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Items: 19

1.

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 Aug 31. pii: S1074-7613(19)30363-2. doi: 10.1016/j.immuni.2019.08.012. [Epub ahead of print]

PMID:
31495665
2.

Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging.

Czech E, Aksoy BA, Aksoy P, Hammerbacher J.

BMC Bioinformatics. 2019 Sep 2;20(1):448. doi: 10.1186/s12859-019-3055-3.

3.

Anti-CTLA-4 Activates Intratumoral NK Cells and Combined with IL15/IL15Rα Complexes Enhances Tumor Control.

Sanseviero E, O'Brien EM, Karras JR, Shabaneh TB, Aksoy BA, Xu W, Zheng C, Yin X, Xu X, Karakousis GC, Amaravadi RK, Nam B, Turk MJ, Hammerbacher J, Rubinstein MP, Schuchter LM, Mitchell TC, Liu Q, Stone EL.

Cancer Immunol Res. 2019 Aug;7(8):1371-1380. doi: 10.1158/2326-6066.CIR-18-0386. Epub 2019 Jun 25.

PMID:
31239316
4.

T cells genetically engineered to overcome death signaling enhance adoptive cancer immunotherapy.

Yamamoto TN, Lee PH, Vodnala SK, Gurusamy D, Kishton RJ, Yu Z, Eidizadeh A, Eil R, Fioravanti J, Gattinoni L, Kochenderfer JN, Fry TJ, Aksoy BA, Hammerbacher JE, Cruz AC, Siegel RM, Restifo NP, Klebanoff CA.

J Clin Invest. 2019 Feb 25;129(4):1551-1565. doi: 10.1172/JCI121491. eCollection 2019 Feb 25.

5.

Mutations in an Innate Immunity Pathway Are Associated with Poor Overall Survival Outcomes and Hypoxic Signaling in Cancer.

Olcina MM, Balanis NG, Kim RK, Aksoy BA, Kodysh J, Thompson MJ, Hammerbacher J, Graeber TG, Giaccia AJ.

Cell Rep. 2018 Dec 26;25(13):3721-3732.e6. doi: 10.1016/j.celrep.2018.11.093.

6.

Joint longitudinal and time-to-event models for multilevel hierarchical data.

Brilleman SL, Crowther MJ, Moreno-Betancur M, Buros Novik J, Dunyak J, Al-Huniti N, Fox R, Hammerbacher J, Wolfe R.

Stat Methods Med Res. 2019 Dec;28(12):3502-3515. doi: 10.1177/0962280218808821. Epub 2018 Oct 31.

PMID:
30378472
7.

Coral: Clear and Customizable Visualization of Human Kinome Data.

Metz KS, Deoudes EM, Berginski ME, Jimenez-Ruiz I, Aksoy BA, Hammerbacher J, Gomez SM, Phanstiel DH.

Cell Syst. 2018 Sep 26;7(3):347-350.e1. doi: 10.1016/j.cels.2018.07.001. Epub 2018 Aug 29.

PMID:
30172842
8.

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction.

O'Donnell TJ, Rubinsteyn A, Bonsack M, Riemer AB, Laserson U, Hammerbacher J.

Cell Syst. 2018 Jul 25;7(1):129-132.e4. doi: 10.1016/j.cels.2018.05.014. Epub 2018 Jun 27.

9.

Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer.

Hellmann MD, Nathanson T, Rizvi H, Creelan BC, Sanchez-Vega F, Ahuja A, Ni A, Novik JB, Mangarin LMB, Abu-Akeel M, Liu C, Sauter JL, Rekhtman N, Chang E, Callahan MK, Chaft JE, Voss MH, Tenet M, Li XM, Covello K, Renninger A, Vitazka P, Geese WJ, Borghaei H, Rudin CM, Antonia SJ, Swanton C, Hammerbacher J, Merghoub T, McGranahan N, Snyder A, Wolchok JD.

Cancer Cell. 2018 May 14;33(5):843-852.e4. doi: 10.1016/j.ccell.2018.03.018. Epub 2018 Apr 12.

10.

Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial.

Rubinsteyn A, Kodysh J, Hodes I, Mondet S, Aksoy BA, Finnigan JP, Bhardwaj N, Hammerbacher J.

Front Immunol. 2018 Jan 18;8:1807. doi: 10.3389/fimmu.2017.01807. eCollection 2017.

11.

Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.

O'Donnell T, Christie EL, Ahuja A, Buros J, Aksoy BA, Bowtell DDL, Snyder A, Hammerbacher J.

BMC Cancer. 2018 Jan 22;18(1):87. doi: 10.1186/s12885-017-3825-0.

12.

Informatics for cancer immunotherapy.

Hammerbacher J, Snyder A.

Ann Oncol. 2017 Dec 1;28(suppl_12):xii56-xii73. doi: 10.1093/annonc/mdx682. Review.

13.

PI3Kδ Inhibition Enhances the Antitumor Fitness of Adoptively Transferred CD8+ T Cells.

Bowers JS, Majchrzak K, Nelson MH, Aksoy BA, Wyatt MM, Smith AS, Bailey SR, Neal LR, Hammerbacher JE, Paulos CM.

Front Immunol. 2017 Sep 29;8:1221. doi: 10.3389/fimmu.2017.01221. eCollection 2017.

14.

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis.

Snyder A, Nathanson T, Funt SA, Ahuja A, Buros Novik J, Hellmann MD, Chang E, Aksoy BA, Al-Ahmadie H, Yusko E, Vignali M, Benzeno S, Boyd M, Moran M, Iyer G, Robins HS, Mardis ER, Merghoub T, Hammerbacher J, Rosenberg JE, Bajorin DF.

PLoS Med. 2017 May 26;14(5):e1002309. doi: 10.1371/journal.pmed.1002309. eCollection 2017 May.

15.

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.

Nathanson T, Ahuja A, Rubinsteyn A, Aksoy BA, Hellmann MD, Miao D, Van Allen E, Merghoub T, Wolchok JD, Snyder A, Hammerbacher J.

Cancer Immunol Res. 2017 Jan;5(1):84-91. doi: 10.1158/2326-6066.CIR-16-0019. Epub 2016 Dec 12.

16.

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.

Vanderkam D, Aksoy BA, Hodes I, Perrone J, Hammerbacher J.

Bioinformatics. 2016 Aug 1;32(15):2378-9. doi: 10.1093/bioinformatics/btw167. Epub 2016 Mar 29.

17.

Using a Machine Learning Approach to Predict Outcomes after Radiosurgery for Cerebral Arteriovenous Malformations.

Oermann EK, Rubinsteyn A, Ding D, Mascitelli J, Starke RM, Bederson JB, Kano H, Lunsford LD, Sheehan JP, Hammerbacher J, Kondziolka D.

Sci Rep. 2016 Feb 9;6:21161. doi: 10.1038/srep21161.

18.

How Will Big Data Improve Clinical and Basic Research in Radiation Therapy?

Rosenstein BS, Capala J, Efstathiou JA, Hammerbacher J, Kerns SL, Kong FS, Ostrer H, Prior FW, Vikram B, Wong J, Xiao Y.

Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):895-904. doi: 10.1016/j.ijrobp.2015.11.009. Epub 2015 Nov 11. No abstract available.

19.

Mutation-Derived Tumor Antigens: Novel Targets in Cancer Immunotherapy.

Finnigan JP Jr, Rubinsteyn A, Hammerbacher J, Bhardwaj N.

Oncology (Williston Park). 2015 Dec;29(12):970-2, 974-5. Review. No abstract available.

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