Related literature

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Full list

Please add your reference here when adding it as a new post.
This will allow us to track them per theme and eventually to check if read or not, etc.

Previous works:

• The landscape of natural product diversity and their pharmacological relevance from a focus on the Dictionary of Natural Products®
• Predicting medicinal resources in Ranunculaceae family by a combined approach using DNA barcodes and chemical metabolites

Biodiversity:

• The number of tree species on Earth

Phylogeny:

• Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant ‘tree of life’
• Comparative analysis of four medicinal floras: Phylogenetic methods to identify cross-cultural patterns
• Phylogenies reveal predictive power of traditional medicine in bioprospecting
• How to measure and test phylogenetic signal
• Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae
• Global plant diversity as a reservoir of
  micronutrients for humanity

Bayesian approaches and related probabilistic frameworks:

• Bayesian Algorithm for Retrosynthesis
• Bayesian molecular design with a chemical language model
• A Bayesian Approach to Incorporating Spatiotemporal Variation and Uncertainty Limits into Modeling of Predicted Environmental Concentrations from Chemical Monitoring Campaigns
• A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
• Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data
• A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny
• The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
• Bayesian analytical approaches for metabolomics

Machine Learning and Natural Products:

• Machine learning discovery of missing links that mediate alternative branches to plant alkaloids
• Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience

Graphs:

• Learning to Predict Graphs with Fused Gromov-Wasserstein

In silico LC-MS:

• ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics

Quantitative NP:

• Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics

Varia:

• CACONET: a novel classification framework for microbial correlation networks

[oolonek]

The landscape of natural product diversity and their pharmacological relevance from a focus on the Dictionary of Natural Products®

https://doi.org/10.1007/s11101-019-09606-2

An analysis of the composition of the commercial DNP

[Adafede]

The number of tree species on Earth

https://doi.org/10.1073/pnas.2115329119

TODO add summary

[Adafede]

Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant ‘tree of life’

https://doi.org/10.1093/nsr/nwaa105

TODO add summary

[Adafede]

Comparative analysis of four medicinal floras: Phylogenetic methods to identify cross-cultural patterns

https://doi.org/10.1002/ppp3.10131

TODO add summary

[Adafede]

Phylogenies reveal predictive power of traditional medicine in bioprospecting

https://doi.org/10.1073/pnas.1202242109

TODO add summary

[Adafede]

How to measure and test phylogenetic signal

https://doi.org/10.1111/j.2041-210X.2012.00196.x

TODO add summary

[Adafede]

Learning to Predict Graphs with Fused Gromov-Wasserstein

Barycenters

https://arxiv.org/abs/2202.03813

TODO add summary

[Adafede]

CACONET: a novel classification framework for microbial correlation networks

https://doi.org/10.1093/bioinformatics/btab879

TODO add summary

[oolonek]

Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

https://doi.org/10.1093/sysbio/syu006

TODO add summary

[oolonek]

A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny

https://doi.org/10.1371/journal.pcbi.1000868

[oolonek]

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

https://doi.org/10.1093/sysbio/syp017

[oolonek]

Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of amaryllidaceae

https://doi.org/10.1186/1471-2148-12-182

[oolonek]

Bayesian analytical approaches for metabolomics

A PhD thesis, not exactly our goals but some aligned interests
https://ir.library.louisville.edu/cgi/viewcontent.cgi?article=4211&context=etd

[Adafede]

Global plant diversity as a reservoir of micronutrients for humanity

https://doi.org/10.1038/s41477-022-01100-6

TODO add summary

[Adafede]

Machine learning discovery of missing links that mediate alternative branches to plant alkaloids

https://doi.org/10.1038/s41467-022-28883-8

TODO add summary

[oolonek]

Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.18095

Summary
●Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments.
●Here, we combined multi-species ecological metabolomics and machine learning-based generalised linear model predictions to link the metabolome to the plant environment in a set of 24 species and belonging to 14 families growing along an altitudinal gradient in the Atacama Desert.
●Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors like freezing temperature, water deficit and high solar irradiance.
●These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.

[Adafede]

ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics

https://joss.theoj.org/papers/10.21105/joss.03990

[Adafede]

Predicting medicinal resources in Ranunculaceae family by a combined approach using DNA barcodes and chemical metabolites

https://doi.org/10.1016/j.phytol.2022.04.009

[oolonek]

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

https://doi.org/10.1186/1471-2105-5-76

[oolonek]

A Bayesian Approach to Incorporating Spatiotemporal Variation and Uncertainty Limits into Modeling of Predicted Environmental Concentrations from Chemical Monitoring Campaigns

https://doi.org/10.1021/acs.est.0c06268

[oolonek]

Bayesian Algorithm for Retrosynthesis

https://doi.org/10.1021/acs.jcim.0c00320

[oolonek]

Bayesian molecular design with a chemical language model

https://doi.org/10.1007/s10822-016-0008-z

[Adafede]

Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics

https://doi.org/10.1021/acs.jcim.2c01459

[oolonek]

Global probabilistic annotation of metabolic networks enables enzyme discovery

https://www.nature.com/articles/nchembio.1063

[oolonek]

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

https://www.nature.com/articles/nrmicro2737

[oolonek]

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data

https://doi.org/10.1371/journal.pone.0009293