| [1] |
Kim BR, Zhang L, Berg A, Fan J, Wu R. 2008. A computational approach to the functional clustering of periodic gene-expression profiles. |
| [2] |
Wu S, Liu X, Dong A, Gragnoli C, Griffin C, et al. 2023. The metabolomic physics of complex diseases. |
| [3] |
Xu R, Wunsch D. 2005. Survey of clustering algorithms. |
| [4] |
Rokach L. 2010. A survey of clustering algorithms. In Data mining and knowledge discovery handbook. Boston, MA: Springer. pp. 269−298 doi: 10.1007/978-0-387-09823-4 |
| [5] |
Xu D, Tian Y. 2015. A comprehensive survey of clustering algorithms. |
| [6] |
Wang Q, Dong A, Jiang L, Griffin C, Wu R. 2022. A single-cell omics network model of cell crosstalk during the formation of primordial follicles. |
| [7] |
Dong A, Meng Y, Yau SST, Yau ST, Wu R. 2026. A Statistical Mechanics model to decode tissue crosstalk during graft formation. |
| [8] |
Misra BB, Langefeld C, Olivier M, Cox LA. 2019. Integrated omics: tools, advances and future approaches. |
| [9] |
Nardini C, Dent J, Tieri P. 2015. Multi-omic data integration. |
| [10] |
Wang D, Gu J. 2016. Integrative clustering methods of multi-omics data for molecule-based cancer classifications. |
| [11] |
Tini G, Marchetti L, Priami C, Scott-Boyer MP. 2019. Multi-omics integration—a comparison of unsupervised clustering methodologies. |
| [12] |
Chauvel C, Novoloaca A, Veyre P, Reynier F, Becker J. 2020. Evaluation of integrative clustering methods for the analysis of multi-omics data. |
| [13] |
Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. 2002. Phylogenies and community ecology. |
| [14] |
Johnson MTJ, Stinchcombe JR. 2007. An emerging synthesis between community ecology and evolutionary biology. |
| [15] |
Cavender‐Bares J, Kozak KH, Fine PVA, Kembel SW. 2009. The merging of community ecology and phylogenetic biology. |
| [16] |
Raes J, Bork P. 2008. Molecular eco-systems biology: towards an understanding of community function. |
| [17] |
Shea K, Chesson P. 2002. Community ecology theory as a framework for biological invasions. |
| [18] |
Chesson P. 2000. Mechanisms of maintenance of species diversity. |
| [19] |
Tilman D. 1982. Resource competition and community structure. Princeton, NJ, USA: Princeton University Press. |
| [20] |
Peterson AT, Soberón J, Pearson RG, Anderson RP, Martínez-Meyer E, et al. 2011. Ecological niches and geographic distributions (MPB-49). Online Edition. Princeton University Press. doi: 10.1515/9781400840670 |
| [21] |
Finlay KW, Wilkinson GN. 1963. The analysis of adaptation in a plant-breeding programme. |
| [22] |
Lobell DB, Roberts MJ, Schlenker W, Braun N, Little BB, et al. 2014. Greater sensitivity to drought accompanies maize yield increase in the US Midwest. |
| [23] |
West GB, Brown JH, Enquist BJ. 1997. A general model for the origin of allometric scaling laws in biology. |
| [24] |
West GB, Brown JH, Enquist BJ. 1999. The fourth dimension of life: fractal geometry and allometric scaling of organisms. |
| [25] |
Shingleton A. 2010. Allometry: the study of biological. Nature Education Knowledge 3(10):2 |
| [26] |
Huxley JS, Teissier G. 1936. Terminology of relative growth. |
| [27] |
Feng L, Yang D, Wu S, Xue C, Sang M, et al. 2025. Network modeling and topology of aging. |
| [28] |
Gong H, Wang Y, Wang H, Sun X, Zhang S, et al. 2025. Towards a better understanding of structural-functional relationships in the forest soil microbiota. Reply to comments on "Topological change of soil microbiota networks for forest resilience under global warming". |
| [29] |
Zhao W, Chen YQ, Casella G, Cheverud JM, Wu R. 2005. A non-stationary model for functional mapping of complex traits. |
| [30] |
Zhao W, Hou W, Littell RC, Wu R. 2005. Structured antedependence models for functional mapping of multiple longitudinal traits. |
| [31] |
Zhao W, Wu R. 2008. Wavelet-based nonparametric functional mapping of longitudinal curves. |
| [32] |
Kingma DP. 2014. Adam: a method for stochastic optimization. |
| [33] |
Schwarz G. 1978. Estimating the dimension of a model. The Annals of Statistics 6(2):461−464 |
| [34] |
Meng J, Li Z, Wang H, Miao R, Liu X, et al. 2025. Haplotype‐resolved genome assembly provides new insights into the genomic origin of purple colour in Prunus mume. |
| [35] |
Dong A, Wu S, Che J, Wang Y, Wu R. 2023. idopNetwork: a network tool to dissect spatial community ecology. |
| [36] |
Mu H, Chen J, Huang W, Huang G, Deng M, et al. 2024. OmicShare tools: a zero-code interactive online platform for biological data analysis and visualization. |
| [37] |
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. 2000. Gene ontology: tool for the unification of biology. |
| [38] |
Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic acids research 28:27−30 |