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Items: 1 to 50 of 59

1.

Dynamics of multiple resistance mechanisms in plasma DNA during EGFR-targeted therapies in non-small cell lung cancer.

Tsui DWY, Murtaza M, Wong ASC, Rueda OM, Smith CG, Chandrananda D, Soo RA, Lim HL, Goh BC, Caldas C, Forshew T, Gale D, Liu W, Morris J, Marass F, Eisen T, Chin TM, Rosenfeld N.

EMBO Mol Med. 2018 Jun;10(6). pii: e7945. doi: 10.15252/emmm.201707945.

2.

MAP3K1 and MAP2K4 mutations are associated with sensitivity to MEK inhibitors in multiple cancer models.

Xue Z, Vis DJ, Bruna A, Sustic T, van Wageningen S, Batra AS, Rueda OM, Bosdriesz E, Caldas C, Wessels LFA, Bernards R.

Cell Res. 2018 Jul;28(7):719-729. doi: 10.1038/s41422-018-0044-4. Epub 2018 May 24.

3.

High USP6NL Levels in Breast Cancer Sustain Chronic AKT Phosphorylation and GLUT1 Stability Fueling Aerobic Glycolysis.

Avanzato D, Pupo E, Ducano N, Isella C, Bertalot G, Luise C, Pece S, Bruna A, Rueda OM, Caldas C, Di Fiore PP, Sapino A, Lanzetti L.

Cancer Res. 2018 Jul 1;78(13):3432-3444. doi: 10.1158/0008-5472.CAN-17-3018. Epub 2018 Apr 24.

4.

RAD51 foci as a functional biomarker of homologous recombination repair and PARP inhibitor resistance in germline BRCA-mutated breast cancer.

Cruz C, Castroviejo-Bermejo M, Gutiérrez-Enríquez S, Llop-Guevara A, Ibrahim YH, Gris-Oliver A, Bonache S, Morancho B, Bruna A, Rueda OM, Lai Z, Polanska UM, Jones GN, Kristel P, de Bustos L, Guzman M, Rodríguez O, Grueso J, Montalban G, Caratú G, Mancuso F, Fasani R, Jiménez J, Howat WJ, Dougherty B, Vivancos A, Nuciforo P, Serres-Créixams X, Rubio IT, Oaknin A, Cadogan E, Barrett JC, Caldas C, Baselga J, Saura C, Cortés J, Arribas J, Jonkers J, Díez O, O'Connor MJ, Balmaña J, Serra V.

Ann Oncol. 2018 May 1;29(5):1203-1210. doi: 10.1093/annonc/mdy099.

5.

Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.

Chin SF, Santonja A, Grzelak M, Ahn S, Sammut SJ, Clifford H, Rueda OM, Pugh M, Goldgraben MA, Bardwell HA, Cho EY, Provenzano E, Rojo F, Alba E, Caldas C.

Exp Mol Pathol. 2018 Jun;104(3):161-169. doi: 10.1016/j.yexmp.2018.03.006. Epub 2018 Mar 31.

6.

Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort.

Mukherjee A, Russell R, Chin SF, Liu B, Rueda OM, Ali HR, Turashvili G, Mahler-Araujo B, Ellis IO, Aparicio S, Caldas C, Provenzano E.

NPJ Breast Cancer. 2018 Mar 7;4:5. doi: 10.1038/s41523-018-0056-8. eCollection 2018.

7.

SILAC identifies LAD1 as a filamin-binding regulator of actin dynamics in response to EGF and a marker of aggressive breast tumors.

Roth L, Srivastava S, Lindzen M, Sas-Chen A, Sheffer M, Lauriola M, Enuka Y, Noronha A, Mancini M, Lavi S, Tarcic G, Pines G, Nevo N, Heyman O, Ziv T, Rueda OM, Gnocchi D, Pikarsky E, Admon A, Caldas C, Yarden Y.

Sci Signal. 2018 Jan 30;11(515). pii: eaan0949. doi: 10.1126/scisignal.aan0949.

PMID:
29382783
8.

Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts.

Callari M, Batra AS, Batra RN, Sammut SJ, Greenwood W, Clifford H, Hercus C, Chin SF, Bruna A, Rueda OM, Caldas C.

BMC Genomics. 2018 Jan 5;19(1):19. doi: 10.1186/s12864-017-4414-y.

9.

PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.

Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ.

Cancer Res. 2017 Nov 1;77(21):e62-e66. doi: 10.1158/0008-5472.CAN-17-0582.

PMID:
29092942
10.

Interrogating open issues in cancer medicine with patient-derived xenografts.

Byrne AT, Alférez DG, Amant F, Annibali D, Arribas J, Biankin AV, Bruna A, Budinská E, Caldas C, Chang DK, Clarke RB, Clevers H, Coukos G, Dangles-Marie V, Eckhardt SG, Gonzalez-Suarez E, Hermans E, Hidalgo M, Jarzabek MA, de Jong S, Jonkers J, Kemper K, Lanfrancone L, Mælandsmo GM, Marangoni E, Marine JC, Medico E, Norum JH, Palmer HG, Peeper DS, Pelicci PG, Piris-Gimenez A, Roman-Roman S, Rueda OM, Seoane J, Serra V, Soucek L, Vanhecke D, Villanueva A, Vinolo E, Bertotti A, Trusolino L.

Nat Rev Cancer. 2017 Sep 15;17(10):632. doi: 10.1038/nrc.2017.85. [Epub ahead of print]

PMID:
28912576
11.

BRCA1 and BRCA2 tumor suppressors protect against endogenous acetaldehyde toxicity.

Tacconi EM, Lai X, Folio C, Porru M, Zonderland G, Badie S, Michl J, Sechi I, Rogier M, Matía García V, Batra AS, Rueda OM, Bouwman P, Jonkers J, Ryan A, Reina-San-Martin B, Hui J, Tang N, Bruna A, Biroccio A, Tarsounas M.

EMBO Mol Med. 2017 Oct;9(10):1398-1414. doi: 10.15252/emmm.201607446.

12.

Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers.

Callari M, Sammut SJ, De Mattos-Arruda L, Bruna A, Rueda OM, Chin SF, Caldas C.

Genome Med. 2017 Apr 18;9(1):35. doi: 10.1186/s13073-017-0425-1.

13.

Modeling Breast Cancer Intertumor and Intratumor Heterogeneity Using Xenografts.

Bruna A, Rueda OM, Caldas C.

Cold Spring Harb Symp Quant Biol. 2016;81:227-230. doi: 10.1101/sqb.2016.81.031112. Epub 2017 Apr 5. Review.

PMID:
28381438
14.

Interrogating open issues in cancer precision medicine with patient-derived xenografts.

Byrne AT, Alférez DG, Amant F, Annibali D, Arribas J, Biankin AV, Bruna A, Budinská E, Caldas C, Chang DK, Clarke RB, Clevers H, Coukos G, Dangles-Marie V, Eckhardt SG, Gonzalez-Suarez E, Hermans E, Hidalgo M, Jarzabek MA, de Jong S, Jonkers J, Kemper K, Lanfrancone L, Mælandsmo GM, Marangoni E, Marine JC, Medico E, Norum JH, Palmer HG, Peeper DS, Pelicci PG, Piris-Gimenez A, Roman-Roman S, Rueda OM, Seoane J, Serra V, Soucek L, Vanhecke D, Villanueva A, Vinolo E, Bertotti A, Trusolino L.

Nat Rev Cancer. 2017 Apr;17(4):254-268. doi: 10.1038/nrc.2016.140. Epub 2017 Jan 20. Review. Erratum in: Nat Rev Cancer. 2017 Sep 15;:.

PMID:
28104906
15.

p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis.

van de Ven RA, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer MW, Sahai E, Derksen PW.

Nat Commun. 2016 Dec 22;7:13874. doi: 10.1038/ncomms13874.

16.

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds.

Bruna A, Rueda OM, Greenwood W, Batra AS, Callari M, Batra RN, Pogrebniak K, Sandoval J, Cassidy JW, Tufegdzic-Vidakovic A, Sammut SJ, Jones L, Provenzano E, Baird R, Eirew P, Hadfield J, Eldridge M, McLaren-Douglas A, Barthorpe A, Lightfoot H, O'Connor MJ, Gray J, Cortes J, Baselga J, Marangoni E, Welm AL, Aparicio S, Serra V, Garnett MJ, Caldas C.

Cell. 2016 Sep 22;167(1):260-274.e22. doi: 10.1016/j.cell.2016.08.041. Epub 2016 Sep 15.

17.

Stratification and therapeutic potential of PML in metastatic breast cancer.

Martín-Martín N, Piva M, Urosevic J, Aldaz P, Sutherland JD, Fernández-Ruiz S, Arreal L, Torrano V, Cortazar AR, Planet E, Guiu M, Radosevic-Robin N, Garcia S, Macías I, Salvador F, Domenici G, Rueda OM, Zabala-Letona A, Arruabarrena-Aristorena A, Zúñiga-García P, Caro-Maldonado A, Valcárcel-Jiménez L, Sánchez-Mosquera P, Varela-Rey M, Martínez-Chantar ML, Anguita J, Ibrahim YH, Scaltriti M, Lawrie CH, Aransay AM, Iovanna JL, Baselga J, Caldas C, Barrio R, Serra V, Vivanco Md, Matheu A, Gomis RR, Carracedo A.

Nat Commun. 2016 Aug 24;7:12595. doi: 10.1038/ncomms12595.

18.
19.

SPAG5 as a prognostic biomarker and chemotherapy sensitivity predictor in breast cancer: a retrospective, integrated genomic, transcriptomic, and protein analysis.

Abdel-Fatah TMA, Agarwal D, Liu DX, Russell R, Rueda OM, Liu K, Xu B, Moseley PM, Green AR, Pockley AG, Rees RC, Caldas C, Ellis IO, Ball GR, Chan SYT.

Lancet Oncol. 2016 Jul;17(7):1004-1018. doi: 10.1016/S1470-2045(16)00174-1. Epub 2016 Jun 14.

PMID:
27312051
20.

Erratum: The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes.

Pereira B, Chin SF, Rueda OM, Vollan HK, Provenzano E, Bardwell HA, Pugh M, Jones L, Russell R, Sammut SJ, Tsui DW, Liu B, Dawson SJ, Abraham J, Northen H, Peden JF, Mukherjee A, Turashvili G, Green AR, McKinney S, Oloumi A, Shah S, Rosenfeld N, Murphy L, Bentley DR, Ellis IO, Purushotham A, Pinder SE, Børresen-Dale AL, Earl HM, Pharoah PD, Ross MT, Aparicio S, Caldas C.

Nat Commun. 2016 Jun 6;7:11908. doi: 10.1038/ncomms11908. No abstract available.

21.

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes.

Pereira B, Chin SF, Rueda OM, Vollan HK, Provenzano E, Bardwell HA, Pugh M, Jones L, Russell R, Sammut SJ, Tsui DW, Liu B, Dawson SJ, Abraham J, Northen H, Peden JF, Mukherjee A, Turashvili G, Green AR, McKinney S, Oloumi A, Shah S, Rosenfeld N, Murphy L, Bentley DR, Ellis IO, Purushotham A, Pinder SE, Børresen-Dale AL, Earl HM, Pharoah PD, Ross MT, Aparicio S, Caldas C.

Nat Commun. 2016 May 10;7:11479. doi: 10.1038/ncomms11479.

22.

Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.

Michaut M, Chin SF, Majewski I, Severson TM, Bismeijer T, de Koning L, Peeters JK, Schouten PC, Rueda OM, Bosma AJ, Tarrant F, Fan Y, He B, Xue Z, Mittempergher L, Kluin RJ, Heijmans J, Snel M, Pereira B, Schlicker A, Provenzano E, Ali HR, Gaber A, O'Hurley G, Lehn S, Muris JJ, Wesseling J, Kay E, Sammut SJ, Bardwell HA, Barbet AS, Bard F, Lecerf C, O'Connor DP, Vis DJ, Benes CH, McDermott U, Garnett MJ, Simon IM, Jirström K, Dubois T, Linn SC, Gallagher WM, Wessels LF, Caldas C, Bernards R.

Sci Rep. 2016 Jan 5;6:18517. doi: 10.1038/srep18517.

23.

Context-Specific Effects of TGF-β/SMAD3 in Cancer Are Modulated by the Epigenome.

Tufegdzic Vidakovic A, Rueda OM, Vervoort SJ, Sati Batra A, Goldgraben MA, Uribe-Lewis S, Greenwood W, Coffer PJ, Bruna A, Caldas C.

Cell Rep. 2015 Dec 22;13(11):2480-2490. doi: 10.1016/j.celrep.2015.11.040. Epub 2015 Dec 10.

24.

Double-stranded microRNA mimics can induce length- and passenger strand-dependent effects in a cell type-specific manner.

Goldgraben MA, Russell R, Rueda OM, Caldas C, Git A.

RNA. 2016 Feb;22(2):193-203. doi: 10.1261/rna.054072.115. Epub 2015 Dec 15.

25.

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

Murtaza M, Dawson SJ, Pogrebniak K, Rueda OM, Provenzano E, Grant J, Chin SF, Tsui DW, Marass F, Gale D, Ali HR, Shah P, Contente-Cuomo T, Farahani H, Shumansky K, Kingsbury Z, Humphray S, Bentley D, Shah SP, Wallis M, Rosenfeld N, Caldas C.

Nat Commun. 2015 Nov 4;6:8760. doi: 10.1038/ncomms9760.

26.

Expression profiling of nuclear receptors in breast cancer identifies TLX as a mediator of growth and invasion in triple-negative breast cancer.

Lin ML, Patel H, Remenyi J, Banerji CR, Lai CF, Periyasamy M, Lombardo Y, Busonero C, Ottaviani S, Passey A, Quinlan PR, Purdie CA, Jordan LB, Thompson AM, Finn RS, Rueda OM, Caldas C, Gil J, Coombes RC, Fuller-Pace FV, Teschendorff AE, Buluwela L, Ali S.

Oncotarget. 2015 Aug 28;6(25):21685-703.

27.

Corrigendum: Progesterone receptor modulates ERα action in breast cancer.

Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D'Santos C, Robinson JL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS.

Nature. 2015 Oct 1;526(7571):144. doi: 10.1038/nature14959. Epub 2015 Aug 5. No abstract available.

PMID:
26245370
28.

Progesterone receptor modulates ERα action in breast cancer.

Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D'Santos C, Robinson JL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS.

Nature. 2015 Jul 16;523(7560):313-7. doi: 10.1038/nature14583. Epub 2015 Jul 8. Erratum in: Nature. 2015 Oct 1;526(7571):144. Serandour, Aurelien A A[Corrected to Serandour, Aurelien A].

29.

Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.

Schouten PC, Grigoriadis A, Kuilman T, Mirza H, Watkins JA, Cooke SA, van Dyk E, Severson TM, Rueda OM, Hoogstraat M, Verhagen CV, Natrajan R, Chin SF, Lips EH, Kruizinga J, Velds A, Nieuwland M, Kerkhoven RM, Krijgsman O, Vens C, Peeper D, Nederlof PM, Caldas C, Tutt AN, Wessels LF, Linn SC.

Mol Oncol. 2015 Aug;9(7):1274-86. doi: 10.1016/j.molonc.2015.03.002. Epub 2015 Mar 20.

30.

BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells.

Khaled WT, Choon Lee S, Stingl J, Chen X, Raza Ali H, Rueda OM, Hadi F, Wang J, Yu Y, Chin SF, Stratton M, Futreal A, Jenkins NA, Aparicio S, Copeland NG, Watson CJ, Caldas C, Liu P.

Nat Commun. 2015 Jan 9;6:5987. doi: 10.1038/ncomms6987.

31.

A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.

Vollan HK, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN; METABRIC Group, Brenton JD, Pharoah PD, Børresen-Dale AL, Aparicio S, Caldas C.

Mol Oncol. 2015 Jan;9(1):115-27. doi: 10.1016/j.molonc.2014.07.019. Epub 2014 Aug 8.

32.

Genome-driven integrated classification of breast cancer validated in over 7,500 samples.

Ali HR, Rueda OM, Chin SF, Curtis C, Dunning MJ, Aparicio SA, Caldas C.

Genome Biol. 2014 Aug 28;15(8):431. doi: 10.1186/s13059-014-0431-1.

33.

JARID1B is a luminal lineage-driving oncogene in breast cancer.

Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C, Zhao X, Moen Vollan HK, Maruyama R, Ekram MB, Sun H, Kim JH, Carver K, Zucca M, Feng J, Almendro V, Bessarabova M, Rueda OM, Nikolsky Y, Caldas C, Liu XS, Polyak K.

Cancer Cell. 2014 Jun 16;25(6):762-77. doi: 10.1016/j.ccr.2014.04.024.

34.

Genomic and protein expression analysis reveals flap endonuclease 1 (FEN1) as a key biomarker in breast and ovarian cancer.

Abdel-Fatah TM, Russell R, Albarakati N, Maloney DJ, Dorjsuren D, Rueda OM, Moseley P, Mohan V, Sun H, Abbotts R, Mukherjee A, Agarwal D, Illuzzi JL, Jadhav A, Simeonov A, Ball G, Chan S, Caldas C, Ellis IO, Wilson DM 3rd, Madhusudan S.

Mol Oncol. 2014 Oct;8(7):1326-38. doi: 10.1016/j.molonc.2014.04.009. Epub 2014 May 13.

35.

TP53 mutation spectrum in breast cancer is subtype specific and has distinct prognostic relevance.

Silwal-Pandit L, Vollan HK, Chin SF, Rueda OM, McKinney S, Osako T, Quigley DA, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Langerød A.

Clin Cancer Res. 2014 Jul 1;20(13):3569-80. doi: 10.1158/1078-0432.CCR-13-2943. Epub 2014 May 6. Erratum in: Clin Cancer Res. 2015 Mar 15;21(6):1502.

36.

Amplification of TRIM44: pairing a prognostic target with potential therapeutic strategy.

Ong CA, Shannon NB, Ross-Innes CS, O'Donovan M, Rueda OM, Hu DE, Kettunen MI, Walker CE, Noorani A, Hardwick RH, Caldas C, Brindle K, Fitzgerald RC.

J Natl Cancer Inst. 2014 Apr 28;106(5). pii: dju050. doi: 10.1093/jnci/dju050.

37.

A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients.

Lee U, Frankenberger C, Yun J, Bevilacqua E, Caldas C, Chin SF, Rueda OM, Reinitz J, Rosner MR.

PLoS One. 2013 Dec 11;8(12):e82125. doi: 10.1371/journal.pone.0082125. eCollection 2013.

38.

Master regulators of FGFR2 signalling and breast cancer risk.

Fletcher MN, Castro MA, Wang X, de Santiago I, O'Reilly M, Chin SF, Rueda OM, Caldas C, Ponder BA, Markowetz F, Meyer KB.

Nat Commun. 2013;4:2464. doi: 10.1038/ncomms3464.

39.

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA.

PLoS Comput Biol. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9.

40.

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer.

Margolin AA, Bilal E, Huang E, Norman TC, Ottestad L, Mecham BH, Sauerwine B, Kellen MR, Mangravite LM, Furia MD, Vollan HK, Rueda OM, Guinney J, Deflaux NA, Hoff B, Schildwachter X, Russnes HG, Park D, Vang VO, Pirtle T, Youseff L, Citro C, Curtis C, Kristensen VN, Hellerstein J, Friend SH, Stolovitzky G, Aparicio S, Caldas C, Børresen-Dale AL.

Sci Transl Med. 2013 Apr 17;5(181):181re1. doi: 10.1126/scitranslmed.3006112.

41.

Analysis of circulating tumor DNA to monitor metastatic breast cancer.

Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, Halsall D, Wallis M, Bentley D, Caldas C, Rosenfeld N.

N Engl J Med. 2013 Mar 28;368(13):1199-209. doi: 10.1056/NEJMoa1213261. Epub 2013 Mar 13.

42.

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.

Nilsen G, Liestøl K, Van Loo P, Moen Vollan HK, Eide MB, Rueda OM, Chin SF, Russell R, Baumbusch LO, Caldas C, Børresen-Dale AL, Lingjaerde OC.

BMC Genomics. 2012 Nov 4;13:591. doi: 10.1186/1471-2164-13-591.

43.

Finding common regions of alteration in copy number data.

Rueda OM, Diaz-Uriarte R, Caldas C.

Methods Mol Biol. 2013;973:339-53. doi: 10.1007/978-1-62703-281-0_21. Review.

PMID:
23412800
44.

Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor.

Mohammed H, D'Santos C, Serandour AA, Ali HR, Brown GD, Atkins A, Rueda OM, Holmes KA, Theodorou V, Robinson JL, Zwart W, Saadi A, Ross-Innes CS, Chin SF, Menon S, Stingl J, Palmieri C, Caldas C, Carroll JS.

Cell Rep. 2013 Feb 21;3(2):342-9. doi: 10.1016/j.celrep.2013.01.010. Epub 2013 Feb 9.

45.

A new genome-driven integrated classification of breast cancer and its implications.

Dawson SJ, Rueda OM, Aparicio S, Caldas C.

EMBO J. 2013 Mar 6;32(5):617-28. doi: 10.1038/emboj.2013.19. Epub 2013 Feb 8. Review.

46.

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

Yuan Y, Failmezger H, Rueda OM, Ali HR, Gräf S, Chin SF, Schwarz RF, Curtis C, Dunning MJ, Bardwell H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F.

Sci Transl Med. 2012 Oct 24;4(157):157ra143. doi: 10.1126/scitranslmed.3004330. Erratum in: Sci Transl Med. 2012 Oct 24;4(157):161er6.

47.

TGFβ induces the formation of tumour-initiating cells in claudinlow breast cancer.

Bruna A, Greenwood W, Le Quesne J, Teschendorff A, Miranda-Saavedra D, Rueda OM, Sandoval JL, Vidakovic AT, Saadi A, Pharoah P, Stingl J, Caldas C.

Nat Commun. 2012;3:1055. doi: 10.1038/ncomms2039.

PMID:
22968701
48.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S.

Nature. 2012 Apr 18;486(7403):346-52. doi: 10.1038/nature10983.

49.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S.

Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933.

50.

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.

Yuan Y, Rueda OM, Curtis C, Markowetz F.

Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.

PMID:
21804112

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