Molecular portraits of human breast tumours

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Cited by:

1. Zinab O. Doha & Xiaoyan Wang & Nicholas L. Calistri & Jennifer Eng & Colin J. Daniel & Luke Ternes & Eun Na Kim & Carl Pelz & Michael Munks & Courtney Betts & Sunjong Kwon & Elmar Bucher & Xi Li & Tre, 2023. "MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
2. Yang, Xi & Hoadley, Katherine A. & Hannig, Jan & Marron, J.S., 2023. "Jackstraw inference for AJIVE data integration," Computational Statistics & Data Analysis, Elsevier, vol. 180(C).
3. UnJin Lee & Casey Frankenberger & Jieun Yun & Elena Bevilacqua & Carlos Caldas & Suet-Feung Chin & Oscar M Rueda & John Reinitz & Marsha Rich Rosner, 2013. "A Prognostic Gene Signature for Metastasis-Free Survival of Triple Negative Breast Cancer Patients," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-13, December.
4. Erhan Bilal & Janusz Dutkowski & Justin Guinney & In Sock Jang & Benjamin A Logsdon & Gaurav Pandey & Benjamin A Sauerwine & Yishai Shimoni & Hans Kristian Moen Vollan & Brigham H Mecham & Oscar M Rue, 2013. "Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-16, May.
5. M. G. Filippone & D. Gaglio & R. Bonfanti & F. A. Tucci & E. Ceccacci & R. Pennisi & M. Bonanomi & G. Jodice & M. Tillhon & F. Montani & G. Bertalot & S. Freddi & M. Vecchi & A. Taglialatela & M. Roma, 2022. "CDK12 promotes tumorigenesis but induces vulnerability to therapies inhibiting folate one-carbon metabolism in breast cancer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
6. Junhee Seok & Ronald W Davis & Wenzhong Xiao, 2015. "A Hybrid Approach of Gene Sets and Single Genes for the Prediction of Survival Risks with Gene Expression Data," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-15, May.
7. Lingsong Meng & Dorina Avram & George Tseng & Zhiguang Huo, 2022. "Outcome‐guided sparse K‐means for disease subtype discovery via integrating phenotypic data with high‐dimensional transcriptomic data," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 71(2), pages 352-375, March.
8. Wenbin Zhou & Zhongyuan He & Jialei Xue & Minghai Wang & Xiaoming Zha & Lijun Ling & Lin Chen & Shui Wang & Xiaoan Liu, 2012. "Molecular Subtype Classification Is a Determinant of Non-Sentinel Lymph Node Metastasis in Breast Cancer Patients with Positive Sentinel Lymph Nodes," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-5, April.
9. Qing Qu & Yan Mao & Xiao-chun Fei & Kun-wei Shen, 2013. "The Impact of Androgen Receptor Expression on Breast Cancer Survival: A Retrospective Study and Meta-Analysis," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-1, December.
10. G. Gambardella & G. Viscido & B. Tumaini & A. Isacchi & R. Bosotti & D. di Bernardo, 2022. "A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
11. J Matthew Mahoney & Jaclyn Taroni & Viktor Martyanov & Tammara A Wood & Casey S Greene & Patricia A Pioli & Monique E Hinchcliff & Michael L Whitfield, 2015. "Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms," PLOS Computational Biology, Public Library of Science, vol. 11(1), pages 1-20, January.
12. John P Lloyd & Matthew B Soellner & Sofia D Merajver & Jun Z Li, 2021. "Impact of between-tissue differences on pan-cancer predictions of drug sensitivity," PLOS Computational Biology, Public Library of Science, vol. 17(2), pages 1-25, February.
13. Marron, J.S., 2017. "Big Data in context and robustness against heterogeneity," Econometrics and Statistics, Elsevier, vol. 2(C), pages 73-80.
14. I Díaz & O Savenkov & K Ballman, 2018. "Targeted learning ensembles for optimal individualized treatment rules with time-to-event outcomes," Biometrika, Biometrika Trust, vol. 105(3), pages 723-738.
15. David Ascheid & Magdalena Baumann & Jürgen Pinnecker & Mike Friedrich & Daniel Szi-Marton & Cornelia Medved & Maja Bundalo & Vanessa Ortmann & Asli Öztürk & Rajender Nandigama & Katherina Hemmen & Sül, 2024. "A vascularized breast cancer spheroid platform for the ranked evaluation of tumor microenvironment-targeted drugs by light sheet fluorescence microscopy," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
16. Manish G & Anil Kumar Badana & Rama Rao Malla, 2017. "Emerging Diagnostic and Prognostic Biomarkers of Triple Negative Breast Cancer," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 1(3), pages 561-565, August.
17. Maurizio Callari & Antonio Lembo & Giampaolo Bianchini & Valeria Musella & Vera Cappelletti & Luca Gianni & Maria Grazia Daidone & Paolo Provero, 2014. "Accurate Data Processing Improves the Reliability of Affymetrix Gene Expression Profiles from FFPE Samples," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-10, January.
18. Jacob Elnaggar & Fern Tsien & Lucio Miele & Chindo Hicks & Clayton Yates & Melisa Davis, 2019. "An Integrative Genomics Approach for Associating Genetic Susceptibility with the Tumor Immune Microenvironment in Triple Negative Breast Cancer," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 15(1), pages 1-12, February.
19. Deepak Poduval & Zuzana Sichmanova & Anne Hege Straume & Per Eystein Lønning & Stian Knappskog, 2020. "The novel microRNAs hsa-miR-nov7 and hsa-miR-nov3 are over-expressed in locally advanced breast cancer," PLOS ONE, Public Library of Science, vol. 15(4), pages 1-23, April.
20. Daniel Couch & Zhenning Yu & Jin Hyun Nam & Carter Allen & Paula S Ramos & Willian A da Silveira & Kelly J Hunt & Edward S Hazard & Gary Hardiman & Andrew Lawson & Dongjun Chung, 2019. "GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-19, July.
21. Markus Ringnér & Erik Fredlund & Jari Häkkinen & Åke Borg & Johan Staaf, 2011. "GOBO: Gene Expression-Based Outcome for Breast Cancer Online," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-11, March.
22. Egashira, Kento & Yata, Kazuyoshi & Aoshima, Makoto, 2024. "Asymptotic properties of hierarchical clustering in high-dimensional settings," Journal of Multivariate Analysis, Elsevier, vol. 199(C).
23. Mark Reimers, 2010. "Making Informed Choices about Microarray Data Analysis," PLOS Computational Biology, Public Library of Science, vol. 6(5), pages 1-7, May.
24. Yoo-Ah Kim & Stefan Wuchty & Teresa M Przytycka, 2011. "Identifying Causal Genes and Dysregulated Pathways in Complex Diseases," PLOS Computational Biology, Public Library of Science, vol. 7(3), pages 1-13, March.
25. Mariana Segovia-Mendoza & Margarita Isabel Palacios-Arreola & Luz María Monroy-Escamilla & Alexandra Estela Soto-Piña & Karen Elizabeth Nava-Castro & Yizel Becerril-Alarcón & Roberto Camacho-Beiza & D, 2022. "Association of Serum Levels of Plasticizers Compounds, Phthalates and Bisphenols, in Patients and Survivors of Breast Cancer: A Real Connection?," IJERPH, MDPI, vol. 19(13), pages 1-22, June.
26. Zhiguang Huo & Ying Ding & Silvia Liu & Steffi Oesterreich & George Tseng, 2016. "Meta-Analytic Framework for Sparse K -Means to Identify Disease Subtypes in Multiple Transcriptomic Studies," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(513), pages 27-42, March.
27. Alan A. Arslan & Yian Zhang & Nedim Durmus & Sultan Pehlivan & Adrienne Addessi & Freya Schnabel & Yongzhao Shao & Joan Reibman, 2021. "Breast Cancer Characteristics in the Population of Survivors Participating in the World Trade Center Environmental Health Center Program 2002–2019," IJERPH, MDPI, vol. 18(14), pages 1-11, July.
28. María Elena Martínez & Jonathan T Unkart & Li Tao & Candyce H Kroenke & Richard Schwab & Ian Komenaka & Scarlett Lin Gomez, 2017. "Prognostic significance of marital status in breast cancer survival: A population-based study," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-14, May.
29. Marie Tuomarila & Kaisa Luostari & Ylermi Soini & Vesa Kataja & Veli-Matti Kosma & Arto Mannermaa, 2014. "Overexpression of MicroRNA-200c Predicts Poor Outcome in Patients with PR-Negative Breast Cancer," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-8, October.
30. Danijel Sikic & Bastian Keck & Sven Wach & Helge Taubert & Bernd Wullich & Peter J Goebell & Andreas Kahlmeyer & Peter Olbert & Philipp Isfort & Wilhelm Nimphius & Arndt Hartmann & Johannes Giedl & on, 2017. "Immunohistochemiocal subtyping using CK20 and CK5 can identify urothelial carcinomas of the upper urinary tract with a poor prognosis," PLOS ONE, Public Library of Science, vol. 12(6), pages 1-13, June.
31. Peter Eirew & Ciara O’Flanagan & Jerome Ting & Sohrab Salehi & Jazmine Brimhall & Beixi Wang & Justina Biele & Teresa Algara & So Ra Lee & Corey Hoang & Damian Yap & Steven McKinney & Cherie Bates & E, 2022. "Accurate determination of CRISPR-mediated gene fitness in transplantable tumours," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
32. Yishai Shimoni, 2018. "Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification," PLOS Computational Biology, Public Library of Science, vol. 14(2), pages 1-15, February.
33. Eun Young Chae & Woo Kyung Moon & Hak Hee Kim & Won Hwa Kim & Joo Hee Cha & Hee Jung Shin & Woo Jung Choi & Wonshik Han & Dong-Young Noh & Sae Byul Lee & Sei Hyun Ahn, 2016. "Association between Ultrasound Features and the 21-Gene Recurrence Score Assays in Patients with Oestrogen Receptor-Positive, HER2-Negative, Invasive Breast Cancer," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-14, June.
34. Sun Jiehuan & Warren Joshua L. & Zhao Hongyu, 2017. "A Bayesian semiparametric factor analysis model for subtype identification," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(2), pages 145-158, April.
35. Karama Asleh & Gian Luca Negri & Sandra E. Spencer Miko & Shane Colborne & Christopher S. Hughes & Xiu Q. Wang & Dongxia Gao & C. Blake Gilks & Stephen K. L. Chia & Torsten O. Nielsen & Gregg B. Morin, 2022. "Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
36. Sandra M. Rocha & Sílvia Socorro & Luís A. Passarinha & Cláudio J. Maia, 2022. "Comprehensive Landscape of STEAP Family Members Expression in Human Cancers: Unraveling the Potential Usefulness in Clinical Practice Using Integrated Bioinformatics Analysis," Data, MDPI, vol. 7(5), pages 1-48, May.
37. Ausra Milano & Sarah A Pendergrass & Jennifer L Sargent & Lacy K George & Timothy H McCalmont & M Kari Connolly & Michael L Whitfield, 2008. "Molecular Subsets in the Gene Expression Signatures of Scleroderma Skin," PLOS ONE, Public Library of Science, vol. 3(7), pages 1-19, July.
38. Casey S Greene & Olga G Troyanskaya, 2012. "Chapter 2: Data-Driven View of Disease Biology," PLOS Computational Biology, Public Library of Science, vol. 8(12), pages 1-8, December.
39. Li Li & Chang Liu & Fang Wang & Wei Miao & Jie Zhang & Zhiqian Kang & Yihan Chen & Luying Peng, 2014. "Unraveling the Hidden Heterogeneities of Breast Cancer Based on Functional miRNA Cluster," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-6, January.
40. Silje Kjølle & Kenneth Finne & Even Birkeland & Vandana Ardawatia & Ingeborg Winge & Sura Aziz & Gøril Knutsvik & Elisabeth Wik & Joao A. Paulo & Heidrun Vethe & Dimitrios Kleftogiannis & Lars A. Aksl, 2023. "Hypoxia induced responses are reflected in the stromal proteome of breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
41. Andrew E Teschendorff & Michel Journée & Pierre A Absil & Rodolphe Sepulchre & Carlos Caldas, 2007. "Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis," PLOS Computational Biology, Public Library of Science, vol. 3(8), pages 1-16, August.
42. Marcin Pilarczyk & Mehdi Fazel-Najafabadi & Michal Kouril & Behrouz Shamsaei & Juozas Vasiliauskas & Wen Niu & Naim Mahi & Lixia Zhang & Nicholas A. Clark & Yan Ren & Shana White & Rashid Karim & Huan, 2022. "Connecting omics signatures and revealing biological mechanisms with iLINCS," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
43. Xiao-song Chen & Ying Yuan & David H Garfield & Jia-yi Wu & Ou Huang & Kun-wei Shen, 2014. "Both Carboplatin and Bevacizumab Improve Pathological Complete Remission Rate in Neoadjuvant Treatment of Triple Negative Breast Cancer: A Meta-Analysis," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-8, September.
44. Radu Vidra & Tudor Eliade Ciuleanu & Adina Nemeș & Oana Pascu & Ana Maria Heroiu & Nicoleta Antone & Andreea Iulia Vidrean & Cristina Marinela Oprean & Laura Ancuta Pop & Ioana Berindan-Neagoe & Rares, 2022. "Spectrum of BRCA1/2 Mutations in Romanian Breast and Ovarian Cancer Patients," IJERPH, MDPI, vol. 19(7), pages 1-13, April.
45. Daniel Rodrigues de Bastos & Maria A Nagai, 2020. "In silico analyses identify lncRNAs: WDFY3-AS2, BDNF-AS and AFAP1-AS1 as potential prognostic factors for patients with triple-negative breast tumors," PLOS ONE, Public Library of Science, vol. 15(5), pages 1-16, May.
46. Pauliina M. Munne & Lahja Martikainen & Iiris Räty & Kia Bertula & Nonappa & Janika Ruuska & Hanna Ala-Hongisto & Aino Peura & Babette Hollmann & Lilya Euro & Kerim Yavuz & Linda Patrikainen & Maria S, 2021. "Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
47. Martin H van Vliet & Christiaan N Klijn & Lodewyk F A Wessels & Marcel J T Reinders, 2007. "Module-Based Outcome Prediction Using Breast Cancer Compendia," PLOS ONE, Public Library of Science, vol. 2(10), pages 1-10, October.
48. Herman M J Sontrop & Wim F J Verhaegh & Marcel J T Reinders & Perry D Moerland, 2011. "An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-12, July.
49. Gary K Chen & Eric C Chi & John Michael O Ranola & Kenneth Lange, 2015. "Convex Clustering: An Attractive Alternative to Hierarchical Clustering," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-31, May.
50. Elisabetta Crippa & Lara Lusa & Loris De Cecco & Edoardo Marchesi & George Adrian Calin & Paolo Radice & Siranoush Manoukian & Bernard Peissel & Maria Grazia Daidone & Manuela Gariboldi & Marco Alessa, 2014. "miR-342 Regulates BRCA1 Expression through Modulation of ID4 in Breast Cancer," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-12, January.
51. John Fadul & Teresa Zulueta-Coarasa & Gloria M. Slattum & Nadja M. Redd & Mauricio Franco Jin & Michael J. Redd & Stephan Daetwyler & Danielle Hedeen & Jan Huisken & Jody Rosenblatt, 2021. "KRas-transformed epithelia cells invade and partially dedifferentiate by basal cell extrusion," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
52. Zheqi Li & Olivia McGinn & Yang Wu & Amir Bahreini & Nolan M. Priedigkeit & Kai Ding & Sayali Onkar & Caleb Lampenfeld & Carol A. Sartorius & Lori Miller & Margaret Rosenzweig & Ofir Cohen & Nikhil Wa, 2022. "ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
53. Bourret, Pascale & Keating, Peter & Cambrosio, Alberto, 2011. "Regulating diagnosis in post-genomic medicine: Re-aligning clinical judgment?," Social Science & Medicine, Elsevier, vol. 73(6), pages 816-824, September.
54. Chen, Xi & Wang, Lily & Ishwaran, Hemant, 2010. "An integrative pathway-based clinical-genomic model for cancer survival prediction," Statistics & Probability Letters, Elsevier, vol. 80(17-18), pages 1313-1319, September.
55. Leann A. Lovejoy & Craig D. Shriver & Svasti Haricharan & Rachel E. Ellsworth, 2023. "Survival Disparities in US Black Compared to White Women with Hormone Receptor Positive-HER2 Negative Breast Cancer," IJERPH, MDPI, vol. 20(4), pages 1-15, February.
56. Gøril Knutsvik & Ingunn M Stefansson & Sura Aziz & Jarle Arnes & Johan Eide & Karin Collett & Lars A Akslen, 2014. "Evaluation of Ki67 Expression across Distinct Categories of Breast Cancer Specimens: A Population-Based Study of Matched Surgical Specimens, Core Needle Biopsies and Tissue Microarrays," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-11, November.
57. Sung Gwe Ahn & Minkyung Lee & Tae Joo Jeon & Kyunghwa Han & Hak Min Lee & Seung Ah Lee & Young Hoon Ryu & Eun Ju Son & Joon Jeong, 2014. "[18F]-Fluorodeoxyglucose Positron Emission Tomography Can Contribute to Discriminate Patients with Poor Prognosis in Hormone Receptor-Positive Breast Cancer," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-7, August.
58. Cambrosio, Alberto & Campbell, Jonah & Keating, Peter & Bourret, Pascale, 2022. "Multi-polar scripts: Techno-regulatory environments and the rise of precision oncology diagnostic tests," Social Science & Medicine, Elsevier, vol. 304(C).
59. Chi-Cheng Huang & Shih-Hsin Tu & Heng-Hui Lien & Jaan-Yeh Jeng & Ching-Shui Huang & Chi-Jung Huang & Liang-Chuan Lai & Eric Y Chuang, 2013. "Concurrent Gene Signatures for Han Chinese Breast Cancers," PLOS ONE, Public Library of Science, vol. 8(10), pages 1-1, October.
60. Erika S. Helgeson & David M. Vock & Eric Bair, 2021. "Nonparametric cluster significance testing with reference to a unimodal null distribution," Biometrics, The International Biometric Society, vol. 77(4), pages 1215-1226, December.
61. Amina Amadou & Thomas Coudon & Delphine Praud & Pietro Salizzoni & Karen Leffondré & Emilie Lévêque & Marie-Christine Boutron-Ruault & Aurélie Danjou & Xavier Morelli & Charlotte Le Cornet & Lionel Pe, 2020. "Chronic Low-Dose Exposure to Xenoestrogen Ambient Air Pollutants and Breast Cancer Risk: XENAIR Protocol for a Case-Control Study Nested Within the French E3N Cohort," Post-Print halshs-03003523, HAL.
62. Fadia Gujam & Katie Dickson & Pamela McCall & Donald McMillan & Joanne Edwards, 2018. "The Relationship Between Androgen Receptor, Components of Tumour Microenvironment and Survival in Breast Cancer Molecular Subtypes," Cancer Therapy & Oncology International Journal, Juniper Publishers Inc., vol. 11(3), pages 77-85, July.
63. Zhiguang Huo & Li Zhu & Tianzhou Ma & Hongcheng Liu & Song Han & Daiqing Liao & Jinying Zhao & George Tseng, 2020. "Two-Way Horizontal and Vertical Omics Integration for Disease Subtype Discovery," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 12(1), pages 1-22, April.
64. Felipe Ades & Christelle Senterre & Dimitrios Zardavas & Evandro de Azambuja & Razvan Popescu & Martine Piccart, 2017. "Are life-saving anticancer drugs reaching all patients? Patterns and discrepancies of trastuzumab use in the European Union and the USA," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-11, March.
65. Radhakrishnan Nagarajan & Marco Scutari, 2013. "Impact of Noise on Molecular Network Inference," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-12, December.
66. R Joseph Bender & Feilim Mac Gabhann, 2013. "Expression of VEGF and Semaphorin Genes Define Subgroups of Triple Negative Breast Cancer," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-15, May.