Volume 54, Issue D1, 6 January 2026

View issue

MAJOR MULTI-DATABASE RESOURCES

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025

Matthew Thakur and others

Database resources of the National Center for Biotechnology Information in 2026

Eric W Sayers and others

Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2026

NUCLEIC ACID SEQUENCE, STRUCTURE AND REGULATION

ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse

Qiao-Li Fang and others

CircleBase V2: an eccDNA annotation platform across cancers and species

Ling Wei and others

CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration

Si-Nan Zhai and others

CircTarget: a comprehensive database of circRNA'target RNA interactions across multiple cell types

Hongmei Zhang and others

CisBP-RNA: a web resource for eukaryotic RNA-binding proteins and their motifs

Diego A Rosado-Tristani and others

DDBJ update in 2025: system integration for global data-sharing including pathogen surveillance

Takeshi Ara and others

ENSURE: the encyclopedia of suppressor tRNA with an AI assistant

Zhuo Ouyang and others

EVmiRNA2.0: an updated database for miRNA expression in comprehensive human extracellular vesicles

Gui-Yan Xie and others

exoRBase 3.0: an updated resource for extracellular RNAs from human biofluids

Wenqian Yu and others

Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration

Pedro Madrigal and others

GlycoRNAdb: a database of glycoRNA sequences, structures, abundance, and glycan information across tissues and cell lines

Chuxin Zheng and others

groov^DB in 2026: a community-editable database of small molecule biosensors

Joshua D Love and others

Human-scATAC-Corpus: a comprehensive database of scATAC-seq data

Xiaoyang Chen and others

JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models

Damla Ovek Baydar and others

LnCeVar 2.0: an updated resource and web tools for genomic variations disrupting ceRNA networks from single-cell/spatial transcriptomics data

Qiuyan Guo and others

m6AConquer: a consistently quantified and orthogonally validated database for the N⁶-methyladenosine (m⁶A) epitranscriptome

Xichen Zhao and others

PROTEIN SEQUENCE AND STRUCTURE, MOTIFS AND DOMAINS

AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage

Damian Bertoni and others

APD6: the antimicrobial peptide database is expanded to promote research and development by deploying an unprecedented information pipeline

Guangshun Wang and others

CD-CODE 2.0: an enhanced condensate knowledgebase integrating pathobiology, condensate modulating drugs, and host'pathogen interactions

Ksenia Kuznetsova and others

DisProt in 2026: enhancing intrinsically disordered proteins accessibility, deposition, and annotation

Maria Victoria Nugnes and others

DynaRepo: the repository of macromolecular conformational dynamics

Omid Mokhtari and others

eggNOG v7: phylogeny-based orthology predictions and functional annotations

Ana HernÃ¡ndez-Plaza and others

FireProt^DB 2.0: large-scale manually curated database of the protein stability data

Milos Musil and others

GeneFamily: a comprehensive mammalian gene family database with extensive annotation and interactive visualization

Yinan Wang and others

Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale

Mario Picciani and others

METABOLIC AND SIGNALLING PATHWAYS, ENZYMES

BRENDA in 2026: a Global Core Biodata Resource for functional enzyme and metabolic data within the DSMZ Digital Diversity

Julia Hauenstein and others

CCCdb: a comprehensive manually curated database for cell'cell communication in human and mouse

Mingcong Xu and others

connectomeDB2025: a rigorously curated, multi-species resource of experimentally supported ligand'receptor interactions

Peiwen Liu and others

dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations

Yuchen Yan and others

Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence'function relationships across protein engineering campaigns

Yueming Long and others

FerrDb V3: expanding the manually curated resource for regulators and disease associations from ferroptosis to regulated cell death

Nan Zhou and others

GotEnzymes2: expanding coverage of enzyme kinetics and thermal properties

Bingxue Lyu and others

IID 2025: Physical protein interaction data with detection types, co-purified protein sets, molecular docking, and immune cell networks

Max Kotlyar and others

MassBank: an open and FAIR mass spectral data resource

Steffen Neumann and others

MetabFlow: a comprehensive metabolic map for exogenous natural products

Sisi Zhu and others

MetaNetX: a bridge between metabolic resources for enhanced curation and multi-omics data harmonization

SÃ©bastien Moretti and others

MiMeDB 2.0: the Human Microbial Metabolome Database for 2026

Ray Kruger and others

VIRUSES, BACTERIA, PROTOZOA AND FUNGI

AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance

Louise T Cerdeira and others

ARKbase: Antimicrobial Resistance Knowledgebase^1.0

Simran Gambhir and others

BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration

Maulik Shukla and others

gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research

Yan Sun and others

GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis

Can Liu and others

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes

Donovan H Parks and others

gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms

Kai Qian and others

HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data

Zhaoyu Zhai and others

IVCDB: a comprehensive database of iridoviruses for epidemiology, genetic evolution, and disease management

Mincong Liang and others

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Mateus B Fiamenghi and others

Metalog: curated and harmonised contextual data for global metagenomics samples

Michael Kuhn and others

metaTraits: a large-scale integration of microbial phenotypic trait information

Daniel Podlesny and others

MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses

Xikang Feng and others

HUMAN GENOME, MODEL ORGANISMS, COMPARATIVE GENOMICS

ASTRA: a comprehensive resource of stress-induced transcriptional activity in human cell lines

Margaritis Tsifintaris and others

Bovine Genome Database: new curated collection of selective sweeps in bovine populations across the world

Sumaya Kambal and others

CellSNVReg: a multidimensional resource for SNV-mediated regulatory perturbations in single-cell and spatial omics

Jingyi Shi and others

ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomics

Min Chen and others

CRESTA: a comprehensive transcriptome atlas for cellular response to external stressors

Hongge Wang and others

DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments

Vladyslav Honcharuk and others

DOO: integrated multi-omics resources for deep ocean organisms

Jiajie She and others

enhancer3D: 3D chromatin structures and enhancer-promoter distance profiles for archaic and modern human genomes

Michal Wlasnowolski and others

Ensembl 2026

Andrew D Yates and others

EWAS Open Platform 2026: a deeply integrated resource for epigenome-wide association studies

Fei Yang and others

Gene4Denovo2: an updated platform for human de novo mutations discovery and interpretation

Zhaopo Zhu and others

GPSAdb 2.0: an expanded atlas of gene-perturbation transcriptomes with enhanced tools for regulatory gene discovery

Shipeng Guo and others

HapScoreDB: a database of protein language model functional scores for haplotype-resolved protein sequences

Fabio Mazza and others

Genenames.org: the HGNC and PGNC resources in 2026

Ruth L Seal and others

iFish: a comprehensive multi-omics database for fish genetics, transcriptional regulation, and epigenetic research

Ruoyan Liu and others

IMGT® at scale: FAIR, dynamic, and automated tools for immune locus analysis

Gaoussou Sanou and others

International Mouse Phenotyping Consortium Portal: facilitating investigation of gene function and providing insights into human disease

Robert Wilson and others

InsectBase 3.0: a comprehensive multi-omics resource for insects

Zuoqi Wang and others

JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes

Masao Nagasaki and others

KnockRBP: an integrated multi-omics database of functional perturbation profiles for RNA-binding proteins

Mengyuan Yang and others

Charting the expression landscape of human long non-coding RNAs across diverse biological contexts with LncExpDB 2.0

Yue Qi and others

Genome Variation Map: a platform for the analysis and integration of genomic variation

Xue Bai and others

RNAPaceDB: a dedicated database to dissect RNA velocity across diverse cell types

Hui Liu and others

GENOMIC VARIATION, DISEASES AND DRUGS

African Natural Products Database (ANPDB): A resource for exploring the therapeutic potential of natural compounds from Africa

Jude Y Betow and others

CellMiner cross-database (CellMinerCDB) version 2.2 for explorations of patient-derived cancer cell line pharmacogenomics

Fathi Elloumi and others

ClinMAVE: a curated database for clinical application of data from multiplexed assays of variant effect

Chenyu Ma and others

CNAScope: pan-cancer copy number aberration database with functional annotation and interactive visualization

Xikang Feng and others

DisCP-Atlas: a comprehensive resource mapping cellular processes to complex diseases

Frank Qingyun Wang and others

DRESIS 2.0: the comprehensive landscape of drug resistance information

Xiuna Sun and others

EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment

Ashenafi Legehar and others

FAVOR 2.0: A reengineered functional annotation of variants online resource for interpreting genomic variation

Hufeng Zhou and others

GENEasso: a curated resource of credible disease'gene associations across complex diseases from GWAS summary statistics

Tao Jiang and others

M6AREG 2.0: the landscape of m⁶A-centered crosstalk with diverse epigenetic regulation

Mengjie Yang and others

Macrocycle-DB: a comprehensive database for macrocycle-based drug discovery

Minchuan Jiang and others

Medicines, Diseases, Indications, and Contraindications (MeDIC): a foundational resource to support drug repurposing

Marcello DeLuca and others

MGDB: a curated database for molecular glues

Chenxin Li and others

MGTbind: a comprehensive database of molecular glue ternary interactome

Jintao Zhu and others

PLANTS

GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana

Motomu Endo and others

Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research

Andrew Olson and others

metagRoot: a comprehensive database of protein families associated with plant root microbiomes

Maria N Chasapi and others

MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops

OTHER DATABASES

BioSamples database: the global hub for sample metadata and multi-omics integration

Dipayan Gupta and others

ChEBI: re-engineered for a sustainable future

Adnan Malik and others

MediaAssist: database to support the design and optimization of cell culture medium

Kalyani Thakar and others

CORRECTIONS

Correction to "PersADE: a database of personalized adverse drug events and their underlying molecular mechanisms"

Correction to ˜GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes'

Correction to ˜CellMiner cross-database (CellMinerCDB) version 2.2 for explorations of patient-derived cancer cell line pharmacogenomics'

There are more items than can be listed in this email. You may view the full list on Oxford Academic.

View search results

This email is intended for bionet@evol.mcmaster.ca.