arXiv - QuanBio - Molecular Networks最新文献_第7页

Information propagation in far-from-equilibrium molecular templating networks is optimised by pseudo-equilibrium systems with negligible dissipation 通过可忽略耗散的伪平衡系统优化远非平衡分子模板网络中的信息传播

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-03 DOI: arxiv-2404.02791

Benjamin Qureshi, Jenny M. Poulton, Thomas E. Ouldridge

{"title":"Information propagation in far-from-equilibrium molecular templating networks is optimised by pseudo-equilibrium systems with negligible dissipation","authors":"Benjamin Qureshi, Jenny M. Poulton, Thomas E. Ouldridge","doi":"arxiv-2404.02791","DOIUrl":"https://doi.org/arxiv-2404.02791","url":null,"abstract":"Far-from equilibrium molecular templating networks, like those that maintain\u0000the populations of RNA and protein molecules in the cell, are key biological\u0000motifs. These networks share the general property that assembled products are\u0000produced and degraded via complex pathways controlled by catalysts, including\u0000molecular templates. Although it has been suggested that the information\u0000propagated from templates to products sets a lower bound on the thermodynamic\u0000cost of these networks, this bound has not been explored rigorously to date. We\u0000show that, for an arbitrarily catalytic reaction network in steady state, the\u0000specificity with which a single product can dominate the ensemble is upper\u0000bounded, and the entropy of the product ensemble lower bounded, by a function\u0000of $Delta G$, the difference between the maximal and minimal free-energy\u0000changes along pathways to assembly. These simple bounds are particularly\u0000restrictive for systems with a smaller number of possible products $M$.\u0000Remarkably, however, although $Delta G$ constrains the information propagated\u0000to the product distribution, the systems that saturate the bound operate in a\u0000pseudo-equilibrium fashion, and there is no minimal entropy production rate for\u0000maintaining this non-equilibrium distribution. Moreover, for large systems, a\u0000vanishingly small subset of the possible products can dominate the product\u0000ensemble even for small values of $Delta G/ln M$.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140569392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Embedding-based comparison of reaction networks of Wnt signaling 基于嵌入式的 Wnt 信号传递反应网络比较

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-01 DOI: arxiv-2404.06515

Bryan S. Hernandez, Patrick Vincent N. Lubenia, Eduardo R. Mendoza

{"title":"Embedding-based comparison of reaction networks of Wnt signaling","authors":"Bryan S. Hernandez, Patrick Vincent N. Lubenia, Eduardo R. Mendoza","doi":"arxiv-2404.06515","DOIUrl":"https://doi.org/arxiv-2404.06515","url":null,"abstract":"This work introduces a new method for comparing two reaction networks of the\u0000same or closely related systems through their embedded networks in terms of the\u0000shared set of species. Hence, we call this method the Common Species Embedded\u0000Networks (CSEN) analysis. Using this approach, we conduct a comparison of\u0000existing reaction networks associated with Wnt signaling models (Lee, Schmitz,\u0000MacLean, and Feinberg) that we have identified. The analysis yields three\u0000important results for these Wnt models. First, the CSEN analysis of the Lee\u0000(mono-stationary) and Feinberg (multi-stationary) shows a strong similarity,\u0000justifying the study of the Feinberg model, which was a modified Lee model\u0000constructed to study an important network property called \"concordance\". It\u0000also challenge the absoluteness of discrimination of the models into\u0000mono-stationarity versus multi-stationarity, which is a main result of Maclean\u0000et al. (PNAS USA 2015). Second, the CSEN analysis provides evidence supporting\u0000a strong similarity between the Schmitz and MacLean models, as indicated by the\u0000\"proximate equivalence\" that we have identified. Third, the analysis\u0000underscores the absence of a comparable relationship between the Feinberg and\u0000MacLean models, highlighting distinctive differences between the two. Thus, our\u0000approach could be a useful tool to compare mathematical models of the same or\u0000closely related systems.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"47 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140594861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction ProLLM：用于蛋白质-蛋白质相互作用预测的蛋白质思维链增强型 LLM

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-30 DOI: arxiv-2405.06649

Mingyu Jin, Haochen Xue, Zhenting Wang, Boming Kang, Ruosong Ye, Kaixiong Zhou, Mengnan Du, Yongfeng Zhang

{"title":"ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction","authors":"Mingyu Jin, Haochen Xue, Zhenting Wang, Boming Kang, Ruosong Ye, Kaixiong Zhou, Mengnan Du, Yongfeng Zhang","doi":"arxiv-2405.06649","DOIUrl":"https://doi.org/arxiv-2405.06649","url":null,"abstract":"The prediction of protein-protein interactions (PPIs) is crucial for\u0000understanding biological functions and diseases. Previous machine learning\u0000approaches to PPI prediction mainly focus on direct physical interactions,\u0000ignoring the broader context of nonphysical connections through intermediate\u0000proteins, thus limiting their effectiveness. The emergence of Large Language\u0000Models (LLMs) provides a new opportunity for addressing this complex biological\u0000challenge. By transforming structured data into natural language prompts, we\u0000can map the relationships between proteins into texts. This approach allows\u0000LLMs to identify indirect connections between proteins, tracing the path from\u0000upstream to downstream. Therefore, we propose a novel framework ProLLM that\u0000employs an LLM tailored for PPI for the first time. Specifically, we propose\u0000Protein Chain of Thought (ProCoT), which replicates the biological mechanism of\u0000signaling pathways as natural language prompts. ProCoT considers a signaling\u0000pathway as a protein reasoning process, which starts from upstream proteins and\u0000passes through several intermediate proteins to transmit biological signals to\u0000downstream proteins. Thus, we can use ProCoT to predict the interaction between\u0000upstream proteins and downstream proteins. The training of ProLLM employs the\u0000ProCoT format, which enhances the model's understanding of complex biological\u0000problems. In addition to ProCoT, this paper also contributes to the exploration\u0000of embedding replacement of protein sites in natural language prompts, and\u0000instruction fine-tuning in protein knowledge datasets. We demonstrate the\u0000efficacy of ProLLM through rigorous validation against benchmark datasets,\u0000showing significant improvement over existing methods in terms of prediction\u0000accuracy and generalizability. The code is available at:\u0000https://github.com/MingyuJ666/ProLLM.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140931165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The generic temperature response of large biochemical networks 大型生化网络的一般温度响应

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-25 DOI: arxiv-2403.17202

Julian B. VoitsHeidelberg University, Ulrich S. SchwarzHeidelberg University

{"title":"The generic temperature response of large biochemical networks","authors":"Julian B. VoitsHeidelberg University, Ulrich S. SchwarzHeidelberg University","doi":"arxiv-2403.17202","DOIUrl":"https://doi.org/arxiv-2403.17202","url":null,"abstract":"Biological systems are remarkably susceptible to relatively small temperature\u0000changes. The most obvious example is fever, when a modest rise in body\u0000temperature of only few Kelvin has strong effects on our immune system and how\u0000it fights pathogens. Another very important example is climate change, when\u0000even smaller temperature changes lead to dramatic shifts in ecosystems.\u0000Although it is generally accepted that the main effect of an increase in\u0000temperature is the acceleration of biochemical reactions according to the\u0000Arrhenius equation, it is not clear how it effects large biochemical networks\u0000with complicated architectures. For developmental systems like fly and frog, it\u0000has been shown that the system response to temperature deviates in a\u0000characteristic manner from the linear Arrhenius plot of single reactions, but a\u0000rigorous explanation has not been given yet. Here we use a graph theoretical\u0000interpretation of the mean first passage times of a biochemical master equation\u0000to give a statistical description. We find that in the limit of large system\u0000size and if the network has a bias towards a target state, then the Arrhenius\u0000plot is generically quadratic, in excellent agreement with experimental data\u0000for developmental times in fly and frog.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140313219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Connectivity of Parameter Regions of Multistationarity for Multisite Phosphorylation Networks 多位点磷酸化网络多态性参数区域的连接性

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-25 DOI: arxiv-2403.16556

Nidhi Kaihnsa, Máté L. Telek

引用次数: 0

Stability distillation hypothesis for the origin of life 生命起源的稳定蒸馏假说

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-25 DOI: arxiv-2403.17072

Cheng Bi

{"title":"Stability distillation hypothesis for the origin of life","authors":"Cheng Bi","doi":"arxiv-2403.17072","DOIUrl":"https://doi.org/arxiv-2403.17072","url":null,"abstract":"The essence of life is a frequency distribution conversion process of\u0000molecules accompanied by changes in information. In wet-dry cycling hot\u0000springs, RNA of different sequences continuously undergoes polymerization and\u0000decomposition reactions, products with stable configurations will accumulate\u0000their frequency among all RNA molecules and finally become an important source\u0000of DNA coding and non-coding regions in primitive cells. This periodic extreme\u0000environmental change narrows the frequency distribution of macromolecules\u0000through the distillation process and new potential catalysts are searched. When\u0000enough macromolecules are accumulated and reliable reaction pathways are built,\u0000phospholipids randomly wrap the macromolecules in the hot springs which I would\u0000call it the pioneer pools, and these protocells become parallel calculators of\u0000molecule frequency distribution. Through the selective permeability of the cell\u0000membrane to different molecular weights and properties, cells with appropriate\u0000distribution have more opportunities to absorb small molecule substances and\u0000increase its intracellular frequencies of molecules. This will strongly induce\u0000the occurrence of macromolecules that can widely catalyze the synthesis of\u0000other macromolecules or themselves, such as ribosomes, etc. Rupture and fusion\u0000during cell division make all protocells share the same frequency distribution\u0000of molecules during the origin of life, thus ensuring that all present cells\u0000have very similar genetic materials and protein translation systems. This also\u0000suggests that viruses may have originated and evolved together with cells.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140313233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exact analytic expressions for discrete first-passage time probability distributions in Markov networks 马尔可夫网络中离散首过时间概率分布的精确解析表达式

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-21 DOI: arxiv-2403.14149

Jaroslav Albert

{"title":"Exact analytic expressions for discrete first-passage time probability distributions in Markov networks","authors":"Jaroslav Albert","doi":"arxiv-2403.14149","DOIUrl":"https://doi.org/arxiv-2403.14149","url":null,"abstract":"The first-passage time (FPT) is the time it takes a system variable to cross\u0000a given boundary for the first time. In the context of Markov networks, the FPT\u0000is the time a random walker takes to reach a particular node (target) by\u0000hopping from one node to another. If the walker pauses at each node for a\u0000period of time drawn from a continuous distribution, the FPT will be a\u0000continuous variable; if the pauses last exactly one unit of time, the FPT will\u0000be discrete and equal to the number of hops. We derive an exact analytical\u0000expression for the discrete first-passage time (DFPT) in Markov networks. Our\u0000approach is as follows: first, we divide each edge (connection between two\u0000nodes) of the network into $h$ unidirectional edges connecting a cascade of $h$\u0000fictitious nodes and compute the continuous FPT (CFPT). Second, we set the\u0000transition rates along the edges to $h$, and show that as $htoinfty$, the\u0000distribution of travel times between any two nodes of the original network\u0000approaches a delta function centered at 1, which is equivalent to pauses\u0000lasting 1 unit of time. Using this approach, we also compute the\u0000joint-probability distributions for the DFPT, the target node, and the node\u0000from which the target node was reached. A comparison with simulation confirms\u0000the validity of our approach.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140199305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Competition for binding targets results in paradoxical effects for simultaneous activator and repressor action -- Extended Version 对结合目标的竞争导致激活剂和抑制剂同时作用的矛盾效应 -- 扩展版

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-21 DOI: arxiv-2403.14820

M. Ali Al-Radhawi, Krishna Manoj, Dhruv D. Jatkar, Alon Duvall, Domitilla Del Vecchio, Eduardo D. Sontag

{"title":"Competition for binding targets results in paradoxical effects for simultaneous activator and repressor action -- Extended Version","authors":"M. Ali Al-Radhawi, Krishna Manoj, Dhruv D. Jatkar, Alon Duvall, Domitilla Del Vecchio, Eduardo D. Sontag","doi":"arxiv-2403.14820","DOIUrl":"https://doi.org/arxiv-2403.14820","url":null,"abstract":"In the context of epigenetic transformations in cancer metastasis, a puzzling\u0000effect was recently discovered, in which the elimination (knock-out) of an\u0000activating regulatory element leads to increased (rather than decreased)\u0000activity of the element being regulated. It has been postulated that this\u0000paradoxical behavior can be explained by activating and repressing\u0000transcription factors competing for binding to other possible targets. It is\u0000very difficult to prove this hypothesis in mammalian cells, due to the large\u0000number of potential players and the complexity of endogenous intracellular\u0000regulatory networks. Instead, this paper analyzes this issue through an\u0000analogous synthetic biology construct which aims to reproduce the paradoxical\u0000behavior using standard bacterial gene expression networks. The paper first\u0000reviews the motivating cancer biology work, and then describes a proposed\u0000synthetic construct. A mathematical model is formulated, and basic properties\u0000of uniqueness of steady states and convergence to equilibria are established,\u0000as well as an identification of parameter regimes which should lead to\u0000observing such paradoxical phenomena (more activator leads to less activity at\u0000steady state). A proof is also given to show that this is a steady-state\u0000property, and for initial transients the phenomenon will not be observed. This\u0000work adds to the general line of work of resource competition in synthetic\u0000circuits.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140299529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A necessary condition for non-monotonic dose response, with an application to a kinetic proofreading model -- Extended version 非单调剂量反应的必要条件，并应用于动力学校对模型 -- 扩展版

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-20 DOI: arxiv-2403.13862

Polly Y. Yu, Eduardo D. Sontag

引用次数: 0

ScAtt: an Attention based architecture to analyze Alzheimer's disease at cell type level from single-cell RNA-sequencing data ScAtt：基于注意力的架构，从单细胞 RNA 序列数据分析阿尔茨海默病的细胞类型水平

arXiv - QuanBio - Molecular Networks Pub Date : 2024-03-12 DOI: arxiv-2405.17433

Xiaoxia Liu, Robert R Butler III, Prashnna K Gyawali, Frank M Longo, Zihuai He

{"title":"ScAtt: an Attention based architecture to analyze Alzheimer's disease at cell type level from single-cell RNA-sequencing data","authors":"Xiaoxia Liu, Robert R Butler III, Prashnna K Gyawali, Frank M Longo, Zihuai He","doi":"arxiv-2405.17433","DOIUrl":"https://doi.org/arxiv-2405.17433","url":null,"abstract":"Alzheimer's disease (AD) is a pervasive neurodegenerative disorder that leads\u0000to memory and behavior impairment severe enough to interfere with daily life\u0000activities. Understanding this disease pathogenesis can drive the development\u0000of new targets and strategies to prevent and treat AD. Recent advances in\u0000high-throughput single-cell RNA sequencing technology (scRNA-seq) have enabled\u0000the generation of massive amounts of transcriptomic data at the single-cell\u0000level provided remarkable insights into understanding the molecular\u0000pathogenesis of Alzheimer's disease. In this study, we introduce ScAtt, an\u0000innovative Attention-based architecture, devised specifically for the\u0000concurrent identification of cell-type specific AD-related genes and their\u0000associated gene regulatory network. ScAtt incorporates a flexible model capable\u0000of capturing nonlinear effects, leading to the detection of AD-associated genes\u0000that might be overlooked by traditional differentially expressed gene (DEG)\u0000analyses. Moreover, ScAtt effectively infers a gene regulatory network\u0000depicting the combined influences of genes on the targeted disease, as opposed\u0000to examining correlations among genes in conventional gene co-expression\u0000networks. In an application to 95,186 single-nucleus transcriptomes from 17\u0000hippocampus samples, ScAtt shows substantially better performance in modeling\u0000quantitative changes in expression levels between AD and healthy controls.\u0000Consequently, ScAtt performs better than existing methods in the identification\u0000of AD-related genes, with more unique discoveries and less overlap between cell\u0000types. Functional enrichments of the corresponding gene modules detected from\u0000gene regulatory network show significant enrichment of biologically meaningful\u0000AD-related pathways across different cell types.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141166697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0