Transformer technology in molecular science

J Jiang, L Ke, L Chen, B Dou, Y Zhu… - Wiley …, 2024 - Wiley Online Library
A transformer is the foundational architecture behind large language models designed to
handle sequential data by using mechanisms of self‐attention to weigh the importance of …

[HTML][HTML] Liquid chromatography–mass spectrometry-based metabolomics approaches for foodomics research

T Cajka - Current Opinion in Food Science, 2024 - Elsevier
Highlights•LC-MS-based metabolomics approaches for foodomics studies•Sample
preparation of diverse sample types and a multiplatform LC-MS-based approach•Data …

Tandem mass spectrum prediction for small molecules using graph transformers

A Young, H Röst, B Wang - Nature Machine Intelligence, 2024 - nature.com
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 …

Computational methods for processing and interpreting mass spectrometry-based metabolomics

L Perez de Souza, AR Fernie - Essays in Biochemistry, 2024 - portlandpress.com
Metabolomics has emerged as an indispensable tool for exploring complex biological
questions, providing the ability to investigate a substantial portion of the metabolome …

Natural Product Synthesis in the 21st Century: Beyond the Mountain Top

RA Shenvi - ACS Central Science, 2024 - ACS Publications
Research into natural products emerged from humanity's curiosity about the nature of matter
and its role in the materia medica of diverse civilizations. Plants and fungi, in particular …

MassSpecGym: A benchmark for the discovery and identification of molecules

R Bushuiev, A Bushuiev, NF de Jonge, A Young… - arXiv preprint arXiv …, 2024 - arxiv.org
The discovery and identification of molecules in biological and environmental samples is
crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry …

Jestr: Joint embedding space technique for ranking candidate molecules for the annotation of untargeted metabolomics data

A Kalia, D Krishnan, S Hassoun - arXiv preprint arXiv:2411.14464, 2024 - arxiv.org
Motivation: A major challenge in metabolomics is annotation: assigning molecular structures
to mass spectral fragmentation patterns. Despite recent advances in molecule-to-spectra …

Critical review on in silico methods for structural annotation of chemicals detected with LC/HRMS non-targeted screening

H Hupatz, I Rahu, WC Wang, P Peets, EH Palm… - Analytical and …, 2024 - Springer
Non-targeted screening with liquid chromatography coupled to high-resolution mass
spectrometry (LC/HRMS) is increasingly leveraging in silico methods, including machine …

From multi-omics to predictive biomarker: AI in tumor microenvironment

L Hai, Z Jiang, H Zhang, Y Sun - Frontiers in Immunology, 2024 - frontiersin.org
In recent years, tumors have emerged as a major global health threat. An increasing number
of studies indicate that the production, development, metastasis, and elimination of tumor …

基于质谱的未知次生代谢物结构解析研究进展与展望.

纪宏超, 李正艳 - Biotechnology Bulletin, 2024 - search.ebscohost.com
次生代谢产物研究对于植物生长发育, 环境适应以及人类健康和药物研发具有重要意义.
液相色谱-质谱联用平台(LC-MS) 已成为次生代谢研究的首选策略. 然而, 代谢物结构解析仍受限 …