26 papers · ranked by Valyu relevance
Haotian Ma, Xiaoxiao Cheng, Gong Zhang, Tengfei Miao + 2 more
'Wei Zhang'] Title: Abstract New insights are raised to interpret pathway complexity in the supramolecular assembly of chiral triarylamine tris-amide (TATA) monomer. In cosolvent systems, the monomer undergoes entirely different assembly processes depending on the chemical feature of the two solvents. Specifically…
Erik Csikos
Directed networks arise across biological, social, informational, and engineered systems, yet most analyses treat directedness as a binary property: a network is either a directed acyclic graph (DAG) or it is not. This binary classification obscures the rich spectrum of hierarchical, recurrent, and modular structure…
Mildred Visser, Marleen de Mul, Kees Ahaus, Anne Marie Weggelaar-Jansen
'Anne Marie Weggelaar-Jansen'] Abstract Objectives Care pathways (CPs) are widely used to standardise and improve healthcare delivery. However, CP development is often shaped by value (or normative) complexity. This study empirically explores how value complexity unfolds in a CP development programme. Design A…
Neha Talluri, Tristan Figueroa-Reid, Justin Hiemstra, Chris S. Magnano + 19 more
Cells coordinate diverse biological processes through interactions among thousands of molecules, but mapping these interactions comprehensively and systematically remains an open problem. Pathway reconstruction algorithms address this problem by linking molecules of interest, identified from high-throughput omics…
Chathranee Jayathilaka, Robyn Araujo, Lan Nguyen, Mark Flegg
Models of biochemical networks are often large intractable sets of differential equations. To make sense of the complexity, relationships between genes/proteins are presented as connected graphs, the edges of which are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing…
Chathranee Jayathilaka, Robyn P. Araujo, Lan Anh Nguyen, Mark B. Flegg
'Mark B. Flegg'] Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions from the identification of topological features, for example…
Juliette Cooke, Cecilia Wieder, Nathalie Poupin, Clément Frainay + 2 more
Initially developed for transcriptomics data, pathway analysis (PA) methods can introduce biases when applied to metabolomics data, especially if input parameters are not chosen with care. This is particularly true for exometabolomics data, where exported metabolites may be far from internal disruptions in the…
Tunç Başar Köse, Jiarong Li, Anna Ritz
A major challenge in molecular systems biology is to understand how proteins work to transmit external signals to changes in gene expression. Computationally reconstructing these signaling pathways from protein interaction networks can help understand what is missing from existing pathway databases. We formulate a new…
Rikuto Kamiura, Ryo Mizuuchi, Norikazu Ichihashi, Ricardo Martinez-Garcia
'Ricardo Martinez-Garcia'] How the complexity of primitive self-replication molecules develops through Darwinian evolution remains a mystery with regards to the origin of life. Theoretical studies have proposed that coevolution with parasitic replicators increases network complexity by inducing inter-dependent…
Hoai Nguyen Huynh, Muhamad Azfar Ramli
Spatial road networks have been widely employed to model the structure and connectivity of cities. In such representation, the question of spatial scale of the entities in the network, i.e. what its nodes and edges actually embody in reality, is of particular importance so that redundant information can be identified…
Pietro Traversa, Guilherme Ferraz de Arruda, Alexei Vázquez, Yamir Moreno
'Yamir Moreno'] Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we propose a directed hypergraph with edge-dependent vertex weight as…
Cécile Beust, Emmanuelle Becker, Nathalie Théret, Olivier Dameron
In systems biology, the study of biological pathways plays a central role in understanding the complexity of biological systems. The massification of pathway data made available by numerous online databases in recent years has given rise to an important need for standardization of this data. The BioPAX format…
Jay R. Walton, Paul A. Lindahl
Title: Summary This contribution treats linear, steady-state dynamics for a metabolic network within a growing cell. Admissible steady-state reaction fluxes are assumed to form a pointed, convex, polyhedral, conical subset of the stoichiometric null-space. A solution of the problem is defined to consist of a linear…
Elliot M. Butterworth, Tim Rogers, Matthew A. Wills
Attempts to quantify biological complexity often consider intrinsic structural properties at a chosen hierarchical level and resolution, such as counts of body parts and their degree of differentiation. These measures are inherently \emph{syntactic}, being concerned with the information needed to specify an arrangement…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Authors not listed
Selection of efficient multi-step synthesis routes is a fundamental challenge in organic synthesis. Comparing different routes involves numerous parameters, economic considerations, and integration of nuanced chemical knowledge. While computer-aided synthesis planning (CASP) tools can generate synthetic routes…
Pier Luigi Gentili, Pasquale Stano
It is evident that our discussion just scratches the surface of a challenging but stimulating problem: defining the complexity of the structured and functionally rich chemical systems we call ACs. It is worth noting that the issue of defining and measuring the complexity of ACs was briefly put forward in a previous…
Ryan Miller, Sebastian Muraru, Ana Belén Malpartida, Josh Low + 7 more
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while…
Samuel Genheden, Esben Bjerrum
We introduce a framework for benchmarking multi-step retrosynthesis methods, i.e. route predictions, called PaRoutes. The framework consists of two sets of 10,000 synthetic routes extracted from the patent literature, a list of stock compounds, and a curated set of reactions on which one-step retrosynthesis models can…
Abicumaran Uthamacumaran, Héctor Zenil
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires the integration of information dynamics across multidimensional spatiotemporal…
ALESSANDRO ALIPRANDI, Dario Alessi, Luca Morgan, Elisa Pelorosso + 1 more
Self-organization is a key pathway to achieving high levels of matter complexity. However, an energy-consuming active process, such as a dissipative regime, is essential for adaptation and evolution to occur. In this study, we transform the passive self-organization of a luminescent square planar Pt(II) complex into an…
Manjunatha Beduru Krishnamurthy, Harish P S, Abhishek Subramanian
Genome-scale metabolic network (GSMN) models are rigorously curated, cellular-level representations of metabolism that enable flux-based metabolite fate discovery, metabolic engineering, drug target identification and context-specific multi-omics integration. However, the inherent complexity of model architectures…
Chiara Pastrello, Max Kotlyar, Mark Abovsky, Richard Lu + 1 more
Pathway Data Integration Portal (PathDIP) is an integrated pathway database that was developed to increase functional gene annotation coverage and reduce bias in pathway enrichment analysis. PathDIP 5 provides multiple improvements to enable more interpretable analysis: users can perform enrichment analysis using all…
Moushumi Goswami, Divya Dosemane, Sravanthi Davuluri, Akhilesh Bajpai + 1 more
Pathway Databases are essential particularly in the post-genomic era as they provide organized information about biological pathways and processes. However, there are too many pathway databases with varying features. These variations, stemming from multiple factors, create challenges for users in making objective…
Chonghuan Zhang, Qianyue Zhang, Alexei Lapkin
Biochemical transformations may allow significant improvements in synthetic efficiency of complex functional molecules through reduction in the number of synthetic steps or avoidance of harsh conditions and/or toxic solvents/reactants. Yet, there is a limited access to biochemical reaction data, which reduces the…
Authors not listed
Effective visualization of complex synthesis routes is critical for computeraided synthesis planning (CASP), yet current solutions are limited in scope, integration flexibility, and chemical intuition. We introduce RouteWise, a versatile, containerized web application designed to address these unmet needs. Its modular…