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Results: 20

1.

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC.

Ann Oncol. 2014 Oct 15. pii: mdu479. [Epub ahead of print]

PMID:
25319062
[PubMed - as supplied by publisher]
2.

Expression of regulators of mitotic fidelity are associated with intercellular heterogeneity and chromosomal instability in primary breast cancer.

Roylance R, Endesfelder D, Jamal-Hanjani M, Burrell RA, Gorman P, Sander J, Murphy N, Birkbak NJ, Hanby AM, Speirs V, Johnston SR, Kschischo M, Swanton C.

Breast Cancer Res Treat. 2014 Nov;148(1):221-9. doi: 10.1007/s10549-014-3153-x. Epub 2014 Oct 7.

PMID:
25288231
[PubMed - in process]
3.

Systematic Evaluation of the Prognostic Impact and Intratumour Heterogeneity of Clear Cell Renal Cell Carcinoma Biomarkers.

Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M.

Eur Urol. 2014 Jul 18. pii: S0302-2838(14)00627-7. doi: 10.1016/j.eururo.2014.06.053. [Epub ahead of print]

PMID:
25047176
[PubMed - as supplied by publisher]
Free Article
4.

Enhancing reproducibility in cancer drug screening: how do we move forward?

Hatzis C, Bedard PL, Birkbak NJ, Beck AH, Aerts HJ, Stem DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains B.

Cancer Res. 2014 Aug 1;74(15):4016-23. doi: 10.1158/0008-5472.CAN-14-0725. Epub 2014 Jul 11. Erratum in: Cancer Res. 2014 Sep 15;74(18):5348. Stern, David F [corrected to Stem, David F].

PMID:
25015668
[PubMed - in process]
5.

Tracking genomic cancer evolution for precision medicine: the lung TRACERx study.

Jamal-Hanjani M, Hackshaw A, Ngai Y, Shaw J, Dive C, Quezada S, Middleton G, de Bruin E, Le Quesne J, Shafi S, Falzon M, Horswell S, Blackhall F, Khan I, Janes S, Nicolson M, Lawrence D, Forster M, Fennell D, Lee SM, Lester J, Kerr K, Muller S, Iles N, Smith S, Murugaesu N, Mitter R, Salm M, Stuart A, Matthews N, Adams H, Ahmad T, Attanoos R, Bennett J, Birkbak NJ, Booton R, Brady G, Buchan K, Capitano A, Chetty M, Cobbold M, Crosbie P, Davies H, Denison A, Djearman M, Goldman J, Haswell T, Joseph L, Kornaszewska M, Krebs M, Langman G, MacKenzie M, Millar J, Morgan B, Naidu B, Nonaka D, Peggs K, Pritchard C, Remmen H, Rowan A, Shah R, Smith E, Summers Y, Taylor M, Veeriah S, Waller D, Wilcox B, Wilcox M, Woolhouse I, McGranahan N, Swanton C.

PLoS Biol. 2014 Jul 8;12(7):e1001906. doi: 10.1371/journal.pbio.1001906. eCollection 2014 Jul.

PMID:
25003521
[PubMed - in process]
Free PMC Article
6.

STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes.

Xiang M, Birkbak NJ, Vafaizadeh V, Walker SR, Yeh JE, Liu S, Kroll Y, Boldin M, Taganov K, Groner B, Richardson AL, Frank DA.

Sci Signal. 2014 Jan 28;7(310):ra11. doi: 10.1126/scisignal.2004497.

PMID:
24473196
[PubMed - indexed for MEDLINE]
7.

Computational optimisation of targeted DNA sequencing for cancer detection.

Martinez P, McGranahan N, Birkbak NJ, Gerlinger M, Swanton C.

Sci Rep. 2013 Dec 3;3:3309. doi: 10.1038/srep03309.

PMID:
24296834
[PubMed - in process]
8.

Inconsistency in large pharmacogenomic studies.

Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJ, Quackenbush J.

Nature. 2013 Dec 19;504(7480):389-93. doi: 10.1038/nature12831. Epub 2013 Nov 27.

PMID:
24284626
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations.

Birkbak NJ, Kochupurakkal B, Izarzugaza JM, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC.

PLoS One. 2013 Nov 12;8(11):e80023. doi: 10.1371/journal.pone.0080023. eCollection 2013.

PMID:
24265793
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

HELQ promotes RAD51 paralogue-dependent repair to avert germ cell loss and tumorigenesis.

Adelman CA, Lolo RL, Birkbak NJ, Murina O, Matsuzaki K, Horejsi Z, Parmar K, Borel V, Skehel JM, Stamp G, D'Andrea A, Sartori AA, Swanton C, Boulton SJ.

Nature. 2013 Oct 17;502(7471):381-4. doi: 10.1038/nature12565. Epub 2013 Sep 4.

PMID:
24005329
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Parallel evolution of tumour subclones mimics diversity between tumours.

Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell RA, Rowan AJ, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C.

J Pathol. 2013 Aug;230(4):356-64. doi: 10.1002/path.4214.

PMID:
23716380
[PubMed - indexed for MEDLINE]
12.

Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome.

Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, Schwede M, Alsop K, Daniels KE, Piao H, Liu J, Etemadmoghadam D, Miron A, Salvesen HB, Mitchell G, DeFazio A, Quackenbush J, Berkowitz RS, Iglehart JD, Bowtell DD; Australian Ovarian Cancer Study Group, Matulonis UA.

Clin Cancer Res. 2012 Oct 15;18(20):5806-15. doi: 10.1158/1078-0432.CCR-12-0857. Epub 2012 Aug 21.

PMID:
22912389
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents.

Birkbak NJ, Wang ZC, Kim JY, Eklund AC, Li Q, Tian R, Bowman-Colin C, Li Y, Greene-Colozzi A, Iglehart JD, Tung N, Ryan PD, Garber JE, Silver DP, Szallasi Z, Richardson AL.

Cancer Discov. 2012 Apr;2(4):366-75. doi: 10.1158/2159-8290.CD-11-0206. Epub 2012 Mar 22. Erratum in: Cancer Discov. 2013 Aug;3(8):952.

PMID:
22576213
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Jetset: selecting the optimal microarray probe set to represent a gene.

Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC.

BMC Bioinformatics. 2011 Dec 15;12:474. doi: 10.1186/1471-2105-12-474.

PMID:
22172014
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction.

Lee AJ, Roylance R, Sander J, Gorman P, Endesfelder D, Kschischo M, Jones NP, East P, Nicke B, Spassieva S, Obeid LM, Birkbak NJ, Szallasi Z, McKnight NC, Rowan AJ, Speirs V, Hanby AM, Downward J, Tooze SA, Swanton C.

J Pathol. 2012 Feb;226(3):482-94. doi: 10.1002/path.2998. Epub 2011 Oct 19.

PMID:
21953249
[PubMed - indexed for MEDLINE]
16.

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response.

Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z.

BMC Bioinformatics. 2011 Jul 28;12:310. doi: 10.1186/1471-2105-12-310.

PMID:
21798043
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer.

Roylance R, Endesfelder D, Gorman P, Burrell RA, Sander J, Tomlinson I, Hanby AM, Speirs V, Richardson AL, Birkbak NJ, Eklund AC, Downward J, Kschischo M, Szallasi Z, Swanton C.

Cancer Epidemiol Biomarkers Prev. 2011 Oct;20(10):2183-94. doi: 10.1158/1055-9965.EPI-11-0343. Epub 2011 Jul 22.

PMID:
21784954
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables.

Endesfelder D, McGranahan N, Birkbak NJ, Szallasi Z, Kschischo M, Graham TA, Swanton C.

Oncotarget. 2011 Jul;2(7):529-37.

PMID:
21709316
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Chromosomal instability confers intrinsic multidrug resistance.

Lee AJ, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, Downward J, Szallasi Z, Tomlinson IP, Howell M, Kschischo M, Swanton C.

Cancer Res. 2011 Mar 1;71(5):1858-70. doi: 10.1158/0008-5472.CAN-10-3604.

PMID:
21363922
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Paradoxical relationship between chromosomal instability and survival outcome in cancer.

Birkbak NJ, Eklund AC, Li Q, McClelland SE, Endesfelder D, Tan P, Tan IB, Richardson AL, Szallasi Z, Swanton C.

Cancer Res. 2011 May 15;71(10):3447-52. doi: 10.1158/0008-5472.CAN-10-3667. Epub 2011 Jan 26.

PMID:
21270108
[PubMed - indexed for MEDLINE]
Free PMC Article
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