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Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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  1. 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.
  2. 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.
  3. 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).
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. Bastien Lextrait, 2021. "Scaling up SME's credit scoring scope with LightGBM," EconomiX Working Papers 2021-25, University of Paris Nanterre, EconomiX.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
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