Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products
Covering: 1995 to 2023Advances in bioanalytical methods, particularly mass spectrometry,
have provided valuable molecular insights into the mechanisms of life. Non-targeted …
have provided valuable molecular insights into the mechanisms of life. Non-targeted …
Computational methods for processing and interpreting mass spectrometry-based metabolomics
Metabolomics has emerged as an indispensable tool for exploring complex biological
questions, providing the ability to investigate a substantial portion of the metabolome …
questions, providing the ability to investigate a substantial portion of the metabolome …
Scientists' Perspectives on the Potential for Generative AI in their Fields
MR Morris - arxiv preprint arxiv:2304.01420, 2023 - arxiv.org
Generative AI models, including large language models and multimodal models that include
text and other media, are on the cusp of transforming many aspects of modern life, including …
text and other media, are on the cusp of transforming many aspects of modern life, including …
Prefix-tree decoding for predicting mass spectra from molecules
Computational predictions of mass spectra from molecules have enabled the discovery of
clinically relevant metabolites. However, such predictive tools are still limited as they occupy …
clinically relevant metabolites. However, such predictive tools are still limited as they occupy …
Tandem mass spectrum prediction for small molecules using graph transformers
Tandem mass spectra capture fragmentation patterns that provide key structural information
about molecules. Although mass spectrometry is applied in many areas, the vast majority of …
about molecules. Although mass spectrometry is applied in many areas, the vast majority of …
Generating molecular fragmentation graphs with autoregressive neural networks
The accurate prediction of tandem mass spectra from molecular structures has the potential
to unlock new metabolomic discoveries by augmenting the community's libraries of …
to unlock new metabolomic discoveries by augmenting the community's libraries of …
MIST-CF: Chemical formula inference from tandem mass spectra
Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step
toward structurally elucidating unknown metabolites. While great strides have been made …
toward structurally elucidating unknown metabolites. While great strides have been made …
Differentiable modeling and optimization of non-aqueous Li-based battery electrolyte solutions using geometric deep learning
Electrolytes play a critical role in designing next-generation battery systems, by allowing
efficient ion transfer, preventing charge transfer, and stabilizing electrode-electrolyte …
efficient ion transfer, preventing charge transfer, and stabilizing electrode-electrolyte …
Spiers Memorial Lecture: How to do impactful research in artificial intelligence for chemistry and materials science
Machine learning has been pervasively touching many fields of science. Chemistry and
materials science are no exception. While machine learning has been making a great …
materials science are no exception. While machine learning has been making a great …
An Ensemble Spectral Prediction (ESP) model for metabolite annotation
Motivation A key challenge in metabolomics is annotating measured spectra from a
biological sample with chemical identities. Currently, only a small fraction of measurements …
biological sample with chemical identities. Currently, only a small fraction of measurements …