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Items: 1 to 20 of 26

1.

Non-conventional Inhibitory CD4+Foxp3-PD-1hi T Cells as a Biomarker of Immune Checkpoint Blockade Activity.

Zappasodi R, Budhu S, Hellmann MD, Postow MA, Senbabaoglu Y, Manne S, Gasmi B, Liu C, Zhong H, Li Y, Huang AC, Hirschhorn-Cymerman D, Panageas KS, Wherry EJ, Merghoub T, Wolchok JD.

Cancer Cell. 2018 Oct 8;34(4):691. doi: 10.1016/j.ccell.2018.09.007. No abstract available.

PMID:
30300585
2.

Non-conventional Inhibitory CD4+Foxp3-PD-1hi T Cells as a Biomarker of Immune Checkpoint Blockade Activity.

Zappasodi R, Budhu S, Hellmann MD, Postow MA, Senbabaoglu Y, Manne S, Gasmi B, Liu C, Zhong H, Li Y, Huang AC, Hirschhorn-Cymerman D, Panageas KS, Wherry EJ, Merghoub T, Wolchok JD.

Cancer Cell. 2018 Jun 11;33(6):1017-1032.e7. doi: 10.1016/j.ccell.2018.05.009. Erratum in: Cancer Cell. 2018 Oct 8;34(4):691.

PMID:
29894689
3.

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells.

Mariathasan S, Turley SJ, Nickles D, Castiglioni A, Yuen K, Wang Y, Kadel EE III, Koeppen H, Astarita JL, Cubas R, Jhunjhunwala S, Banchereau R, Yang Y, Guan Y, Chalouni C, Ziai J, Şenbabaoğlu Y, Santoro S, Sheinson D, Hung J, Giltnane JM, Pierce AA, Mesh K, Lianoglou S, Riegler J, Carano RAD, Eriksson P, Höglund M, Somarriba L, Halligan DL, van der Heijden MS, Loriot Y, Rosenberg JE, Fong L, Mellman I, Chen DS, Green M, Derleth C, Fine GD, Hegde PS, Bourgon R, Powles T.

Nature. 2018 Feb 22;554(7693):544-548. doi: 10.1038/nature25501. Epub 2018 Feb 14.

4.

Selective autophagy of the adaptor TRIF regulates innate inflammatory signaling.

Samie M, Lim J, Verschueren E, Baughman JM, Peng I, Wong A, Kwon Y, Senbabaoglu Y, Hackney JA, Keir M, Mckenzie B, Kirkpatrick DS, van Lookeren Campagne M, Murthy A.

Nat Immunol. 2018 Mar;19(3):246-254. doi: 10.1038/s41590-017-0042-6. Epub 2018 Jan 22.

PMID:
29358708
5.

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer.

Balachandran VP, Łuksza M, Zhao JN, Makarov V, Moral JA, Remark R, Herbst B, Askan G, Bhanot U, Senbabaoglu Y, Wells DK, Cary CIO, Grbovic-Huezo O, Attiyeh M, Medina B, Zhang J, Loo J, Saglimbeni J, Abu-Akeel M, Zappasodi R, Riaz N, Smoragiewicz M, Kelley ZL, Basturk O; Australian Pancreatic Cancer Genome Initiative; Garvan Institute of Medical Research; Prince of Wales Hospital; Royal North Shore Hospital; University of Glasgow; St Vincent’s Hospital; QIMR Berghofer Medical Research Institute; University of Melbourne, Centre for Cancer Research; University of Queensland, Institute for Molecular Bioscience; Bankstown Hospital; Liverpool Hospital; Royal Prince Alfred Hospital, Chris O’Brien Lifehouse; Westmead Hospital; Fremantle Hospital; St John of God Healthcare; Royal Adelaide Hospital; Flinders Medical Centre; Envoi Pathology; Princess Alexandria Hospital; Austin Hospital; Johns Hopkins Medical Institutes; ARC-Net Centre for Applied Research on Cancer, Gönen M, Levine AJ, Allen PJ, Fearon DT, Merad M, Gnjatic S, Iacobuzio-Donahue CA, Wolchok JD, DeMatteo RP, Chan TA, Greenbaum BD, Merghoub T, Leach SD.

Nature. 2017 Nov 23;551(7681):512-516. doi: 10.1038/nature24462. Epub 2017 Nov 8.

6.

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas.

Cancer Genome Atlas Research Network. Electronic address: elizabeth.demicco@sinaihealthsystem.ca; Cancer Genome Atlas Research Network.

Cell. 2017 Nov 2;171(4):950-965.e28. doi: 10.1016/j.cell.2017.10.014.

7.

Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma.

Cancer Genome Atlas Research Network. Electronic address: andrew_aguirre@dfci.harvard.edu; Cancer Genome Atlas Research Network.

Cancer Cell. 2017 Aug 14;32(2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007.

8.

Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.

Şenbabaoğlu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA.

Genome Biol. 2017 Mar 1;18(1):46. doi: 10.1186/s13059-017-1180-8. No abstract available.

9.

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.

Şenbabaoğlu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA.

Genome Biol. 2016 Nov 17;17(1):231. Erratum in: Genome Biol. 2017 Mar 1;18(1):46.

10.

The head and neck cancer immune landscape and its immunotherapeutic implications.

Mandal R, Şenbabaoğlu Y, Desrichard A, Havel JJ, Dalin MG, Riaz N, Lee KW, Ganly I, Hakimi AA, Chan TA, Morris LG.

JCI Insight. 2016 Oct 20;1(17):e89829. doi: 10.1172/jci.insight.89829.

11.

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.

Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ.

Cell Rep. 2016 Mar 15;14(10):2476-89. doi: 10.1016/j.celrep.2016.02.024. Epub 2016 Mar 3.

12.

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.

Şenbabaoğlu Y, Sümer SO, Sánchez-Vega F, Bemis D, Ciriello G, Schultz N, Sander C.

PLoS Comput Biol. 2016 Feb 29;12(2):e1004765. doi: 10.1371/journal.pcbi.1004765. eCollection 2016 Feb.

13.

Mitochondrial DNA copy number variation across human cancers.

Reznik E, Miller ML, Şenbabaoğlu Y, Riaz N, Sarungbam J, Tickoo SK, Al-Ahmadie HA, Lee W, Seshan VE, Hakimi AA, Sander C.

Elife. 2016 Feb 22;5. pii: e10769. doi: 10.7554/eLife.10769.

14.

Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival.

Morris LG, Riaz N, Desrichard A, Şenbabaoğlu Y, Hakimi AA, Makarov V, Reis-Filho JS, Chan TA.

Oncotarget. 2016 Mar 1;7(9):10051-63. doi: 10.18632/oncotarget.7067.

15.

Graph Curvature for Differentiating Cancer Networks.

Sandhu R, Georgiou T, Reznik E, Zhu L, Kolesov I, Senbabaoglu Y, Tannenbaum A.

Sci Rep. 2015 Jul 14;5:12323. doi: 10.1038/srep12323.

16.

Genomic Classification of Cutaneous Melanoma.

Cancer Genome Atlas Network.

Cell. 2015 Jun 18;161(7):1681-96. doi: 10.1016/j.cell.2015.05.044.

17.

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T Jr, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG Jr, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J.

N Engl J Med. 2015 Jun 25;372(26):2481-98. doi: 10.1056/NEJMoa1402121. Epub 2015 Jun 10.

18.

Notch reporter activity in breast cancer cell lines identifies a subset of cells with stem cell activity.

D'Angelo RC, Ouzounova M, Davis A, Choi D, Tchuenkam SM, Kim G, Luther T, Quraishi AA, Senbabaoglu Y, Conley SJ, Clouthier SG, Hassan KA, Wicha MS, Korkaya H.

Mol Cancer Ther. 2015 Mar;14(3):779-787. doi: 10.1158/1535-7163.MCT-14-0228. Epub 2015 Feb 11.

19.

Integrated genomic characterization of papillary thyroid carcinoma.

Cancer Genome Atlas Research Network.

Cell. 2014 Oct 23;159(3):676-90. doi: 10.1016/j.cell.2014.09.050.

20.

Critical limitations of consensus clustering in class discovery.

Șenbabaoğlu Y, Michailidis G, Li JZ.

Sci Rep. 2014 Aug 27;4:6207. doi: 10.1038/srep06207.

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