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Items: 1 to 50 of 60

1.

Illuminating the Onco-GPCRome: Novel G protein-coupled receptor-driven oncocrine networks and targets for cancer immunotherapy.

Wu V, Yeerna H, Nohata N, Chiou J, Harismendy O, Raimondi F, Inoue A, Russell RB, Tamayo P, Gutkind JS.

J Biol Chem. 2019 Jun 5. pii: jbc.REV119.005601. doi: 10.1074/jbc.REV119.005601. [Epub ahead of print] Review.

2.

Activation of Hedgehog signaling associates with early disease progression in chronic lymphocytic leukemia.

Ghia EM, Rassenti LZ, Neuberg DS, Blanco A, Yousif F, Smith EN, McPherson JD, Hudson TJ, Harismendy O, Frazer KA, Kipps TJ.

Blood. 2019 Mar 28. pii: blood-2018-09-873695. doi: 10.1182/blood-2018-09-873695. [Epub ahead of print]

PMID:
30923040
3.

Evaluating and sharing global genetic ancestry in biomedical datasets.

Harismendy O, Kim J, Xu X, Ohno-Machado L.

J Am Med Inform Assoc. 2019 May 1;26(5):457-461. doi: 10.1093/jamia/ocy194.

4.

Inhibition of mTOR Signaling and Clinical Activity of Rapamycin in Head and Neck Cancer in a Window of Opportunity Trial.

Day TA, Shirai K, O'Brien PE, Matheus MG, Godwin K, Sood AJ, Kompelli A, Vick JA, Martin D, Vitale-Cross L, Callejas-Varela JL, Wang Z, Wu X, Harismendy O, Molinolo AA, Lippman SM, Van Waes C, Szabo E, Gutkind JS.

Clin Cancer Res. 2019 Feb 15;25(4):1156-1164. doi: 10.1158/1078-0432.CCR-18-2024. Epub 2018 Nov 12.

PMID:
30420444
5.

ADAR1-mediated RNA-editing of 3'UTRs in breast cancer.

Sagredo EA, Blanco A, Sagredo AI, Pérez P, Sepúlveda-Hermosilla G, Morales F, Müller B, Verdugo R, Marcelain K, Harismendy O, Armisén R.

Biol Res. 2018 Oct 5;51(1):36. doi: 10.1186/s40659-018-0185-4.

6.

Integrative genomic analysis of mouse and human hepatocellular carcinoma.

Dow M, Pyke RM, Tsui BY, Alexandrov LB, Nakagawa H, Taniguchi K, Seki E, Harismendy O, Shalapour S, Karin M, Carter H, Font-Burgada J.

Proc Natl Acad Sci U S A. 2018 Oct 16;115(42):E9879-E9888. doi: 10.1073/pnas.1811029115. Epub 2018 Oct 4.

7.

Prognostic Importance of Age, Tumor Location, and Tumor Grade in Grade II Astrocytomas: An Integrated Analysis of the Cancer Genome Atlas and the Surveillance, Epidemiology, and End Results Database.

Alattar AA, Carroll KT, Bryant AK, Hirshman B, Joshi R, Carter BS, Harismendy O, Chen CC.

World Neurosurg. 2019 Jan;121:e411-e418. doi: 10.1016/j.wneu.2018.09.124. Epub 2018 Sep 26.

PMID:
30266697
8.

Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas.

Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ.

Genome Med. 2018 Sep 14;10(1):69. doi: 10.1186/s13073-018-0579-5.

9.

Nuclear respiratory factor 1 promotes spheroid survival and mesenchymal transition in mammary epithelial cells.

Zhou Y, Xu Z, Quan D, Zhang F, Zhang H, Xiao T, Hou S, Qiao H, Harismendy O, Wang JYJ, Suo G.

Oncogene. 2018 Nov;37(47):6152-6165. doi: 10.1038/s41388-018-0349-2. Epub 2018 Jul 11.

10.

Interaction Between the Contributions of Tumor Location, Tumor Grade, and Patient Age to the Survival Benefit Associated with Gross Total Resection.

Carroll KT, Bryant AK, Hirshman B, Alattar AA, Joshi R, Gabel B, Carter BS, Harismendy O, Vaida F, Chen CC.

World Neurosurg. 2018 Mar;111:e790-e798. doi: 10.1016/j.wneu.2017.12.165. Epub 2018 Jan 5.

PMID:
29309983
11.

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens.

Spahn PN, Bath T, Weiss RJ, Kim J, Esko JD, Lewis NE, Harismendy O.

Sci Rep. 2017 Nov 20;7(1):15854. doi: 10.1038/s41598-017-16193-9.

12.

Biochemical, Molecular, and Clinical Characterization of Succinate Dehydrogenase Subunit A Variants of Unknown Significance.

Bannon AE, Kent J, Forquer I, Town A, Klug LR, McCann K, Beadling C, Harismendy O, Sicklick JK, Corless C, Shinde U, Heinrich MC.

Clin Cancer Res. 2017 Nov 1;23(21):6733-6743. doi: 10.1158/1078-0432.CCR-17-1397. Epub 2017 Jul 19.

13.

Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ.

BMC Genomics. 2017 Jun 12;18(1):458. doi: 10.1186/s12864-017-3770-y.

14.

Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations.

Zong N, Kim H, Ngo V, Harismendy O.

Bioinformatics. 2017 Aug 1;33(15):2337-2344. doi: 10.1093/bioinformatics/btx160.

15.

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.

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.

Stem Cell Reports. 2017 Apr 11;8(4):1086-1100. doi: 10.1016/j.stemcr.2017.03.012.

16.

Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer.

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.

Nat Commun. 2017 Feb 15;8:14423. doi: 10.1038/ncomms14423.

17.

Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility.

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.

PLoS One. 2017 Feb 2;12(2):e0170977. doi: 10.1371/journal.pone.0170977. eCollection 2017.

18.

Duodenal-Jejunal Flexure GI Stromal Tumor Frequently Heralds Somatic NF1 and Notch Pathway Mutations.

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.

JCO Precis Oncol. 2017;2017. doi: 10.1200/PO.17.00014. Epub 2017 Aug 15.

19.

FGFR1 and NTRK3 actionable alterations in "Wild-Type" gastrointestinal stromal tumors.

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.

J Transl Med. 2016 Dec 14;14(1):339.

20.

Hedgehog pathway dysregulation contributes to the pathogenesis of human gastrointestinal stromal tumors via GLI-mediated activation of KIT expression.

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.

Oncotarget. 2016 Nov 29;7(48):78226-78241. doi: 10.18632/oncotarget.12909.

21.

Nrf2 Induces IL-17D to Mediate Tumor and Virus Surveillance.

Saddawi-Konefka R, Seelige R, Gross ET, Levy E, Searles SC, Washington A Jr, Santosa EK, Liu B, O'Sullivan TE, Harismendy O, Bui JD.

Cell Rep. 2016 Aug 30;16(9):2348-58. doi: 10.1016/j.celrep.2016.07.075. Epub 2016 Aug 18.

22.

Immune DNA signature of T-cell infiltration in breast tumor exomes.

Levy E, Marty R, Gárate Calderón V, Woo B, Dow M, Armisen R, Carter H, Harismendy O.

Sci Rep. 2016 Jul 25;6:30064. doi: 10.1038/srep30064.

23.

Use of Liquid Biopsies in Clinical Oncology: Pilot Experience in 168 Patients.

Schwaederle M, Husain H, Fanta PT, Piccioni DE, Kesari S, Schwab RB, Patel SP, Harismendy O, Ikeda M, Parker BA, Kurzrock R.

Clin Cancer Res. 2016 Nov 15;22(22):5497-5505. doi: 10.1158/1078-0432.CCR-16-0318. Epub 2016 May 16.

24.

Cronkhite Canada Syndrome: Significant Response to Infliximab and a Possible Clue to Pathogenesis.

Boland BS, Bagi P, Valasek MA, Chang JT, Bustamante R, Madlensky L, Sandborn WJ, Harismendy O, Gupta S.

Am J Gastroenterol. 2016 May;111(5):746-8. doi: 10.1038/ajg.2016.92. No abstract available.

25.

Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors.

Bao L, Messer K, Schwab R, Harismendy O, Pu M, Crain B, Yost S, Frazer KA, Rana B, Hasteh F, Wallace A, Parker BA.

PLoS One. 2015 Nov 10;10(11):e0142487. doi: 10.1371/journal.pone.0142487. eCollection 2015.

26.

Both GLUT-1 and GLUT-14 are Independent Prognostic Factors in Gastric Adenocarcinoma.

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.

Ann Surg Oncol. 2015 Dec;22 Suppl 3:S822-31. doi: 10.1245/s10434-015-4730-x. Epub 2015 Jul 17.

PMID:
26183839
27.

Dynamic epigenetic regulation of glioblastoma tumorigenicity through LSD1 modulation of MYC expression.

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.

Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):E4055-64. doi: 10.1073/pnas.1501967112. Epub 2015 Jul 9.

28.

BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma.

Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM, Harismendy O.

J Transl Med. 2015 Apr 16;13:122. doi: 10.1186/s12967-015-0485-1.

29.

Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development.

Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, 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 CH, Carson DA, Kipps TJ, Frazer KA.

Blood Cancer J. 2015 Apr 10;5:e303. doi: 10.1038/bcj.2015.14.

30.

Immunodeficiency and autoimmune enterocolopathy linked to NFAT5 haploinsufficiency.

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.

J Immunol. 2015 Mar 15;194(6):2551-60. doi: 10.4049/jimmunol.1401463. Epub 2015 Feb 9.

31.

Correction: Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin.

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 Med. 2014 Jul 26;6(7):53. doi: 10.1186/s13073-014-0053-y. eCollection 2014. No abstract available.

32.

Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression.

Cheng CP, Kuo IY, Alakus H, Frazer KA, Harismendy O, Wang YC, Tseng VS.

Bioinformatics. 2014 Nov 1;30(21):3054-61. doi: 10.1093/bioinformatics/btu433. Epub 2014 Jul 10.

33.

Homozygous GNAS 393C-allele carriers with locally advanced esophageal cancer fail to benefit from platinum-based preoperative chemoradiotherapy.

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.

Ann Surg Oncol. 2014 Dec;21(13):4375-82. doi: 10.1245/s10434-014-3843-y. Epub 2014 Jul 2.

PMID:
24986238
34.

Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin.

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 Med. 2014 May 29;6(5):43. doi: 10.1186/gm559. eCollection 2014.

35.

Evaluation of ultra-deep targeted sequencing for personalized breast cancer care.

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.

Breast Cancer Res. 2013 Dec 10;15(6):R115. doi: 10.1186/bcr3584.

36.

Identification of liver cancer progenitors whose malignant progression depends on autocrine IL-6 signaling.

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.

Cell. 2013 Oct 10;155(2):384-96. doi: 10.1016/j.cell.2013.09.031.

37.

Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.

DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA.

PLoS One. 2013 Sep 4;8(9):e73956. doi: 10.1371/journal.pone.0073956. eCollection 2013.

38.

Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing.

Yost SE, Alakus H, Matsui H, Schwab RB, Jepsen K, Frazer KA, Harismendy O.

Bioinformatics. 2013 Aug 1;29(15):1908-9. doi: 10.1093/bioinformatics/btt305. Epub 2013 May 27.

39.

Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer.

Barrett CL, Schwab RB, Jung H, Crain B, Goff DJ, Jamieson CH, Thistlethwaite PA, Harismendy O, Carson DA, Frazer KA.

PLoS One. 2013;8(3):e58714. doi: 10.1371/journal.pone.0058714. Epub 2013 Mar 20.

40.

High-resolution mutational profiling suggests the genetic validity of glioblastoma patient-derived pre-clinical models.

Yost SE, Pastorino S, Rozenzhak S, Smith EN, Chao YS, Jiang P, Kesari S, Frazer KA, Harismendy O.

PLoS One. 2013;8(2):e56185. doi: 10.1371/journal.pone.0056185. Epub 2013 Feb 18.

41.

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens.

Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer KA.

Nucleic Acids Res. 2012 Aug;40(14):e107. Epub 2012 Apr 6.

42.

Genomics in 2011: challenges and opportunities.

Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ.

Genome Biol. 2011 Dec 28;12(12):137. doi: 10.1186/gb-2011-12-12-137.

43.

Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.

Harismendy O, Schwab RB, Bao L, Olson J, Rozenzhak S, Kotsopoulos SK, Pond S, Crain B, Chee MS, Messer K, Link DR, Frazer KA.

Genome Biol. 2011 Dec 20;12(12):R124. doi: 10.1186/gb-2011-12-12-r124.

44.

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V.

Bioinformatics. 2011 Apr 15;27(8):1068-75. doi: 10.1093/bioinformatics/btr085. Epub 2011 Feb 16.

45.

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response.

Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA.

Nature. 2011 Feb 10;470(7333):264-8. doi: 10.1038/nature09753.

46.

Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level.

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.

Genome Biol. 2010;11(11):R118. doi: 10.1186/gb-2010-11-11-r118. Epub 2010 Nov 30.

47.

A covering method for detecting genetic associations between rare variants and common phenotypes.

Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V.

PLoS Comput Biol. 2010 Oct 14;6(10):e1000954. doi: 10.1371/journal.pcbi.1000954.

48.

Accurate detection and genotyping of SNPs utilizing population sequencing data.

Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA.

Genome Res. 2010 Apr;20(4):537-45. doi: 10.1101/gr.100040.109. Epub 2010 Feb 11.

49.

Biomarkers of endocannabinoid system activation in severe obesity.

Sipe JC, Scott TM, Murray S, Harismendy O, Simon GM, Cravatt BF, Waalen J.

PLoS One. 2010 Jan 20;5(1):e8792. doi: 10.1371/journal.pone.0008792.

50.

Microdroplet-based PCR enrichment for large-scale targeted sequencing.

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.

Nat Biotechnol. 2009 Nov;27(11):1025-31. doi: 10.1038/nbt.1583. Epub 2009 Nov 1. Erratum in: Nat Biotechnol. 2010 Feb;28(2):178.

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