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Items: 38

1.

Genomic mechanisms of immune evasion in colorectal cancer: from discovery to clinical practice.

Grasso CS, Giannakis M.

Oncotarget. 2018 Sep 18;9(73):33743-33744. doi: 10.18632/oncotarget.26105. eCollection 2018 Sep 18. No abstract available.

2.

Smoking and Risk of Colorectal Cancer Sub-Classified by Tumor-Infiltrating T Cells.

Hamada T, Nowak JA, Masugi Y, Drew DA, Song M, Cao Y, Kosumi K, Mima K, Twombly TS, Liu L, Shi Y, da Silva A, Gu M, Li W, Nosho K, Keum N, Giannakis M, Meyerhardt JA, Wu K, Wang M, Chan AT, Giovannucci EL, Fuchs CS, Nishihara R, Zhang X, Ogino S.

J Natl Cancer Inst. 2018 Oct 11. doi: 10.1093/jnci/djy137. [Epub ahead of print]

PMID:
30312431
3.

The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome.

Kosumi K, Hamada T, Koh H, Borowsky J, Bullman S, Twombly TS, Nevo D, Masugi Y, Liu L, da Silva A, Chen Y, Du C, Gu M, Li C, Li W, Liu H, Shi Y, Mima K, Song M, Nosho K, Nowak JA, Nishihara R, Baba H, Zhang X, Wu K, Wang M, Huttenhower C, Garrett WS, Meyerson ML, Lennerz JK, Giannakis M, Chan AT, Meyerhardt JA, Fuchs CS, Ogino S.

Am J Pathol. 2018 Dec;188(12):2839-2852. doi: 10.1016/j.ajpath.2018.08.015. Epub 2018 Sep 20.

PMID:
30243655
4.

Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status.

Hamada T, Zhang X, Mima K, Bullman S, Sukawa Y, Nowak JA, Kosumi K, Masugi Y, Twombly TS, Cao Y, Song M, Liu L, da Silva A, Shi Y, Gu M, Li W, Koh H, Nosho K, Inamura K, Keum N, Wu K, Meyerhardt JA, Kostic AD, Huttenhower C, Garrett WS, Meyerson M, Giovannucci EL, Chan AT, Fuchs CS, Nishihara R, Giannakis M, Ogino S.

Cancer Immunol Res. 2018 Nov;6(11):1327-1336. doi: 10.1158/2326-6066.CIR-18-0174. Epub 2018 Sep 18.

PMID:
30228205
5.

Vitamin D status after colorectal cancer diagnosis and patient survival according to immune response to tumour.

Hamada T, Liu L, Nowak JA, Mima K, Cao Y, Ng K, Twombly TS, Song M, Jung S, Dou R, Masugi Y, Kosumi K, Shi Y, da Silva A, Gu M, Li W, Keum N, Wu K, Nosho K, Inamura K, Meyerhardt JA, Nevo D, Wang M, Giannakis M, Chan AT, Giovannucci EL, Fuchs CS, Nishihara R, Zhang X, Ogino S.

Eur J Cancer. 2018 Nov;103:98-107. doi: 10.1016/j.ejca.2018.07.130. Epub 2018 Sep 13.

PMID:
30219720
6.

TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PD-L1) expression status and tumor-infiltrating lymphocytes in colorectal carcinomas.

Hamada T, Soong TR, Masugi Y, Kosumi K, Nowak JA, da Silva A, Mu XJ, Twombly TS, Koh H, Yang J, Song M, Liu L, Gu M, Shi Y, Nosho K, Morikawa T, Inamura K, Shukla SA, Wu CJ, Garraway LA, Zhang X, Wu K, Meyerhardt JA, Chan AT, Glickman JN, Rodig SJ, Freeman GJ, Fuchs CS, Nishihara R, Giannakis M, Ogino S.

Oncoimmunology. 2018 Mar 19;7(7):e1442999. doi: 10.1080/2162402X.2018.1442999. eCollection 2018.

PMID:
29900052
7.

Immunoscore for (colorectal) cancer precision medicine.

Ogino S, Giannakis M.

Lancet. 2018 May 26;391(10135):2084-2086. doi: 10.1016/S0140-6736(18)30953-X. Epub 2018 May 10. No abstract available.

PMID:
29754776
8.

Diets That Promote Colon Inflammation Associate With Risk of Colorectal Carcinomas That Contain Fusobacterium nucleatum.

Liu L, Tabung FK, Zhang X, Nowak JA, Qian ZR, Hamada T, Nevo D, Bullman S, Mima K, Kosumi K, da Silva A, Song M, Cao Y, Twombly TS, Shi Y, Liu H, Gu M, Koh H, Li W, Du C, Chen Y, Li C, Li W, Mehta RS, Wu K, Wang M, Kostic AD, Giannakis M, Garrett WS, Hutthenhower C, Chan AT, Fuchs CS, Nishihara R, Ogino S, Giovannucci EL.

Clin Gastroenterol Hepatol. 2018 Oct;16(10):1622-1631.e3. doi: 10.1016/j.cgh.2018.04.030. Epub 2018 Apr 24.

PMID:
29702299
9.

Genetic Mechanisms of Immune Evasion in Colorectal Cancer.

Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U.

Cancer Discov. 2018 Jun;8(6):730-749. doi: 10.1158/2159-8290.CD-17-1327. Epub 2018 Mar 6.

PMID:
29510987
10.

Inherited DNA-Repair Defects in Colorectal Cancer.

AlDubayan SH, Giannakis M, Moore ND, Han GC, Reardon B, Hamada T, Mu XJ, Nishihara R, Qian Z, Liu L, Yurgelun MB, Syngal S, Garraway LA, Ogino S, Fuchs CS, Van Allen EM.

Am J Hum Genet. 2018 Mar 1;102(3):401-414. doi: 10.1016/j.ajhg.2018.01.018. Epub 2018 Feb 22.

11.

Integrative analysis of exogenous, endogenous, tumour and immune factors for precision medicine.

Ogino S, Nowak JA, Hamada T, Phipps AI, Peters U, Milner DA Jr, Giovannucci EL, Nishihara R, Giannakis M, Garrett WS, Song M.

Gut. 2018 Jun;67(6):1168-1180. doi: 10.1136/gutjnl-2017-315537. Epub 2018 Feb 6. Review.

PMID:
29437869
12.

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma.

Miao D, Margolis CA, Gao W, Voss MH, Li W, Martini DJ, Norton C, Bossé D, Wankowicz SM, Cullen D, Horak C, Wind-Rotolo M, Tracy A, Giannakis M, Hodi FS, Drake CG, Ball MW, Allaf ME, Snyder A, Hellmann MD, Ho T, Motzer RJ, Signoretti S, Kaelin WG Jr, Choueiri TK, Van Allen EM.

Science. 2018 Feb 16;359(6377):801-806. doi: 10.1126/science.aan5951. Epub 2018 Jan 4.

13.

Aspirin exerts high anti-cancer activity in PIK3CA-mutant colon cancer cells.

Gu M, Nishihara R, Chen Y, Li W, Shi Y, Masugi Y, Hamada T, Kosumi K, Liu L, da Silva A, Nowak JA, Twombly T, Du C, Koh H, Li W, Meyerhardt JA, Wolpin BM, Giannakis M, Aguirre AJ, Bass AJ, Drew DA, Chan AT, Fuchs CS, Qian ZR, Ogino S.

Oncotarget. 2017 Sep 18;8(50):87379-87389. doi: 10.18632/oncotarget.20972. eCollection 2017 Oct 20.

14.

Aspirin in the era of immunotherapy.

Hamada T, Giannakis M, Ogino S.

Oncotarget. 2017 Sep 14;8(43):73370-73371. doi: 10.18632/oncotarget.20877. eCollection 2017 Sep 26. No abstract available.

15.

Tumor PDCD1LG2 (PD-L2) Expression and the Lymphocytic Reaction to Colorectal Cancer.

Masugi Y, Nishihara R, Hamada T, Song M, da Silva A, Kosumi K, Gu M, Shi Y, Li W, Liu L, Nevo D, Inamura K, Cao Y, Liao X, Nosho K, Chan AT, Giannakis M, Bass AJ, Hodi FS, Freeman GJ, Rodig SJ, Fuchs CS, Qian ZR, Nowak JA, Ogino S.

Cancer Immunol Res. 2017 Nov;5(11):1046-1055. doi: 10.1158/2326-6066.CIR-17-0122. Epub 2017 Oct 16.

16.

Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.

Zhang X, Choi PS, Francis JM, Gao GF, Campbell JD, Ramachandran A, Mitsuishi Y, Ha G, Shih J, Vazquez F, Tsherniak A, Taylor AM, Zhou J, Wu Z, Berger AC, Giannakis M, Hahn WC, Cherniack AD, Meyerson M.

Cancer Discov. 2018 Jan;8(1):108-125. doi: 10.1158/2159-8290.CD-17-0532. Epub 2017 Sep 29.

PMID:
28963353
17.

Aspirin Use and Colorectal Cancer Survival According to Tumor CD274 (Programmed Cell Death 1 Ligand 1) Expression Status.

Hamada T, Cao Y, Qian ZR, Masugi Y, Nowak JA, Yang J, Song M, Mima K, Kosumi K, Liu L, Shi Y, da Silva A, Gu M, Li W, Keum N, Zhang X, Wu K, Meyerhardt JA, Giovannucci EL, Giannakis M, Rodig SJ, Freeman GJ, Nevo D, Wang M, Chan AT, Fuchs CS, Nishihara R, Ogino S.

J Clin Oncol. 2017 Jun 1;35(16):1836-1844. doi: 10.1200/JCO.2016.70.7547. Epub 2017 Apr 13.

18.

To Treat or Not to Treat: Adjuvant Therapy for Stage II Colon Cancer in the Era of Precision Oncology.

Giannakis M, Ng K.

J Oncol Pract. 2017 Apr;13(4):242-244. doi: 10.1200/JOP.2017.022103. No abstract available.

PMID:
28399380
19.

Precancer Atlas to Drive Precision Prevention Trials.

Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM.

Cancer Res. 2017 Apr 1;77(7):1510-1541. doi: 10.1158/0008-5472.CAN-16-2346.

20.

Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study.

Ghazani AA, Oliver NM, St Pierre JP, Garofalo A, Rainville IR, Hiller E, Treacy DJ, Rojas-Rudilla V, Wood S, Bair E, Parello M, Huang F, Giannakis M, Wilson FH, Stover EH, Corsello SM, Nguyen T, Rana HQ, Church AJ, Lowenstein C, Cibulskis C, Amin-Mansour A, Heng J, Brais L, Santos A, Bauer P, Waldron A, Lo P, Gorman M, Lydon CA, Welch M, McNamara P, Gabriel S, Sholl LM, Lindeman NI, Garber JE, Joffe S, Van Allen EM, Gray SW, Ja Nne PA, Garraway LA, Wagle N.

Genet Med. 2017 Jul;19(7):787-795. doi: 10.1038/gim.2016.191. Epub 2017 Jan 26.

PMID:
28125075
21.

Integration of pharmacology, molecular pathology, and population data science to support precision gastrointestinal oncology.

Ogino S, Jhun I, Mata DA, Soong TR, Hamada T, Liu L, Nishihara R, Giannakis M, Cao Y, Manson JE, Nowak JA, Chan AT.

NPJ Precis Oncol. 2017;1. pii: 40. doi: 10.1038/s41698-017-0042-x. Epub 2017 Dec 6.

22.

Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location.

Mima K, Cao Y, Chan AT, Qian ZR, Nowak JA, Masugi Y, Shi Y, Song M, da Silva A, Gu M, Li W, Hamada T, Kosumi K, Hanyuda A, Liu L, Kostic AD, Giannakis M, Bullman S, Brennan CA, Milner DA, Baba H, Garraway LA, Meyerhardt JA, Garrett WS, Huttenhower C, Meyerson M, Giovannucci EL, Fuchs CS, Nishihara R, Ogino S.

Clin Transl Gastroenterol. 2016 Nov 3;7(11):e200. doi: 10.1038/ctg.2016.53.

23.

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.

Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA.

Cell Rep. 2016 Oct 18;17(4):1206. doi: 10.1016/j.celrep.2016.10.009. No abstract available.

24.

The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.

Garofalo A, Sholl L, Reardon B, Taylor-Weiner A, Amin-Mansour A, Miao D, Liu D, Oliver N, MacConaill L, Ducar M, Rojas-Rudilla V, Giannakis M, Ghazani A, Gray S, Janne P, Garber J, Joffe S, Lindeman N, Wagle N, Garraway LA, Van Allen EM.

Genome Med. 2016 Jul 26;8(1):79. doi: 10.1186/s13073-016-0333-9.

25.

An ED pilot intervention to facilitate outpatient acute care for cancer patients.

Brooks GA, Chen EJ, Murakami MA, Giannakis M, Baugh CW, Schrag D.

Am J Emerg Med. 2016 Oct;34(10):1934-1938. doi: 10.1016/j.ajem.2016.06.076. Epub 2016 Jun 24.

PMID:
27412915
26.

The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis.

Gibson WJ, Hoivik EA, Halle MK, Taylor-Weiner A, Cherniack AD, Berg A, Holst F, Zack TI, Werner HM, Staby KM, Rosenberg M, Stefansson IM, Kusonmano K, Chevalier A, Mauland KK, Trovik J, Krakstad C, Giannakis M, Hodis E, Woie K, Bjorge L, Vintermyr OK, Wala JA, Lawrence MS, Getz G, Carter SL, Beroukhim R, Salvesen HB.

Nat Genet. 2016 Aug;48(8):848-55. doi: 10.1038/ng.3602. Epub 2016 Jun 27.

27.

Tumour CD274 (PD-L1) expression and T cells in colorectal cancer.

Masugi Y, Nishihara R, Yang J, Mima K, da Silva A, Shi Y, Inamura K, Cao Y, Song M, Nowak JA, Liao X, Nosho K, Chan AT, Giannakis M, Bass AJ, Hodi FS, Freeman GJ, Rodig S, Fuchs CS, Qian ZR, Ogino S.

Gut. 2017 Aug;66(8):1463-1473. doi: 10.1136/gutjnl-2016-311421. Epub 2016 May 5.

28.

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.

Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA.

Cell Rep. 2016 Apr 26;15(4):857-865. doi: 10.1016/j.celrep.2016.03.075. Epub 2016 Apr 14. Erratum in: Cell Rep. 2016 Oct 18;17 (4):1206.

29.

MicroRNA MIR21 and T Cells in Colorectal Cancer.

Mima K, Nishihara R, Nowak JA, Kim SA, Song M, Inamura K, Sukawa Y, Masuda A, Yang J, Dou R, Nosho K, Baba H, Giovannucci EL, Bowden M, Loda M, Giannakis M, Bass AJ, Dranoff G, Freeman GJ, Chan AT, Fuchs CS, Qian ZR, Ogino S.

Cancer Immunol Res. 2016 Jan;4(1):33-40. doi: 10.1158/2326-6066.CIR-15-0084. Epub 2015 Sep 29.

30.

Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis.

Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, Yang J, Dou R, Masugi Y, Song M, Kostic AD, Giannakis M, Bullman S, Milner DA, Baba H, Giovannucci EL, Garraway LA, Freeman GJ, Dranoff G, Garrett WS, Huttenhower C, Meyerson M, Meyerhardt JA, Chan AT, Fuchs CS, Ogino S.

Gut. 2016 Dec;65(12):1973-1980. doi: 10.1136/gutjnl-2015-310101. Epub 2015 Aug 26.

31.

Fusobacterium nucleatum and T Cells in Colorectal Carcinoma.

Mima K, Sukawa Y, Nishihara R, Qian ZR, Yamauchi M, Inamura K, Kim SA, Masuda A, Nowak JA, Nosho K, Kostic AD, Giannakis M, Watanabe H, Bullman S, Milner DA, Harris CC, Giovannucci E, Garraway LA, Freeman GJ, Dranoff G, Chan AT, Garrett WS, Huttenhower C, Fuchs CS, Ogino S.

JAMA Oncol. 2015 Aug;1(5):653-61. doi: 10.1001/jamaoncol.2015.1377.

32.

Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with JAK3 Activation.

Van Allen EM, Golay HG, Liu Y, Koyama S, Wong K, Taylor-Weiner A, Giannakis M, Harden M, Rojas-Rudilla V, Chevalier A, Thai T, Lydon C, Mach S, Avila AG, Wong JA, Rabin AR, Helmkamp J, Sholl L, Carter SL, Oxnard G, Janne P, Getz G, Lindeman N, Hammerman PS, Garraway LA, Hodi FS, Rodig SJ, Dranoff G, Wong KK, Barbie DA.

Cancer Immunol Res. 2015 Aug;3(8):855-63. doi: 10.1158/2326-6066.CIR-15-0024. Epub 2015 May 26.

33.

RNF43 is frequently mutated in colorectal and endometrial cancers.

Giannakis M, Hodis E, Jasmine Mu X, Yamauchi M, Rosenbluh J, Cibulskis K, Saksena G, Lawrence MS, Qian ZR, Nishihara R, Van Allen EM, Hahn WC, Gabriel SB, Lander ES, Getz G, Ogino S, Fuchs CS, Garraway LA.

Nat Genet. 2014 Dec;46(12):1264-6. doi: 10.1038/ng.3127. Epub 2014 Oct 26.

34.

Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis.

Giannakis M, Bäckhed HK, Chen SL, Faith JJ, Wu M, Guruge JL, Engstrand L, Gordon JI.

J Biol Chem. 2009 Oct 30;284(44):30383-94. doi: 10.1074/jbc.M109.052738. Epub 2009 Sep 1.

35.

Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells.

Giannakis M, Chen SL, Karam SM, Engstrand L, Gordon JI.

Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4358-63. doi: 10.1073/pnas.0800668105. Epub 2008 Mar 10.

36.

The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression.

Oh JD, Kling-Bäckhed H, Giannakis M, Xu J, Fulton RS, Fulton LA, Cordum HS, Wang C, Elliott G, Edwards J, Mardis ER, Engstrand LG, Gordon JI.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9999-10004. Epub 2006 Jun 20.

37.

Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches.

Giannakis M, Stappenbeck TS, Mills JC, Leip DG, Lovett M, Clifton SW, Ippolito JE, Glasscock JI, Arumugam M, Brent MR, Gordon JI.

J Biol Chem. 2006 Apr 21;281(16):11292-300. Epub 2006 Feb 7.

38.

Interactions between gastric epithelial stem cells and Helicobacter pylori in the setting of chronic atrophic gastritis.

Oh JD, Kling-Bäckhed H, Giannakis M, Engstrand LG, Gordon JI.

Curr Opin Microbiol. 2006 Feb;9(1):21-7. Epub 2006 Jan 6. Review.

PMID:
16406776

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