Cargando…

biochem4j: Integrated and extensible biochemical knowledge through graph databases

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between e...

Descripción completa

Detalles Bibliográficos
Autores principales:	Swainston, Neil, Batista-Navarro, Riza, Carbonell, Pablo, Dobson, Paul D., Dunstan, Mark, Jervis, Adrian J., Vinaixa, Maria, Williams, Alan R., Ananiadou, Sophia, Faulon, Jean-Loup, Mendes, Pedro, Kell, Douglas B., Scrutton, Nigel S., Breitling, Rainer
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2017
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510799/ https://www.ncbi.nlm.nih.gov/pubmed/28708831 http://dx.doi.org/10.1371/journal.pone.0179130

Ejemplares similares

Selenzyme: enzyme selection tool for pathway design
por: Carbonell, Pablo, et al.
Publicado: (2018)

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol
por: Dunstan, Mark S, et al.
Publicado: (2020)

SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals
por: Carbonell, Pablo, et al.
Publicado: (2016)

SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production
por: RA, Le Feuvre, et al.
Publicado: (2016)

Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries
por: Currin, Andrew, et al.
Publicado: (2019)

Engineering the “Missing Link” in Biosynthetic (−)-Menthol Production: Bacterial Isopulegone Isomerase
por: Currin, Andrew, et al.
Publicado: (2018)

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals
por: Carbonell, Pablo, et al.
Publicado: (2018)

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
por: Miwa, Makoto, et al.
Publicado: (2013)

An automated pipeline for the screening of diverse monoterpene synthase libraries
por: Leferink, Nicole G. H., et al.
Publicado: (2019)

Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle
por: Carbonell, Pablo, et al.
Publicado: (2016)

Co‐production of biofuel, bioplastics and biochemicals during extended fermentation of Halomonas bluephagenesis
por: Park, Helen, et al.
Publicado: (2022)

A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli
por: Fehér, Tamás, et al.
Publicado: (2015)

Mapping the patent landscape of synthetic biology for fine chemical production pathways
por: Carbonell, Pablo, et al.
Publicado: (2016)

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0
por: Koch, Mathilde, et al.
Publicado: (2017)

SensiPath: computer-aided design of sensing-enabling metabolic pathways
por: Delépine, Baudoin, et al.
Publicado: (2016)

Argo: enabling the development of bespoke workflows and services for disease annotation
por: Batista-Navarro, Riza, et al.
Publicado: (2016)

Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics
por: Batista-Navarro, Riza, et al.
Publicado: (2015)

A retrosynthetic biology approach to metabolic pathway design for therapeutic production
por: Carbonell, Pablo, et al.
Publicado: (2011)

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
por: Carbonell, Pablo, et al.
Publicado: (2012)

RetroRules: a database of reaction rules for engineering biology
por: Duigou, Thomas, et al.
Publicado: (2019)

Hierarchical graphs for rule-based modeling of biochemical systems
por: Lemons, Nathan W, et al.
Publicado: (2011)

Sensitivity analysis of biochemical systems using bond graphs
por: Gawthrop, Peter J., et al.
Publicado: (2023)

Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers
por: Robinson, Christopher J., et al.
Publicado: (2020)

Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows
por: Fu, Xiao, et al.
Publicado: (2015)

Using text mining techniques to extract phenotypic information from the PhenoCHF corpus
por: Alnazzawi, Noha, et al.
Publicado: (2015)

Using uncertainty to link and rank evidence from biomedical literature for model curation
por: Zerva, Chrysoula, et al.
Publicado: (2017)

A plasmid toolset for CRISPR‐mediated genome editing and CRISPRi gene regulation in Escherichia coli
por: Jervis, Adrian J., et al.
Publicado: (2021)

DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach
por: Khemchandani, Yash, et al.
Publicado: (2020)

XTMS: pathway design in an eXTended metabolic space
por: Carbonell, Pablo, et al.
Publicado: (2014)

An analysis of a ‘community-driven’ reconstruction of the human metabolic network
por: Swainston, Neil, et al.
Publicado: (2013)

Syntactically-informed word representations from graph neural network
por: Tran, Thy Thy, et al.
Publicado: (2020)

Mining metabolites: extracting the yeast metabolome from the literature
por: Nobata, Chikashi, et al.
Publicado: (2010)

Optimising protein synthesis in cell‐free systems, a review
por: Batista, Angelo C., et al.
Publicado: (2021)

A Toolbox for Diverse Oxyfunctionalisation of Monoterpenes
por: Hernandez-Ortega, Aitor, et al.
Publicado: (2018)

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling
por: Pauthenier, Cyrille, et al.
Publicado: (2014)

Text-mining-assisted biocuration workflows in Argo
por: Rak, Rafal, et al.
Publicado: (2014)

Processing biological literature with customizable Web services supporting interoperable formats
por: Rak, Rafal, et al.
Publicado: (2014)

Annotation and detection of drug effects in text for pharmacovigilance
por: Thompson, Paul, et al.
Publicado: (2018)

Learning graph representations of biochemical networks and its application to enzymatic link prediction
por: Jiang, Julie, et al.
Publicado: (2020)

Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs
por: Fontanesi, Michele, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_n0pialib5c3tf0pop2rq7c4av1