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

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  1. Hugh Chen & Scott M. Lundberg & Su-In Lee, 2022. "Explaining a series of models by propagating Shapley values," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  2. Aleix Prat & Fara Brasó-Maristany & Olga Martínez-Sáez & Esther Sanfeliu & Youli Xia & Meritxell Bellet & Patricia Galván & Débora Martínez & Tomás Pascual & Mercedes Marín-Aguilera & Anna Rodríguez &, 2023. "Circulating tumor DNA reveals complex biological features with clinical relevance in metastatic breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  3. 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.
  4. Zhe Jiang & YoungJun Ju & Amjad Ali & Philip E. D. Chung & Patryk Skowron & Dong-Yu Wang & Mariusz Shrestha & Huiqin Li & Jeff C. Liu & Ioulia Vorobieva & Ronak Ghanbari-Azarnier & Ethel Mwewa & Maria, 2023. "Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  5. 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.
  6. Lei-Jie Dai & Ding Ma & Yu-Zheng Xu & Ming Li & Yu-Wei Li & Yi Xiao & Xi Jin & Song-Yang Wu & Ya-Xin Zhao & Han Wang & Wen-Tao Yang & Yi-Zhou Jiang & Zhi-Ming Shao, 2023. "Molecular features and clinical implications of the heterogeneity in Chinese patients with HER2-low breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  7. Ha-Linh Nguyen & Tatjana Geukens & Marion Maetens & Samuel Aparicio & Ayse Bassez & Ake Borg & Jane Brock & Annegien Broeks & Carlos Caldas & Fatima Cardoso & Maxim Schepper & Mauro Delorenzi & Caroli, 2023. "Obesity-associated changes in molecular biology of primary breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  8. Songbai Zhang & Ayako Miyakawa & Malin Wickström & Cecilia Dyberg & Lauri Louhivuori & Manuel Varas-Godoy & Kati Kemppainen & Shigeaki Kanatani & Dagmara Kaczynska & Ivar Dehnisch Ellström & Lotta Elf, 2022. "GIT1 protects against breast cancer growth through negative regulation of Notch," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  9. Nils-Petter Rudqvist & Maud Charpentier & Claire Lhuillier & Erik Wennerberg & Sheila Spada & Caroline Sheridan & Xi Kathy Zhou & Tuo Zhang & Silvia C. Formenti & Jennifer S. Sims & Alicia Alonso & Sa, 2023. "Immunotherapy targeting different immune compartments in combination with radiation therapy induces regression of resistant tumors," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
  10. Weihua Guo & Jiayi Tan & Lei Wang & Colt A. Egelston & Diana L. Simons & Aaron Ochoa & Min Hui Lim & Lu Wang & Shawn Solomon & James Waisman & Christina H. Wei & Caroline Hoffmann & Joo Song & Daniel , 2024. "Tumor draining lymph nodes connected to cold triple-negative breast cancers are characterized by Th2-associated microenvironment," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  11. Amanda Fitzpatrick & Marjan Iravani & Adam Mills & David Vicente & Thanussuyah Alaguthurai & Ioannis Roxanis & Nicholas C. Turner & Syed Haider & Andrew N. J. Tutt & Clare M. Isacke, 2023. "Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  12. Liang, Weijuan & Zhang, Qingzhao & Ma, Shuangge, 2024. "Hierarchical false discovery rate control for high-dimensional survival analysis with interactions," Computational Statistics & Data Analysis, Elsevier, vol. 192(C).
  13. 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.
  14. 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.
  15. Jia, Yichen & Jeong, Jong-Hyeon, 2022. "Deep learning for quantile regression under right censoring: DeepQuantreg," Computational Statistics & Data Analysis, Elsevier, vol. 165(C).
  16. Eugene F. Schuster & Elena Lopez-Knowles & Anastasia Alataki & Lila Zabaglo & Elizabeth Folkerd & David Evans & Kally Sidhu & Maggie Chon U. Cheang & Holly Tovey & Manuel Salto-Tellez & Perry Maxwell , 2023. "Molecular profiling of aromatase inhibitor sensitive and resistant ER+HER2- postmenopausal breast cancers," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  17. 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.
  18. 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.
  19. Adam C. Weiner & Marc J. Williams & Hongyu Shi & Ignacio Vázquez-García & Sohrab Salehi & Nicole Rusk & Samuel Aparicio & Sohrab P. Shah & Andrew McPherson, 2024. "Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  20. Marco, Nicholas & Şentürk, Damla & Jeste, Shafali & DiStefano, Charlotte C. & Dickinson, Abigail & Telesca, Donatello, 2024. "Flexible regularized estimation in high-dimensional mixed membership models," Computational Statistics & Data Analysis, Elsevier, vol. 194(C).
  21. Camilla Tombari & Alessandro Zannini & Rebecca Bertolio & Silvia Pedretti & Matteo Audano & Luca Triboli & Valeria Cancila & Davide Vacca & Manuel Caputo & Sara Donzelli & Ilenia Segatto & Simone Vodr, 2023. "Mutant p53 sustains serine-glycine synthesis and essential amino acids intake promoting breast cancer growth," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  22. Louise A. Baldwin & Nenad Bartonicek & Jessica Yang & Sunny Z. Wu & Niantao Deng & Daniel L. Roden & Chia-Ling Chan & Ghamdan Al-Eryani & Damien J. Zanker & Belinda S. Parker & Alexander Swarbrick & S, 2022. "DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and immunotherapy response," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  23. Colin Y. C. Lee & Bethany C. Kennedy & Nathan Richoz & Isaac Dean & Zewen K. Tuong & Fabrina Gaspal & Zhi Li & Claire Willis & Tetsuo Hasegawa & Sarah K. Whiteside & David A. Posner & Gianluca Carless, 2024. "Tumour-retained activated CCR7+ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  24. F. Nadalin & M. J. Marzi & M. Pirra Piscazzi & P. Fuentes-Bravo & S. Procaccia & M. Climent & P. Bonetti & C. Rubolino & B. Giuliani & I. Papatheodorou & J. C. Marioni & F. Nicassio, 2024. "Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
  25. Hipólito Nicolás Cuesta-Hernández & Julia Contreras & Pablo Soriano-Maldonado & Jana Sánchez-Wandelmer & Wayland Yeung & Ana Martín-Hurtado & Inés G. Muñoz & Natarajan Kannan & Marta Llimargas & Javie, 2023. "An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  26. Isabel Tundidor & Marta Seijo-Vila & Sandra Blasco-Benito & María Rubert-Hernández & Sandra Adámez & Clara Andradas & Sara Manzano & Isabel Álvarez-López & Cristina Sarasqueta & María Villa-Morales & , 2023. "Identification of fatty acid amide hydrolase as a metastasis suppressor in breast cancer," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  27. Giovanni Tosi & Alessandro Paoli & Gaia Zuccolotto & Emilia Turco & Manuela Simonato & Daniela Tosoni & Francesco Tucci & Pietro Lugato & Monica Giomo & Nicola Elvassore & Antonio Rosato & Paola Cogo , 2024. "Cancer cell stiffening via CoQ10 and UBIAD1 regulates ECM signaling and ferroptosis in breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
  28. S. Mouron & M. J. Bueno & A. Lluch & L. Manso & I. Calvo & J. Cortes & J. A. Garcia-Saenz & M. Gil-Gil & N. Martinez-Janez & J. V. Apala & E. Caleiras & Pilar Ximénez-Embún & J. Muñoz & L. Gonzalez-Co, 2022. "Phosphoproteomic analysis of neoadjuvant breast cancer suggests that increased sensitivity to paclitaxel is driven by CDK4 and filamin A," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  29. 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.
  30. Joyce V. Lee & Filomena Housley & Christina Yau & Rachel Nakagawa & Juliane Winkler & Johanna M. Anttila & Pauliina M. Munne & Mariel Savelius & Kathleen E. Houlahan & Daniel Mark & Golzar Hemmati & G, 2022. "Combinatorial immunotherapies overcome MYC-driven immune evasion in triple negative breast cancer," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  31. Caroline Hoffmann & Floriane Noel & Maximilien Grandclaudon & Lucile Massenet-Regad & Paula Michea & Philemon Sirven & Lilith Faucheux & Aurore Surun & Olivier Lantz & Mylene Bohec & Jian Ye & Weihua , 2022. "PD-L1 and ICOSL discriminate human Secretory and Helper dendritic cells in cancer, allergy and autoimmunity," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  32. Mohammadamin Edrisi & Xiru Huang & Huw A. Ogilvie & Luay Nakhleh, 2023. "Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  33. You, Na & Dai, Hongsheng & Wang, Xueqin & Yu, Qingyun, 2024. "Sequential estimation for mixture of regression models for heterogeneous population," Computational Statistics & Data Analysis, Elsevier, vol. 194(C).
  34. Jieqiong Zhang & Zhenhua Hu & Hwa Hwa Chung & Yun Tian & Kah Weng Lau & Zheng Ser & Yan Ting Lim & Radoslaw M. Sobota & Hwei Fen Leong & Benjamin Jieming Chen & Clarisse Jingyi Yeo & Shawn Ying Xuan T, 2023. "Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  35. Brian D. Lehmann & Antonio Colaprico & Tiago C. Silva & Jianjiao Chen & Hanbing An & Yuguang Ban & Hanchen Huang & Lily Wang & Jamaal L. James & Justin M. Balko & Paula I. Gonzalez-Ericsson & Melinda , 2021. "Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
  36. Zhang, Xin & Zhao, Junlong, 2024. "Group variable selection via group sparse neural network," Computational Statistics & Data Analysis, Elsevier, vol. 192(C).
  37. Chao-Hui Chang & Feng Liu & Stefania Militi & Svenja Hester & Reshma Nibhani & Siwei Deng & James Dunford & Aniko Rendek & Zahir Soonawalla & Roman Fischer & Udo Oppermann & Siim Pauklin, 2024. "The pRb/RBL2-E2F1/4-GCN5 axis regulates cancer stem cell formation and G0 phase entry/exit by paracrine mechanisms," Nature Communications, Nature, vol. 15(1), pages 1-29, December.
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