive mutations in TRAF7 and CDC42. Mod Pathol. 2019 01; 32(1):88-99. Stevers M, Rabban JT, Garg K, Van Ziffle J, Onodera C, Grenert JP, Yeh I, Bastian BC, Zaloudek C, Solomon DA. PMID: 30171198.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    17. 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 Neuropathol. 2018 08; 136(2):339-343. 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, Grenert JP, Bastian BC, Villanueva-Meyer JE, Pekmezci M, Bollen AW, Perry A. PMID: 30006677.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    18. The genetic landscape of ganglioglioma. Acta Neuropathol Commun. 2018 06 07; 6(1):47. 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 T, Torkildson J, Gupta N, Theodosopoulos P, Chang EF, Berger M, Bollen AW, Perry A, Tihan T, Solomon DA. PMID: 29880043.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    19. A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle. Nat Commun. 2018 02 23; 9(1):810. 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 MB, Rosenblum MK, Butowski N, Tihan T, Bollen AW, Phillips JJ, Wiita AP, Yeh I, Jacobson MP, Bastian BC, Perry A, Solomon DA. PMID: 29476136.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    20. Adenomatoid tumors of the male and female genital tract are defined by TRAF7 mutations that drive aberrant NF-kB pathway activation. Mod Pathol. 2018 04; 31(4):660-673. 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. PMID: 29148537.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    21. Genomic Analysis of Pigmented Epithelioid Melanocytomas Reveals Recurrent Alterations in PRKAR1A, and PRKCA Genes. Am J Surg Pathol. 2017 Oct; 41(10):1333-1346. Cohen JN, Joseph NM, North JP, Onodera C, Zembowicz A, LeBoit PE. PMID: 28796000.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    22. Genomic profiling of breast secretory carcinomas reveals distinct genetics from other breast cancers and similarity to mammary analog secretory carcinomas. Mod Pathol. 2017 08; 30(8):1086-1099. 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. PMID: 28548128.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    23. Targeted next-generation DNA sequencing of paired tumor and normal DNA to reveal frequent actionable germline alterations. Journal of Clinical Oncology. 2017 May 20; 35(15_suppl):11575-11575. 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, Boris C. Bastian. .
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    24. Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy. Neuro Oncol. 2017 05 01; 19(5):699-709. 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, Tihan T, Bollen AW, Phillips JJ, Korn WM, Yeh I, Bastian BC, Gupta N, Mueller S, Perry A, Nicolaides T, Solomon DA. PMID: 28453743.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    25. Genomic profiling of malignant peritoneal mesothelioma reveals recurrent alterations in epigenetic regulatory genes BAP1, SETD2, and DDX3X. Mod Pathol. 2017 02; 30(2):246-254. Joseph NM, Chen YY, Nasr A, Yeh I, Talevich E, Onodera C, Bastian BC, Rabban JT, Garg K, Zaloudek C, Solomon DA. PMID: 27813512.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    26. Genomic profiling of malignant phyllodes tumors reveals aberrations in FGFR1 and PI-3 kinase/RAS signaling pathways and provides insights into intratumoral heterogeneity. Mod Pathol. 2016 09; 29(9):1012-27. 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. PMID: 27255162.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    27. The Cancer Genome Atlas Analysis Predicts MicroRNA for Targeting Cancer Growth and Vascularization in Glioblastoma. Mol Ther. 2015 Jul; 23(7):1234-1247. 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. PMID: 25903473.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    28. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. Development. 2015 Jan 01; 142(1):118-27. Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M. PMID: 25480920.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    29. Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes. Nat Cell Biol. 2013 Dec; 15(12):1415-23. 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. PMID: 24270888.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    30. Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Rep. 2013 Jun 27; 3(6):1777-84. Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M. PMID: 23727241.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
    31. Gene isoform specificity through enhancer-associated antisense transcription. PLoS One. 2012; 7(8):e43511. Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D. PMID: 22937057.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    32. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec; 7(12):995-1001. Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. PMID: 21057495.
      View in: PubMed   Mentions: 138     Fields:    Translation:HumansAnimalsCells
    33. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14; 443(7108):167-72. 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. PMID: 16915236.
      View in: PubMed   Mentions: 295     Fields:    Translation:HumansAnimalsCells
    34. Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. Plant Cell. 2005 Dec; 17(12):3282-300. 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. PMID: 16284307.
      View in: PubMed   Mentions: 106     Fields:    Translation:AnimalsCells
    35. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell. 2005 Feb; 17(2):444-63. 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. PMID: 15659631.
      View in: PubMed   Mentions: 269     Fields:    Translation:AnimalsCells
    36. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003 Oct 31; 302(5646):842-6. 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, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR. PMID: 14593172.
      View in: PubMed   Mentions: 341     Fields:    Translation:AnimalsCells