Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research

JL Baker - FEMS Microbiology Reviews, 2023 - academic.oup.com
The oral microbiota has an enormous impact on human health, with oral dysbiosis now
linked to many oral and systemic diseases. Recent advancements in sequencing, mass …

Computational approaches to enzyme inhibition by marine natural products in the search for new drugs

F Gago - Marine Drugs, 2023 - mdpi.com
The exploration of biologically relevant chemical space for the discovery of small bioactive
molecules present in marine organisms has led not only to important advances in certain …

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

DJ Rigden, XM Fernández - Nucleic Acids Research, 2023 - academic.oup.com
Abstract The 2023 Nucleic Acids Research Database Issue contains 178 papers ranging
across biology and related fields. There are 90 papers reporting on new databases and 82 …

[HTML][HTML] Antifungal activity of Lactiplantibacillus plantarum isolated from fruit and vegetables and detection of novel antifungal VOCs from fungal-LAB co-cultures

N De Simone, L López, CS Ciudad, A Scauro, P Russo… - Food Bioscience, 2024 - Elsevier
Undesired microbiota, such as filamentous fungi, negatively impacts the food sector leading
to huge losses of food produce. For this reason, preservatives are often used to reduce …

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

BE Santangelo, M Apgar, ASB Colorado… - Frontiers in …, 2024 - frontiersin.org
Advances in high-throughput technologies have enhanced our ability to describe microbial
communities as they relate to human health and disease. Alongside the growth in …

The Natural Products Magnetic Resonance Database (NP-MRD) for 2025

DS Wishart, T Sajed, M Pin, EF Poynton… - Nucleic Acids …, 2025 - academic.oup.com
Abstract The Natural Products Magnetic Resonance Database (NP-MRD; https://np-mrd.
org) is a comprehensive, freely accessible, web-based resource for the deposition …

Mining patents with large language models demonstrates congruence of functional labels and chemical structures

CW Kosonocky, CO Wilke, EM Marcotte… - arxiv preprint arxiv …, 2023 - arxiv.org
Predicting chemical function from structure is a major goal of the chemical sciences, from the
discovery and repurposing of novel drugs to the creation of new materials. Recently, new …

Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey

Q Pei, L Wu, K Gao, J Zhu, Y Wang, Z Wang… - arxiv preprint arxiv …, 2024 - arxiv.org
The integration of biomolecular modeling with natural language (BL) has emerged as a
promising interdisciplinary area at the intersection of artificial intelligence, chemistry and …

Promises and Perils of Big Data: Philosophical Constraints on Chemical Ontologies

R Duke, R McCoy, C Risko… - Journal of the American …, 2024 - ACS Publications
Chemistry is experiencing a paradigm shift in the way it interacts with data. So-called “big
data” are collected and used at unprecedented scales with the idea that algorithms can be …

Mining patents with large language models elucidates the chemical function landscape

CW Kosonocky, CO Wilke, EM Marcotte… - Digital Discovery, 2024 - pubs.rsc.org
The fundamental goal of small molecule discovery is to generate chemicals with target
functionality. While this often proceeds through structure-based methods, we set out to …