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Nucleic Acids Research, Volume 51
Volume 51, Number D1, January 2023
- Daniel J. Rigden
, Xosé M. Fernández:
The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection. 1-8 - Matthew Thakur
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. 9-17 - CNCB-NGDC Members:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. 18-28 - Eric W. Sayers
Database resources of the National Center for Biotechnology Information in 2023. 29-38 - Wen-Kang Shen
AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations. 39-45 - Junhong Huang, Wu-Jian Zheng, Ping Zhang, Qiao Lin, Zhi-Rong Chen, Jia-Jia Xuan
ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes. 46-56 - Qiangwei Zhou
ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms. 57-69 - Jiankang Wang
CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells. 70-79 - Takeshi Obayashi
COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations. 80- - Yimeng Zhang, Yuexin Zhang, Chao Song, Xilong Zhao, Bo Ai, Yuezhu Wang, Liwei Zhou, Jiang Zhu, Chenchen Feng, Liyan Xu
CRdb: a comprehensive resource for deciphering chromatin regulators in human. 88-100 - Yasuhiro Tanizawa
DNA Data Bank of Japan (DDBJ) update report 2022. 101-105 - Yuxin Zhang, Jie Jiang
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. 106-116 - Mei-Jing Dong, Hao Luo
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes. 117-120 - Josephine Burgin
The European Nucleotide Archive in 2022. 121-125 - Haopeng Yu
G4Atlas: a comprehensive transcriptome-wide G-quadruplex database. 126-134 - Anaïs Vannutelli, Lauriane lucienne noele Schell, Jean-Pierre Perreault, Aïda Ouangraoua:
GAIA: G-quadruplexes in alive creature database. 135-140 - Eric W. Sayers
GenBank 2023 update. 141-144 - Priyanka Raina, Rodrigo Guinea
GeneFriends: gene co-expression databases and tools for humans and model organisms. 145-158 - Wanwen Zeng
HiChIPdb: a comprehensive database of HiChIP regulatory interactions. 159-166 - Sonia García-Ruíz
IntroVerse: a comprehensive database of introns across human tissues. 167-178 - Ernesto Aparicio-Puerta
isomiRdb: microRNA expression at isoform resolution. 179-185 - Zhao Li
LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. 186-191 - Yanbo Yang, Dongyang Wang, Ya-Ru Miao, Xiaohong Wu, Haohui Luo, Wen Cao, Wenqian Yang, Jianye Yang, An-Yuan Guo
lncRNASNP v3: an updated database for functional variants in long non-coding RNAs. 192-198 - Hongying Zhao, Xiangzhe Yin, Haotian Xu, Kailai Liu
LncTarD 2.0: an updated comprehensive database for experimentally-supported functional lncRNA-target regulations in human diseases. 199-207 - Mochen Zhang
MethBank 4.0: an updated database of DNA methylation across a variety of species. 208-2016 - Anne-Christin Hauschild
MirDIP 5.2: tissue context annotation and novel microRNA curation. 217-225 - Andrea Cappannini
NACDDB: Nucleic Acid Circular Dichroism Database. 226-231 - Yu Zheng, Huaxia Luo
NPInter v5.0: ncRNA interaction database in a new era. 232-239 - Sébastien Bourdon, Pauline Herviou
QUADRatlas: the RNA G-quadruplex and RG4-binding proteins database. 240-247 - Qi Liu, Xin Peng, Mengyuan Shen
Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling. 248-261 - Jie Deng, Yaohuang Shi, Xuemei Peng, Yuanlin He, Xiaoxue Chen, Mengxiao Li, Xiaowei Lin, Wenjian Liao
Ribocentre: a database of ribozymes. 262-268 - Xiaoqiong Bao, Yin Zhang, Huiqin Li, Yuyan Teng, Lixia Ma, Zhihang Chen, Xiaotong Luo, Jian Zheng
RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications. 269-279 - Yuezhu Wang, Chao Song, Jun Zhao, Yuexin Zhang, Xilong Zhao, Chenchen Feng, Guorui Zhang, Jiang Zhu, Fan Wang, Fengcui Qian, Liwei Zhou, Jian Zhang, Xuefeng Bai, Bo Ai, Xinyu Liu, Qiuyu Wang, Chunquan Li
SEdb 2.0: a comprehensive super-enhancer database of human and mouse. 280-290 - Danny Bergeron, Hermes Paraqindes
snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs. 291-296 - Lingyu Guan
tatDB: a database of Ago1-mediated targets of transfer RNA fragments. 297-305 - Yongbing Zhao
TFSyntax: a database of transcription factors binding syntax in mammalian genomes. 306-314 - Hao-Tian Lei, Zhang-Hao Wang, Bin Li
tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data. 315-327 - Felix Manske
The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. 328-336 - Claudio Lo Giudice
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions. 337-344 - Zhen Wah Tan, Wei-Ven Tee, Enrico Guarnera, Igor N. Berezovsky
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design. 345-351 - Michal Burdukiewicz
AmyloGraph: a comprehensive database of amyloid-amyloid interactions. 352-357 - Anita E. Bandrowski
The Antibody Registry: ten years of registering antibodies. 358-367 - Jeffrey C. Hoch
Biological Magnetic Resonance Data Bank. 368-376 - Ulka Gawde, Shuvechha Chakraborty, Faiza Hanif Waghu, Ram Shankar Barai
CAMPR4: a database of natural and synthetic antimicrobial peptides. 377-383 - Jiyao Wang, Farideh Chitsaz, Myra K. Derbyshire, Noreen R. Gonzales, Marc Gwadz, Shennan Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J. Lanczycki, Aron Marchler-Bauer
The conserved domain database in 2023. 384-388 - Ana Hernández-Plaza
eggNOG 6.0: enabling comparative genomics across 12 535 organisms. 389-394 - Gáspár Pándy-Szekeres, Jimmy Caroli, Alibek Mamyrbekov, Ali A Kermani, György M. Keserü, Albert J. Kooistra
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources. 395-402 - Jiho Sim, Sohee Kwon
HProteome-BSite: predicted binding sites and ligands in human 3D proteome. 403-408 - Yangyang Cai, Dezhong Lv, Donghao Li, Jiaqi Yin, Yingying Ma, Ya Luo, Limei Fu, Na Ding, Yongsheng Li
IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions. 409-417 - Typhaine Paysan-Lafosse
InterPro in 2022. 418-427 - Daniel M. Tadros
The MHC Motif Atlas: a database of MHC binding specificities and ligands. 428-437 - Damiano Piovesan
MobiDB: 10 years of intrinsically disordered proteins. 438-444 - Dmitry Kuznetsov, Fredrik Tegenfeldt, Mosè Manni, Mathieu Seppey
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. 445-451 - Ya Liu, Sheng Liu, Zhuo Pan, Yu Ren, Yiru Jiang, Feng Wang, Dan-dan Li, Yue-zhong Li
PAT: a comprehensive database of prokaryotic antimicrobial toxins. 452-459 - Chao Hou
PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information. 460-465 - Qifang Xu
The protein common assembly database (ProtCAD) - a comprehensive structural resource of protein complexes. 466-478 - Kai Yu
qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast. 479-487 - Stephen K. Burley
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. 488-508 - Artem Kushner
RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures. 509-516 - Laszlo Dobson
TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures. 517-522 - The UniProt Consortium:
UniProt: the Universal Protein Knowledgebase in 2023. 523-531 - Xavier B. Tao
ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design. 532-538 - George Tsitsiridis, Ralph Steinkamp, Madalina Giurgiu
CORUM: the comprehensive resource of mammalian protein complexes-2022. 539-545 - Kuerbannisha Amahong, Wei Zhang
CovInter: interaction data between coronavirus RNAs and host proteins. 546-556 - Jinfang Zheng
dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes. 557-563 - Daria Marakulina
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes. 564-570 - Nan Zhou
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations. 571-582 - Feiran Li
GotEnzymes: an extensive database of enzyme parameter predictions. 583-586 - Minoru Kanehisa
KEGG for taxonomy-based analysis of pathways and genomes. 587-592 - Jun-Lin Yu, Song Wu, Cong Zhou, Qing-Qing Dai, Christopher J. Schofield, Guo-Bo Li
MeDBA: the Metalloenzyme Data Bank and Analysis platform. 593-602 - Barbara R. Terlouw
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. 603-610 - David S. Wishart
MiMeDB: the Human Microbial Metabolome Database. 611-620 - Hui Zhao, Yuan Yang, Shuaiqi Wang, Xue Yang, Kaicheng Zhou, Caili Xu, Xuyao Zhang
NPASS database update 2023: quantitative natural product activity and species source database for biomedical research. 621-628 - Richard J. Roberts
REBASE: a database for DNA restriction and modification: enzymes, genes and genomes. 629-630 - Prisca Lo Surdo
SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update. 631-637 - Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. 638-646 - Mark Stam, Pernelle Lelièvre, Mark Hoebeke
SulfAtlas, the sulfatase database: state of the art and new developments. 647-653 - Kathleen Gallo, Emanuel Kemmler
SuperNatural 3.0 - a database of natural products and natural product-based derivatives. 654-659 - Nozomu Sakurai
The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites. 660-677 - Robert D. Olson, Rida Assaf, Thomas S. Brettin, Neal Conrad, Clark Cucinell, James J. Davis
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. 678-689 - Brian P. Alcock
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. 690-699 - Bingbing Lei, Yueren Xu, Yunjiao Lei, Cunyuan Li, Ping Zhou, Limin Wang, Qing Yang, Xiaoyue Li, Fulin Li, Chuyang Liu, Chaowen Cui, Tong Chen, Wei Ni, Shengwei Hu
CRAMdb: a comprehensive database for composition and roles of microbiome in animals. 700-707 - Fang Wang, Ke Wang, Lei Cai
Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy. 708-716 - Changlu Qi, Yiting Cai, Kai Qian, Xuefeng Li, Jialiang Ren, Ping Wang
gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions. 717-722 - I-Min A. Chen
The IMG/M data management and analysis system v.7: content updates and new features. 723-732 - Antonio Pedro Camargo
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. 733-743 - Nathalie Bonin
MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. 744-752 - Lorna J. Richardson
MGnify: the microbiome sequence data analysis resource in 2023. 753-759 - Anthony Fullam
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. 760-766 - Yadong Zhang, Hao Zhang, Zaichao Zhang, Qiheng Qian, Zhewen Zhang, Jing-Fa Xiao:
ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics. 767-776 - Dongwook Kim
UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. 777-784 - Miguel Cacho Teixeira
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. 785-791 - Xin Gao
ABC portal: a single-cell database and web server for blood cells. 792-804 - Kexin Huang
AgeAnno: a knowledgebase of single-cell annotation of aging in human. 805-815 - Yingjie Gao, Guanghui Jiang, Wenqian Yang, Weiwei Jin, Jing Gong
Animal-SNPAtlas: a comprehensive SNP database for multiple animals. 816-826 - Yi-Min Zheng
Aquila: a spatial omics database and analysis platform. 827-834 - Siyu Pan
Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits. 835-844 - Zeynep Kosaloglu-Yalçin
The Cancer Epitope Database and Analysis Resource (CEDAR). 845-852 - Shuai Jiang
Cell Taxonomy: a curated repository of cell types with multifaceted characterization. 853-860 - Qiuyan Guo, Peng Wang
CellTracer: a comprehensive database to dissect the causative multilevel interplay contributing to cell development trajectories. 861-869 - Congxue Hu, Tengyue Li, Yingqi Xu, Xinxin Zhang, Feng Li, Jing Bai, Jing Chen, Wenqi Jiang, Kaiyue Yang, Qi Ou, Xia Li
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data. 870-876 - Menglin Zheng, Satoshi Okawa
ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells. 877-889 - Zhichao Li
CMDB: the comprehensive population genome variation database of China. 890-895 - Dapeng Wang
COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas. 896-905 - Jianguo Lu
DupScan: predicting and visualizing vertebrate genome duplication database. 906-912 - Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang
EDomics: a comprehensive and comparative multi-omics database for animal evo-devo. 913-923 - Lei Zheng
EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis. 924-932 - Fergal J. Martin
Ensembl 2023. 933-941 - Adam Frankish
GENCODE: reference annotation for the human and mouse genomes in 2023. 942-949 - Fan Feng, Feitong Tang, Yijia Gao, Dongyu Zhu, Tianjun Li, Shuyuan Yang, Yuan Yao, Yuanhao Huang, Jie Liu
GenomicKB: a knowledge graph for the human genome. 950-956 - Supratim Mukherjee
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9. 957-963 - Shipeng Guo
GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets. 964-968 - Xiaonan Liu
GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals. 969-976 - Elliot Sollis
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. 977-985 - Tim Beck
GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies. 986-993 - Guangya Duan, Gangao Wu
HGD: an integrated homologous gene database across multiple species. 994-1002 - Ruth L. Seal
Genenames.org: the HGNC resources in 2023. 1003-1009 - Youngseok Choi, Sojin Ahn
HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method. 1010-1018 - Lu Pan
HTCA: a database with an in-depth characterization of the single-cell human transcriptome. 1019-1028 - Xiaoying Shi, Zhiguang Yu, Pengfei Ren, Xin Dong, Xuanxin Ding, Jiaming Song, Jing Zhang, Taiwen Li, Chenfei Wang:
HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses. 1029-1037 - Tudor Groza
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. 1038-1045 - Xuelian Ma
ipaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues. 1046-1052 - Dominic J. Barker
The IPD-IMGT/HLA Database. 1053-1060 - Haoteng Yan
Lineage Landscape: a comprehensive database that records lineage commitment across species. 1061-1066 - Molly A. Bogue
Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes. 1067-1074 - Seth A. Ament
The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain. 1075-1085 - Qinfeng Ma, Haodong Tao
OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids. 1086-1093 - Zhaoyu Zhai, Xuelu Zhang, Lu Zhou, Zhewei Lin, Ni Kuang, Qiang Li, Qinfeng Ma, Haodong Tao
PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation. 1094-1101 - Xiaohan Zhao, Sen Ma, Baonan Wang, Xuetong Jiang, Shuhua Xu
PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations. 1102-1108 - Yimin Wang, Yunchao Ling, Jiao Gong, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin
PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. 1109-1116 - Lance C. Novak, Juihsuan Chou, Medina Colic
PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens. 1117-1121 - Dandan Huang, Xiangling Feng, Hongxi Yang, Jianhua Wang, Wenwen Zhang, Xutong Fan, Xiaobao Dong, Kexin Chen, Ying Yu, Xin Ma, Xianfu Yi, Mulin Jun Li
QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes. 1122-1128 - Henry E. Miller
Exploration and analysis of R-loop mapping data with RLBase. 1129-1137 - Zhiwei Fan, Yangyang Luo
SPASCER: spatial transcriptomics annotation at single-cell resolution. 1138-1149 - Yangfeng Chen
SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases. 1150-1159 - Junyi Xin, Dongying Gu, Silu Chen, Shuai Ben, Huiqin Li, Zhengdong Zhang
SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival. 1160-1167 - Ziheng Zhou, Cong Tan, Matthew Hoi Kin Chau
TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms. 1168-1178 - Mingming Lu, Yadong Zhang, Fengchun Yang
TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. 1179-1187 - Luis R. Nassar
The UCSC Genome Browser database: 2023 update. 1188-1195 - Song Wu
ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers. 1196-1204 - Kai-Pu Chen, Chia-Lang Hsu, Yen-Jen Oyang, Hsuan-Cheng Huang
BIC: a database for the transcriptional landscape of bacteria in cancer. 1205-1211 - Patrizio Di Micco
canSAR: update to the cancer translational research and drug discovery knowledgebase. 1212-1219 - David S. Wishart
ChemFOnt: the chemical functional ontology resource. 1220-1229 - Kilannin Krysiak
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. 1230-1241 - Hatairat Yingtaweesittikul
CREAMMIST: an integrative probabilistic database for cancer drug response prediction. 1242-1248 - Jibiao Fan, Leisheng Shi
Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase. 1249-1256 - Allan Peter Davis
Comparative Toxicogenomics Database (CTD): update 2023. 1257-1262 - Xiuna Sun, Yintao Zhang
DRESIS: the first comprehensive landscape of drug resistance information. 1263-1275 - Sorin I. Avram
DrugCentral 2023 extends human clinical data and integrates veterinary drugs. 1276-1287 - Fengcheng Li
DrugMAP: molecular atlas and pharma-information of all drugs. 1288-1299 - Hufeng Zhou, Theodore Arapoglou, Xihao Li, Zilin Li, Xiuwen Zheng, Jill Moore, Abhijith Asok, Sushant Kumar, Elizabeth E. Blue, Steven Buyske, Nancy J. Cox, Adam Felsenfeld, Mark Gerstein, Eimear Kenny, Bingshan Li, Tara Cox Matise, Anthony Philippakis, Heidi L. Rehm, Heidi J. Sofia, Grace Snyder, Zhiping Weng, Benjamin M. Neale, Shamil R. Sunyaev, Xihong Lin:
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. 1300-1311 - Yuhua Fu, Hong Liu, Jingwen Dou, Yue Wang, Yong Liao, Xin Huang, Zhenshuang Tang, Jingya Xu, Dong Yin, Shilin Zhu, Yangfan Liu, Xiong Shen, Hengyi Liu, Jiaqi Liu, Xin Yang, Yi Zhang, Yue Xiang, Jingjin Li, Zhuqing Zheng, Yunxia Zhao, Yunlong Ma, Haiyan Wang, Xiaoyong Du, Shengsong Xie
IAnimal: a cross-species omics knowledgebase for animals. 1312-1324 - Tiantongfei Jiang, Weiwei Zhou
ImmCluster: an ensemble resource for immunology cell type clustering and annotations in normal and cancerous tissues. 1325-1332 - Shuiping Liu
M6AREG: m6A-centered regulation of disease development and drug response. 1333-1344 - Ping Wang
microbioTA: an atlas of the microbiome in multiple disease tissues of Homo sapiens and Mus musculus. 1345-1352 - David Ochoa
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt. 1353-1359 - Zinaida Perova
PDCM Finder: an open global research platform for patient-derived cancer models. 1360-1366 - Gaoqi Weng
PROTAC-DB 2.0: an updated database of PROTACs. 1367-1372 - Sunghwan Kim
PubChem 2023 update. 1373-1380 - Haiyan Chen, Jing Xu, Siyu Wei, Zhe Jia, Chen Sun, Jingxuan Kang, Xuying Guo, Nan Zhang, Junxian Tao, Yu Dong, Chen Zhang, Yingnan Ma, Wenhua Lv, Hongsheng Tian, Shuo Bi, Hongchao Lv, Chen Huang, Fanwu Kong, Guoping Tang, Yongshuai Jiang
RABC: Rheumatoid Arthritis Bioinformatics Center. 1381-1387 - Bowen Song
RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. 1388-1396 - Jia Chen, Jiahao Lin
RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. 1397-1404 - Keith J. Kelleher
Pharos 2023: an integrated resource for the understudied human proteome. 1405-1416 - Xueying Wang
TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization. 1417-1424 - Ya Han
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment. 1425-1431 - Lianlian Wu
TOXRIC: a comprehensive database of toxicological data and benchmarks. 1432-1445 - Zhiquan Yang
CottonMD: a multi-omics database for cotton biological study. 1446-1456 - Jingyin Yu, Shan Wu, Honghe Sun, Xin Wang, Xuemei Tang, Shaogui Guo, Zhonghua Zhang
CuGenDBv2: an updated database for cucurbit genomics. 1457-1464 - Pragna Kotni, Theo J. L. van Hintum
EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material. 1465-1469 - Eliza C. Martin
NLRscape: an atlas of plant NLR proteins. 1470-1482 - Jinding Liu
PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples. 1483-1491 - Albert A. Antolin
The Chemical Probes Portal: an expert review-based public resource to empower chemical probe assessment, selection and use. 1492-1502 - Andrii Iudin
EMPIAR: the Electron Microscopy Public Image Archive. 1503-1511 - Qingyu Chen
LitCovid in 2022: an information resource for the COVID-19 literature. 1512-1518 - Xinhao Shao, Clarissa D. Gomez, Nandini Kapoor, James M. Considine, Christopher Grams, Yu (Tom) Gao, Alexandra Naba
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. 1519-1530 - Julia Koblitz
MediaDive: the expert-curated cultivation media database. 1531-1538 - Eric W. Deutsch, Nuno Bandeira, Yasset Pérez-Riverol
The ProteomeXchange consortium at 10 years: 2023 update. 1539-1548 - Louis Philip Benoit Bouvrette, Xiaofeng Wang, Jonathan Boulais, Jian Kong, Easin Uddin Syed
RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins. 1549-1557 - Esteban Martínez-García
SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. 1558-1567
Volume 51, Number W1, July 2023
- Dominik Seelow
Editorial: the 21st annual Nucleic Acids Research Web Server Issue 2023. 1-4 - Michal Wlasnowolski
3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome. 5-10 - Ondrej Schindler
αCharges: partial atomic charges for AlphaFold structures in high quality. 11-16 - Fanjie Zong, Chenyu Long, Wanxin Hu, Shuang Chen, Wentao Dai, Zhi-Xiong Xiao, Yang Cao
Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. 17-24 - Xing-Xing Shi, Zhi-Zheng Wang
ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy. 25-32 - Jinyin Zha, Qian Li, Xinyi Liu, Weidong Lin, Tingting Wang, Jiacheng Wei, Ziliang Zhang, Xun Lu, Jing Wu, Duan Ni
AlloReverse: multiscale understanding among hierarchical allosteric regulations. 33-38 - Véronique Geoffroy, Jean-Baptiste Lamouche, Thomas Guignard, Samuel Nicaise, Arnaud Kress, Sophie Scheidecker, Antony Le Béchec, Jean Muller
The AnnotSV webserver in 2023: updated visualization and ranking. 39-45 - Kai Blin
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. 46-50 - Joshua S. Martin Beem, Sravani Venkatayogi
ARMADiLLO: a web server for analyzing antibody mutation probabilities. 51-56 - Potdar Swapnil
Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. 57-61 - Alessio Del Conte
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. 62-69 - Zhitao Mao
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. 70-77 - Alexandre Borrel
ChemMaps.com v2.0: exploring the environmental chemical universe. 78-82 - Ottavio Croci
ChroKit: a Shiny-based framework for interactive analysis, visualization and integration of genomic data. 83-92 - Fengxia Zhou, Xiaorong Yu
CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing. 93-107 - Kristian Barrett
Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes. 108-114 - Jinfang Zheng
dbCAN3: automated carbohydrate-active enzyme and substrate annotation. 115-121 - Yunzhuo Zhou
DDMut: predicting effects of mutations on protein stability using deep learning. 122-128 - Qianqian Song
DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations. 129-133 - Jeong Yeon Kim, Hyoeun Bang, Seung-Jae Noh, Jung Kyoon Choi
DeepNeo: a webserver for predicting immunogenic neoantigens. 134-140 - Sushmita Basu
DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction. 141-147 - Spyros Tastsoglou, Athanasios Alexiou, Dimitra Karagkouni, Giorgos Skoufos, Elissavet Zacharopoulou, Artemis G. Hatzigeorgiou
DIANA-microT 2023: including predicted targets of virally encoded miRNAs. 148-153 - Spyros Tastsoglou, Giorgos Skoufos, Marios Miliotis, Dimitra Karagkouni, Ioannis Koutsoukos, Anna Karavangeli, Filippos S. Kardaras, Artemis G. Hatzigeorgiou
DIANA-miRPath v4.0: expanding target-based miRNA functional analysis in cell-type and tissue contexts. 154-159 - Volodymyr Tsybulskyi
e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features. 160-167 - John Erol Evangelista
Enrichr-KG: bridging enrichment analysis across multiple libraries. 168-179 - Zixuan Zhang, Haiqi Zhu, Pengtao Dang, Jia Wang, Wennan Chang, Xiao Wang, Norah Alghamdi, Alex Lu, Yong Zang, Wenzhuo Wu
FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data. 180-190 - Turgut Mesut Yilmaz
FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi. 191-197 - András Hatos
FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins. 198-206 - Liis Kolberg
g:Profiler - interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update). 207-212 - Giacomo B. Marino
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. 213-224 - Alan M. Cleary
Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes. 225-231 - Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothée Huchon
GenomeFLTR: filtering reads made easy. 232-236 - Erik Faessler
GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions. 237-242 - Miaomiao Chen, Weizhi Zhang, Yujie Gou, Danyang Xu, Yuxiang Wei, Dan Liu, Cheng Han, Xinhe Huang, Chengzhi Li, Wanshan Ning
GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins. 243-250 - Urszula Orzel
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex. 251-262 - Sebastian Schönherr, Hansi Weißensteiner
Haplogrep 3 - an interactive haplogroup classification and analysis platform. 263-268 - Lukasz Ciecierski, Ireneusz Stolarek, Marek Figlerowicz
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics. 269-273 - Liam J. McGuffin
Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers. 274-280 - Guillaume Postic
IRSOM2: a web server for predicting bifunctional RNAs. 281-288 - João Victor da Silva Guerra
KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities. 289-297 - Brian Jiménez-García
The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions. 298-304 - Javier López-Ibáñez, Florencio Pazos
MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. 305-309 - Yao Lu, Guangyan Zhou, Jessica Ewald
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data. 310-318 - Ernesto Aparicio-Puerta
miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations. 319-325 - Aliaksei Chareshneu
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. 326-330 - Ferdous Nasri
MpoxRadar: a worldwide MPXV genomic surveillance dashboard. 331-337 - Arthur Declercq
Updated MS²PIP web server supports cutting-edge proteomics applications. 338-342 - Yuexu Jiang, Lei Jiang, Chopparapu Sai Akhil, Duolin Wang, Ziyang Zhang, Weinan Zhang, Dong Xu
MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels. 343-349 - Ricardo Avila
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes. 350-356 - Qi Xu
NBBC: a non-B DNA burden explorer in cancer. 357-364 - Kai Liu, Xufeng Lu, Hang Shi, Xiaojun Xu
nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands. 365-371 - Chantal Scheepbouwer
NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods. 372-378 - Oriol Fornes
OnTarget: in silico design of MiniPromoters for targeted delivery of expression. 379-386 - Chaohui Bao
OpenXGR: a web-server update for genomic summary data interpretation. 387-396 - Jiahe Sun, Fang Lu, Yongjiang Luo, Lingzi Bie, Ling Xu, Yi Wang
OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. 397-403 - Christoph Elfmann
PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks. 404-410 - María José Jiménez-Santos, Alba Nogueira-Rodríguez
PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data. 411-418 - Yanhui Hu
PANGEA: a new gene set enrichment tool for Drosophila and common research organisms. 419-426 - Hao Tian
PASSer: fast and accurate prediction of protein allosteric sites. 427-431 - Julien Rey, Samuel Murail
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution. 432-437 - Anastasija Zaiko
Pest Alert Tool - a web-based application for flagging species of concern in metabarcoding datasets. 438-442 - David S. Wishart
PHASTEST: faster than PHASTER, better than PHAST. 443-450 - Emidio Capriotti
PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants. 451-458 - David S. Wishart
PlasMapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps. 459-467 - Yiran Xu, Jianghui Zhu, Wenze Huang
PrismNet: predicting protein-RNA interaction using in vivo RNA structural information. 468-477 - Moran Sharon
ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts. 478-483 - Jason R. Grant, Eric Enns, Eric Marinier, Arnab Mandal, Emily K. Herman, Chih-Yu Chen
Proksee: in-depth characterization and visualization of bacterial genomes. 484-492 - Rémi Gschwind
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. 493-500 - Philip Z. Johnson
RNAcanvas: interactive drawing and exploration of nucleic acid structures. 501-508 - Yunxia Wang
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. 509-519 - Fengcui Qian, Li-Wei Zhou, Yanyu Li, Zhengmin Yu, Li-Dong Li, Yuezhu Wang, Mingcong Xu, Qiuyu Wang, Chunquan Li
SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse. 520-527 - Tianyi Qiu
SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs. 528-534 - Simon Mendelsohn, David Froelicher, Denis Loginov, David Bernick, Bonnie Berger
sfkit: a web-based toolkit for secure and federated genomic analysis. 535-541 - Dávid Bajusz
SH2db, an information system for the SH2 domain. 542-552 - Ruifang Cao, Yunchao Ling, Jiayue Meng, Ao Jiang, Ruijin Luo, Qinwen He, Anan Li, Yujie Chen, Zoutao Zhang, Feng Liu, Yixue Li, Guoqing Zhang
SMDB: a Spatial Multimodal Data Browser. 553-559 - Xiangshang Li
STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data. 560-568 - Rui Yin
TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning. 569-576 - Tomasz Wozniak
TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs. 577-586 - Jianmin Xie
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees. 587-592 - Ahmed Mohamed
vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis. 593-600 - Alla Mikheenko
WebQUAST: online evaluation of genome assemblies. 601-606 - Bartosz Adamczyk, Michal Zurkowski
WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. 607-612
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