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Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction.

Abelin JG, Harjanto D, Malloy M, Suri P, Colson T, Goulding SP, Creech AL, Serrano LR, Nasir G, Nasrullah Y, McGann CD, Velez D, Ting YS, Poran A, Rothenberg DA, Chhangawala S, Rubinsteyn A, Hammerbacher J, Gaynor RB, Fritsch EF, Greshock J, Oslund RC, Barthelme D, Addona TA, Arieta CM, Rooney MS.

Immunity. 2019 Oct 15;51(4):766-779.e17. doi: 10.1016/j.immuni.2019.08.012. Epub 2019 Sep 5.


High-Order Drug Combinations Are Required to Effectively Kill Colorectal Cancer Cells.

Horn T, Ferretti S, Ebel N, Tam A, Ho S, Harbinski F, Farsidjani A, Zubrowski M, Sellers WR, Schlegel R, Porter D, Morris E, Wuerthner J, Jeay S, Greshock J, Halilovic E, Garraway LA, Caponigro G, Lehár J.

Cancer Res. 2016 Dec 1;76(23):6950-6963. Epub 2016 Sep 22.


Targeted Exome Sequencing of the Cancer Genome in Patients with Very High-risk Bladder Cancer.

Longo T, McGinley KF, Freedman JA, Etienne W, Wu Y, Sibley A, Owzar K, Gresham J, Moy C, Szabo S, Greshock J, Zhou H, Bai Y, Inman BA.

Eur Urol. 2016 Nov;70(5):714-717. doi: 10.1016/j.eururo.2016.07.049. Epub 2016 Aug 9.


Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors.

Frampton GM, Ali SM, Rosenzweig M, Chmielecki J, Lu X, Bauer TM, Akimov M, Bufill JA, Lee C, Jentz D, Hoover R, Ou SH, Salgia R, Brennan T, Chalmers ZR, Jaeger S, Huang A, Elvin JA, Erlich R, Fichtenholtz A, Gowen KA, Greenbowe J, Johnson A, Khaira D, McMahon C, Sanford EM, Roels S, White J, Greshock J, Schlegel R, Lipson D, Yelensky R, Morosini D, Ross JS, Collisson E, Peters M, Stephens PJ, Miller VA.

Cancer Discov. 2015 Aug;5(8):850-9. doi: 10.1158/2159-8290.CD-15-0285. Epub 2015 May 13.


A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer.

Hu X, Feng Y, Zhang D, Zhao SD, Hu Z, Greshock J, Zhang Y, Yang L, Zhong X, Wang LP, Jean S, Li C, Huang Q, Katsaros D, Montone KT, Tanyi JL, Lu Y, Boyd J, Nathanson KL, Li H, Mills GB, Zhang L.

Cancer Cell. 2014 Sep 8;26(3):344-357. doi: 10.1016/j.ccr.2014.07.009.


Good practice guidelines for biomarker discovery from array data: a case study for breast cancer prognosis.

Cheng J, Greshock J, Shi L, Zheng S, Menius A, Lee K.

BMC Syst Biol. 2013;7 Suppl 4:S2. doi: 10.1186/1752-0509-7-S4-S2. Epub 2013 Oct 23.


Quinoline 3-sulfonamides inhibit lactate dehydrogenase A and reverse aerobic glycolysis in cancer cells.

Billiard J, Dennison JB, Briand J, Annan RS, Chai D, Colón M, Dodson CS, Gilbert SA, Greshock J, Jing J, Lu H, McSurdy-Freed JE, Orband-Miller LA, Mills GB, Quinn CJ, Schneck JL, Scott GF, Shaw AN, Waitt GM, Wooster RF, Duffy KJ.

Cancer Metab. 2013 Sep 6;1(1):19. doi: 10.1186/2049-3002-1-19.


Tumor genetic analyses of patients with metastatic melanoma treated with the BRAF inhibitor dabrafenib (GSK2118436).

Nathanson KL, Martin AM, Wubbenhorst B, Greshock J, Letrero R, D'Andrea K, O'Day S, Infante JR, Falchook GS, Arkenau HT, Millward M, Brown MP, Pavlick A, Davies MA, Ma B, Gagnon R, Curtis M, Lebowitz PF, Kefford R, Long GV.

Clin Cancer Res. 2013 Sep 1;19(17):4868-78. doi: 10.1158/1078-0432.CCR-13-0827. Epub 2013 Jul 5.


Lapatinib inhibits the growth of esophageal squamous cell carcinoma and synergistically interacts with 5-fluorouracil in patient-derived xenograft models.

Hou W, Qin X, Zhu X, Fei M, Liu P, Liu L, Moon H, Zhang P, Greshock J, Bachman KE, Ye BC, Wang H, Zang CY.

Oncol Rep. 2013 Aug;30(2):707-14. doi: 10.3892/or.2013.2500. Epub 2013 May 27.


Loss and reduced expression of PTEN correlate with advanced-stage gastric carcinoma.

Zhu X, Qin X, Fei M, Hou W, Greshock J, Bachman KE, Kang J, Qin CY.

Exp Ther Med. 2013 Jan;5(1):57-64. Epub 2012 Oct 15.


High overexpression of fatty acid synthase is associated with poor survival in Chinese patients with gastric carcinoma.

Hou W, Fei M, Qin X, Zhu X, Greshock J, Liu P, Zhou Y, Wang H, Ye BC, Qin CY.

Exp Ther Med. 2012 Dec;4(6):999-1004. Epub 2012 Sep 27.


Genomic DNA copy-number alterations of the let-7 family in human cancers.

Wang Y, Hu X, Greshock J, Shen L, Yang X, Shao Z, Liang S, Tanyi JL, Sood AK, Zhang L.

PLoS One. 2012;7(9):e44399. doi: 10.1371/journal.pone.0044399. Epub 2012 Sep 6.


Combined phosphatase and tensin homolog (PTEN) loss and fatty acid synthase (FAS) overexpression worsens the prognosis of Chinese patients with hepatocellular carcinoma.

Zhu X, Qin X, Fei M, Hou W, Greshock J, Bachman KE, Wooster R, Kang J, Qin CY.

Int J Mol Sci. 2012;13(8):9980-91. doi: 10.3390/ijms13089980. Epub 2012 Aug 10.


Predicting breast cancer chemotherapeutic response using a novel tool for microarray data analysis.

Cheng J, Greshock J, Painter J, Lin X, Lee K, Zheng S, Menius A.

J Integr Bioinform. 2012 Aug 2;9(2):209. doi: 10.2390/biecoll-jib-2012-209.


Systematic analysis of genotype-specific drug responses in cancer.

Kim N, He N, Kim C, Zhang F, Lu Y, Yu Q, Stemke-Hale K, Greshock J, Wooster R, Yoon S, Mills GB.

Int J Cancer. 2012 Nov 15;131(10):2456-64. doi: 10.1002/ijc.27529. Epub 2012 Mar 29.


Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood.

Higgins MJ, Jelovac D, Barnathan E, Blair B, Slater S, Powers P, Zorzi J, Jeter SC, Oliver GR, Fetting J, Emens L, Riley C, Stearns V, Diehl F, Angenendt P, Huang P, Cope L, Argani P, Murphy KM, Bachman KE, Greshock J, Wolff AC, Park BH.

Clin Cancer Res. 2012 Jun 15;18(12):3462-9. doi: 10.1158/1078-0432.CCR-11-2696. Epub 2012 Mar 15.


Comprehensive predictive biomarker analysis for MEK inhibitor GSK1120212.

Jing J, Greshock J, Holbrook JD, Gilmartin A, Zhang X, McNeil E, Conway T, Moy C, Laquerre S, Bachman K, Wooster R, Degenhardt Y.

Mol Cancer Ther. 2012 Mar;11(3):720-9. doi: 10.1158/1535-7163.MCT-11-0505. Epub 2011 Dec 14.


A combined array-based comparative genomic hybridization and functional library screening approach identifies mir-30d as an oncomir in cancer.

Li N, Kaur S, Greshock J, Lassus H, Zhong X, Wang Y, Leminen A, Shao Z, Hu X, Liang S, Katsaros D, Huang Q, Bützow R, Weber BL, Coukos G, Zhang L.

Cancer Res. 2012 Jan 1;72(1):154-64. doi: 10.1158/0008-5472.CAN-11-2484. Epub 2011 Nov 4.


Subtype and pathway specific responses to anticancer compounds in breast cancer.

Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, Jakkula L, Korkola JE, Durinck S, Pepin F, Guan Y, Purdom E, Neuvial P, Bengtsson H, Wood KW, Smith PG, Vassilev LT, Hennessy BT, Greshock J, Bachman KE, Hardwicke MA, Park JW, Marton LJ, Wolf DM, Collisson EA, Neve RM, Mills GB, Speed TP, Feiler HS, Wooster RF, Haussler D, Stuart JM, Gray JW, Spellman PT.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2724-9. doi: 10.1073/pnas.1018854108. Epub 2011 Oct 14.


High chromosome number in hematological cancer cell lines is a negative predictor of response to the inhibition of Aurora B and C by GSK1070916.

Moy C, Oleykowski CA, Plant R, Greshock J, Jing J, Bachman K, Hardwicke MA, Wooster R, Degenhardt Y.

J Transl Med. 2011 Jul 15;9:110. doi: 10.1186/1479-5876-9-110.


Mutation and copy number detection in human cancers using a custom genotyping assay.

Moy C, Aziz MU, Greshock J, Szabo S, McNeil E, Jing J, Conway T, Degenhardt Y, Wooster R, Bachman K.

Genomics. 2011 Oct;98(4):296-301. doi: 10.1016/j.ygeno.2011.04.008. Epub 2011 May 7.


Frequent genetic abnormalities of the PI3K/AKT pathway in primary ovarian cancer predict patient outcome.

Huang J, Zhang L, Greshock J, Colligon TA, Wang Y, Ward R, Katsaros D, Lassus H, Butzow R, Godwin AK, Testa JR, Nathanson KL, Gimotty PA, Coukos G, Weber BL, Degenhardt Y.

Genes Chromosomes Cancer. 2011 Aug;50(8):606-18. doi: 10.1002/gcc.20883. Epub 2011 May 11.


Sensitivity of cancer cells to Plk1 inhibitor GSK461364A is associated with loss of p53 function and chromosome instability.

Degenhardt Y, Greshock J, Laquerre S, Gilmartin AG, Jing J, Richter M, Zhang X, Bleam M, Halsey W, Hughes A, Moy C, Liu-Sullivan N, Powers S, Bachman K, Jackson J, Weber B, Wooster R.

Mol Cancer Ther. 2010 Jul;9(7):2079-89. doi: 10.1158/1535-7163.MCT-10-0095. Epub 2010 Jun 22.


Molecular target class is predictive of in vitro response profile.

Greshock J, Bachman KE, Degenhardt YY, Jing J, Wen YH, Eastman S, McNeil E, Moy C, Wegrzyn R, Auger K, Hardwicke MA, Wooster R.

Cancer Res. 2010 May 1;70(9):3677-86. doi: 10.1158/0008-5472.CAN-09-3788. Epub 2010 Apr 20.


Antitumor activity of an allosteric inhibitor of centromere-associated protein-E.

Wood KW, Lad L, Luo L, Qian X, Knight SD, Nevins N, Brejc K, Sutton D, Gilmartin AG, Chua PR, Desai R, Schauer SP, McNulty DE, Annan RS, Belmont LD, Garcia C, Lee Y, Diamond MA, Faucette LF, Giardiniere M, Zhang S, Sun CM, Vidal JD, Lichtsteiner S, Cornwell WD, Greshock JD, Wooster RF, Finer JT, Copeland RA, Huang PS, Morgans DJ Jr, Dhanak D, Bergnes G, Sakowicz R, Jackson JR.

Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5839-44. doi: 10.1073/pnas.0915068107. Epub 2010 Feb 18.


Distinct MHC gene expression patterns during progression of melanoma.

Degenhardt Y, Huang J, Greshock J, Horiates G, Nathanson K, Yang X, Herlyn M, Weber B.

Genes Chromosomes Cancer. 2010 Feb;49(2):144-54. doi: 10.1002/gcc.20728.


Inhibition of tumor cell growth, invasion, and metastasis by EXEL-2880 (XL880, GSK1363089), a novel inhibitor of HGF and VEGF receptor tyrosine kinases.

Qian F, Engst S, Yamaguchi K, Yu P, Won KA, Mock L, Lou T, Tan J, Li C, Tam D, Lougheed J, Yakes FM, Bentzien F, Xu W, Zaks T, Wooster R, Greshock J, Joly AH.

Cancer Res. 2009 Oct 15;69(20):8009-16. doi: 10.1158/0008-5472.CAN-08-4889. Epub 2009 Oct 6.


Novel mechanism of lapatinib resistance in HER2-positive breast tumor cells: activation of AXL.

Liu L, Greger J, Shi H, Liu Y, Greshock J, Annan R, Halsey W, Sathe GM, Martin AM, Gilmer TM.

Cancer Res. 2009 Sep 1;69(17):6871-8. doi: 10.1158/0008-5472.CAN-08-4490. Epub 2009 Aug 11.


Distinct patterns of DNA copy number alterations associate with BRAF mutations in melanomas and melanoma-derived cell lines.

Greshock J, Nathanson K, Medina A, Ward MR, Herlyn M, Weber BL, Zaks TZ.

Genes Chromosomes Cancer. 2009 May;48(5):419-28. doi: 10.1002/gcc.20651.


MicroRNA microarray identifies Let-7i as a novel biomarker and therapeutic target in human epithelial ovarian cancer.

Yang N, Kaur S, Volinia S, Greshock J, Lassus H, Hasegawa K, Liang S, Leminen A, Deng S, Smith L, Johnstone CN, Chen XM, Liu CG, Huang Q, Katsaros D, Calin GA, Weber BL, Bützow R, Croce CM, Coukos G, Zhang L.

Cancer Res. 2008 Dec 15;68(24):10307-14. doi: 10.1158/0008-5472.CAN-08-1954.


Ultraconserved elements: genomics, function and disease.

Baira E, Greshock J, Coukos G, Zhang L.

RNA Biol. 2008 Jul-Sep;5(3):132-4. Epub 2008 Jul 25. Review.


Method of primary tumor detection as a risk factor for local and distant recurrence after breast-conservation treatment for early-stage breast cancer.

Tchou J, Greshock J, Bergey MR, Sonnad SS, Sargen M, Weinstein S, Czerniecki BJ, Boraas M, Fraker DL, Rosato E, Fox K, Weber B, Solin LJ.

Clin Breast Cancer. 2008 Apr;8(2):143-8. doi: 10.3816/CBC.2008.n.014.


Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer.

Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, Yang N, Liu CG, Giannakakis A, Alexiou P, Hasegawa K, Johnstone CN, Megraw MS, Adams S, Lassus H, Huang J, Kaur S, Liang S, Sethupathy P, Leminen A, Simossis VA, Sandaltzopoulos R, Naomoto Y, Katsaros D, Gimotty PA, DeMichele A, Huang Q, Bützow R, Rustgi AK, Weber BL, Birrer MJ, Hatzigeorgiou AG, Croce CM, Coukos G.

Proc Natl Acad Sci U S A. 2008 May 13;105(19):7004-9. doi: 10.1073/pnas.0801615105. Epub 2008 May 5.


Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines.

Greshock J, Cheng J, Rusnak D, Martin AM, Wooster R, Gilmer T, Lee K, Weber BL, Zaks T.

Mol Cancer Ther. 2008 Apr;7(4):935-43. doi: 10.1158/1535-7163.MCT-07-2072.


Transcriptional regulation of PIK3CA oncogene by NF-kappaB in ovarian cancer microenvironment.

Yang N, Huang J, Greshock J, Liang S, Barchetti A, Hasegawa K, Kim S, Giannakakis A, Li C, O'Brien-Jenkins A, Katsaros D, Bützow R, Coukos G, Zhang L.

PLoS One. 2008 Mar 12;3(3):e1758. doi: 10.1371/journal.pone.0001758.


miR-210 links hypoxia with cell cycle regulation and is deleted in human epithelial ovarian cancer.

Giannakakis A, Sandaltzopoulos R, Greshock J, Liang S, Huang J, Hasegawa K, Li C, O'Brien-Jenkins A, Katsaros D, Weber BL, Simon C, Coukos G, Zhang L.

Cancer Biol Ther. 2008 Feb;7(2):255-64. Epub 2007 Nov 14.


DNA copy number data analysis using the CGHAnalyzer software suite.

Greshock J.

Methods Mol Biol. 2007;396:255-66.


A comparison of DNA copy number profiling platforms.

Greshock J, Feng B, Nogueira C, Ivanova E, Perna I, Nathanson K, Protopopov A, Weber BL, Chin L.

Cancer Res. 2007 Nov 1;67(21):10173-80. Epub 2007 Oct 29.


Integrative genomic analysis of phosphatidylinositol 3'-kinase family identifies PIK3R3 as a potential therapeutic target in epithelial ovarian cancer.

Zhang L, Huang J, Yang N, Greshock J, Liang S, Hasegawa K, Giannakakis A, Poulos N, O'Brien-Jenkins A, Katsaros D, Butzow R, Weber BL, Coukos G.

Clin Cancer Res. 2007 Sep 15;13(18 Pt 1):5314-21.


Cancer cell lines as genetic models of their parent histology: analyses based on array comparative genomic hybridization.

Greshock J, Nathanson K, Martin AM, Zhang L, Coukos G, Weber BL, Zaks TZ.

Cancer Res. 2007 Apr 15;67(8):3594-600.


STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments.

Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr, Weber BL, Maris JM, Grant GR.

Genome Res. 2006 Sep;16(9):1149-58. Epub 2006 Aug 9.


microRNAs exhibit high frequency genomic alterations in human cancer.

Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O'brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G.

Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9136-41. Epub 2006 Jun 5.


High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization.

Naylor TL, Greshock J, Wang Y, Colligon T, Yu QC, Clemmer V, Zaks TZ, Weber BL.

Breast Cancer Res. 2005;7(6):R1186-98. Epub 2005 Nov 24.


Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization.

Jönsson G, Naylor TL, Vallon-Christersson J, Staaf J, Huang J, Ward MR, Greshock JD, Luts L, Olsson H, Rahman N, Stratton M, Ringnér M, Borg A, Weber BL.

Cancer Res. 2005 Sep 1;65(17):7612-21.


Measurement and relevance of neuroblastoma DNA copy number changes in the post-genome era.

Mosse YP, Greshock J, Weber BL, Maris JM.

Cancer Lett. 2005 Oct 18;228(1-2):83-90. Review.


CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.

Margolin AA, Greshock J, Naylor TL, Mosse Y, Maris JM, Bignell G, Saeed AI, Quackenbush J, Weber BL.

Bioinformatics. 2005 Aug 1;21(15):3308-11. Epub 2005 May 19.


High-resolution detection and mapping of genomic DNA alterations in neuroblastoma.

Mosse YP, Greshock J, Margolin A, Naylor T, Cole K, Khazi D, Hii G, Winter C, Shahzad S, Asziz MU, Biegel JA, Weber BL, Maris JM.

Genes Chromosomes Cancer. 2005 Aug;43(4):390-403.


Array based CGH and FISH fail to confirm duplication of 8p22-p23.1 in association with Kabuki syndrome.

Hoffman JD, Zhang Y, Greshock J, Ciprero KL, Emanuel BS, Zackai EH, Weber BL, Ming JE.

J Med Genet. 2005 Jan;42(1):49-53.


High-resolution analysis of DNA copy number using oligonucleotide microarrays.

Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR, Futreal PA, Weber B, Shapero MH, Wooster R.

Genome Res. 2004 Feb;14(2):287-95.


1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis.

Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL.

Genome Res. 2004 Jan;14(1):179-87. Epub 2003 Dec 12.

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