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Items: 34

1.

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.

2.

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis.

Vedanayagam J, Chatila WK, Aksoy BA, Majumdar S, Skanderup AJ, Demir E, Schultz N, Sander C, Lai EC.

Nat Commun. 2019 Aug 15;10(1):3682. doi: 10.1038/s41467-019-11610-1.

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.

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.

7.

KMT2C Mutations in Diffuse-Type Gastric Adenocarcinoma Promote Epithelial-to-Mesenchymal Transition.

Cho SJ, Yoon C, Lee JH, Chang KK, Lin JX, Kim YH, Kook MC, Aksoy BA, Park DJ, Ashktorab H, Smoot DT, Schultz N, Yoon SS.

Clin Cancer Res. 2018 Dec 15;24(24):6556-6569. doi: 10.1158/1078-0432.CCR-17-1679. Epub 2018 Aug 14.

PMID:
30108106
8.

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.

9.

A Landscape of Metabolic Variation across Tumor Types.

Reznik E, Luna A, Aksoy BA, Liu EM, La K, Ostrovnaya I, Creighton CJ, Hakimi AA, Sander C.

Cell Syst. 2018 Mar 28;6(3):301-313.e3. doi: 10.1016/j.cels.2017.12.014. Epub 2018 Jan 27.

10.

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.

11.

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network.

Aksoy BA, Dancík V, Smith K, Mazerik JN, Ji Z, Gross B, Nikolova O, Jaber N, Califano A, Schreiber SL, Gerhard DS, Hermida LC, Jagu S, Sander C, Floratos A, Clemons PA.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax054.

12.

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.

13.

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.

14.

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.

15.

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.

16.

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains.

Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C.

Cell Syst. 2015 Sep 23;1(3):197-209. doi: 10.1016/j.cels.2015.08.014. Epub 2015 Sep 23.

17.

An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma.

Hakimi AA, Reznik E, Lee CH, Creighton CJ, Brannon AR, Luna A, Aksoy BA, Liu EM, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen YB, Tickoo SK, Reuter VE, Cheng EH, Sander C, Hsieh JJ.

Cancer Cell. 2016 Jan 11;29(1):104-116. doi: 10.1016/j.ccell.2015.12.004.

18.

PaxtoolsR: pathway analysis in R using Pathway Commons.

Luna A, Babur Ö, Aksoy BA, Demir E, Sander C.

Bioinformatics. 2016 Apr 15;32(8):1262-4. doi: 10.1093/bioinformatics/btv733. Epub 2015 Dec 18.

19.

Chemotherapy Resistance in Diffuse-Type Gastric Adenocarcinoma Is Mediated by RhoA Activation in Cancer Stem-Like Cells.

Yoon C, Cho SJ, Aksoy BA, Park DJ, Schultz N, Ryeom SW, Yoon SS.

Clin Cancer Res. 2016 Feb 15;22(4):971-83. doi: 10.1158/1078-0432.CCR-15-1356. Epub 2015 Oct 19.

20.

Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells.

Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Onur Sumer S, Solit DB, Pratilas CA, Sander C.

Elife. 2015 Aug 18;4. doi: 10.7554/eLife.04640.

21.

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.

22.

SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur Ö, Demir E.

PLoS One. 2015 Jun 1;10(6):e0128985. doi: 10.1371/journal.pone.0128985. eCollection 2015.

23.

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.

Babur Ö, Gönen M, Aksoy BA, Schultz N, Ciriello G, Sander C, Demir E.

Genome Biol. 2015 Feb 26;16:45. doi: 10.1186/s13059-015-0612-6.

24.

Integrating biological pathways and genomic profiles with ChiBE 2.

Babur Ö, Dogrusoz U, Çakır M, Aksoy BA, Schultz N, Sander C, Demir E.

BMC Genomics. 2014 Aug 3;15:642. doi: 10.1186/1471-2164-15-642.

25.

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.

Aksoy BA, Demir E, Babur Ö, Wang W, Jing X, Schultz N, Sander C.

Bioinformatics. 2014 Jul 15;30(14):2051-9. doi: 10.1093/bioinformatics/btu164. Epub 2014 Mar 24.

26.

Emerging landscape of oncogenic signatures across human cancers.

Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C.

Nat Genet. 2013 Oct;45(10):1127-33. doi: 10.1038/ng.2762.

27.

Using biological pathway data with paxtools.

Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.

PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19.

28.

Pattern search in BioPAX models.

Babur Ö, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E.

Bioinformatics. 2014 Jan 1;30(1):139-40. doi: 10.1093/bioinformatics/btt539. Epub 2013 Sep 16.

29.

PiHelper: an open source framework for drug-target and antibody-target data.

Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C.

Bioinformatics. 2013 Aug 15;29(16):2071-2. doi: 10.1093/bioinformatics/btt345. Epub 2013 Jun 12.

30.

Genome-wide inference of natural selection on human transcription factor binding sites.

Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A.

Nat Genet. 2013 Jul;45(7):723-9. doi: 10.1038/ng.2658. Epub 2013 Jun 9.

31.

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N.

Sci Signal. 2013 Apr 2;6(269):pl1. doi: 10.1126/scisignal.2004088.

32.

Using MEMo to discover mutual exclusivity modules in cancer.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N.

Curr Protoc Bioinformatics. 2013 Mar;Chapter 8:Unit 8.17. doi: 10.1002/0471250953.bi0817s41.

33.

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N.

Cancer Discov. 2012 May;2(5):401-4. doi: 10.1158/2159-8290.CD-12-0095. Erratum in: Cancer Discov. 2012 Oct;2(10):960.

34.

Effect of electromagnetic field induced by radio frequency waves at 900 to 1800 MHz on bone mineral density of iliac bone wings.

Atay T, Aksoy BA, Aydogan NH, Baydar ML, Yildiz M, Ozdemir R.

J Craniofac Surg. 2009 Sep;20(5):1556-60. doi: 10.1097/SCS.0b013e3181b78559.

PMID:
19816295

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