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Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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  1. Cecilia Pessoa Rodrigues & Aindrila Chatterjee & Meike Wiese & Thomas Stehle & Witold Szymanski & Maria Shvedunova & Asifa Akhtar, 2021. "Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice," Nature Communications, Nature, vol. 12(1), pages 1-21, December.
  2. Jérémie Kalfon & Jules Samaran & Gabriel Peyré & Laura Cantini, 2025. "scPRINT: pre-training on 50 million cells allows robust gene network predictions," Nature Communications, Nature, vol. 16(1), pages 1-23, December.
  3. Hinako M Takase & Tappei Mishina & Tetsutaro Hayashi & Mika Yoshimura & Mariko Kuse & Itoshi Nikaido & Tomoya S Kitajima, 2024. "Transcriptomic signatures of WNT-driven pathways and granulosa cell-oocyte interactions during primordial follicle activation," PLOS ONE, Public Library of Science, vol. 19(10), pages 1-26, October.
  4. Fei Wang & Peiwen Ding & Xue Liang & Xiangning Ding & Camilla Blunk Brandt & Evelina Sjöstedt & Jiacheng Zhu & Saga Bolund & Lijing Zhang & Laura P. M. H. Rooij & Lihua Luo & Yanan Wei & Wandong Zhao , 2022. "Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  5. Li, Jiawen & Meng, Lu & Zhang, Zelin & Yang, Kejia, 2023. "Low-frequency, high-impact: Discovering important rare events from UGC," Journal of Retailing and Consumer Services, Elsevier, vol. 70(C).
  6. Maghsoodi, Masoume, 2016. "A New Method to Build Gene Regulation Network Based on Fuzzy Hierarchical Clustering Methods," MPRA Paper 79743, University Library of Munich, Germany.
  7. Edoardo Bertolini & Brian R. Rice & Max Braud & Jiani Yang & Sarah Hake & Josh Strable & Alexander E. Lipka & Andrea L. Eveland, 2025. "Regulatory variation controlling architectural pleiotropy in maize," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  8. Yichi Niu & Jiayi Luo & Chenghang Zong, 2024. "Single-cell total-RNA profiling unveils regulatory hubs of transcription factors," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  9. Marius Arend & Yizhong Yuan & M. Águila Ruiz-Sola & Nooshin Omranian & Zoran Nikoloski & Dimitris Petroutsos, 2023. "Widening the landscape of transcriptional regulation of green algal photoprotection," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  10. Lingfei Wang & Tom Michoel, 2017. "Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data," PLOS Computational Biology, Public Library of Science, vol. 13(8), pages 1-26, August.
  11. Mingyi Wang & Jerome Verdier & Vagner A Benedito & Yuhong Tang & Jeremy D Murray & Yinbing Ge & Jörg D Becker & Helena Carvalho & Christian Rogers & Michael Udvardi & Ji He, 2013. "LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-7, July.
  12. Takeshi Hase & Samik Ghosh & Ryota Yamanaka & Hiroaki Kitano, 2013. "Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-16, November.
  13. Qiao Wen Tan & Peng Ken Lim & Zhong Chen & Asher Pasha & Nicholas Provart & Marius Arend & Zoran Nikoloski & Marek Mutwil, 2023. "Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  14. Ze Yan & Ji Yang & Wen-Tian Wei & Ming-Liang Zhou & Dong-Xin Mo & Xing Wan & Rui Ma & Mei-Ming Wu & Jia-Hui Huang & Ya-Jing Liu & Feng-Hua Lv & Meng-Hua Li, 2024. "A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  15. Dongsheng Chen & Jian Sun & Jiacheng Zhu & Xiangning Ding & Tianming Lan & Xiran Wang & Weiying Wu & Zhihua Ou & Linnan Zhu & Peiwen Ding & Haoyu Wang & Lihua Luo & Rong Xiang & Xiaoling Wang & Jiayin, 2021. "Single cell atlas for 11 non-model mammals, reptiles and birds," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
  16. Kinzy Tyler G. & Starr Timothy K. & Tseng George C. & Ho Yen-Yi, 2019. "Meta-analytic framework for modeling genetic coexpression dynamics," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(1), pages 1-13, February.
  17. Natalie M. Clark & Trevor M. Nolan & Ping Wang & Gaoyuan Song & Christian Montes & Conner T. Valentine & Hongqing Guo & Rosangela Sozzani & Yanhai Yin & Justin W. Walley, 2021. "Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  18. Ruonan Wu & Michelle R. Davison & William C. Nelson & Montana L. Smith & Mary S. Lipton & Janet K. Jansson & Ryan S. McClure & Jason E. McDermott & Kirsten S. Hofmockel, 2023. "Hi-C metagenome sequencing reveals soil phage–host interactions," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  19. Rachael M. Zemek & Wee Loong Chin & Vanessa S. Fear & Ben Wylie & Thomas H. Casey & Cath Forbes & Caitlin M. Tilsed & Louis Boon & Belinda B. Guo & Anthony Bosco & Alistair R. R. Forrest & Michael J. , 2022. "Temporally restricted activation of IFNβ signaling underlies response to immune checkpoint therapy in mice," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  20. Holger Weishaupt & Patrik Johansson & Christopher Engström & Sven Nelander & Sergei Silvestrov & Fredrik J Swartling, 2017. "Loss of Conservation of Graph Centralities in Reverse-engineered Transcriptional Regulatory Networks," Methodology and Computing in Applied Probability, Springer, vol. 19(4), pages 1089-1105, December.
  21. Lulu Shang & Jennifer A Smith & Xiang Zhou, 2020. "Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies," PLOS Genetics, Public Library of Science, vol. 16(4), pages 1-30, April.
  22. Qingfei Pan & Liang Ding & Siarhei Hladyshau & Xiangyu Yao & Jiayu Zhou & Lei Yan & Yogesh Dhungana & Hao Shi & Chenxi Qian & Xinran Dong & Chad Burdyshaw & Joao Pedro Veloso & Alireza Khatamian & Zhe, 2025. "scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
  23. Jie Xiong & Tong Zhou, 2012. "Gene Regulatory Network Inference from Multifactorial Perturbation Data Using both Regression and Correlation Analyses," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-13, September.
  24. Bastien Lextrait, 2021. "Scaling up SME's credit scoring scope with LightGBM," EconomiX Working Papers 2021-25, University of Paris Nanterre, EconomiX.
  25. Alfonso Monaco & Nicola Amoroso & Loredana Bellantuono & Eufemia Lella & Angela Lombardi & Anna Monda & Andrea Tateo & Roberto Bellotti & Sabina Tangaro, 2019. "Shannon entropy approach reveals relevant genes in Alzheimer’s disease," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-29, December.
  26. Marco Grimaldi & Roberto Visintainer & Giuseppe Jurman, 2011. "RegnANN: Reverse Engineering Gene Networks Using Artificial Neural Networks," PLOS ONE, Public Library of Science, vol. 6(12), pages 1-19, December.
  27. Hyunje Yang & Honggeun Lim & Haewon Moon & Qiwen Li & Sooyoun Nam & Jaehoon Kim & Hyung Tae Choi, 2022. "Simple Optimal Sampling Algorithm to Strengthen Digital Soil Mapping Using the Spatial Distribution of Machine Learning Predictive Uncertainty: A Case Study for Field Capacity Prediction," Land, MDPI, vol. 11(11), pages 1-18, November.
  28. Yu Chang & Yujie Fang & Jiahan Liu & Tiantian Ye & Xiaokai Li & Haifu Tu & Ying Ye & Yao Wang & Lizhong Xiong, 2024. "Stress-induced nuclear translocation of ONAC023 improves drought and heat tolerance through multiple processes in rice," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  29. Natalie Jane de Vries & Rodrigo Reis & Pablo Moscato, 2015. "Clustering Consumers Based on Trust, Confidence and Giving Behaviour: Data-Driven Model Building for Charitable Involvement in the Australian Not-For-Profit Sector," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-28, April.
  30. Meichen Dong & Yiping He & Yuchao Jiang & Fei Zou, 2023. "Joint gene network construction by single‐cell RNA sequencing data," Biometrics, The International Biometric Society, vol. 79(2), pages 915-925, June.
  31. Fei Liu & Shao-Wu Zhang & Wei-Feng Guo & Ze-Gang Wei & Luonan Chen, 2016. "Inference of Gene Regulatory Network Based on Local Bayesian Networks," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-17, August.
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