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这篇博客集合了31篇关于生物信息学中高阶关系的研究论文，涵盖了从微生物组学、生态组学到网络理论等多个领域。论文探讨了合作自组装网络的几何特性、细胞信息处理、复杂群落中未解的复杂性、竞争网络模型的稳定性以及口腔生物膜中的病原体交互等主题。研究还揭示了高阶相互作用在稳定生态系统动态、解析微生物社区结构和功能以及预测口腔生物膜疾病过程中的关键作用。此外，还讨论了细菌群体感应的进展和未来潜力，以及如何使用高阶相关性从节点输出重构非线性网络，以揭示隐藏在复杂系统数据中的高阶依赖性。
生物信息中High-Order高阶关系研究论文集锦（2）
- 31. Hidden geometries in networks arising from cooperative self-assembly
- 32. Higher-Order Cellular Information Processing with Synthetic RNA Devices
- 33. Higher-order interactions capture unexplained complexity in diverse communities
- 34. Higher-order interactions stabilize dynamics in competitive network models
- 35. Higher-order organization of complex networks
- 36. High-Order Affinity Extension of Normalized Cut and Its Applications
- 37. High-order species interactions shape ecosystem diversity
- 38. How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience
- 39. Indirect effects drive coevolution in mutualistic networks
- 40. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections
- 41. Iterative random forests to discover predictive and stable high-order interactions
- 42. Linear Association in Compositional Data Analysis
- 43. Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions
- 44. Making a microbiome: the many determinants of host-associated microbial community composition
- 45. Mapping the ecological networks of microbial communities
- 46. Metabolic dependencies drive species co-occurrence in diverse microbial communities
- 47. Metabolic division of labor in microbial systems
- 48. Metabolic interactions in microbial communities: untangling the Gordian knot
- 49. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
- 50. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
- 51. Microbial community structure predicted by the stable marriage problem
- 52. Microbiome, metabolites and host immunity
- 53. Multilayer networks reveal the spatial structure of seed-dispersal interactions across the Great Rift landscapes
- 54. Network structure embracing mutualism–antagonism continuums increases community robustness
- 55. Non-random coextinctions in phylogenetically structured mutualistic networks
- 56. Overcoming catastrophic forgetting in neural networks
- 57. Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments
- 58. Progress in and promise of bacterial quorum sensing research
- 59. Reconstruction of noise-driven nonlinear networks from node outputs by using high-order correlations
- 60. Representing higher-order dependencies in networks
31. Hidden geometries in networks arising from cooperative self-assembly
- 协同自组装网络中隐藏的几何形状
Abstract：Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and compatibility of the building blocks are decisive factors in each phase of growth. Therefore, a comprehensive understanding of these processes is essential for the design of large assemblies of desired properties. Here, we introduce a computational model for cooperative self-assembly with simultaneous attachment of structure
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