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ArticlesPeer ReviewedFull Text
Multi-omic machine learning predictor of breast cancer therapy response
Author / Creator:Sammut, Stephen-John ; Crispin-Ortuzar, Mireia ; Chin, Suet-Feung ; Provenzano, Elena ; Bardwell, Helen A. ; Ma, Wenxin ; Cope, Wei ; Dariush, Ali ; Dawson, Sarah-Jane ; Abraham, Jean E. ; Dunn, Janet ; Hiller, Louise ; Thomas, Jeremy ; Cameron, David A. ; Bartlett, John M. S. ; Hayward, Larry ; Pharoah, Paul D. ; Markowetz, Florian ; Rueda, Oscar M. ; Earl, Helena M. ; Caldas, Carlos
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2022-01, Vol.601 (7894), p.623-629
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Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups
Author / Creator:Rueda, Oscar M. ; Sammut, Stephen-John ; Seoane, Jose A. ; Chin, Suet-Feung ; Caswell-Jin, Jennifer L. ; Callari, Maurizio ; Batra, Rajbir ; Pereira, Bernard ; Bruna, Alejandra ; Ali, H. Raza ; Provenzano, Elena ; Liu, Bin ; Parisien, Michelle ; Gillett, Cheryl ; McKinney, Steven ; Green, Andrew R. ; Murphy, Leigh ; Purushotham, Arnie ; Ellis, Ian O. ; Pharoah, Paul D. ; Rueda, Cristina ; Aparicio, Samuel ; Caldas, Carlos ; Curtis, Christina
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2019-03, Vol.567 (7748), p.399-404
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Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer
Author / Creator:Dawson, Sarah-Jane ; Tsui, Dana W.Y ; Murtaza, Muhammed ; Biggs, Heather ; Rueda, Oscar M ; Chin, Suet-Feung ; Dunning, Mark J ; Gale, Davina ; Forshew, Tim ; Mahler-Araujo, Betania ; Rajan, Sabrina ; Humphray, Sean ; Becq, Jennifer ; Halsall, David ; Wallis, Matthew ; Bentley, David ; Caldas, Carlos ; Rosenfeld, Nitzan
Publisher:Waltham, MA: Massachusetts Medical Society
Journal title:The New England journal of medicine, 2013-03, Vol.368 (13), p.1199-1209
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Evaluation and comparison of different breast cancer prognosis scores based on gene expression data
Author / Creator:Chowdhury, Avirup ; Pharoah, Paul D ; Rueda, Oscar M
Publisher:England: BioMed Central Ltd
Journal title:Breast cancer research : BCR, 2023-02, Vol.25 (1), p.17-8, Article 17
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The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences
Author / Creator:Pan, Jia-Wern ; Zabidi, Muhammad Mamduh Ahmad ; Ng, Pei-Sze ; Meng, Mei-Yee ; Hasan, Siti Norhidayu ; Sandey, Bethan ; Sammut, Stephen-John ; Yip, Cheng-Har ; Rajadurai, Pathmanathan ; Rueda, Oscar M. ; Caldas, Carlos ; Chin, Suet-Feung ; Teo, Soo-Hwang
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-12, Vol.11 (1), p.6433-6433, Article 6433
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Copynumber: Efficient algorithms for single- and multi-track copy number segmentation
Author / Creator:Nilsen, Gro ; Liestøl, Knut ; Van Loo, Peter ; Moen Vollan, Hans Kristian ; Eide, Marianne B ; Rueda, Oscar M ; Chin, Suet-Feung ; Russell, Roslin ; Baumbusch, Lars O ; Caldas, Carlos ; Børresen-Dale, Anne-Lise ; Lingjaerde, Ole Christian
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2012-11, Vol.13 (1), p.591-591, Article 591
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FGFR1 amplification or overexpression and hormonal resistance in luminal breast cancer: rationale for a triple blockade of ER, CDK4/6, and FGFR1
Author / Creator:Mouron, Silvana ; Manso, Luis ; Caleiras, Eduardo ; Rodriguez-Peralto, Jose L ; Rueda, Oscar M ; Caldas, Carlos ; Colomer, Ramon ; Quintela-Fandino, Miguel ; Bueno, Maria J
Publisher:England: BioMed Central Ltd
Journal title:Breast cancer research : BCR, 2021-02, Vol.23 (1), p.21-16, Article 21
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Predicting COVID-19 progression from diagnosis to recovery or death linking primary care and hospital records in Castilla y León (Spain)
Author / Creator:Álvarez-Esteban, Pedro C ; Del Barrio, Eustasio ; Rueda, Oscar M ; Rueda, Cristina
Publisher:United States: Public Library of Science
Journal title:PloS one, 2021-09, Vol.16 (9), p.e0257613-e0257613
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DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation
Author / Creator:Batra, Rajbir Nath ; Lifshitz, Aviezer ; Vidakovic, Ana Tufegdzic ; Chin, Suet-Feung ; Sati-Batra, Ankita ; Sammut, Stephen-John ; Provenzano, Elena ; Ali, H. Raza ; Dariush, Ali ; Bruna, Alejandra ; Murphy, Leigh ; Purushotham, Arnie ; Ellis, Ian ; Green, Andrew ; Garrett-Bakelman, Francine E. ; Mason, Chris ; Melnick, Ari ; Aparicio, Samuel A. J. R. ; Rueda, Oscar M. ; Tanay, Amos ; Caldas, Carlos
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-09, Vol.12 (1), p.5406-13, Article 5406
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ArticlesPeer ReviewedFull Text
Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts
Author / Creator:Callari, Maurizio ; Batra, Ankita Sati ; Batra, Rajbir Nath ; Sammut, Stephen-John ; Greenwood, Wendy ; Clifford, Harry ; Hercus, Colin ; Chin, Suet-Feung ; Bruna, Alejandra ; Rueda, Oscar M ; Caldas, Carlos
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2018-01, Vol.19 (1), p.19-19, Article 19
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Development and validation of a reliable DNA copy-number-based machine learning algorithm (CopyClust) for breast cancer integrative cluster classification
Author / Creator:Young, Cameron C. ; Eason, Katherine ; Manzano Garcia, Raquel ; Moulange, Richard ; Mukherjee, Sach ; Chin, Suet-Feung ; Caldas, Carlos ; Rueda, Oscar M.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-05, Vol.14 (1), p.11861-11861, Article 11861
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Positive correlation between transcriptomic stemness and PI3K/AKT/mTOR signaling scores in breast cancer, and a counterintuitive relationship with PIK3CA genotype
Author / Creator:Madsen, Ralitsa R ; Erickson, Emily C ; Rueda, Oscar M ; Robin, Xavier ; Caldas, Carlos ; Toker, Alex ; Semple, Robert K ; Vanhaesebroeck, Bart
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2021-11, Vol.17 (11), p.e1009876-e1009876
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A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients
Author / Creator:Lee, Unjin ; Frankenberger, Casey ; Yun, Jieun ; Bevilacqua, Elena ; Caldas, Carlos ; Chin, Suet-Feung ; Rueda, Oscar M ; Reinitz, John ; Rosner, Marsha Rich
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-12, Vol.8 (12), p.e82125-e82125
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Dynamics of multiple resistance mechanisms in plasma DNA during EGFR‐targeted therapies in non‐small cell lung cancer
Author / Creator:Tsui, Dana Wai Yi ; Murtaza, Muhammed ; Wong, Alvin Seng Cheong ; Rueda, Oscar M ; Smith, Christopher G ; Chandrananda, Dineika ; Soo, Ross A ; Lim, Hong Liang ; Goh, Boon Cher ; Caldas, Carlos ; Forshew, Tim ; Gale, Davina ; Liu, Wei ; Morris, James ; Marass, Francesco ; Eisen, Tim ; Chin, Tan Min ; Rosenfeld, Nitzan
Publisher:London: Nature Publishing Group UK
Journal title:EMBO molecular medicine, 2018-06, Vol.10 (6), p.1-n/a
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NRG1 fusions in breast cancer
Author / Creator:Howarth, Karen D ; Mirza, Tashfina ; Cooke, Susanna L ; Chin, Suet-Feung ; Pole, Jessica C ; Turro, Ernest ; Eldridge, Matthew D ; Garcia, Raquel Manzano ; Rueda, Oscar M ; Boursnell, Chris ; Abraham, Jean E ; Caldas, Carlos ; Edwards, Paul A W
Publisher:England: BioMed Central Ltd
Journal title:Breast cancer research : BCR, 2021-01, Vol.23 (1), p.3-12, Article 3
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Clustering of HR + /HER2- breast cancer in an Asian cohort is driven by immune phenotypes
Author / Creator:Pan, Jia-Wern ; Ragu, Mohana ; Chan, Wei-Qin ; Hasan, Siti Norhidayu ; Islam, Tania ; Teoh, Li-Ying ; Jamaris, Suniza ; See, Mee-Hoong ; Yip, Cheng-Har ; Rajadurai, Pathmanathan ; Looi, Lai-Meng ; Taib, Nur Aishah Mohd ; Rueda, Oscar M ; Caldas, Carlos ; Chin, Suet-Feung ; Lim, Joanna ; Teo, Soo-Hwang
Publisher:England: BioMed Central Ltd
Journal title:Breast cancer research : BCR, 2024-04, Vol.26 (1), p.67-14, Article 67
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Comparison of tumor‐informed and tumor‐naïve sequencing assays for ctDNA detection in breast cancer
Author / Creator:Santonja, Angela ; Cooper, Wendy N ; Eldridge, Matthew D ; Edwards, Paul A W ; Morris, James A ; Edwards, Abigail R ; Zhao, Hui ; Heider, Katrin ; Couturier, Dominique‐Laurent ; Vijayaraghavan, Aadhitthya ; Mennea, Paulius ; Ditter, Emma‐Jane ; Smith, Christopher G ; Boursnell, Chris ; Manzano García, Raquel ; Rueda, Oscar M ; Beddowes, Emma ; Biggs, Heather ; Sammut, Stephen‐John ; Rosenfeld, Nitzan ; Caldas, Carlos ; Abraham, Jean E ; Gale, Davina
Publisher:London: Nature Publishing Group UK
Journal title:EMBO molecular medicine, 2023-06, Vol.15 (6), p.e16505-n/a
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Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers
Author / Creator:Callari, Maurizio ; Sammut, Stephen-John ; De Mattos-Arruda, Leticia ; Bruna, Alejandra ; Rueda, Oscar M ; Chin, Suet-Feung ; Caldas, Carlos
Publisher:England: BioMed Central
Journal title:Genome medicine, 2017-04, Vol.9 (1), p.35-11, Article 35
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Genomic and protein expression analysis reveals flap endonuclease 1 (FEN1) as a key biomarker in breast and ovarian cancer
Author / Creator:Abdel-Fatah, Tarek M.A. ; Russell, Roslin ; Albarakati, Nada ; Maloney, David J. ; Dorjsuren, Dorjbal ; Rueda, Oscar M. ; Moseley, Paul ; Mohan, Vivek ; Sun, Hongmao ; Abbotts, Rachel ; Mukherjee, Abhik ; Agarwal, Devika ; Illuzzi, Jennifer L. ; Jadhav, Ajit ; Simeonov, Anton ; Ball, Graham ; Chan, Stephen ; Caldas, Carlos ; Ellis, Ian O. ; Wilson, David M. ; Madhusudan, Srinivasan
Publisher:United States: Elsevier B.V
Journal title:Molecular oncology, 2014-10, Vol.8 (7), p.1326-1338
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BRCA1 and BRCA2 tumor suppressors protect against endogenous acetaldehyde toxicity
Author / Creator:Tacconi, Eliana MC ; Lai, Xianning ; Folio, Cecilia ; Porru, Manuela ; Zonderland, Gijs ; Badie, Sophie ; Michl, Johanna ; Sechi, Irene ; Rogier, Mélanie ; Matía García, Verónica ; Batra, Ankita Sati ; Rueda, Oscar M ; Bouwman, Peter ; Jonkers, Jos ; Ryan, Anderson ; Reina‐San‐Martin, Bernardo ; Hui, Joannie ; Tang, Nelson ; Bruna, Alejandra ; Biroccio, Annamaria ; Tarsounas, Madalena
Publisher:London: Nature Publishing Group UK
Journal title:EMBO molecular medicine, 2017-10, Vol.9 (10), p.1398-1414
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Multi-omic machine learning predictor of breast cancer therapy response

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Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups

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Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

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Evaluation and comparison of different breast cancer prognosis scores based on gene expression data

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The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences

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

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FGFR1 amplification or overexpression and hormonal resistance in luminal breast cancer: rationale for a triple blockade of ER, CDK4/6, and FGFR1

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Predicting COVID-19 progression from diagnosis to recovery or death linking primary care and hospital records in Castilla y León (Spain)

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DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation

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

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Development and validation of a reliable DNA copy-number-based machine learning algorithm (CopyClust) for breast cancer integrative cluster classification

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Positive correlation between transcriptomic stemness and PI3K/AKT/mTOR signaling scores in breast cancer, and a counterintuitive relationship with PIK3CA genotype

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

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

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NRG1 fusions in breast cancer

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Clustering of HR + /HER2- breast cancer in an Asian cohort is driven by immune phenotypes

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Comparison of tumor‐informed and tumor‐naïve sequencing assays for ctDNA detection in breast cancer

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

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

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BRCA1 and BRCA2 tumor suppressors protect against endogenous acetaldehyde toxicity

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