Subject: Nucleic Acids Research Table of Contents for 6 January 2025 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
NAR Invites Submissions for the 2025 Web Server Issue
 

In July of each year, NAR devotes a single issue to papers describing web-based software resources of value to the biological community. This issue focuses on web servers offering computations for DNA, RNA, and protein sequences, high-throughput sequencing data, and biological network analysis, and includes a special section for Web Services. The deadline for submitting your proposal is 20th December. 

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Nucleic Acids Research  
Volume 53 Issue D1
 
6 January 2025
 
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EDITORIAL
 
 
 
 
The 2025 Nucleic Acids Research database issue and the online molecular biology database collection border= 
 
Daniel J Rigden, Xosé M Fernández
 
 
 
MAJOR MULTI-DATABASE RESOURCES
 
 
 
 
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024 border= 
 
Matthew Thakur, Catherine Brooksbank, Robert D Finn, Helen V Firth, Julia Foreman ...
 
 
 
Database resources of the National Center for Biotechnology Information in 2025 
 
Eric W Sayers, Jeffrey Beck, Evan E Bolton, J Rodney Brister, Jessica Chan ...
 
 
 
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025 border= 
 
Yiming Bao, Xue Bai, Congfan Bu, Haobin Chen, Huanxin Chen ...
 
 
 
DDBJ update in 2024: the DDBJ Group Cloud service for sharing pre-publication data border= 
 
Yuichi Kodama, Takeshi Ara, Asami Fukuda, Toshiaki Tokimatsu, Jun Mashima ...
 
 
 
 
The European Nucleotide Archive in 2024 border= 
 
Colman O'Cathail, Alisha Ahamed, Josephine Burgin, Carla Cummins, Rajkumar Devaraj ...
 
 
 
GenBank 2025 update 
 
Eric W Sayers, Mark Cavanaugh, Linda Frisse, Kim D Pruitt, Valerie A Schneider ...
 
 
 
The international nucleotide sequence database collaboration (INSDC): enhancing global participation 
 
Ilene Karsch-Mizrachi, Masanori Arita, Tony Burdett, Guy Cochrane, Yasukazu Nakamura ...
 
 
 
NUCLEIC ACID SEQUENCE, STRUCTURE AND REGULATION
 
 
 
 
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species border= 
 
Xingchen Zhu, Xiao Han, Zhijin Li, Xiaobo Zhou, Seung-Hee Yoo ...
 
 
 
EXPRESSO: a multi-omics database to explore multi-layered 3D genomic organization border= 
 
Liuyang Cai, Jun Qiao, Ruixin Zhou, Xinyi Wang, Yelan Li ...
 
 
 
 
G4LDB 3.0: a database for discovering and studying G-quadruplex and i-motif ligands border= 
 
Qian-Fan Yang, Xu-Rui Wang, Yu-Huan Wang, Xing-Hong Wu, Run-Yu Shi ...
 
 
 
iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets border= 
 
Edward A Catoiu, Jayanth Krishnan, Gaoyuan Li, Xuwen A Lou, Kevin Rychel ...
 
 
 
LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data border= 
 
Qiuyan Guo, Qian Liu, Danni He, Mengyu Xin, Yifan Dai ...
 
 
 
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models border= 
 
Alexander W Clarke, Eirik Høye, Anju Angelina Hembrom, Vanessa Molin Paynter, Jakob Vinther ...
 
 
 
miRNATissueAtlas 2025: an update to the uniformly processed and annotated human and mouse non-coding RNA tissue atlas border= 
 
Shusruto Rishik, Pascal Hirsch, Friederike Grandke, Tobias Fehlmann, Andreas Keller
 
 
 
miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification border= 
 
Jiatong Xu, Jingting Wan, Hsi-Yuan Huang, Yigang Chen, Yixian Huang ...
 
 
 
miRTarBase 2025: updates to the collection of experimentally validated microRNA'target interactions border= 
 
Shidong Cui, Sicong Yu, Hsi-Yuan Huang, Yang-Chi-Dung Lin, Yixian Huang ...
 
 
 
NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids border= 
 
Elsa Balduzzi, Frédéric Geinguenaud, Dominik Sordyl, Satyabrata Maiti, Masoud Amiri Farsani ...
 
 
 
oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements border= 
 
Guitian Liu, Xiaobin Li, Jiahao Guan, Cui Tai, Yuqing Weng ...
 
 
 
PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes border= 
 
Qianhui Zhu, Qi Chen, Shenghan Gao, Zhenpeng Li, Haijian Zhou ...
 
 
 
PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools border= 
 
Yinhu Li, Xikang Feng, Xuhua Chen, Shuo Yang, Zicheng Zhao ...
 
 
 
The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research border= 
 
Leidy-Alejandra G Molano, Pascal Hirsch, Matthias Hannig, Rolf Müller, Andreas Keller
 
 
 
PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data border= 
 
Youngbin Moon, Christina J Herrmann, Aleksei Mironov, Mihaela Zavolan
 
 
 
qPrimerDB 2.0: an updated comprehensive gene-specific qPCR primer database for 1172 organisms border= 
 
Xiaodong Li, Boyu Meng, Zhi Zhang, Lijuan Wei, Wei Chang ...
 
 
 
RASP v2.0: an updated atlas for RNA structure probing data border=  
 
Kunting Mu, Yuhan Fei, Yiran Xu, Qiangfeng Cliff Zhang
 
 
 
RBPWorld for exploring functions and disease associations of RNA-binding proteins across species border= 
 
Jian-You Liao, Bing Yang, Chuan-Ping Shi, Wei-Xi Deng, Jin-Si Deng ...
 
 
 
REDIportal: toward an integrated view of the A-to-I editing border=  
 
Pietro D'Addabbo, Roni Cohen-Fultheim, Itamar Twersky, Adriano Fonzino, Domenico Alessandro Silvestris ...
 
 
 
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation 
 
Tamara Goldfarb, Vamsi K Kodali, Shashikant Pujar, Vyacheslav Brover, Barbara Robbertse ...
 
 
 
Rfam 15: RNA families database in 2025 border=  
 
Nancy Ontiveros-Palacios, Emma Cooke, Eric P Nawrocki, Sandra Triebel, Manja Marz ...
 
 
 
RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization border= 
 
Jack A S Tierney, MichaÅ‚ I Åšwirski, Håkon Tjeldnes, Anmol M Kiran, Gionmattia Carancini ...
 
 
 
RMVar 2.0: an updated database of functional variants in RNA modifications border=  
 
Yuantai Huang, Luowanyue Zhang, Weiping Mu, Mohan Zheng, Xiaoqiong Bao ...
 
 
 
RNALocate v3.0: Advancing the Repository of RNA Subcellular Localization with Dynamic Analysis and Prediction border= 
 
Le Wu, Luqi Wang, Shijie Hu, Guangjue Tang, Jia Chen ...
 
 
 
RPFdb v3.0: an enhanced repository for ribosome profiling data and related content border= 
 
Yan Wang, Yuewen Tang, Zhi Xie, Hongwei Wang
 
 
 
RPS 2.0: an updated database of RNAs involved in liquid'liquid phase separation border= 
 
Yongxin He, Xiaoqiong Bao, Tianjian Chen, Qi Jiang, Luowanyue Zhang ...
 
 
 
Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites border= 
 
Etienne Boileau, Harald Wilhelmi, Anne Busch, Andrea Cappannini, Andreas Hildebrand ...
 
 
 
TransmiR v3.0: an updated transcription factor-microRNA regulation database border=  
 
Maodi Liang, Chenhao Zhang, Yang Yang, Qinghua Cui, Jun Zhang ...
 
 
 
VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers border= 
 
Michael Kosicki, Fotis A Baltoumas, Guy Kelman, Joshua Boverhof, Yeongshnn Ong ...
 
 
 
PROTEIN SEQUENCE AND STRUCTURE, MOTIFS AND DOMAINS
 
 
 
 
ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures border= 
 
Yuntao Yang, Himansu Kumar, Yuhan Xie, Zhao Li, Rongbin Li ...
 
 
 
BFVD'a large repository of predicted viral protein structures border=  
 
Rachel Seongeun Kim, Eli Levy Karin, Milot Mirdita, Rayan Chikhi, Martin Steinegger
 
 
 
CATH v4.4: major expansion of CATH by experimental and predicted structural data border= 
 
Vaishali P Waman, Nicola Bordin, Andy Lau, Shaun Kandathil, Jude Wells ...
 
 
 
COG database update 2024 
 
Michael Y Galperin, Roberto Vera Alvarez, Svetlana Karamycheva, Kira S Makarova, Yuri I Wolf ...
 
 
 
dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era border= 
 
Lantian Yao, Jiahui Guan, Peilin Xie, Chia-Ru Chung, Zhihao Zhao ...
 
 
 
dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research border= 
 
Chia-Ru Chung, Yun Tang, Yen-Peng Chiu, Shangfu Li, Wen-Kai Hsieh ...
 
 
 
DIONYSUS: a database of protein'carbohydrate interfaces border=  
 
Aria Gheeraert, Thomas Bailly, Yani Ren, Ali Hamraoui, Julie Te ...
 
 
 
DNAproDB: an updated database for the automated and interactive analysis of protein'DNA complexes border= 
 
Raktim Mitra, Ari S Cohen, Jared M Sagendorf, Helen M Berman, Remo Rohs
 
 
 
DRAMP 4.0: an open-access data repository dedicated to the clinical translation of antimicrobial peptides border= 
 
Tianyue Ma, Yanchao Liu, Bingxin Yu, Xin Sun, Huiyuan Yao ...
 
 
 
ECOD: integrating classifications of protein domains from experimental and predicted structures border= 
 
R Dustin Schaeffer, Kirill E Medvedev, Antonina Andreeva, Sara Rocio Chuguransky, Beatriz Lazaro Pinto ...
 
 
 
Update of the FANTOM web resource: enhancement for studying noncoding genomes border= 
 
Tomoe Nobusada, Chi Wai Yip, Saumya Agrawal, Jessica Severin, Imad Abugessaisa ...
 
 
 
GPCRdb in 2025: adding odorant receptors, data mapper, structure similarity search and models of physiological ligand complexes border= 
 
Luis P Taracena Herrera, Søren N Andreassen, Jimmy Caroli, Ismael Rodríguez-Espigares, Ali A Kermani ...
 
 
 
The Immune Epitope Database (IEDB): 2024 update border=  
 
Randi Vita, Nina Blazeska, Daniel Marrama, Deborah Shackelford, Leora Zalman ...
 
 
 
InterPro: the protein sequence classification resource in 2025 border=  
 
Matthias Blum, Antonina Andreeva, Laise Cavalcanti Florentino, Sara Rocio Chuguransky, Tiago Grego ...
 
 
 
The 2024 IPD-MHC database update: a comprehensive resource for major histocompatibility complex studies border= 
 
Giuseppe Maccari, James Robinson, Dominic J Barker, Andrew D Yates, John A Hammond ...
 
 
 
jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data border= 
 
Shujiro Okuda, Akiyasu C Yoshizawa, Daiki Kobayashi, Yushi Takahashi, Yu Watanabe ...
 
 
 
LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNAs border= 
 
Xinyuan Zhou, Yanxia Qin, Jiangxue Li, Linyuan Fan, Shun Zhang ...
 
 
 
MDRepo'an open data warehouse for community-contributed molecular dynamics simulations of proteins border= 
 
Amitava Roy, Ethan Ward, Illyoung Choi, Michele Cosi, Tony Edgin ...
 
 
 
MFIB 2.0: a major update of the database of protein complexes formed by mutual folding of the constituting protein chains border= 
 
Erzsébet Fichó, Rita Pancsa, Csaba Magyar, Zsofia E Kalman, Éva Schád ...
 
 
 
MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins border= 
 
Damiano Piovesan, Alessio Del Conte, Mahta Mehdiabadi, Maria Cristina Aspromonte, Matthias Blum ...
 
 
 
OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft border= 
 
Yintao Zhang, Xichen Lian, Hangwei Xu, Sisi Zhu, Hao Zhang ...
 
 
 
OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes border= 
 
Fredrik Tegenfeldt, Dmitry Kuznetsov, Mosè Manni, Matthew Berkeley, Evgeny M Zdobnov ...
 
 
 
The Pfam protein families database: embracing AI/ML border=  
 
Typhaine Paysan-Lafosse, Antonina Andreeva, Matthias Blum, Sara Rocio Chuguransky, Tiago Grego ...
 
 
 
PLAbDab-nano: a database of camelid and shark nanobodies from patents and literature border= 
 
Gemma L Gordon, Alexander Greenshields-Watson, Parth Agarwal, Ashley Wong, Fergus Boyles ...
 
 
 
The PRIDE database at 20 years: 2025 update border=  
 
Yasset Perez-Riverol, Chakradhar Bandla, Deepti J Kundu, Selvakumar Kamatchinathan, Jingwen Bai ...
 
 
 
PTMD 2.0: an updated database of disease-associated post-translational modifications border= 
 
Xinhe Huang, Zihao Feng, Dan Liu, Yujie Gou, Miaomiao Chen ...
 
 
 
Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank border= 
 
Stephen K Burley, Rusham Bhatt, Charmi Bhikadiya, Chunxiao Bi, Alison Biester ...
 
 
 
RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB border= 
 
Damiano Clementel, Paula Nazarena Arrías, Soroush Mozaffari, Zarifa Osmanli, Ximena Aixa Castro ...
 
 
 
scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues border= 
 
Tiangang Wang, Xuanmin Chen, Yujuan Han, Jiahao Yi, Xi Liu ...
 
 
 
SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation border= 
 
Yanlin Li, Fengcheng Li, Zixin Duan, Ruihan Liu, Wantong Jiao ...
 
 
 
TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions border= 
 
Valerie Lin, Melyssa Cheung, Ragul Gowthaman, Maya Eisenberg, Brian M Baker ...
 
 
 
UniProt: the Universal Protein Knowledgebase in 2025 border=  
 
Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Aduragbemi Adesina ...
 
 
 
METABOLIC AND SIGNALLING PATHWAYS, ENZYMES
 
 
 
 
BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes border= 
 
Caner Bağcı, Matin Nuhamunada, Hemant Goyat, Casimir Ladanyi, Ludek Sehnal ...
 
 
 
CAZac: an activity descriptor for carbohydrate-active enzymes border=  
 
Vincent Lombard, Bernard Henrissat, Marie-Line Garron
 
 
 
COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database border= 
 
Venkata Chandrasekhar, Kohulan Rajan, Sri Ram Sagar Kanakam, Nisha Sharma, Viktor Weißenborn ...
 
 
 
Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes border= 
 
Sucharitha Balu, Susie Huget, Juan Jose Medina Reyes, Eliot Ragueneau, Kalpana Panneerselvam ...
 
 
 
CORUM in 2024: protein complexes as drug targets border=  
 
Ralph Steinkamp, George Tsitsiridis, Barbara Brauner, Corinna Montrone, Gisela Fobo ...
 
 
 
FunCoup 6: advancing functional association networks across species with directed links and improved user experience border= 
 
Davide Buzzao, Emma Persson, Dimitri Guala, Erik L L Sonnhammer
 
 
 
KEGG: biological systems database as a model of the real world border=  
 
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Yuriko Matsuura, Mari Ishiguro-Watanabe
 
 
 
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration border= 
 
Mitja M Zdouc, Kai Blin, Nico L L Louwen, Jorge Navarro, Catarina Loureiro ...
 
 
 
The Natural Products Atlas 3.0: extending the database of microbially derived natural products border= 
 
Ella F Poynton, Jeffrey A van Santen, Matthew Pin, Marla Macias Contreras, Emily McMann ...
 
 
 
The Natural Products Magnetic Resonance Database (NP-MRD) for 2025 border=  
 
David S Wishart, Tanvir Sajed, Matthew Pin, Ella F Poynton, Bharat Goel ...
 
 
 
RDBSB: a database for catalytic bioparts with experimental evidence border=  
 
Wan Liu, Pingping Wang, Xinhao Zhuang, Yunchao Ling, Haiyan Liu ...
 
 
 
The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters 
 
Daniel W Udwary, Drew T Doering, Bryce Foster, Tatyana Smirnova, Satria A Kautsar ...
 
 
 
StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization border= 
 
Yue Feng, Ammar Qaseem, Aurélien F A Moumbock, Shuling Pan, Pascal A Kirchner ...
 
 
 
The STRING database in 2025: protein networks with directionality of regulation border= 
 
Damian Szklarczyk, Katerina Nastou, Mikaela Koutrouli, Rebecca Kirsch, Farrokh Mehryary ...
 
 
 
SubCELL: the landscape of subcellular compartment-specific molecular interactions border= 
 
Yintao Zhang, Wanghao Jiang, Teng Li, Hangwei Xu, Yimiao Zhu ...
 
 
 
VIRUSES, BACTERIA, PROTOZOA AND FUNGI
 
 
 
 
BacDive in 2025: the core database for prokaryotic strain data border= 
 
Isabel Schober, Julia Koblitz, Joaquim Sardà Carbasse, Christian Ebeling, Marvin Leon Schmidt ...
 
 
 
EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens border= 
 
Nigel P Dyer, Birgitta Päuker, Laura Baxter, Anshul Gupta, Boyke Bunk ...
 
 
 
GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data border= 
 
Guomei Fan, Qinglan Sun, Yan Sun, Dongmei Liu, Shiwen Li ...
 
 
 
GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome border= 
 
Yiqi Jiang, Yanfei Wang, Lijia Che, Shuo Yang, Xianglilan Zhang ...
 
 
 
gutMGene v2.0: an updated comprehensive database for target genes of gut microbes and microbial metabolites border= 
 
Changlu Qi, Guoyou He, Kai Qian, Siyuan Guan, Zhaohai Li ...
 
 
 
MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights border= 
 
Yao Lu, Fiona Hui, Guangyan Zhou, Jianguo Xia
 
 
 
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities border= 
 
Marija Dmitrijeva, Hans-Joachim Ruscheweyh, Lilith Feer, Kang Li, Samuel Miravet-Verde ...
 
 
 
PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining border= 
 
Binhuan Sun, Liubov Pashkova, Pascal Aldo Pieters, Archana Sanjay Harke, Omkar Satyavan Mohite ...
 
 
 
PhageDive : the comprehensive strain database of prokaryotic viral diversity border= 
 
Clara Rolland, Johannes Wittmann, Lorenz C Reimer, Joaquim Sardà Carbasse, Isabel Schober ...
 
 
 
PHI-base ' the multi-species pathogen'host interaction database in 2025 border=  
 
Martin Urban, Alayne Cuzick, James Seager, Nagashree Nonavinakere, Jahobanta Sahoo ...
 
 
 
PneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae border= 
 
Axel B Janssen, Paddy S Gibson, Afonso M Bravo, Vincent de Bakker, Jelle Slager ...
 
 
 
ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel border= 
 
Zepu Miao, Yifan Ren, Andrea Tarabini, Ludong Yang, Huihui Li ...
 
 
 
A new framework for SubtiWiki, the database for the model organism Bacillus subtilis border= 
 
Christoph Elfmann, Vincenz Dumann, Tim van den Berg, Jörg Stülke
 
 
 
VFDB 2025: an integrated resource for exploring anti-virulence compounds border=  
 
Siyu Zhou, Bo Liu, Dandan Zheng, Lihong Chen, Jian Yang
 
 
 
HUMAN GENOME, MODEL ORGANISMS, COMPARATIVE GENOMICS
 
 
 
 
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools border= 
 
Frederic B Bastian, Alessandro Brandulas Cammarata, Sara Carsanaro, Harald Detering, Wan-Ting Huang ...
 
 
 
CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data border= 
 
Shibla Abdulla, Brian Aevermann, Pedro Assis, Seve Badajoz, Sidney M Bell ...
 
 
 
CRISPRepi: a multi-omic atlas for CRISPR-based epigenome editing border=  
 
Leisheng Shi, Shasha Li, Rongyi Zhu, Chenyang Lu, Xintian Xu ...
 
 
 
CRISPRoffT: comprehensive database of CRISPR/Cas off-targets border=  
 
Grant Wang, Xiaona Liu, Aoqi Wang, Jianguo Wen, Pora Kim ...
 
 
 
The evolution of dbSNP: 25 years of impact in genomic research 
 
Lon Phan, Hua Zhang, Qiang Wang, Ricardo Villamarin, Tim Hefferon ...
 
 
 
Rediscovering publicly available single-cell data with the DISCO platform border=  
 
Mengwei Li, Kok Siong Ang, Brian Teo, Uddamvathanak Rom, Minh N Nguyen ...
 
 
 
Dog10K: an integrated Dog10K database summarizing canine multi-omics border=  
 
Tong Zhou, Shao-Yan Pu, Shao-Jie Zhang, Qi-Jun Zhou, Min Zeng ...
 
 
 
Ensembl 2025 border= 
 
Sarah C Dyer, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes ...
 
 
 
FlyRNAi.org 2025 update'expanded resources for new technologies and species border=  
 
Yanhui Hu, Aram Comjean, Jonathan Rodiger, Weihang Chen, Ah-Ram Kim ...
 
 
 
GENCODE 2025: reference gene annotation for human and mouse border=  
 
Jonathan M Mudge, Sílvia Carbonell-Sala, Mark Diekhans, Jose Gonzalez Martinez, Toby Hunt ...
 
 
 
GoFCards: an integrated database and analytic platform for gain of function variants in humans border= 
 
Wenjing Zhao, Youfu Tao, Jiayi Xiong, Lei Liu, Zhongqing Wang ...
 
 
 
Genomes OnLine Database (GOLD) v.10: new features and updates 
 
Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Mahathi Kandimalla ...
 
 
 
The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity border= 
 
Maria Cerezo, Elliot Sollis, Yue Ji, Elizabeth Lewis, Ala Abid ...
 
 
 
GWAShug: a comprehensive platform for decoding the shared genetic basis between complex traits based on summary statistics border= 
 
Chen Cao, Min Tian, Zhenghui Li, Wenyan Zhu, Peng Huang ...
 
 
 
Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources border= 
 
Ido Diamant, Daniel J B Clarke, John Erol Evangelista, Nathania Lingam, Avi Ma'ayan
 
 
 
HSCGD: a comprehensive database of single-cell whole-genome data and metadata border= 
 
Jiye Fu, Shiyang He, Yixuan Yang, Zitong Chen, Yi Qiao ...
 
 
 
iDog: a multi-omics resource for canids study border=  
 
Yanhu Liu, Yibo Wang, Jiani Sun, Demian Kong, Bowen Zhou ...
 
 
 
Immunosenescence Inventory'a multi-omics database for immune aging research border=  
 
Hao Li, Wei Zhao, Fei Yang, Qin Qiao, Shuai Ma ...
 
 
 
MAPbrain: a multi-omics atlas of the primate brain border=  
 
Liangchen Zhuo, Mengdi Wang, Tingrui Song, Suijuan Zhong, Bo Zeng ...
 
 
 
miRNASNP-v4: a comprehensive database for miRNA-related SNPs across 17 species border= 
 
Wen Cao, Jiaxin He, Jing Feng, Xiaohong Wu, Tian Wu ...
 
 
 
MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species border= 
 
Fuyun Liu, Bingcheng Cai, Shanshan Lian, Xinyao Chang, Dongsheng Chen ...
 
 
 
Pairpot: a database with real-time lasso-based analysis tailored for paired single-cell and spatial transcriptomics border= 
 
Zhihan Ruan, Fan Lin, Zhenjie Zhang, Jiayue Cao, Wenting Xiang ...
 
 
 
PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization border= 
 
Zhiting Wei, Duanmiao Si, Bin Duan, Yicheng Gao, Qian Yu ...
 
 
 
PerturbAtlas: a comprehensive atlas of public genetic perturbation bulk RNA-seq datasets border= 
 
Yiming Zhang, Ting Zhang, Gaoxia Yang, Zhenzhong Pan, Min Tang ...
 
 
 
PerturbDB for unraveling gene functions and regulatory networks border=  
 
Bing Yang, Man Zhang, Yanmei Shi, Bing-Qi Zheng, Chuanping Shi ...
 
 
 
PWAS Hub: exploring gene-based associations of complex diseases with sex dependency border= 
 
Roei Zucker, Guy Kelman, Michal Linial
 
 
 
The RodentGPOmics Atlas: a comprehensive database of rodent biology for genomes and pathogens border= 
 
Zhiwen Jiang, Ziqing Yan, Yali Hou, Jia Tang, Mengdi Zheng ...
 
 
 
sc2GWAS: a comprehensive platform linking single cell and GWAS traits of human border= 
 
Mingxue Yin, Chenchen Feng, Zhengmin Yu, Yuexin Zhang, Ye Li ...
 
 
 
scImmOmics: a manually curated resource of single-cell multi-omics immune data border= 
 
Yan-Yu Li, Li-Wei Zhou, Feng-Cui Qian, Qiao-Li Fang, Zheng-Min Yu ...
 
 
 
scLTdb: a comprehensive single-cell lineage tracing database border=  
 
Junyao Jiang, Xing Ye, Yunhui Kong, Chenyu Guo, Mingyuan Zhang ...
 
 
 
scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics border= 
 
Wenwen Cheng, Changhui Yin, Shiya Yu, Xi Chen, Ni Hong ...
 
 
 
scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies border= 
 
Jialin Mai, Qiheng Qian, Hao Gao, Zhuojing Fan, Jingyao Zeng ...
 
 
 
SPathDB: a comprehensive database of spatial pathway activity atlas border=  
 
Feng Li, Xinyu Song, Wenli Fan, Liying Pei, Jiaqi Liu ...
 
 
 
SpatialRef: a reference of spatial omics with known spot annotation border=  
 
Ting Cui, Yan-Yu Li, Bing-Long Li, Han Zhang, Ting-Ting Yu ...
 
 
 
stSNV: a comprehensive resource of SNVs in spatial transcriptome border=  
 
Changbo Yang, Yujie Liu, Xiaohua Wang, Qing Jia, Yuqi Fan ...
 
 
 
TranscriptDB: a transcript-centric database to study eukaryotic transcript conservation and evolution border= 
 
Wend Yam D D Ouedraogo, Aida Ouangraoua
 
 
 
The UCSC Genome Browser database: 2025 update border=  
 
Gerardo Perez, Galt P Barber, Anna Benet-Pages, Jonathan Casper, Hiram Clawson ...
 
 
 
VDGE: a data repository of variation database for gene-edited animals across multiple species border= 
 
Wenwen Shi, Enhui Jin, Lu Fang, Yanling Sun, Zhuojing Fan ...
 
 
 
webTWAS 2.0: update platform for identifying complex disease susceptibility genes through transcriptome-wide association study border= 
 
Chen Cao, Mengting Shao, Jianhua Wang, Zhenghui Li, Haoran Chen ...
 
 
 
xQTLatlas: a comprehensive resource for human cellular-resolution multi-omics genetic regulatory landscape border= 
 
Yuran Jia, Hongchao Dong, Linhao Li, Fang Wang, Liran Juan ...
 
 
 
GENOMIC VARIATION, DISEASES AND DRUGS
 
 
 
 
CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers border= 
 
Jingyao Zeng, Zhi Nie, Yunfei Shang, Jialin Mai, Yadong Zhang ...
 
 
 
canSAR 2024'an update to the public drug discovery knowledgebase border=  
 
Phillip W Gingrich, Rezvan Chitsazi, Ansuman Biswas, Chunjie Jiang, Li Zhao ...
 
 
 
CAUSALdb2: an updated database for causal variants of complex traits border=  
 
Jianhua Wang, Liao Ouyang, Tianyi You, Nianling Yang, Xinran Xu ...
 
 
 
ChiTaRS 8.0: the comprehensive database of chimeric transcripts and RNA-seq data with applications in liquid biopsy border= 
 
Dylan DSouza, Lihi Bik, Olawumi Giwa, Shahaf Cohen, Hilit Levy Barazany ...
 
 
 
ClinVar: updates to support classifications of both germline and somatic variants 
 
Melissa J Landrum, Shanmuga Chitipiralla, Kuljeet Kaur, Garth Brown, Chao Chen ...
 
 
 
CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening border= 
 
Hongyan Du, Xujun Zhang, Zhenxing Wu, Odin Zhang, Shukai Gu ...
 
 
 
Comparative Toxicogenomics Database's 20th anniversary: update 2025 border=  
 
Allan Peter Davis, Thomas C Wiegers, Daniela Sciaky, Fern Barkalow, Melissa Strong ...
 
 
 
CTR-DB 2.0: an updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers border= 
 
Jianzhou Jiang, Yajie Ma, Lele Yang, Shurui Ma, Zixuan Yu ...
 
 
 
CVD Atlas: a multi-omics database of cardiovascular disease border=  
 
Qiheng Qian, Ruikun Xue, Chenle Xu, Fengyu Wang, Jingyao Zeng ...
 
 
 
DDInter 2.0: an enhanced drug interaction resource with expanded data coverage, new interaction types, and improved user interface border= 
 
Yao Tian, Jiacai Yi, Ningning Wang, Chengkun Wu, Jinfu Peng ...
 
 
 
DMRdb: a disease-centric Mendelian randomization database for systematically assessing causal relationships of diseases with genes, proteins, CpG sites, metabolites and other diseases border= 
 
Xiao Zheng, Zhihao Tian, Xiaohui Che, Xu Zhang, Yu Xiang ...
 
 
 
DrugMAP 2.0: molecular atlas and pharma-information of all drugs border=  
 
Fengcheng Li, Minjie Mou, Xiaoyi Li, Weize Xu, Jiayi Yin ...
 
 
 
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