Research graph
References from Advances in flux balance analysis by integrating machine learning and mechanism-based models. Local targets link to admitted publications; unresolved targets remain external evidence.
Current state and applications of microbial genome-scale metabolic models
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Reconstruction of genome-scale human metabolic models using omics data
10.1039/c5ib00002e · 2015 · External reference
10.1016/j.copbio.2012.08.007
10.1016/j.copbio.2012.08.007 · External reference
Are we ready for genome-scale modeling in plants?
10.1016/j.plantsci.2012.04.010 · 2012 · External reference
10.1016/j.copbio.2017.07.009
10.1016/j.copbio.2017.07.009 · External reference
10.3389/fpls.2011.00038
10.3389/fpls.2011.00038 · External reference
Environment-coupled models of leaf metabolism
10.1042/bst20200059 · 2021 · External reference
10.1007/978-1-4939-7295-1
10.1007/978-1-4939-7295-1 · 2018 · External reference
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10.1002/wsbm.1393
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Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits
10.1111/tpj.14707 · 2020 · External reference
10.1105/tpc.20.00132
10.1105/tpc.20.00132 · External reference
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10.3390/metabo9020022
10.3390/metabo9020022 · External reference
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes
2017 · External reference
10.1038/nbt.3703
10.1038/nbt.3703 · External reference
Reconstruction of context-specific genome-scale metabolic models using multiomics data to study metabolic rewiring
10.1016/j.coisb.2019.02.009 · 2019 · External reference
10.1016/j.copbio.2017.11.014
10.1016/j.copbio.2017.11.014 · External reference
A genome-scale metabolic model of soybean (Glycine max) highlights metabolic fluxes in seedlings
10.1104/pp.19.00122 · 2019 · External reference
A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants
10.1186/s12859-019-2941-z · 2019 · External reference
Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
10.1038/s41598-018-26232-8 · 2018 · External reference
Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale
10.1104/pp.113.224006 · 2013 · External reference
10.1073/pnas.1100358109
10.1073/pnas.1100358109 · External reference
10.3389/fpls.2015.00004
10.3389/fpls.2015.00004 · External reference
10.3389/fpls.2018.00884
10.3389/fpls.2018.00884 · External reference
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10.1038/nbt.1614 · External reference
10.1016/j.mib.2010.03.003
10.1016/j.mib.2010.03.003 · External reference
Methods and advances in metabolic flux analysis: a mini-review
10.1007/s10295-015-1585-x · 2015 · External reference
Inference and prediction of metabolic network fluxes
2015 · External reference
10.1016/j.ymben.2016.09.005
10.1016/j.ymben.2016.09.005 · External reference
A diel flux balance model captures interactions between light and dark metabolism during day-night cycles in C3 and crassulacean acid metabolism leaves
10.1104/pp.113.234468 · 2014 · External reference
10.1016/s0006-3495(02)73903-9
10.1016/s0006-3495(02)73903-9 · External reference
10.3389/fmicb.2015.00409
10.3389/fmicb.2015.00409 · External reference
A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
10.1042/bst20190840 · 2020 · External reference
10.3389/fphys.2012.00299
10.3389/fphys.2012.00299 · External reference
10.1016/j.csbj.2014.08.009 · Admitted local publication
10.3389/fpls.2014.00491
10.3389/fpls.2014.00491 · External reference
10.3389/fpls.2015.00049
10.3389/fpls.2015.00049 · External reference
Unresolved reference
2018 · External reference
10.15252/msb.20167411
10.15252/msb.20167411 · External reference
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
10.1073/pnas.0609845104 · 2007 · External reference
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Cell design in bacteria as a convex optimization problem
10.1016/j.automatica.2011.02.038 · 2011 · External reference
10.1042/bst20160436
10.1042/bst20160436 · External reference
10.1038/msb.2013.52
10.1038/msb.2013.52 · External reference
10.1016/j.cels.2017.11.013
10.1016/j.cels.2017.11.013 · External reference
Recent advances on constraint-based models by integrating machine learning
10.1016/j.copbio.2019.11.007 · 2020 · External reference
10.1186/s13059-019-1689-0
10.1186/s13059-019-1689-0 · External reference
10.1126/science.aaa8415
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Learning dynamics from large biological datasets: machine learning meets systems biology. Curr Opin
2020 · External reference
10.1371/journal.pcbi.1004977
10.1371/journal.pcbi.1004977 · External reference
10.1371/journal.pcbi.1007084
10.1371/journal.pcbi.1007084 · External reference
Principal metabolic flux mode analysis
10.1093/bioinformatics/bty049 · 2018 · External reference
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
2016 · External reference
10.1038/srep46249
10.1038/srep46249 · External reference
Points of significance: Principal component analysis
10.1038/nmeth.4346 · 2017 · External reference
10.1016/j.neucom.2017.06.053
10.1016/j.neucom.2017.06.053 · External reference
Research and implementation of SVD in machine learning
2017 · External reference
10.1016/b978-0-12-815739-8.00013-4
10.1016/b978-0-12-815739-8.00013-4 · External reference
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
10.1186/s12918-018-0673-8 · 2019 · External reference
10.3390/pr6080132
10.3390/pr6080132 · External reference
10.1007/s10479-018-2865-4
10.1007/s10479-018-2865-4 · External reference
Unresolved reference
2016 · External reference
Unresolved reference
2021 · External reference
Unresolved reference
2012 · External reference
Overview of use of decision tree algorithms in machine learning
2011 · External reference
Artificial neural networks as models of neural information processing
10.3389/fncom.2017.00114 · 2017 · External reference
Applications of support vector machine (SVM) learning in cancer genomics
2018 · External reference
Recurrent neural networks
10.4249/scholarpedia.1888 · 2013 · External reference
A survey on ensemble learning
10.1007/s11704-019-8208-z · 2020 · External reference
10.15252/msb.20145108
10.15252/msb.20145108 · External reference
In silico method for modelling metabolism and gene product expression at genome scale
10.1038/ncomms1928 · 2012 · External reference
10.1038/msb.2013.52
10.1038/msb.2013.52 · External reference
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10.7717/peerj.6046 · External reference
Metabolic network prediction of drug side effects
10.1016/j.cels.2016.03.001 · 2016 · External reference
Machine learning reveals missing edges and putative interaction mechanisms in microbial ecosystem networks
10.1128/msystems.00181-18 · 2018 · External reference
10.3390/jpm11060496
10.3390/jpm11060496 · External reference
The poly-omics of ageing through individual-based metabolic modelling
10.1186/s12859-018-2383-z · 2018 · External reference
10.1016/j.isci.2020.101818
10.1016/j.isci.2020.101818 · External reference
10.1073/pnas.2002959117
10.1073/pnas.2002959117 · External reference
Multimodal regularised linear models with flux balance analysis for mechanistic integration of omics data
2021 · External reference
10.1038/nature14539
10.1038/nature14539 · External reference
Deep learning meets metabolomics: A methodological perspective
2020 · External reference
10.15252/msb.20156651
10.15252/msb.20156651 · External reference
10.1016/j.neucom.2016.12.038
10.1016/j.neucom.2016.12.038 · External reference
Unresolved reference
2020 · External reference
Unresolved reference
2020 · External reference
DeepMetabolism: a deep learning system to predict phenotype from genome sequencing
2017 · External reference
10.1101/365643
10.1101/365643 · External reference
10.1016/s0006-3495(02)73903-9
10.1016/s0006-3495(02)73903-9 · External reference
Elucidating temporal resource allocation and diurnal dynamics in phototrophic metabolism using conditional FBA
10.1038/srep15247 · 2015 · External reference
10.3389/fmicb.2018.01690
10.3389/fmicb.2018.01690 · External reference
μbialSim: constraint-based dynamic simulation of complex microbiomes. Front Bioeng
2020 · External reference
10.3389/fmicb.2016.00673
10.3389/fmicb.2016.00673 · External reference
10.3389/fgene.2017.00088
10.3389/fgene.2017.00088 · External reference
PBPK models for the prediction of in vivo performance of oral dosage forms
10.1016/j.ejps.2013.09.008 · 2014 · External reference
Physiologically based pharmacokinetic (PBPK) modeling and simulation approaches: a systematic review of published models, applications, and model verification
10.1124/dmd.115.065920 · 2015 · External reference
Applications of physiologically based pharmacokinetic (PBPK) modeling and simulation during regulatory review
10.1038/clpt.2010.298 · 2011 · External reference
MUFINS: multi-formalism interaction network simulator
2016 · External reference
10.1371/journal.pcbi.1002750
10.1371/journal.pcbi.1002750 · External reference
Multiscale metabolic modeling approach for predicting blood alcohol concentration
10.1109/lls.2016.2644647 · 2016 · External reference
10.1109/embc.2016.7590974
10.1109/embc.2016.7590974 · External reference
A multi-scale model of the whole human body based on dynamic parsimonious flux balance analysis
2016 · External reference
Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology
2017 · External reference
Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation
10.1038/s41540-018-0048-1 · 2018 · External reference
Systems pharmacology of levodopa absorption
2015 · External reference
Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients
10.1038/npjsba.2016.13 · 2016 · External reference
Computational modeling of quiescent platelet energy metabolism in the context of whole-body glucose turnover
10.1051/mmnp/201611606 · 2016 · External reference
10.1002/psp4.12230
10.1002/psp4.12230 · External reference
Genome-scale metabolic networks in time and space
10.1016/j.coisb.2017.12.003 · 2018 · External reference
10.3389/fmolb.2016.00003
10.3389/fmolb.2016.00003 · External reference
10.1016/j.coisb.2017.06.001
10.1016/j.coisb.2017.06.001 · External reference
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10.1073/pnas.1919250117 · External reference
10.1049/iet-syb.2013.0021
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Constraint-based stoichiometric modelling from single organisms to microbial communities
10.1098/rsif.2016.0627 · 2016 · External reference
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10.1021/sb4001307 · External reference
10.1186/1472-6750-13-8
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10.1186/s12918-016-0259-2 · External reference
10.1016/j.celrep.2014.03.070
10.1016/j.celrep.2014.03.070 · External reference
Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species
10.1186/s12918-016-0334-8 · 2016 · External reference
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Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
10.1093/bioinformatics/btn352 · 2008 · External reference
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10.1109/pma.2012.6524848 · External reference
Unresolved reference
External reference
Biochemical models of leaf photosynthesis
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10.1093/bioinformatics/bti145 · 2005 · External reference
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2004 · External reference
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10.3389/fgene.2017.00085 · External reference
Large-scale metabolic models: From reconstruction to differential equations
10.1089/ind.2013.0003 · 2013 · External reference
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SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks
10.1093/bioinformatics/btq679 · 2011 · External reference
Unresolved reference
2016 · External reference
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice
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Unresolved reference
2014 · External reference
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Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models
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Unresolved reference
External reference
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A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks
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Unresolved reference
2012 · External reference
Charlie–an extensible Petri net analysis tool
2015 · External reference
MARCIE–model checking and reachability analysis done efficiently
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