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Items: 25

1.

Machine-Learning Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes.

Smith CC, Chai S, Washington AR, Lee SJ, Landoni E, Field K, Garness J, Bixby LM, Selitsky SR, Parker JS, Savoldo B, Serody JS, Vincent BG.

Cancer Immunol Res. 2019 Oct;7(10):1591-1604. doi: 10.1158/2326-6066.CIR-19-0155. Epub 2019 Sep 12.

PMID:
31515258
2.

Using RNA Sequencing to Characterize the Tumor Microenvironment.

Smith CC, Bixby LM, Miller KL, Selitsky SR, Bortone DS, Hoadley KA, Vincent BG, Serody JS.

Methods Mol Biol. 2020;2055:245-272. doi: 10.1007/978-1-4939-9773-2_12.

PMID:
31502156
3.

Alternative tumour-specific antigens.

Smith CC, Selitsky SR, Chai S, Armistead PM, Vincent BG, Serody JS.

Nat Rev Cancer. 2019 Aug;19(8):465-478. doi: 10.1038/s41568-019-0162-4. Epub 2019 Jul 5. Review.

PMID:
31278396
4.

Prognostic value of B cells in cutaneous melanoma.

Selitsky SR, Mose LE, Smith CC, Chai S, Hoadley KA, Dittmer DP, Moschos SJ, Parker JS, Vincent BG.

Genome Med. 2019 May 28;11(1):36. doi: 10.1186/s13073-019-0647-5.

5.

Basal expression of interferon regulatory factor 1 drives intrinsic hepatocyte resistance to multiple RNA viruses.

Yamane D, Feng H, Rivera-Serrano EE, Selitsky SR, Hirai-Yuki A, Das A, McKnight KL, Misumi I, Hensley L, Lovell W, González-López O, Suzuki R, Matsuda M, Nakanishi H, Ohto-Nakanishi T, Hishiki T, Wauthier E, Oikawa T, Morita K, Reid LM, Sethupathy P, Kohara M, Whitmire JK, Lemon SM.

Nat Microbiol. 2019 Jul;4(7):1096-1104. doi: 10.1038/s41564-019-0425-6. Epub 2019 Apr 15.

6.

Epstein-Barr Virus-Positive Cancers Show Altered B-Cell Clonality.

Selitsky SR, Marron D, Mose LE, Parker JS, Dittmer DP.

mSystems. 2018 Sep 25;3(5). pii: e00081-18. doi: 10.1128/mSystems.00081-18. eCollection 2018 Sep-Oct.

7.

Male breast cancer: a disease distinct from female breast cancer.

Gucalp A, Traina TA, Eisner JR, Parker JS, Selitsky SR, Park BH, Elias AD, Baskin-Bey ES, Cardoso F.

Breast Cancer Res Treat. 2019 Jan;173(1):37-48. doi: 10.1007/s10549-018-4921-9. Epub 2018 Sep 28. Review.

PMID:
30267249
8.

Clinical and Molecular Factors Associated With Histologic Response to Topical Steroid Treatment in Patients With Eosinophilic Esophagitis.

Eluri S, Selitsky SR, Perjar I, Hollyfield J, Betancourt R, Randall C, Rusin S, Woosley JT, Shaheen NJ, Dellon ES.

Clin Gastroenterol Hepatol. 2019 May;17(6):1081-1088.e2. doi: 10.1016/j.cgh.2018.09.005. Epub 2018 Sep 10.

PMID:
30213583
9.

Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma.

Smith CC, Beckermann KE, Bortone DS, De Cubas AA, Bixby LM, Lee SJ, Panda A, Ganesan S, Bhanot G, Wallen EM, Milowsky MI, Kim WY, Rathmell WK, Swanstrom R, Parker JS, Serody JS, Selitsky SR, Vincent BG.

J Clin Invest. 2018 Nov 1;128(11):4804-4820. doi: 10.1172/JCI121476. Epub 2018 Oct 2.

10.

Gene expression-phenotype associations in adults with eosinophilic esophagitis.

Dellon ES, Selitsky SR, Genta RM, Lash RH, Parker JS.

Dig Liver Dis. 2018 Aug;50(8):804-811. doi: 10.1016/j.dld.2018.03.021. Epub 2018 Mar 27.

11.

Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2018 Feb 5;9(1):572. doi: 10.1038/s41467-017-02383-6.

12.

Identification of Germline Variants in Tumor Genomic Sequencing Analysis.

Montgomery ND, Selitsky SR, Patel NM, Hayes DN, Parker JS, Weck KE.

J Mol Diagn. 2018 Jan;20(1):123-125. doi: 10.1016/j.jmoldx.2017.09.008.

PMID:
29249243
13.

Combating subclonal evolution of resistant cancer phenotypes.

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH.

Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. Erratum in: Nat Commun. 2018 Feb 5;9(1):572.

14.

A Gene Expression Panel is Accurate for Diagnosis and Monitoring Treatment of Eosinophilic Esophagitis in Adults.

Dellon ES, Veerappan R, Selitsky SR, Parker JS, Higgins LL, Beitia R, Genta RM, Lash RH.

Clin Transl Gastroenterol. 2017 Feb 9;8(2):e74. doi: 10.1038/ctg.2017.2.

15.

Differential hepatitis C virus RNA target site selection and host factor activities of naturally occurring miR-122 3΄ variants.

Yamane D, Selitsky SR, Shimakami T, Li Y, Zhou M, Honda M, Sethupathy P, Lemon SM.

Nucleic Acids Res. 2017 May 5;45(8):4743-4755. doi: 10.1093/nar/gkw1332.

16.

Claudin-low bladder tumors are immune infiltrated and actively immune suppressed.

Kardos J, Chai S, Mose LE, Selitsky SR, Krishnan B, Saito R, Iglesia MD, Milowsky MI, Parker JS, Kim WY, Vincent BG.

JCI Insight. 2016 Mar 17;1(3):e85902. doi: 10.1172/jci.insight.85902.

17.

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.

Mose LE, Selitsky SR, Bixby LM, Marron DL, Iglesia MD, Serody JS, Perou CM, Vincent BG, Parker JS.

Bioinformatics. 2016 Dec 15;32(24):3729-3734. Epub 2016 Aug 24.

18.

Prospective assessment of serum periostin as a biomarker for diagnosis and monitoring of eosinophilic oesophagitis.

Dellon ES, Higgins LL, Beitia R, Rusin S, Woosley JT, Veerappan R, Selitsky SR, Parker JS, Genta RM, Lash RH, Aranda R, Peach RJ, Grimm M.

Aliment Pharmacol Ther. 2016 Jul;44(2):189-97. doi: 10.1111/apt.13672. Epub 2016 May 18.

19.

Transcriptomic Analysis of Chronic Hepatitis B and C and Liver Cancer Reveals MicroRNA-Mediated Control of Cholesterol Synthesis Programs.

Selitsky SR, Dinh TA, Toth CL, Kurtz CL, Honda M, Struck BR, Kaneko S, Vickers KC, Lemon SM, Sethupathy P.

MBio. 2015 Dec 8;6(6):e01500-15. doi: 10.1128/mBio.01500-15.

20.

tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data.

Selitsky SR, Sethupathy P.

BMC Bioinformatics. 2015 Nov 4;16:354. doi: 10.1186/s12859-015-0800-0.

21.

Model of fibrolamellar hepatocellular carcinomas reveals striking enrichment in cancer stem cells.

Oikawa T, Wauthier E, Dinh TA, Selitsky SR, Reyna-Neyra A, Carpino G, Levine R, Cardinale V, Klimstra D, Gaudio E, Alvaro D, Carrasco N, Sethupathy P, Reid LM.

Nat Commun. 2015 Oct 6;6:8070. doi: 10.1038/ncomms9070.

22.

Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C.

Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T, Kaneko S, Lanford RE, Lemon SM, Sethupathy P.

Sci Rep. 2015 Jan 8;5:7675. doi: 10.1038/srep07675.

23.

microRNA-122 abundance in hepatocellular carcinoma and non-tumor liver tissue from Japanese patients with persistent HCV versus HBV infection.

Spaniel C, Honda M, Selitsky SR, Yamane D, Shimakami T, Kaneko S, Lanford RE, Lemon SM.

PLoS One. 2013 Oct 9;8(10):e76867. doi: 10.1371/journal.pone.0076867. eCollection 2013.

24.

A novel intronic single nucleotide polymorphism in the myosin heavy polypeptide 4 gene is responsible for the mini-muscle phenotype characterized by major reduction in hind-limb muscle mass in mice.

Kelly SA, Bell TA, Selitsky SR, Buus RJ, Hua K, Weinstock GM, Garland T Jr, Pardo-Manuel de Villena F, Pomp D.

Genetics. 2013 Dec;195(4):1385-95. doi: 10.1534/genetics.113.154476. Epub 2013 Sep 20.

25.

Identification of driver genes in hepatocellular carcinoma by exome sequencing.

Cleary SP, Jeck WR, Zhao X, Chen K, Selitsky SR, Savich GL, Tan TX, Wu MC, Getz G, Lawrence MS, Parker JS, Li J, Powers S, Kim H, Fischer S, Guindi M, Ghanekar A, Chiang DY.

Hepatology. 2013 Nov;58(5):1693-702. doi: 10.1002/hep.26540. Epub 2013 Sep 24.

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