AIMC Topic: Metabolic Networks and Pathways
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Discriminating early- and late-stage cancers using multiple kernel learning on gene sets.
Bioinformatics (Oxford, England)
Jul 1, 2018
MOTIVATION: Identifying molecular mechanisms that drive cancers from early to late stages is highly important to develop new preventive and therapeutic strategies. Standard machine learning algorithms could be used to discriminate early- and late-sta...
Reactome diagram viewer: data structures and strategies to boost performance.
Bioinformatics (Oxford, England)
Apr 1, 2018
MOTIVATION: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. He...
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease.
Bioinformatics (Oxford, England)
Mar 15, 2018
SUMMARY: Gene-based supervised machine learning classification models have been widely used to differentiate disease states, predict disease progression and determine effective treatment options. However, many of these classifiers are sensitive to no...
Gramene 2018: unifying comparative genomics and pathway resources for plant research.
Nucleic acids research
Jan 4, 2018
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,...
The Reactome Pathway Knowledgebase.
Nucleic acids research
Jan 4, 2018
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended version of a clas...
A Network Integration Method for Deciphering the Types of Metabolic Pathway of Chemicals with Heterogeneous Information.
Combinatorial chemistry & high throughput screening
Jan 1, 2018
AIM AND OBJECTIVE: A metabolic pathway is an important type of biological pathway, which is composed of a series of chemical reactions. It provides essential molecules and energies for living organisms. To date, several metabolic pathways have been u...
Graph-based semi-supervised learning with genomic data integration using condition-responsive genes applied to phenotype classification.
Journal of the American Medical Informatics Association : JAMIA
Jan 1, 2018
OBJECTIVE: Data integration methods that combine data from different molecular levels such as genome, epigenome, transcriptome, etc., have received a great deal of interest in the past few years. It has been demonstrated that the synergistic effects ...
An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features.
Molecular bioSystems
Jul 25, 2017
Prediction of essential genes helps to identify a minimal set of genes that are absolutely required for the appropriate functioning and survival of a cell. The available machine learning techniques for essential gene prediction have inherent problems...
A fuzzy logic controller based approach to model the switching mechanism of the mammalian central carbon metabolic pathway in normal and cancer cells.
Molecular bioSystems
Jul 19, 2016
Dynamics of large nonlinear complex systems, like metabolic networks, depend on several parameters. A metabolic pathway may switch to another pathway in accordance with the current state of parameters in both normal and cancer cells. Here, most of th...
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