Publications

Dr Harismendy's full publications record is available on Google Scholar

2017

  • Waszak SM, Tiao G, Zhu B, Rausch T, Muyas F, Rodriguez-Martin B, Rabionet R, Yakneen S, Escaramis G, Li Y, Saini N, Roberts SA, Demidov GM, Pitkanen E, Delaneau O, Heredia-Genestar JM, Weischenfeldt J, Shringarpure SS, Chen J, Nakagawa H, Alexandrov LB, Drechsel O, Dursi LJ, Segre A V, Garrison E, Erkek S, Habermann N, Urban L, Khurana E, Cafferkey A, Hayashi S, Imoto S, Aaltonen LA, Alvarez EG, Baez-Ortega A, Bailey M, Bosio M, Bruzos AL, Buchhalter I, Bustamante CD, Calabrese C, DiBiase A, Gerstein M, Holik AZ, Hua X, Huang K, Letunic I, Klimczak LJ, Koster R, Kumar S, McLellan M, Mashl J, Mirabello L, Newhouse S, Prasad A, Raetsch G, Schlesner M, Schwarz R, Sharma P, Shmaya T, Sidiropoulos N, Song L, Susak H, Tanskanen T, Tojo M, Wedge DC, Wright M, Wu Y, Ye K, Yellapantula VD, Zamora J, Butte AJ, Getz G, Simpson J, Ding L, Marques-Bonet T, Navarro A, Brazma A, Campbell P, Chanock SJ, Chatterjee N, Stegle O, Siebert R, Ossowski S, Harismendy O, Gordenin DA, Tubio JMC, De La Vega FM, Easton DF, Estivill X, Korbel J. Germline determinants of the somatic mutation landscape in 2,642 cancer genomes. bioRxiv. 2017 Jan 1; 
  • Harismendy O, Kim J, Xu X, Ohno-Machado L. Sharing genetic admixture and diversity of public biomedical datasets. bioRxiv. 2017 Jan 1; 
  • 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
  • Yung CK, O'Connor BD, Yakneen S, Zhang J, Ellrott K, Kleinheinz K, Miyoshi N, Raine KM, Royo R, Saksena GB, Schlesner M, Shorser SI, Vazquez M, Weischenfeldt J, Yuen D, Butler AP, Davis-Dusenbery BN, Eils R, Ferretti V, Grossman RL, Harismendy O, Kim Y, Nakagawa H, Newhouse SJ, Torrents D, Stein LD. Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments. bioRxiv. 2017 Jan 1; 
  • Bannon AE, Kent J, Forquer I, Town A, Klug LR, McCann K, Beadling C, Harismendy O, Sicklick JK, Corless C, Shinde U, Heinrich MC. Biochemical, Molecular, and Clinical Characterization of Succinate Dehydrogenase Subunit A Variants of Unknown Significance. Clin Cancer Res. 2017 Nov 1;23(21):6733–6743. PMID: 28724664
  • Zong N, Kim H, Ngo V, Harismendy O. Deep mining heterogeneous networks of biomedical linked data to predict novel drug–target associations. Bioinformatics. 2017 Apr 18;33(15):2337–2344. PMID: 28430977
  • 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
  • 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
  • Champa D, Sun S, Tsai C-Y, Howell SB, Harismendy O. Evolution and characterization of carboplatin resistance at single cell resolution. bioRxiv. 2017 Jan 1; 
  • 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, Muller F-J, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D’Antonio-Chronowska A, Smith EN, Frazer KA, Müller F-J, 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 Apr 11;8(4):1086–1100. PMID: 28410642


2016

  • Shi E, Chmielecki J, Tang C-M, 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 Dec 14;14(1):339. PMID: 27974047
  • Tang C-M, 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 De, 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
  • 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 May;111(5):746–8. PMID: 27151126
  • Saddawi-Konefka R, Seelige R, Gross E, 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 Aug 30;(9):2348–58. PMID: 27545889
  • 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


2015

  • 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 Jan;10(11):e0142487. PMID: 26554380
  • 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 Jul 17; PMID: 26183839
  • 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 C-H, 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
  • 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(1):122. PMID: 25889843
  • 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 E V, 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 Feb 9;194(6):2551–60. PMID: 25667416
  • Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon K-A, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, Bina M, Gunderson KL, Messer K, Muthuswamy L, Hudson TJ, Harismendy O, Barrett CL, Jamieson CHM, Carson DA, Kipps TJ, Frazer KA. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. Blood Cancer J. 2015 Jan;5:e303. PMID: 25860294

2014

  • Alakus H, Bollschweiler E, Hölscher AH, Warnecke-Eberz U, Frazer KA, Harismendy O, Lowy AM, Mönig SP, Eberz PM, Maus M, others. Homozygous GNAS 393C-allele carriers with locally advanced esophageal cancer fail to benefit from platinum-based preoperative chemoradiotherapy. Ann Surg Oncol. Springer US; 2014;21(13):4375–4382. PMID:24986238
  • Cheng C-P, Kuo I-Y, Alakus H, Frazer KA, Harismendy O, Wang Y-C, Tseng VS. Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. Bioinformatics. Oxford University Press; 2014;30(21):3054–3061. PMID:25015989
  • 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 (2014) Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med. 6: 43. doi:10.1186/gm559 PMID:24944587

2013

  • Olivier Harismendy, Richard B Schwab, Hakan Alakus, Shawn E Yost, Hiroko Matsui, Farnaz Hasteh, Anne M Wallace, Hannah L Park, Lisa Madlensky, Barbara Parker, Philip M Carpenter, Kristen Jepsen, Hoda Anton-Culver and Kelly A Frazer. Evaluation of Ultra-Deep Targeted Sequencing for Personalized Breast Cancer Care. Breast Cancer Research.2013 Dec 10; 15(6):R115, doi:10.1186/bcr3584. Pubmed PMID:24326041
  • Guobin He, Debanjan Dhar, Hayato Nakagawa, Joan Font-Burgada, Hisanobu Ogata, Yuhong Jiang, Shabnam Shalapour, Ekihiro Seki, Shawn E Yost, Kristen Jepsen, Kelly A Frazer, Olivier Harismendy, Maria Hatziapostolou, Dimitrios Iliopoulos, Atsushi Suetsugu, Robert M Hoffman, Ryosuke Tateishi, Kazuhiko Koike, Michael Karin. Identification of Liver Cancer Progenitors Whose Malignant Progression Depends on Autocrine IL-6 Signaling. Cell. 2013 Oct 10; 155(2): 384-396, doi: 10.1016/j.cell.2013.09.031. Epub 2013 Oct 11. Pubmed PMID:24120137
  • Christopher DeBoever, Erin G. Reid, Erin N. Smith, Xiaoyun Wang, Wilmar Dumaop, Olivier Harismendy, Dennis Carson, Douglas Richman, Eliezer Masliah, Kelly A. Frazer. Whole Transcriptome Sequencing Enables Discovery and Analysis of Viruses in Archived Primary Central Nervous System Lymphomas. PLoS ONE. 2013 Sept 4: 8(9): e73956. doi:10.1371/journal.pone.0073956. Pubmed PMID:24023918
  • Shawn E. Yost, Hakan Alakus, Hiroko Matsui, Richard B. Schwab, Kristen Jepsen, Kelly A. Frazer, and Olivier Harismendy. Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing. Bioinformatics. 2013 May 27: 29(15) 1908–1909. doi: 10.1093/bioinformatics/btt305. Epub 2013 May 27. Pubmed PMID:23712659
  • Barrett CL, Schwab RB, Jung H, Crain B, Goff DJ, et al. (2013) Transcriptome Sequencing of Tumor Subpopulations Reveals a Spectrum of Therapeutic Options for Squamous Cell Lung Cancer. PLoS ONE 8(3): e58714. doi:10.1371/journal.pone.0058714
  • Yost SE, Pastorino S, Rozenzhak S, Smith EN, Chao YS, et al. (2013) High-Resolution Mutational Profiling Suggests the Genetic Validity of Glioblastoma Patient-Derived Pre-Clinical Models. PLoS ONE 8(2): e56185. doi:10.1371/journal.pone.0056185. Pubmed PMID: 23441165

2012

  • 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. Epub 2012 Apr 6. Pubmed PMID: 22492626

2011

  • Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, et al. Genome Biol. 2011 12: 137. Genomics in 2011: challenges and opportunities. Pubmed PMD: 22204305
  • 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. [Epub ahead of print]. Pubmed PMID: 22185227
  • 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):1068-1075. Epub 2011 Feb 16. PubMed PMID: 21330288
  • 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.PubMed PMID: 21307941

2010

  • Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang XC, 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 Nov 30;11(11):R118. PubMed PMID: 21118518
  • 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. PubMed PMID: 20976246.
  • 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. Epub 2010 Feb 11. PubMed PMID: 20150320.

2009

  • 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. Epub 2009 Nov 1. PubMed PMID: 19881494.
  • 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 Oct 16;10(10):R116. PubMed PMID: 19835619.
  • Harismendy O, Frazer KA. Elucidating the role of 8q24 in colorectal cancer. Nat Genet. 2009 Aug;41(8):868-9. Erratum in: Nat Genet. 2009 Oct;41(10):1156. PubMed PMID: 19639026.
  • 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. Epub 2009 Mar 27. PubMed PMID: 19327155; PubMed Central PMCID: PMC2691003.
  • 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.
  • Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet. 2009 Apr;10(4):241-51. Review. PubMed PMID: 19293820.

2008

  • Rahim NG, Harismendy O, Topol EJ, Frazer KA. Genetic determinants of phenotypic diversity in humans. Genome Biol. 2008 Apr 24;9(4):215. [Epub ahead of print] PubMed PMID: 18439327; PubMed Central PMCID: PMC2643926.