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Olivier Harismendy

TitleAssistant Adjunct Professor
InstitutionUniversity of California San Diego
DepartmentMedicine
Address9500 Gilman Drive #0819
La Jolla CA 92093
Phone858-246-0248
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    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    In vivo detection and genome-wide location analysis of DNA-adducts
    NIH/NCI R21CA177519Sep 3, 2013 - Aug 31, 2016
    Role: Principal Investigator
    Identification of Somatic Mutations in Rare Subclones of Solid Tumors
    NIH/NCI R21CA155615Sep 22, 2011 - Aug 31, 2013
    Role: Principal Investigator
    REGULATORY GENOMIC STUDIES IN A COHORT OF IPS CELL DERIVED CARDIOMYOCYTES
    NIH/NHLBI U01HL107442Jul 15, 2011 - Jun 30, 2017
    Role: Principal Investigator

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    Collapse Publications
    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. Zhou Y, Xu Z, Quan D, Zhang F, Zhang H, Xiao T, Hou S, Qiao H, Harismendy O, Wang JYJ, Suo G. Nuclear respiratory factor 1 promotes spheroid survival and mesenchymal transition in mammary epithelial cells. Oncogene. 2018 Jul 11. PMID: 29995872.
      View in: PubMed
    2. Carroll KT, Bryant AK, Hirshman B, Alattar AA, Joshi R, Gabel B, Carter BS, Harismendy O, Vaida F, Chen CC. Interaction Between the Contributions of Tumor Location, Tumor Grade, and Patient Age to the Survival Benefit Associated with Gross Total Resection. World Neurosurg. 2018 Mar; 111:e790-e798. PMID: 29309983.
      View in: PubMed
    3. Spahn PN, Bath T, Weiss RJ, Kim J, Esko JD, Lewis NE, Harismendy O. PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep. 2017 Nov 20; 7(1):15854. PMID: 29158538.
      View in: PubMed
    4. Burgoyne AM, De Siena M, Alkhuziem M, Tang CM, Medina B, Fanta PT, Belinsky MG, von Mehren M, Thorson JA, Madlensky L, Bowler T, D'Angelo F, Stupack DG, Harismendy O, DeMatteo RP, Sicklick JK. Duodenal-Jejunal Flexure GI Stromal Tumor Frequently Heralds Somatic NF1 and Notch Pathway Mutations. JCO Precis Oncol. 2017; 2017. PMID: 29938249.
      View in: PubMed
    5. Zong N, Kim H, Ngo V, Harismendy O. Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations. Bioinformatics. 2017 Aug 01; 33(15):2337-2344. PMID: 28430977.
      View in: PubMed
    6. Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics. 2017 06 12; 18(1):458. PMID: 28606096.
      View in: PubMed
    7. Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA. iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Stem Cell Reports. 2017 04 11; 8(4):1086-1100. PMID: 28410642.
      View in: PubMed
    8. Delaney JR, Patel CB, Willis KM, Haghighiabyaneh M, Axelrod J, Tancioni I, Lu D, Bapat J, Young S, Cadassou O, Bartakova A, Sheth P, Haft C, Hui S, Saenz C, Schlaepfer DD, Harismendy O, Stupack DG. Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer. Nat Commun. 2017 Feb 15; 8:14423. PMID: 28198375.
      View in: PubMed
    9. Kim J, Shimizu C, Kingsmore SF, Veeraraghavan N, Levy E, Ribeiro Dos Santos AM, Yang H, Flatley J, Hoang LT, Hibberd ML, Tremoulet AH, Harismendy O, Ohno-Machado L, Burns JC. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLoS One. 2017; 12(2):e0170977. PMID: 28151979.
      View in: PubMed
    10. Shi E, Chmielecki J, Tang CM, Wang K, Heinrich MC, Kang G, Corless CL, Hong D, Fero KE, Murphy JD, Fanta PT, Ali SM, De Siena M, Burgoyne AM, Movva S, Madlensky L, Heestand GM, Trent JC, Kurzrock R, Morosini D, Ross JS, Harismendy O, Sicklick JK. FGFR1 and NTRK3 actionable alterations in "Wild-Type" gastrointestinal stromal tumors. J Transl Med. 2016 12 14; 14(1):339. PMID: 27974047.
      View in: PubMed
    11. Tang CM, Lee TE, Syed SA, Burgoyne AM, Leonard SY, Gao F, Chan JC, Shi E, Chmielecki J, Morosini D, Wang K, Ross JS, Kendrick ML, Bardsley MR, Siena M, Mao J, Harismendy O, Ordog T, Sicklick JK. Hedgehog pathway dysregulation contributes to the pathogenesis of human gastrointestinal stromal tumors via GLI-mediated activation of KIT expression. Oncotarget. 2016 Nov 29; 7(48):78226-78241. PMID: 27793025.
      View in: PubMed
    12. Saddawi-Konefka R, Seelige R, Gross ET, Levy E, Searles SC, Washington A, Santosa EK, Liu B, O'Sullivan TE, Harismendy O, Bui JD. Nrf2 Induces IL-17D to Mediate Tumor and Virus Surveillance. Cell Rep. 2016 08 30; 16(9):2348-58. PMID: 27545889; PMCID: PMC5007173.
    13. Levy E, Marty R, Gárate Calderón V, Woo B, Dow M, Armisen R, Carter H, Harismendy O. Immune DNA signature of T-cell infiltration in breast tumor exomes. Sci Rep. 2016 07 25; 6:30064. PMID: 27452728.
      View in: PubMed
    14. Schwaederle M, Husain H, Fanta PT, Piccioni DE, Kesari S, Schwab RB, Patel SP, Harismendy O, Ikeda M, Parker BA, Kurzrock R. Use of Liquid Biopsies in Clinical Oncology: Pilot Experience in 168 Patients. Clin Cancer Res. 2016 Nov 15; 22(22):5497-5505. PMID: 27185373.
      View in: PubMed
    15. Boland BS, Bagi P, Valasek MA, Chang JT, Bustamante R, Madlensky L, Sandborn WJ, Harismendy O, Gupta S. Cronkhite Canada Syndrome: Significant Response to Infliximab and a Possible Clue to Pathogenesis. Am J Gastroenterol. 2016 05; 111(5):746-8. PMID: 27151126.
      View in: PubMed
    16. Bao L, Messer K, Schwab R, Harismendy O, Pu M, Crain B, Yost S, Frazer KA, Rana B, Hasteh F, Wallace A, Parker BA. Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors. PLoS One. 2015; 10(11):e0142487. PMID: 26554380; PMCID: PMC4640562.
    17. Berlth F, Mönig S, Pinther B, Grimminger P, Maus M, Schlösser H, Plum P, Warnecke-Eberz U, Harismendy O, Drebber U, Bollschweiler E, Hölscher A, Alakus H. Both GLUT-1 and GLUT-14 are Independent Prognostic Factors in Gastric Adenocarcinoma. Ann Surg Oncol. 2015 Dec; 22 Suppl 3:S822-31. PMID: 26183839.
      View in: PubMed
    18. Kozono D, Li J, Nitta M, Sampetrean O, Gonda D, Kushwaha DS, Merzon D, Ramakrishnan V, Zhu S, Zhu K, Matsui H, Harismendy O, Hua W, Mao Y, Kwon CH, Saya H, Nakano I, Pizzo DP, VandenBerg SR, Chen CC. Dynamic epigenetic regulation of glioblastoma tumorigenicity through LSD1 modulation of MYC expression. Proc Natl Acad Sci U S A. 2015 Jul 28; 112(30):E4055-64. PMID: 26159421; PMCID: PMC4522819.
    19. Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM, Harismendy O. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. J Transl Med. 2015 Apr 16; 13:122. PMID: 25889843; PMCID: PMC4422481.
    20. Boland BS, Widjaja CE, Banno A, Zhang B, Kim SH, Stoven S, Peterson MR, Jones MC, Su HI, Crowe SE, Bui JD, Ho SB, Okugawa Y, Goel A, Marietta EV, Khosroheidari M, Jepsen K, Aramburu J, López-Rodríguez C, Sandborn WJ, Murray JA, Harismendy O, Chang JT. Immunodeficiency and autoimmune enterocolopathy linked to NFAT5 haploinsufficiency. J Immunol. 2015 Mar 15; 194(6):2551-60. PMID: 25667416; PMCID: PMC4355235.
    21. Alakus H, Babicky ML, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels ML, Mose ES, Schwab RB, Peterson MR, Lowy AM, Frazer KA, Harismendy O. Correction: Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med. 2014; 6(7):53. PMID: 25228923; PMCID: PMC4165363.
    22. Cheng CP, Kuo IY, Alakus H, Frazer KA, Harismendy O, Wang YC, Tseng VS. Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. Bioinformatics. 2014 Nov 01; 30(21):3054-61. PMID: 25015989; PMCID: PMC4609006.
    23. Alakus H, Bollschweiler E, Hölscher AH, Warnecke-Eberz U, Frazer KA, Harismendy O, Lowy AM, Mönig SP, Eberz PM, Maus M, Drebber U, Siffert W, Metzger R. Homozygous GNAS 393C-allele carriers with locally advanced esophageal cancer fail to benefit from platinum-based preoperative chemoradiotherapy. Ann Surg Oncol. 2014 Dec; 21(13):4375-82. PMID: 24986238.
      View in: PubMed
    24. Alakus H, Babicky ML, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels ML, Mose ES, Schwab RB, Peterson MR, Lowy AM, Frazer KA, Harismendy O. Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med. 2014; 6(5):43. PMID: 24944587; PMCID: PMC4062050.
    25. Harismendy O, Schwab RB, Alakus H, Yost SE, Matsui H, Hasteh F, Wallace AM, Park HL, Madlensky L, Parker B, Carpenter PM, Jepsen K, Anton-Culver H, Frazer KA. Evaluation of ultra-deep targeted sequencing for personalized breast cancer care. Breast Cancer Res. 2013 Dec 10; 15(6):R115. PMID: 24326041; PMCID: PMC3978701.
    26. He G, Dhar D, Nakagawa H, Font-Burgada J, Ogata H, Jiang Y, Shalapour S, Seki E, Yost SE, Jepsen K, Frazer KA, Harismendy O, Hatziapostolou M, Iliopoulos D, Suetsugu A, Hoffman RM, Tateishi R, Koike K, Karin M. Identification of liver cancer progenitors whose malignant progression depends on autocrine IL-6 signaling. Cell. 2013 Oct 10; 155(2):384-96. PMID: 24120137; PMCID: PMC4015514.
    27. DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. PLoS One. 2013; 8(9):e73956. PMID: 24023918; PMCID: PMC3762708.
    28. Yost SE, Alakus H, Matsui H, Schwab RB, Jepsen K, Frazer KA, Harismendy O. Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing. Bioinformatics. 2013 Aug 01; 29(15):1908-9. PMID: 23712659; PMCID: PMC3712217.
    29. Barrett CL, Schwab RB, Jung H, Crain B, Goff DJ, Jamieson CH, Thistlethwaite PA, Harismendy O, Carson DA, Frazer KA. Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. PLoS One. 2013; 8(3):e58714. PMID: 23527012; PMCID: PMC3604164.
    30. Yost SE, Pastorino S, Rozenzhak S, Smith EN, Chao YS, Jiang P, Kesari S, Frazer KA, Harismendy O. High-resolution mutational profiling suggests the genetic validity of glioblastoma patient-derived pre-clinical models. PLoS One. 2013; 8(2):e56185. PMID: 23441165; PMCID: PMC3575368.
    31. Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer KA. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res. 2012 Aug; 40(14):e107. PMID: 22492626; PMCID: PMC3413110.
    32. Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ. Genomics in 2011: challenges and opportunities. Genome Biol. 2011 Dec 28; 12(12):137. PMID: 22204305; PMCID: PMC3334607.
    33. Harismendy O, Schwab RB, Bao L, Olson J, Rozenzhak S, Kotsopoulos SK, Pond S, Crain B, Chee MS, Messer K, Link DR, Frazer KA. Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol. 2011 Dec 20; 12(12):R124. PMID: 22185227; PMCID: PMC3334619.
    34. Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011 Apr 15; 27(8):1068-75. PMID: 21330288; PMCID: PMC3072550.
    35. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA. 9p21 DNA variants associated with coronary artery disease impair interferon-? signalling response. Nature. 2011 Feb 10; 470(7333):264-8. PMID: 21307941; PMCID: PMC3079517.
    36. Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Sipe JC, Murray SS, Deleuze JF, Bafna V, Topol EJ, Frazer KA. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol. 2010; 11(11):R118. PMID: 21118518; PMCID: PMC3156957.
    37. Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010 Oct 14; 6(10):e1000954. PMID: 20976246.
      View in: PubMed
    38. Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 2010 Apr; 20(4):537-45. PMID: 20150320; PMCID: PMC2847757.
    39. Sipe JC, Scott TM, Murray S, Harismendy O, Simon GM, Cravatt BF, Waalen J. Biomarkers of endocannabinoid system activation in severe obesity. PLoS One. 2010 Jan 20; 5(1):e8792. PMID: 20098695.
      View in: PubMed
    40. Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol. 2009 Nov; 27(11):1025-31. PMID: 19881494; PMCID: PMC2779736.
    41. Tewhey R, Nakano M, Wang X, Pabón-Peña C, Novak B, Giuffre A, Lin E, Happe S, Roberts DN, LeProust EM, Topol EJ, Harismendy O, Frazer KA. Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol. 2009; 10(10):R116. PMID: 19835619; PMCID: PMC2784331.
    42. Harismendy O, Frazer KA. Elucidating the role of 8q24 in colorectal cancer. Nat Genet. 2009 Aug; 41(8):868-9. PMID: 19639026.
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    43. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009; 10(3):R32. PMID: 19327155; PMCID: PMC2691003.
    44. Harismendy O, Frazer K. Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques. 2009 Mar; 46(3):229-31. PMID: 19317667.
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    45. Rahim NG, Harismendy O, Topol EJ, Frazer KA. Genetic determinants of phenotypic diversity in humans. Genome Biol. 2008 Apr 24; 9(4):215. PMID: 18439327.
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    46. Ciesla M, Towpik J, Graczyk D, Oficjalska-Pham D, Harismendy O, Suleau A, Balicki K, Conesa C, Lefebvre O, Boguta M. Maf1 is involved in coupling carbon metabolism to RNA polymerase III transcription. Mol Cell Biol. 2007 Nov; 27(21):7693-702. PMID: 17785443; PMCID: PMC2169064.
    47. Guffanti E, Percudani R, Harismendy O, Soutourina J, Werner M, Iacovella MG, Negri R, Dieci G. Nucleosome depletion activates poised RNA polymerase III at unconventional transcription sites in Saccharomyces cerevisiae. J Biol Chem. 2006 Sep 29; 281(39):29155-64. PMID: 16816405.
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    48. Guffanti E, Ferrari R, Preti M, Forloni M, Harismendy O, Lefebvre O, Dieci G. A minimal promoter for TFIIIC-dependent in vitro transcription of snoRNA and tRNA genes by RNA polymerase III. J Biol Chem. 2006 Aug 18; 281(33):23945-57. PMID: 16787917.
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    49. Oficjalska-Pham D, Harismendy O, Smagowicz WJ, Gonzalez de Peredo A, Boguta M, Sentenac A, Lefebvre O. General repression of RNA polymerase III transcription is triggered by protein phosphatase type 2A-mediated dephosphorylation of Maf1. Mol Cell. 2006 Jun 09; 22(5):623-32. PMID: 16762835.
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    50. Harismendy O, Gendrel CG, Soularue P, Gidrol X, Sentenac A, Werner M, Lefebvre O. Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J. 2003 Sep 15; 22(18):4738-47. PMID: 12970186; PMCID: PMC212732.