UniProt: the universal protein knowledgebase in 2023

Nucleic acids research, 2023 - academic.oup.com
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-
quality and freely accessible set of protein sequences annotated with functional information …

A survey on the algorithm and development of multiple sequence alignment

Y Zhang, Q Zhang, J Zhou, Q Zou - Briefings in bioinformatics, 2022 - academic.oup.com
Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can
reveal the potential information in biological sequences, such as function, evolution and …

The 2022 Nucleic Acids Research database issue and the online molecular biology database collection

DJ Rigden, XM Fernández - Nucleic acids research, 2022 - academic.oup.com
Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including
87 papers reporting on new databases and 85 updates from resources previously published …

CROST: a comprehensive repository of spatial transcriptomics

G Wang, S Wu, Z **ong, H Qu, X Fang… - Nucleic Acids …, 2024 - academic.oup.com
The development of spatial transcriptome sequencing technology has revolutionized our
comprehension of complex tissues and propelled life and health sciences into an era of …

[HTML][HTML] Methods in DNA methylation array dataset analysis: A review

K Sahoo, V Sundararajan - Computational and Structural Biotechnology …, 2024 - Elsevier
Understanding the intricate relationships between gene expression levels and epigenetic
modifications in a genome is crucial to comprehending the pathogenic mechanisms of many …

2022 updates to the rat genome database: a findable, accessible, interoperable, and reusable (FAIR) resource

M Vedi, JR Smith, G Thomas Hayman, M Tutaj… - Genetics, 2023 - academic.oup.com
Abstract The Rat Genome Database (RGD, https://rgd. mcw. edu) has evolved from simply a
resource for rat genetic markers, maps, and genes, by adding multiple genomic data types …

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

A Fernández-Torras, M Duran-Frigola, M Bertoni… - Nature …, 2022 - nature.com
Biomedical data is accumulating at a fast pace and integrating it into a unified framework is a
major challenge, so that multiple views of a given biological event can be considered …

gutMDisorder v2. 0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions

C Qi, Y Cai, K Qian, X Li, J Ren, P Wang… - Nucleic acids …, 2023 - academic.oup.com
Gut microbiota plays a significant role in maintaining host health, and conversely, disorders
potentially lead to dysbiosis, an imbalance in the composition of the gut microbial …

AGIDB: a versatile database for genotype imputation and variant decoding across species

K Zhang, J Liang, Y Fu, J Chu, L Fu… - Nucleic Acids …, 2024 - academic.oup.com
The high cost of large-scale, high-coverage whole-genome sequencing has limited its
application in genomics and genetics research. The common approach has been to impute …

An ontology-based knowledge graph for representing interactions involving RNA molecules

E Cavalleri, A Cabri, M Soto-Gomez, S Bonfitto… - Scientific Data, 2024 - nature.com
The “RNA world” represents a novel frontier for the study of fundamental biological
processes and human diseases and is paving the way for the development of new drugs …