CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection
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DOI: 10.1038/s41467-024-50426-6
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- Chaoxiong Wang & Xichen Zheng & Jinlan Zhang & Xiaoyi Jiang & Jia Wang & Yuwei Li & Xiaonan Li & Guanghui Shen & Jiayin Peng & Peixuan Zheng & Yunqing Gu & Jiaojiao Chen & Moubin Lin & Changwen Deng &, 2023. "CD300ld on neutrophils is required for tumour-driven immune suppression," Nature, Nature, vol. 621(7980), pages 830-839, September.
- Ralph Stadhouders & Guillaume J. Filion & Thomas Graf, 2019. "Transcription factors and 3D genome conformation in cell-fate decisions," Nature, Nature, vol. 569(7756), pages 345-354, May.
- Christina V. Theodoris & Ling Xiao & Anant Chopra & Mark D. Chaffin & Zeina R. Al Sayed & Matthew C. Hill & Helene Mantineo & Elizabeth M. Brydon & Zexian Zeng & X. Shirley Liu & Patrick T. Ellinor, 2023. "Transfer learning enables predictions in network biology," Nature, Nature, vol. 618(7965), pages 616-624, June.
- Norio Chihara & Asaf Madi & Takaaki Kondo & Huiyuan Zhang & Nandini Acharya & Meromit Singer & Jackson Nyman & Nemanja D. Marjanovic & Monika S. Kowalczyk & Chao Wang & Sema Kurtulus & Travis Law & Ya, 2018. "Induction and transcriptional regulation of the co-inhibitory gene module in T cells," Nature, Nature, vol. 558(7710), pages 454-459, June.
- Kenji Kamimoto & Blerta Stringa & Christy M. Hoffmann & Kunal Jindal & Lilianna Solnica-Krezel & Samantha A. Morris, 2023. "Dissecting cell identity via network inference and in silico gene perturbation," Nature, Nature, vol. 614(7949), pages 742-751, February.
- Nir Yosef & Alex K. Shalek & Jellert T. Gaublomme & Hulin Jin & Youjin Lee & Amit Awasthi & Chuan Wu & Katarzyna Karwacz & Sheng Xiao & Marsela Jorgolli & David Gennert & Rahul Satija & Arvind Shakya , 2013. "Dynamic regulatory network controlling TH17 cell differentiation," Nature, Nature, vol. 496(7446), pages 461-468, April.
- Sepideh Sadegh & James Skelton & Elisa Anastasi & Judith Bernett & David B. Blumenthal & Gihanna Galindez & Marisol Salgado-Albarrán & Olga Lazareva & Keith Flanagan & Simon Cockell & Cristian Nogales, 2021. "Network medicine for disease module identification and drug repurposing with the NeDRex platform," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- Mark B. Gerstein & Anshul Kundaje & Manoj Hariharan & Stephen G. Landt & Koon-Kiu Yan & Chao Cheng & Xinmeng Jasmine Mu & Ekta Khurana & Joel Rozowsky & Roger Alexander & Renqiang Min & Pedro Alves & , 2012. "Architecture of the human regulatory network derived from ENCODE data," Nature, Nature, vol. 489(7414), pages 91-100, September.
- Jie Xu & Fan Song & Huijue Lyu & Mikoto Kobayashi & Baozhen Zhang & Ziyu Zhao & Ye Hou & Xiaotao Wang & Yu Luan & Bei Jia & Lena Stasiak & Josiah Hiu-yuen Wong & Qixuan Wang & Qi Jin & Qiushi Jin & Yi, 2022. "Subtype-specific 3D genome alteration in acute myeloid leukaemia," Nature, Nature, vol. 611(7935), pages 387-398, November.
- Ting Yan & Heyang Cui & Yong Zhou & Bin Yang & Pengzhou Kong & Yingchun Zhang & Yiqian Liu & Bin Wang & Yikun Cheng & Jiayi Li & Shixing Guo & Enwei Xu & Huijuan Liu & Caixia Cheng & Ling Zhang & Ling, 2019. "Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
- Devan Diwanji & Raphael Trenker & Tarjani M. Thaker & Feng Wang & David A. Agard & Kliment A. Verba & Natalia Jura, 2021. "Structures of the HER2–HER3–NRG1β complex reveal a dynamic dimer interface," Nature, Nature, vol. 600(7888), pages 339-343, December.
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