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Article
Open AccessProtein function prediction through multi-view multi-label latent tensor reconstruction
In last two decades, the use of high-throughput sequencing technologies has accelerated the pace of discovery of proteins. However, due to the time and resource limitations of rigorous experimental functional ...
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Article
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is limited to structures present in libraries or databa...
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Article
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
Mass spectrometry is a predominant experimental technique in metabolomics and related fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 (https://bio.informatik.uni-jena....
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Article
Open AccessSelected proceedings of Machine Learning in Systems Biology: MLSB 2016
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Article
Open AccessInferring branching pathways in genome-scale metabolic networks
A central problem in computational metabolic modelling is how to find biochemically plausible pathways between metabolites in a metabolic network. Two general, complementary frameworks have been utilized to fi...
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Article
Open AccessAn analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Metabolic fluxes provide invaluable insight on the integrated response of a cell to environmental stimuli or genetic modifications. Current computational methods for estimating the metabolic fluxes from 13C isoto...
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Article
Open AccessProbabilistic modeling and machine learning in structural and systems biology
This supplement contains extended versions of a selected subset of papers presented at the workshop PMSB 2007, Probabilistic Modeling and Machine Learning in Structural and Systems Biology, Tuusula, Finland, f...