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Items: 16

1.

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data.

Chiu R, Nip KM, Chu J, Birol I.

BMC Med Genomics. 2018 Sep 10;11(1):79. doi: 10.1186/s12920-018-0402-6.

2.

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

Xue Z, Warren RL, Gibb EA, MacMillan D, Wong J, Chiu R, Hammond SA, Yang C, Nip KM, Ennis CA, Hahn A, Reynolds S, Birol I.

BMC Genomics. 2018 Jul 13;19(1):536. doi: 10.1186/s12864-018-4903-7.

3.

Targeting Prostate Cancer Subtype 1 by Forkhead Box M1 Pathway Inhibition.

Ketola K, Munuganti RSN, Davies A, Nip KM, Bishop JL, Zoubeidi A.

Clin Cancer Res. 2017 Nov 15;23(22):6923-6933. doi: 10.1158/1078-0432.CCR-17-0901. Epub 2017 Sep 12.

4.

Targeting Lyn regulates Snail family shuttling and inhibits metastasis.

Thaper D, Vahid S, Nip KM, Moskalev I, Shan X, Frees S, Roberts ME, Ketola K, Harder KW, Gregory-Evans C, Bishop JL, Zoubeidi A.

Oncogene. 2017 Jul 13;36(28):3964-3975. doi: 10.1038/onc.2017.5. Epub 2017 Mar 13.

PMID:
28288135
5.

The Master Neural Transcription Factor BRN2 Is an Androgen Receptor-Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer.

Bishop JL, Thaper D, Vahid S, Davies A, Ketola K, Kuruma H, Jama R, Nip KM, Angeles A, Johnson F, Wyatt AW, Fazli L, Gleave ME, Lin D, Rubin MA, Collins CC, Wang Y, Beltran H, Zoubeidi A.

Cancer Discov. 2017 Jan;7(1):54-71. doi: 10.1158/2159-8290.CD-15-1263. Epub 2016 Oct 26.

6.

Inhibition of the HER2-YB1-AR axis with Lapatinib synergistically enhances Enzalutamide anti-tumor efficacy in castration resistant prostate cancer.

Shiota M, Bishop JL, Takeuchi A, Nip KM, Cordonnier T, Beraldi E, Kuruma H, Gleave ME, Zoubeidi A.

Oncotarget. 2015 Apr 20;6(11):9086-98.

7.

A low carbohydrate, high protein diet suppresses intratumoral androgen synthesis and slows castration-resistant prostate tumor growth in mice.

Fokidis HB, Yieng Chin M, Ho VW, Adomat HH, Soma KK, Fazli L, Nip KM, Cox M, Krystal G, Zoubeidi A, Tomlinson Guns ES.

J Steroid Biochem Mol Biol. 2015 Jun;150:35-45. doi: 10.1016/j.jsbmb.2015.03.006. Epub 2015 Mar 19.

PMID:
25797030
8.

Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis.

Shoshan E, Mobley AK, Braeuer RR, Kamiya T, Huang L, Vasquez ME, Salameh A, Lee HJ, Kim SJ, Ivan C, Velazquez-Torres G, Nip KM, Zhu K, Brooks D, Jones SJ, Birol I, Mosqueda M, Wen YY, Eterovic AK, Sood AK, Hwu P, Gershenwald JE, Robertson AG, Calin GA, Markel G, Fidler IJ, Bar-Eli M.

Nat Cell Biol. 2015 Mar;17(3):311-21. doi: 10.1038/ncb3110. Epub 2015 Feb 16.

9.

Kleat: cleavage site analysis of transcriptomes.

Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A.

Pac Symp Biocomput. 2015:347-58.

10.

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.

Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, Mar R, Mohamadi H, Butterfield YS, Robertson AG, Birol I.

Bioinformatics. 2014 Dec 1;30(23):3402-4. doi: 10.1093/bioinformatics/btu558. Epub 2014 Aug 20.

11.

Lyn tyrosine kinase regulates androgen receptor expression and activity in castrate-resistant prostate cancer.

Zardan A, Nip KM, Thaper D, Toren P, Vahid S, Beraldi E, Fazli L, Lamoureux F, Gust KM, Cox ME, Bishop JL, Zoubeidi A.

Oncogenesis. 2014 Aug 18;3:e115. doi: 10.1038/oncsis.2014.30.

12.

Hsp27 regulates EGF/β-catenin mediated epithelial to mesenchymal transition in prostate cancer.

Cordonnier T, Bishop JL, Shiota M, Nip KM, Thaper D, Vahid S, Heroux D, Gleave M, Zoubeidi A.

Int J Cancer. 2015 Mar 15;136(6):E496-507. doi: 10.1002/ijc.29122. Epub 2014 Dec 4.

13.

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.

Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JD, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, Hoodless PA, Sahinalp SC, Karsan A, Birol I.

BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.

14.

Complete genomic landscape of a recurring sporadic parathyroid carcinoma.

Kasaian K, Wiseman SM, Thiessen N, Mungall KL, Corbett RD, Qian JQ, Nip KM, He A, Tse K, Chuah E, Varhol RJ, Pandoh P, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao Y, Hirst M, Marra MA, Walker BA, Jones SJ.

J Pathol. 2013 Jul;230(3):249-60. doi: 10.1002/path.4203.

PMID:
23616356
15.

Hsp27 regulates epithelial mesenchymal transition, metastasis, and circulating tumor cells in prostate cancer.

Shiota M, Bishop JL, Nip KM, Zardan A, Takeuchi A, Cordonnier T, Beraldi E, Bazov J, Fazli L, Chi K, Gleave M, Zoubeidi A.

Cancer Res. 2013 May 15;73(10):3109-19. doi: 10.1158/0008-5472.CAN-12-3979. Epub 2013 Mar 14.

16.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD.

Nature. 2012 Aug 2;488(7409):49-56. doi: 10.1038/nature11327.

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