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Items: 27

1.

Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer.

Bielski CM, Donoghue MTA, Gadiya M, Hanrahan AJ, Won HH, Chang MT, Jonsson P, Penson AV, Gorelick A, Harris C, Schram AM, Syed A, Zehir A, Chapman PB, Hyman DM, Solit DB, Shannon K, Chandarlapaty S, Berger MF, Taylor BS.

Cancer Cell. 2018 Nov 12;34(5):852-862.e4. doi: 10.1016/j.ccell.2018.10.003. Epub 2018 Nov 1.

PMID:
30393068
2.

Clonal Relatedness and Mutational Differences between Upper Tract and Bladder Urothelial Carcinoma.

Audenet F, Isharwal S, Cha EK, Donoghue MTA, Drill EN, Ostrovnaya I, Pietzak EJ, Sfakianos JP, Bagrodia A, Murugan P, Dalbagni G, Donahue TF, Rosenberg JE, Bajorin DF, Arcila ME, Hechtman JF, Berger MF, Taylor BS, Al-Ahmadie H, Iyer G, Bochner BH, Coleman JA, Solit DB.

Clin Cancer Res. 2019 Feb 1;25(3):967-976. doi: 10.1158/1078-0432.CCR-18-2039. Epub 2018 Oct 23.

PMID:
30352907
3.

The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers.

Razavi P, Chang MT, Xu G, Bandlamudi C, Ross DS, Vasan N, Cai Y, Bielski CM, Donoghue MTA, Jonsson P, Penson A, Shen R, Pareja F, Kundra R, Middha S, Cheng ML, Zehir A, Kandoth C, Patel R, Huberman K, Smyth LM, Jhaveri K, Modi S, Traina TA, Dang C, Zhang W, Weigelt B, Li BT, Ladanyi M, Hyman DM, Schultz N, Robson ME, Hudis C, Brogi E, Viale A, Norton L, Dickler MN, Berger MF, Iacobuzio-Donahue CA, Chandarlapaty S, Scaltriti M, Reis-Filho JS, Solit DB, Taylor BS, Baselga J.

Cancer Cell. 2018 Sep 10;34(3):427-438.e6. doi: 10.1016/j.ccell.2018.08.008.

4.

Clinical Utility of Prospective Molecular Characterization in Advanced Endometrial Cancer.

Soumerai TE, Donoghue MTA, Bandlamudi C, Srinivasan P, Chang MT, Zamarin D, Cadoo KA, Grisham RN, O'Cearbhaill RE, Tew WP, Konner JA, Hensley ML, Makker V, Sabbatini P, Spriggs DR, Troso-Sandoval TA, Charen AS, Friedman C, Gorsky M, Schweber SJ, Middha S, Murali R, Chiang S, Park KJ, Soslow RA, Ladanyi M, Li BT, Mueller J, Weigelt B, Zehir A, Berger MF, Abu-Rustum NR, Aghajanian C, DeLair DF, Solit DB, Taylor BS, Hyman DM.

Clin Cancer Res. 2018 Dec 1;24(23):5939-5947. doi: 10.1158/1078-0432.CCR-18-0412. Epub 2018 Aug 1.

PMID:
30068706
5.

Genome doubling shapes the evolution and prognosis of advanced cancers.

Bielski CM, Zehir A, Penson AV, Donoghue MTA, Chatila W, Armenia J, Chang MT, Schram AM, Jonsson P, Bandlamudi C, Razavi P, Iyer G, Robson ME, Stadler ZK, Schultz N, Baselga J, Solit DB, Hyman DM, Berger MF, Taylor BS.

Nat Genet. 2018 Aug;50(8):1189-1195. doi: 10.1038/s41588-018-0165-1. Epub 2018 Jul 16.

6.

Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer.

Yaeger R, Chatila WK, Lipsyc MD, Hechtman JF, Cercek A, Sanchez-Vega F, Jayakumaran G, Middha S, Zehir A, Donoghue MTA, You D, Viale A, Kemeny N, Segal NH, Stadler ZK, Varghese AM, Kundra R, Gao J, Syed A, Hyman DM, Vakiani E, Rosen N, Taylor BS, Ladanyi M, Berger MF, Solit DB, Shia J, Saltz L, Schultz N.

Cancer Cell. 2018 Jan 8;33(1):125-136.e3. doi: 10.1016/j.ccell.2017.12.004.

7.

Accelerating Discovery of Functional Mutant Alleles in Cancer.

Chang MT, Bhattarai TS, Schram AM, Bielski CM, Donoghue MTA, Jonsson P, Chakravarty D, Phillips S, Kandoth C, Penson A, Gorelick A, Shamu T, Patel S, Harris C, Gao J, Sumer SO, Kundra R, Razavi P, Li BT, Reales DN, Socci ND, Jayakumaran G, Zehir A, Benayed R, Arcila ME, Chandarlapaty S, Ladanyi M, Schultz N, Baselga J, Berger MF, Rosen N, Solit DB, Hyman DM, Taylor BS.

Cancer Discov. 2018 Feb;8(2):174-183. doi: 10.1158/2159-8290.CD-17-0321. Epub 2017 Dec 15.

8.

Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making.

Abida W, Armenia J, Gopalan A, Brennan R, Walsh M, Barron D, Danila D, Rathkopf D, Morris M, Slovin S, McLaughlin B, Curtis K, Hyman DM, Durack JC, Solomon SB, Arcila ME, Zehir A, Syed A, Gao J, Chakravarty D, Vargas HA, Robson ME, Joseph V, Offit K, Donoghue MTA, Abeshouse AA, Kundra R, Heins ZJ, Penson AV, Harris C, Taylor BS, Ladanyi M, Mandelker D, Zhang L, Reuter VE, Kantoff PW, Solit DB, Berger MF, Sawyers CL, Schultz N, Scher HI.

JCO Precis Oncol. 2017 Jul;2017. doi: 10.1200/PO.17.00029. Epub 2017 May 31.

9.

AKT Inhibition in Solid Tumors With AKT1 Mutations.

Hyman DM, Smyth LM, Donoghue MTA, Westin SN, Bedard PL, Dean EJ, Bando H, El-Khoueiry AB, Pérez-Fidalgo JA, Mita A, Schellens JHM, Chang MT, Reichel JB, Bouvier N, Selcuklu SD, Soumerai TE, Torrisi J, Erinjeri JP, Ambrose H, Barrett JC, Dougherty B, Foxley A, Lindemann JPO, McEwen R, Pass M, Schiavon G, Berger MF, Chandarlapaty S, Solit DB, Banerji U, Baselga J, Taylor BS.

J Clin Oncol. 2017 Jul 10;35(20):2251-2259. doi: 10.1200/JCO.2017.73.0143. Epub 2017 May 10. Erratum in: J Clin Oncol. 2019 Feb 1;37(4):360.

10.

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.

Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE.

Genome Biol. 2015 Oct 26;16:234. doi: 10.1186/s13059-015-0790-2.

11.

ALCAM is indirectly modulated by miR-125b in MCF7 cells.

Akman HB, Selcuklu SD, Donoghue MT, Akhavantabasi S, Sapmaz A, Spillane C, Yakicier MC, Erson-Bensan AE.

Tumour Biol. 2015 May;36(5):3511-20. doi: 10.1007/s13277-014-2987-5. Epub 2014 Dec 25.

PMID:
25539763
12.

Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication.

Jacob Y, Bergamin E, Donoghue MT, Mongeon V, LeBlanc C, Voigt P, Underwood CJ, Brunzelle JS, Michaels SD, Reinberg D, Couture JF, Martienssen RA.

Science. 2014 Mar 14;343(6176):1249-53. doi: 10.1126/science.1248357.

13.

Molecular adaptation of telomere associated genes in mammals.

Morgan CC, Mc Cartney AM, Donoghue MT, Loughran NB, Spillane C, Teeling EC, O'Connell MJ.

BMC Evol Biol. 2013 Nov 15;13:251. doi: 10.1186/1471-2148-13-251.

14.

C(m)CGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants.

Donoghue MT, Fort A, Clifton R, Zhang X, McKeown PC, Voigt-Zielinksi ML, Borevitz JO, Spillane C.

DNA Res. 2014;21(2):141-51. doi: 10.1093/dnares/dst046. Epub 2013 Nov 7.

15.

Computational identification and evolutionary relationships of the microRNA gene cluster miR-71/2 in protostomes.

de Souza Gomes M, Donoghue MT, Muniyappa M, Pereira RV, Guerra-Sá R, Spillane C.

J Mol Evol. 2013 Jun;76(6):353-8. doi: 10.1007/s00239-013-9563-2. Epub 2013 Jun 6.

PMID:
23740160
16.

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.

Regulski M, Lu Z, Kendall J, Donoghue MT, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D, Martienssen RA.

Genome Res. 2013 Oct;23(10):1651-62. doi: 10.1101/gr.153510.112. Epub 2013 Jun 5.

17.

Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA.

Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, Martienssen RA.

Cell. 2012 Sep 28;151(1):194-205. doi: 10.1016/j.cell.2012.09.001. Epub 2012 Sep 20.

18.

In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure.

O'Connell MJ, Doyle AM, Juenger TE, Donoghue MT, Keshavaiah C, Tuteja R, Spillane C.

BMC Res Notes. 2012 Jul 17;5:359. doi: 10.1186/1756-0500-5-359.

19.

MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells.

Selcuklu SD, Donoghue MT, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C.

J Biol Chem. 2012 Aug 24;287(35):29516-28. doi: 10.1074/jbc.M111.335943. Epub 2012 Jul 2.

20.

Regulatory interplay between miR-21, JAG1 and 17beta-estradiol (E2) in breast cancer cells.

Selcuklu SD, Donoghue MT, Kerin MJ, Spillane C.

Biochem Biophys Res Commun. 2012 Jun 29;423(2):234-9. doi: 10.1016/j.bbrc.2012.05.074. Epub 2012 May 19.

PMID:
22618231
21.

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers.

Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang SP, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X, Jackson SA.

Nat Biotechnol. 2011 Nov 6;30(1):83-9. doi: 10.1038/nbt.2022.

PMID:
22057054
22.

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds.

McKeown PC, Laouielle-Duprat S, Prins P, Wolff P, Schmid MW, Donoghue MT, Fort A, Duszynska D, Comte A, Lao NT, Wennblom TJ, Smant G, Köhler C, Grossniklaus U, Spillane C.

BMC Plant Biol. 2011 Aug 12;11:113. doi: 10.1186/1471-2229-11-113.

23.

High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm.

Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MT, Spillane C, Nordborg M, Rehmsmeier M, Köhler C.

PLoS Genet. 2011 Jun;7(6):e1002126. doi: 10.1371/journal.pgen.1002126. Epub 2011 Jun 16.

24.

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana.

Donoghue MT, Keshavaiah C, Swamidatta SH, Spillane C.

BMC Evol Biol. 2011 Feb 18;11:47. doi: 10.1186/1471-2148-11-47.

25.

A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals.

O'Connell MJ, Loughran NB, Walsh TA, Donoghue MT, Schmid KJ, Spillane C.

Mamm Genome. 2010 Oct;21(9-10):486-98. doi: 10.1007/s00335-010-9283-5. Epub 2010 Oct 8.

PMID:
20931201
26.

miR-21 as a key regulator of oncogenic processes.

Selcuklu SD, Donoghue MT, Spillane C.

Biochem Soc Trans. 2009 Aug;37(Pt 4):918-25. doi: 10.1042/BST0370918. Review.

PMID:
19614619
27.

Ceftizoxime-induced hemolysis secondary to combined drug adsorption and immune-complex mechanisms.

Calhoun BW, Junsanto T, Donoghue MT, Naureckas E, Baron JM, Baron BW.

Transfusion. 2001 Jul;41(7):893-7.

PMID:
11452157

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