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A General Framework for Weighted Gene Co-Expression Network Analysis

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  1. Ville-Petteri Mäkinen & Mete Civelek & Qingying Meng & Bin Zhang & Jun Zhu & Candace Levian & Tianxiao Huan & Ayellet V Segrè & Sujoy Ghosh & Juan Vivar & Majid Nikpay & Alexandre F R Stewart & Christ, 2014. "Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease," PLOS Genetics, Public Library of Science, vol. 10(7), pages 1-14, July.
  2. Tiffany C Armenta & Steve W Cole & Daniel H Geschwind & Daniel T Blumstein & Robert K Wayne, 2019. "Gene expression shifts in yellow-bellied marmots prior to natal dispersal," Behavioral Ecology, International Society for Behavioral Ecology, vol. 30(2), pages 267-277.
  3. Wu, Cen & Zhang, Qingzhao & Jiang, Yu & Ma, Shuangge, 2018. "Robust network-based analysis of the associations between (epi)genetic measurements," Journal of Multivariate Analysis, Elsevier, vol. 168(C), pages 119-130.
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  5. Elva María Novoa-del-Toro & Efrén Mezura-Montes & Matthieu Vignes & Morgane Térézol & Frédérique Magdinier & Laurent Tichit & Anaïs Baudot, 2021. "A multi-objective genetic algorithm to find active modules in multiplex biological networks," PLOS Computational Biology, Public Library of Science, vol. 17(8), pages 1-24, August.
  6. Tabak, Benjamin M. & Serra, Thiago R. & Cajueiro, Daniel O., 2009. "The expectation hypothesis of interest rates and network theory: The case of Brazil," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 388(7), pages 1137-1149.
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  9. Li, Jie & Wang, Lidan & Zhou, Zhong-Qiang & Zhang, Yongjie, 2021. "Monitoring or tunneling? Information interaction among large shareholders and the crash risk of the stock price," Pacific-Basin Finance Journal, Elsevier, vol. 65(C).
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  11. Shujuan Zhao & Kedous Y. Mekbib & Martijn A. Ent & Garrett Allington & Andrew Prendergast & Jocelyn E. Chau & Hannah Smith & John Shohfi & Jack Ocken & Daniel Duran & Charuta G. Furey & Le Thi Hao & P, 2023. "Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
  12. Clemente, G.P. & Grassi, R., 2018. "Directed clustering in weighted networks: A new perspective," Chaos, Solitons & Fractals, Elsevier, vol. 107(C), pages 26-38.
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  16. Tingting Bo & Jie Li & Ganlu Hu & Ge Zhang & Wei Wang & Qian Lv & Shaoling Zhao & Junjie Ma & Meng Qin & Xiaohui Yao & Meiyun Wang & Guang-Zhong Wang & Zheng Wang, 2023. "Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  17. Raihanul Bari Tanvir & Tasmia Aqila & Mona Maharjan & Abdullah Al Mamun & Ananda Mohan Mondal, 2019. "Graph Theoretic and Pearson Correlation-Based Discovery of Network Biomarkers for Cancer," Data, MDPI, vol. 4(2), pages 1-12, June.
  18. Bahman Panahi & Mohammad Farhadian & Mohammad Amin Hejazi, 2020. "Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after transition from autotrophic to heterotrophic growth condition in microalg," PLOS ONE, Public Library of Science, vol. 15(2), pages 1-15, February.
  19. Mandel, Antoine & Landini, Simone & Gallegati, Mauro & Gintis, Herbert, 2015. "Price dynamics, financial fragility and aggregate volatility," Journal of Economic Dynamics and Control, Elsevier, vol. 51(C), pages 257-277.
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  22. Yiming Hu & Hongyu Zhao, 2016. "CCor: A whole genome network‐based similarity measure between two genes," Biometrics, The International Biometric Society, vol. 72(4), pages 1216-1225, December.
  23. Matias Nehuen Iglesias, 2021. "The Overlooked Insights from Correlation Structures in Economic Geography," Papers in Evolutionary Economic Geography (PEEG) 2105, Utrecht University, Department of Human Geography and Spatial Planning, Group Economic Geography, revised Jan 2021.
  24. Jong Victor L. & Novianti Putri W. & Roes Kit C.B. & Eijkemans Marinus J.C., 2014. "Exploring homogeneity of correlation structures of gene expression datasets within and between etiological disease categories," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 13(6), pages 1-16, December.
  25. Peter Langfelder & Fuying Gao & Nan Wang & David Howland & Seung Kwak & Thomas F Vogt & Jeffrey S Aaronson & Jim Rosinski & Giovanni Coppola & Steve Horvath & X William Yang, 2018. "MicroRNA signatures of endogenous Huntingtin CAG repeat expansion in mice," PLOS ONE, Public Library of Science, vol. 13(1), pages 1-20, January.
  26. Afshin Saffari & Barbara Brechmann & Cedric Böger & Wardiya Afshar Saber & Hellen Jumo & Dosh Whye & Delaney Wood & Lara Wahlster & Julian E. Alecu & Marvin Ziegler & Marlene Scheffold & Kellen Winden, 2024. "High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  27. Chuan Gao & Ian C McDowell & Shiwen Zhao & Christopher D Brown & Barbara E Engelhardt, 2016. "Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-39, July.
  28. Liesbeth François & Alessia Romagnolo & Mark J. Luinenburg & Jasper J. Anink & Patrice Godard & Marek Rajman & Jonathan Eyll & Angelika Mühlebner & Andrew Skelton & James D. Mills & Stefanie Dedeurwae, 2024. "Identification of gene regulatory networks affected across drug-resistant epilepsies," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  29. Matthew V DiLeo & Gary D Strahan & Meghan den Bakker & Owen A Hoekenga, 2011. "Weighted Correlation Network Analysis (WGCNA) Applied to the Tomato Fruit Metabolome," PLOS ONE, Public Library of Science, vol. 6(10), pages 1-10, October.
  30. Moohan Kim & Jong-Sang Sung & Jin-Wook Lee, 2017. "Perspectives on the Direction of the Suncheon Bay National Garden from Local Residents and Non-Local Visitors," Sustainability, MDPI, vol. 9(10), pages 1-10, October.
  31. Victor Forman & Dan Luo & Fernando Geu-Flores & René Lemcke & David R. Nelson & Sotirios C. Kampranis & Dan Staerk & Birger Lindberg Møller & Irini Pateraki, 2022. "A gene cluster in Ginkgo biloba encodes unique multifunctional cytochrome P450s that initiate ginkgolide biosynthesis," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  32. Wang, Tao & Xiao, Shiying & Yan, Jun & Zhang, Panpan, 2021. "Regional and sectoral structures of the Chinese economy: A network perspective from multi-regional input–output tables," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 581(C).
  33. Khang Tsung Fei & Yap Von Bing, 2010. "The Apportionment of Total Genetic Variation by Categorical Analysis of Variance," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-34, January.
  34. Shaoshuo Li & Baixing Chen & Hao Chen & Zhen Hua & Yang Shao & Heng Yin & Jianwei Wang, 2021. "Analysis of potential genetic biomarkers and molecular mechanism of smoking-related postmenopausal osteoporosis using weighted gene co-expression network analysis and machine learning," PLOS ONE, Public Library of Science, vol. 16(9), pages 1-18, September.
  35. Gianluca Ursini & Pasquale Di Carlo & Sreya Mukherjee & Qiang Chen & Shizhong Han & Jiyoung Kim & Maya Deyssenroth & Carmen J. Marsit & Jia Chen & Ke Hao & Giovanna Punzi & Daniel R. Weinberger, 2023. "Prioritization of potential causative genes for schizophrenia in placenta," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  36. Miecznikowski Jeffrey C. & Gaile Daniel P. & Chen Xiwei & Tritchler David L., 2016. "Identification of consistent functional genetic modules," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 1-18, March.
  37. Zhixiang Lin & Tao Wang & Can Yang & Hongyu Zhao, 2017. "On joint estimation of Gaussian graphical models for spatial and temporal data," Biometrics, The International Biometric Society, vol. 73(3), pages 769-779, September.
  38. Li, Wenyuan & Lin, Yongjing & Liu, Ying, 2007. "The structure of weighted small-world networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 376(C), pages 708-718.
  39. Haim Bar & Seojin Bang, 2021. "A mixture model to detect edges in sparse co-expression graphs with an application for comparing breast cancer subtypes," PLOS ONE, Public Library of Science, vol. 16(2), pages 1-20, February.
  40. Yixuan Qiu & Jing Lei & Kathryn Roeder, 2023. "Gradient-based sparse principal component analysis with extensions to online learning," Biometrika, Biometrika Trust, vol. 110(2), pages 339-360.
  41. Nicola Magnavita & Carlo Chiorri, 2022. "Development and Validation of a New Measure of Work Annoyance Using a Psychometric Network Approach," IJERPH, MDPI, vol. 19(15), pages 1-25, July.
  42. Siwei Xia & Yuehan Yang & Hu Yang, 2022. "Sparse Laplacian Shrinkage with the Graphical Lasso Estimator for Regression Problems," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 31(1), pages 255-277, March.
  43. Mandel, Antoine & Landini, Simone & Gallegati, Mauro & Gintis, Herbert, 2015. "Price dynamics, financial fragility and aggregate volatility," Journal of Economic Dynamics and Control, Elsevier, vol. 51(C), pages 257-277.
  44. 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.
  45. Luu, Duc Thi & Lux, Thomas & Yanovski, Boyan, 2017. "Structural correlations in the Italian overnight money market: An analysis based on network configuration models," Economics Working Papers 2017-02, Christian-Albrechts-University of Kiel, Department of Economics.
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  47. Ruiz Vargas, E. & Mitchell, D.G.V. & Greening, S.G. & Wahl, L.M., 2014. "Topology of whole-brain functional MRI networks: Improving the truncated scale-free model," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 405(C), pages 151-158.
  48. Bruce A Desmarais & Skyler J Cranmer, 2012. "Statistical Inference for Valued-Edge Networks: The Generalized Exponential Random Graph Model," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-12, January.
  49. Chang Su & Zichun Xu & Xinning Shan & Biao Cai & Hongyu Zhao & Jingfei Zhang, 2023. "Cell-type-specific co-expression inference from single cell RNA-sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  50. Atle van Beelen Granlund & Arnar Flatberg & Ann E Østvik & Ignat Drozdov & Bjørn I Gustafsson & Mark Kidd & Vidar Beisvag & Sverre H Torp & Helge L Waldum & Tom Christian Martinsen & Jan Kristian Damå, 2013. "Whole Genome Gene Expression Meta-Analysis of Inflammatory Bowel Disease Colon Mucosa Demonstrates Lack of Major Differences between Crohn's Disease and Ulcerative Colitis," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-14, February.
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