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Search · four archives
25 papers · ranked by Valyu relevance
Tommi Aho, Olli-Pekka Smolander, Jari Niemi, Olli Yli-Harja
Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model…
Kevin Schwahn, Romina Beleggia, Nooshin Omranian, Zoran Nikoloski
Recent advances in metabolomics technologies have resulted in high-quality (time-resolved) metabolic profiles with an increasing coverage of metabolic pathways. These data profiles represent read-outs from often non-linear dynamics of metabolic networks. Yet, metabolic profiles have largely been explored with…
Yosef Bedaso, Frank T. Bergmann, Kiri Choi, Herbert M. Sauro
The topology of a reaction network can have a significant influence on the network’s dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the…
Mona Yousofshahi, Ehsan Ullah, Russell Stern, Soha Hassoun
Background Stoichiometric models provide a structural framework for analyzing steady-state cellular behavior. Models are developed either through augmentations of existing models or more recently through automatic reconstruction tools. There is currently no standardized practice or method for validating the properties…
Shodhan Rao, Arjan van der Schaft, Bayu Jayawardhana
In this paper we derive a compact mathematical formulation describing the dynamics of chemical reaction networks that are complex-balanced and are governed by mass action kinetics. The formulation is based on the graph of (substrate and product) complexes and the stoichiometric information of these complexes, and…
Daisy Duan, Meretta Hanson, David O. Holland, Margaret E Johnson
Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at various copy numbers within a cell, from hundreds (e.g. auxilin) to millions (e.g. clathrin). Between cell types with identical genomes, copy numbers further vary significantly both in absolute and relative abundance. These…
Hadjar Rahou, Hulda S. Haraldsdottir, Filippo Martinelli, Ines Thiele + 1 more
'Ines Thiele' 'Ronan M. T. Fleming'] A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and chemical bonds. To address combinatorial…
Hulda S. Haraldsdóttir, Ronan M. T. Fleming, Costas D. Maranas
Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer…
Shu Wang, Jia-Ren Lin, Eduardo D. Sontag, Peter K. Sorger
The goal of many single-cell studies on eukaryotic cells is to gain insight into the biochemical reactions that control cell fate and state. In this paper we introduce the concept of effective stoichiometric space (ESS) to guide the reconstruction of biochemical networks from multiplexed, fixed time-point, single-cell…
Exequiel Jun V. Villejo, Aurelio A. de los Reyes, Bryan S. Hernandez
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical tools for computing these equilibria, such as COMPILES, are limited by computational…
P.J. Gawthrop, Edmund J. Crampin
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked…
Hulda S. Haraldsdóttir, Ronan M. T. Fleming
Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer…
P.J. Gawthrop
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Shodhan Rao, Arjan van der Schaft, Karen van Eunen, Barbara M. Bakker + 1 more
'Barbara M. Bakker' 'Bayu Jayawardhana'] Abstract— In this paper we propose a model-order reduction method for chemical reaction networks governed by general enzyme kinetics, including the mass-action and Michaelis-Menten kinetics. The model-order reduction method is based on the Kron reduction of the weighted…
Bryan S. Hernandez, Patrick Vincent N. Lubenia, Matthew D. Johnston, Jae Kyoung Kim + 1 more
'Jae Kyoung Kim' 'Mark Alber'] The long-term behaviors of biochemical systems are often described by their steady states. Deriving these states directly for complex networks arising from real-world applications, however, is often challenging. Recent work has consequently focused on network-based approaches.…
Damoun Langary, Anika Küken, Zoran Nikoloski
Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation…
Michael Weitzel, Wolfgang Wiechert, Katharina Nöh
Background Metabolic Flux Analysis (MFA) based on isotope labeling experiments (ILEs) is a widely established tool for determining fluxes in metabolic pathways. Isotope labeling networks (ILNs) contain all essential information required to describe the flow of labeled material in an ILE. Whereas recent experimental…
Kuo Kan Liang
Metabolic reaction networks usually include a large number of enzymatic reaction steps. Nowadays, people desire to work on larger and larger metabolic networks, in the research fields of for example systems or synthetic biology. With the growing sizes of the metabolic networks considered, it is more and more tedious…
Yusuke Himeoka, Julius B. Kirkegaard, Namiko Mitarai, Sandeep Krishna
Understanding the relationship between the structure of chemical reaction networks and their reaction dynamics is essential for the functioning of living organisms. However, while some network-structural features are known to relate to the steady-state characteristics of chemical reaction networks, mathematical…
Authors not listed
Identifying synthesis routes from knowledge graphs poses challenges beyond retrosynthesis, including path–finding artifacts and data issues. We introduce “SynGPS”, a novel algorithm that overcomes these limitations by identifying viable routes even with common artifacts. SynGPS can resolve nonsensical cycles…
Daniel Barter, Evan Walter Clark Spotte-Smith, Nikita S. Redkar, Shyam Dwaraknath + 2 more
Chemical reaction networks (CRNs) are powerful tools for obtaining mechanistic insight into complex reactive processes. However, they are limited in their applicability where reaction mechanisms are not well understood and products are unknown. Here we report new methods of CRN generation and analysis that overcome…
Daniel Barter, Evan Walter Clark Spotte-Smith, Nikita S. Redkar, Shyam Dwaraknath + 2 more
Chemical reaction networks (CRNs) are powerful tools for obtaining mechanistic insight into complex reactive processes. However, they are limited in their applicability where reaction mechanisms are unintuitive, and products are unknown. Here we report new methods of CRN generation and analysis that overcome these…
Authors not listed
A dataset derived from 35 sources was used to analyze the changes to acid:extractant and metal:extractant stoichiometric ratios as a function of aqueous acid concentration. The presence and location of the critical micelle concentration is easily identified by sharp changes to the stoichiometric ratios. This is…
Daniel Barter, Evan Walter Clark Spotte-Smith, Nikita S. Redkar, Aniruddh Khanwale + 3 more
Chemical reaction networks (CRNs) are powerful tools for obtaining insight into complex reactive processes. However, they are difficult to employ when reaction mechanisms and products are not thoroughly understood. Here we report new methods of CRN generation and analysis that seek to overcome these limitations. We…
Santiago Morandi, Oliver Loveday, Tim Renningholtz, Sergio Pablo-García + 6 more
Process optimization in heterogeneous catalysis relies on the control of competing reactions. The reaction mechanisms based on chemical knowledge can be evaluated via density functional theory unveiling experimental catalytic trends. However, this approach finds its limits when applied to complex reaction networks or…