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Items: 39

1.

Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas.

Zhao SG, Chen WS, Das R, Chang SL, Tomlins SA, Chou J, Quigley DA, Dang HX, Barnard TJ, Mahal BA, Gibb EA, Liu Y, Davicioni E, Duska LR, Posadas EM, Jolly S, Spratt DE, Nguyen PL, Maher CA, Small EJ, Feng FY.

Clin Cancer Res. 2018 Dec 20. pii: clincanres.3121.2018. doi: 10.1158/1078-0432.CCR-18-3121. [Epub ahead of print]

PMID:
30573691
2.

Molecular tumor heterogeneity in muscle invasive bladder cancer: Biomarkers, subtypes, and implications for therapy.

da Costa JB, Gibb EA, Nykopp TK, Mannas M, Wyatt AW, Black PC.

Urol Oncol. 2018 Dec 8. pii: S1078-1439(18)30463-0. doi: 10.1016/j.urolonc.2018.11.015. [Epub ahead of print] Review.

PMID:
30528886
3.

Integrative Molecular Characterization of Malignant Pleural Mesothelioma.

Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, Tarpey P, Danilova L, Drill E, Gibb EA, Bowlby R, Kanchi R, Osmanbeyoglu HU, Sekido Y, Takeshita J, Newton Y, Graim K, Gupta M, Gay CM, Diao L, Gibbs DL, Thorsson V, Iype L, Kantheti H, Severson DT, Ravegnini G, Desmeules P, Jungbluth AA, Travis WD, Dacic S, Chirieac LR, Galateau-Sallé F, Fujimoto J, Husain AN, Silveira HC, Rusch VW, Rintoul RC, Pass H, Kindler H, Zauderer MG, Kwiatkowski DJ, Bueno R, Tsao AS, Creaney J, Lichtenberg T, Leraas K, Bowen J; TCGA Research Network, Felau I, Zenklusen JC, Akbani R, Cherniack AD, Byers LA, Noble MS, Fletcher JA, Robertson AG, Shen R, Aburatani H, Robinson BW, Campbell P, Ladanyi M.

Cancer Discov. 2018 Dec;8(12):1548-1565. doi: 10.1158/2159-8290.CD-18-0804. Epub 2018 Oct 15.

PMID:
30322867
4.

Selective Inhibition of the Lactate Transporter MCT4 Reduces Growth of Invasive Bladder Cancer.

Todenhöfer T, Seiler R, Stewart C, Moskalev I, Gao J, Ladhar S, Kamjabi A, Al Nakouzi N, Hayashi T, Choi S, Wang Y, Frees S, Daugaard M, Oo HZ, Fisel P, Schwab M, Schaeffeler E, Douglas J, Hennenlotter J, Bedke J, Gibb EA, Fazli L, Stenzl A, Black PC.

Mol Cancer Ther. 2018 Dec;17(12):2746-2755. doi: 10.1158/1535-7163.MCT-18-0107. Epub 2018 Sep 27.

PMID:
30262589
5.

Divergent Biological Response to Neoadjuvant Chemotherapy in Muscle-invasive Bladder Cancer.

Seiler R, Gibb EA, Wang NQ, Oo HZ, Lam HM, van Kessel KE, Voskuilen CS, Winters B, Erho N, Takhar MM, Douglas J, Vakar-Lopez F, Crabb SJ, van Rhijn BWG, Fransen van de Putte EE, Zwarthoff EC, Thalmann GN, Davicioni E, Boormans JL, Dall'Era M, van der Heijden MS, Wright JL, Black PC.

Clin Cancer Res. 2018 Sep 17. doi: 10.1158/1078-0432.CCR-18-1106. [Epub ahead of print]

PMID:
30224344
6.

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.

Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ; TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP.

Cell. 2018 Aug 9;174(4):1033. doi: 10.1016/j.cell.2018.07.036. No abstract available.

7.

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.

8.

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG; Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM.

Cell Rep. 2018 Jun 19;23(12):3698. doi: 10.1016/j.celrep.2018.06.032. No abstract available.

9.

Mechanistic target of rapamycin (MTOR) protein expression in the tumor and its microenvironment correlates with more aggressive pathology at cystectomy.

Winters BR, Vakar-Lopez F, Brown L, Montgomery B, Seiler R, Black PC, Boormans JL, Dall Era M, Davincioni E, Douglas J, Gibb EA, van Rhijn BWG, van der Heijden MS, Hsieh AC, Wright JL, Lam HM.

Urol Oncol. 2018 Jul;36(7):342.e7-342.e14. doi: 10.1016/j.urolonc.2018.03.016. Epub 2018 Apr 12.

10.

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG; Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM.

Cell Rep. 2018 Apr 3;23(1):313-326.e5. doi: 10.1016/j.celrep.2018.03.075. Erratum in: Cell Rep. 2018 Jun 19;23(12):3698.

11.

Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma.

Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE.

Cancer Cell. 2018 Jan 8;33(1):151. doi: 10.1016/j.ccell.2017.12.013. No abstract available.

12.

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.

Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao Y, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I.

Nat Commun. 2017 Nov 10;8(1):1433. doi: 10.1038/s41467-017-01316-7.

13.

APELA promotes tumour growth and cell migration in ovarian cancer in a p53-dependent manner.

Yi Y, Tsai SH, Cheng JC, Wang EY, Anglesio MS, Cochrane DR, Fuller M, Gibb EA, Wei W, Huntsman DG, Karsan A, Hoodless PA.

Gynecol Oncol. 2017 Dec;147(3):663-671. doi: 10.1016/j.ygyno.2017.10.016. Epub 2017 Oct 24.

PMID:
29079036
14.

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.

Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ; TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP.

Cell. 2017 Oct 19;171(3):540-556.e25. doi: 10.1016/j.cell.2017.09.007. Epub 2017 Oct 5. Erratum in: Cell. 2018 Aug 9;174(4):1033.

15.

Low PCA3 expression is a marker of poor differentiation in localized prostate tumors: exploratory analysis from 12,076 patients.

Alshalalfa M, Verhaegh GW, Gibb EA, Santiago-Jiménez M, Erho N, Jordan J, Yousefi K, Lam LLC, Kolisnik T, Chelissery J, Seiler R, Ross AE, Karnes RJ, Schaeffer EM, Lotan TT, Den RB, Freedland SJ, Davicioni E, Klein EA, Schalken JA.

Oncotarget. 2017 Feb 7;8(31):50804-50813. doi: 10.18632/oncotarget.15133. eCollection 2017 Aug 1.

16.

Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma.

Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE.

Cancer Cell. 2017 Aug 14;32(2):204-220.e15. doi: 10.1016/j.ccell.2017.07.003. Erratum in: Cancer Cell. 2018 Jan 8;33(1):151.

17.

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN.

Cell Rep. 2017 Jun 27;19(13):2878-2880. doi: 10.1016/j.celrep.2017.06.008. No abstract available.

18.

Impact of Molecular Subtypes in Muscle-invasive Bladder Cancer on Predicting Response and Survival after Neoadjuvant Chemotherapy.

Seiler R, Ashab HAD, Erho N, van Rhijn BWG, Winters B, Douglas J, Van Kessel KE, Fransen van de Putte EE, Sommerlad M, Wang NQ, Choeurng V, Gibb EA, Palmer-Aronsten B, Lam LL, Buerki C, Davicioni E, Sjödahl G, Kardos J, Hoadley KA, Lerner SP, McConkey DJ, Choi W, Kim WY, Kiss B, Thalmann GN, Todenhöfer T, Crabb SJ, North S, Zwarthoff EC, Boormans JL, Wright J, Dall'Era M, van der Heijden MS, Black PC.

Eur Urol. 2017 Oct;72(4):544-554. doi: 10.1016/j.eururo.2017.03.030. Epub 2017 Apr 5.

PMID:
28390739
19.

Comprehensive Determination of Prostate Tumor ETS Gene Status in Clinical Samples Using the CLIA Decipher Assay.

Torres A, Alshalalfa M, Tomlins SA, Erho N, Gibb EA, Chelliserry J, Lim L, Lam LLC, Faraj SF, Bezerra SM, Davicioni E, Yousefi K, Ross AE, Netto GJ, Schaeffer EM, Lotan TL.

J Mol Diagn. 2017 May;19(3):475-484. doi: 10.1016/j.jmoldx.2017.01.007. Epub 2017 Mar 21.

20.

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN.

Cell Rep. 2017 Mar 14;18(11):2780-2794. doi: 10.1016/j.celrep.2017.02.033. Erratum in: Cell Rep. 2017 Jun 27;19(13):2878-2880.

21.

Tumour-suppressor microRNAs regulate ovarian cancer cell physical properties and invasive behaviour.

Chan CK, Pan Y, Nyberg K, Marra MA, Lim EL, Jones SJ, Maar D, Gibb EA, Gunaratne PH, Robertson AG, Rowat AC.

Open Biol. 2016 Nov;6(11). pii: 160275.

22.

Stiffness of pancreatic cancer cells is associated with increased invasive potential.

Nguyen AV, Nyberg KD, Scott MB, Welsh AM, Nguyen AH, Wu N, Hohlbauch SV, Geisse NA, Gibb EA, Robertson AG, Donahue TR, Rowat AC.

Integr Biol (Camb). 2016 Dec 5;8(12):1232-1245.

23.

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJ, Bohlmann J, Birol I.

Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244.

24.

Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.

Gibb EA, Warren RL, Wilson GW, Brown SD, Robertson GA, Morin GB, Holt RA.

Genome Med. 2015 Mar 5;7(1):22. doi: 10.1186/s13073-015-0142-6. eCollection 2015.

25.

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.

Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, Nelson BH, Holt RA.

Genome Res. 2014 May;24(5):743-50. doi: 10.1101/gr.165985.113. Epub 2014 Apr 29.

26.

Mapping free-standing homing endonuclease promoters using 5'RLM-RACE.

Gibb EA.

Methods Mol Biol. 2014;1123:69-76. doi: 10.1007/978-1-62703-968-0_5.

PMID:
24510260
27.

Aberrant expression of long noncoding RNAs in cervical intraepithelial neoplasia.

Gibb EA, Becker-Santos DD, Enfield KS, Guillaud M, Niekerk Dv, Matisic JP, Macaulay CE, Lam WL.

Int J Gynecol Cancer. 2012 Nov;22(9):1557-63. doi: 10.1097/IGC.0b013e318272f2c9.

PMID:
23095774
28.

Human cancer long non-coding RNA transcriptomes.

Gibb EA, Vucic EA, Enfield KS, Stewart GL, Lonergan KM, Kennett JY, Becker-Santos DD, MacAulay CE, Lam S, Brown CJ, Lam WL.

PLoS One. 2011;6(10):e25915. doi: 10.1371/journal.pone.0025915. Epub 2011 Oct 3.

29.

Long non-coding RNAs are expressed in oral mucosa and altered in oral premalignant lesions.

Gibb EA, Enfield KS, Stewart GL, Lonergan KM, Chari R, Ng RT, Zhang L, MacAulay CE, Rosin MP, Lam WL.

Oral Oncol. 2011 Nov;47(11):1055-61. doi: 10.1016/j.oraloncology.2011.07.008. Epub 2011 Aug 10.

PMID:
21835683
30.

The functional role of long non-coding RNA in human carcinomas.

Gibb EA, Brown CJ, Lam WL.

Mol Cancer. 2011 Apr 13;10:38. doi: 10.1186/1476-4598-10-38. Review.

31.

Deciphering squamous cell carcinoma using multidimensional genomic approaches.

Gibb EA, Enfield KS, Tsui IF, Chari R, Lam S, Alvarez CE, Lam WL.

J Skin Cancer. 2011;2011:541405. doi: 10.1155/2011/541405. Epub 2010 Dec 27.

32.

Mobile DNA elements in T4 and related phages.

Edgell DR, Gibb EA, Belfort M.

Virol J. 2010 Oct 28;7:290. doi: 10.1186/1743-422X-7-290. Review.

33.

Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron.

Gibb EA, Edgell DR.

Mol Microbiol. 2010 Oct;78(1):35-46. doi: 10.1111/j.1365-2958.2010.07216.x. Epub 2010 May 19.

34.

The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases.

Monteiro-Vitorello CB, Hausner G, Searles DB, Gibb EA, Fulbright DW, Bertrand H.

Fungal Genet Biol. 2009 Nov;46(11):837-48. doi: 10.1016/j.fgb.2009.07.005. Epub 2009 Jul 14.

PMID:
19607930
35.

An RNA hairpin sequesters the ribosome binding site of the homing endonuclease mobE gene.

Gibb EA, Edgell DR.

J Bacteriol. 2009 Apr;191(7):2409-13. doi: 10.1128/JB.01751-08. Epub 2009 Jan 30.

37.

Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase that retains function.

Friedrich NC, Torrents E, Gibb EA, Sahlin M, Sjöberg BM, Edgell DR.

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6176-81. Epub 2007 Mar 29.

38.
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