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Courtney Onodera, PhD

Title(s)Bioinformatics Scientist Supvr, Pathology
SchoolSchool of Medicine
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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.
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    1. Joseph NM, Tsokos CG, Umetsu SE, Shain AH, Kelley RK, Onodera C, Bowman S, Talevich E, Ferrell LD, Kakar S, Krings G. Genomic profiling of combined hepatocellular-cholangiocarcinoma reveals similar genetics to hepatocellular carcinoma. J Pathol. 2019 Jan 28. PMID: 30690729.
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    2. 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. 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 Jan 16. PMID: 30649606.
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    3. Lee J, Putnam AR, Chesier SH, Banerjee A, Raffel C, Van Ziffle J, Onodera C, Grenert JP, Bastian BC, Perry A, Solomon DA. 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 Sep 19; 6(1):95. PMID: 30231927.
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    4. 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. The genetic landscape of gliomas arising after therapeutic radiation. Acta Neuropathol. 2018 Sep 08. PMID: 30196423.
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    5. Stevers M, Rabban JT, Garg K, Van Ziffle J, Onodera C, Grenert JP, Yeh I, Bastian BC, Zaloudek C, Solomon DA. Well-differentiated papillary mesothelioma of the peritoneum is genetically defined by mutually exclusive mutations in TRAF7 and CDC42. Mod Pathol. 2019 Jan; 32(1):88-99. PMID: 30171198.
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    6. 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. 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 Aug; 136(2):339-343. PMID: 30006677.
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    7. 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. The genetic landscape of ganglioglioma. Acta Neuropathol Commun. 2018 Jun 07; 6(1):47. PMID: 29880043.
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    8. 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. A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle. Nat Commun. 2018 02 23; 9(1):810. PMID: 29476136.
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    9. 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. 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. PMID: 29148537.
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    10. Cohen JN, Joseph NM, North JP, Onodera C, Zembowicz A, LeBoit PE. Genomic Analysis of Pigmented Epithelioid Melanocytomas Reveals Recurrent Alterations in PRKAR1A, and PRKCA Genes. Am J Surg Pathol. 2017 Oct; 41(10):1333-1346. PMID: 28796000.
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    11. 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. 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. PMID: 28548128.
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    12. 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. 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. PMID: 28453743.
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    13. 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 peritoneal mesothelioma reveals recurrent alterations in epigenetic regulatory genes BAP1, SETD2, and DDX3X. Mod Pathol. 2017 02; 30(2):246-254. PMID: 27813512.
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    14. 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. 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. PMID: 27255162.
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    15. 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. The Cancer Genome Atlas Analysis Predicts MicroRNA for Targeting Cancer Growth and Vascularization in Glioblastoma. Mol Ther. 2015 Jul; 23(7):1234-1247. PMID: 25903473; PMCID: PMC4817797.
    16. Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. Development. 2015 Jan 01; 142(1):118-27. PMID: 25480920; PMCID: PMC4299150.
    17. 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. Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes. Nat Cell Biol. 2013 Dec; 15(12):1415-23. PMID: 24270888; PMCID: PMC4066669.
    18. Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M. Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Rep. 2013 Jun 27; 3(6):1777-84. PMID: 23727241.
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    19. Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D. Gene isoform specificity through enhancer-associated antisense transcription. PLoS One. 2012; 7(8):e43511. PMID: 22937057; PMCID: PMC3427357.
    20. Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec; 7(12):995-1001. PMID: 21057495; PMCID: PMC3247016.
    21. 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. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14; 443(7108):167-72. PMID: 16915236.
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    22. 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/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. Plant Cell. 2005 Dec; 17(12):3282-300. PMID: 16284307; PMCID: PMC1315369.
    23. 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. 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. PMID: 15659631; PMCID: PMC548818.
    24. 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. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003 Oct 31; 302(5646):842-6. PMID: 14593172.
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