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摘要翻译：
生物现象的上下文依赖性质在生物学的各个分支都有很好的记录。虽然以前很少有人试图（隐含地）对生物上下文依赖的各个方面进行建模，但对生物学生来说，没有一个正式的、通用的数学结构来建模广泛的上下文依赖。本文从自下而上和自上而下两个角度提出了一个客观而严格的模型，作为描述生物学不同分支中所遇到的各种上下文依赖关系的模板。生物环境之间的相互作用被发现是传递性的，但非交换性的。研究发现，生物背景之间依赖的层次性有效地模拟了新出现的生物属性。这些发现的原因提供了一个描述生物现实的一般模型。通过一个名为“上下文树”的结构，实现了生物上下文组织的层次结构的算法实现方案。对影响蛋白质结构的生物物理因素之间的上下文交互作用进行了基于上下文树的分析。
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英文标题：
《A (possible) mathematical model to describe biological
"context-dependence" : case study with protein structure》
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作者：
Anirban Banerji
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最新提交年份：
2011
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分类信息：
一级分类：Quantitative Biology 数量生物学
二级分类：Other Quantitative Biology 其他定量生物学
分类描述：Work in quantitative biology that does not fit into the other q-bio classifications
不适合其他q-bio分类的定量生物学工作
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英文摘要：
Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general mathematical construct to model the wide spectrum of context-dependence, eludes the students of biology. An objective and rigorous model, from both 'bottom-up' as well as 'top-down' perspective, is proposed here to serve as the template to describe the various kinds of context-dependence that we encounter in different branches of biology. Interactions between biological contexts was found to be transitive but non-commutative. It is found that a hierarchical nature of dependence amongst the biological contexts models the emergent biological properties efficiently. Reasons for these findings are provided with a general model to describe biological reality. Scheme to algorithmically implement the hierarchic structure of organization of biological contexts was achieved with a construct named 'Context tree'. A 'Context tree' based analysis of context interactions among biophysical factors influencing protein structure was performed.
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PDF链接：
https://arxiv.org/pdf/0902.0664
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