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Nucleic Acids Research, Volume 50
Volume 50, Number D1, January 2022
- Daniel J. Rigden
, Xosé M. Fernández:
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. 1-10 - Gaia Cantelli
The European Bioinformatics Institute (EMBL-EBI) in 2021. 11-19 - Eric W. Sayers
Database resources of the national center for biotechnology information. 20-26 - Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Jingyao Zeng, Yadong Zhang, Yunfei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zhenglin Du, Yinying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Peilin Jia, Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Tong Jin, Yuansheng Zhang, Dong Zou, Qiang Du, Changrui Feng, Lina Ma, Sisi Zhang, Anke Wang, Lili Dong, Yanqing Wang, Wan Liu, Xing Yan, Yunchao Ling, Zhihua Zhou, Wang Kang, Tao Zhang, Shuai Ma, Haoteng Yan, Zunpeng Liu, Zejun Ji, Yusheng Cai, Si Wang, Moshi Song, Jie Ren, Qi Zhou, Jing Qu, Weiqi Zhang, Guanghui Liu, Xu Chen, Tingting Chen, Yanling Sun, Caixia Yu, Bixia Tang, Junwei Zhu, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yingke Ma, Yaokai Jia, Xinchang Zheng, Meili Chen, Ming Chen, Guangyi Niu, Rong Pan, Wei Jing, Jian Sang, Chang Liu, Yujia Xiong, Mochen Zhang, Guoliang Wang, Lizhi Yi, Wei Zhao, Song Wu, Zhuang Xiong, Rujiao Li, Zheng Gong, Lin Liu, Zhao Li, Qianpeng Li, Sicheng Luo, Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Yanyan Li, Fei Yang, Mengwei Li, Zhaohua Li, Dongmei Tian, Xiaonan Liu, Cuiping Li, Xufei Teng, Shuhui Song, Yang Zhang, Ruru Chen, Rongqin Zhang, Feng Xu, Yifan Wang, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yungang He, Zhen Yang, Lun Li, Na Li, Ying Cui, Guangya Duan, Gangao Wu, Tianhao Huang, Enhui Jin, Hailong Kang, Zhonghuang Wang, Hua Chen, Mingkun Li, Wanshan Ning, Yu Xue, Yanhu Liu, Qijun Zhou, Xingyan Liu, Longlong Zhang, Bingyu Mao, Shihua Zhang, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Haichun Jing, Yitong Pan, Leisheng Shi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Shaofeng Lin, Chuijie Liu, Anyuan Guo, Hao Yuan, Tianhan Su, Yong E. Zhang, Yincong Zhou, Guoji Guo, Shanshan Fu, Xiaodan Tan, Weizhi Zhang, Mei Luo, Yubin Xie, Chenwei Wang, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Feng Tian, Dechang Yang, Ge Gao, Dachao Tang, Wenyi Wu, Yujie Gou, Cheng Han, Qinghua Cui, Xiangshang Li, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. 27-38 - Ya Cui
3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues. 39-45 - Weiwei Jin, Guanghui Jiang, Yanbo Yang, Jianye Yang, Wenqian Yang, Dongyang Wang, Xiaohui Niu, Rong Zhong
Animal-eRNAdb: a comprehensive animal enhancer RNA database. 46-53 - Jose Manuel Rodriguez, Fernando Pozo
APPRIS: selecting functionally important isoforms. 54-59 - Qiangwei Zhou
ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms. 60-71 - Xiaolu Zhao, Leisheng Shi
CircleBase: an integrated resource and analysis platform for human eccDNAs. 72-82 - Wenliang Zhang
circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome. 83-92 - Yi-Gang Chen
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers. 93-101 - Toshihisa Okido
DNA Data Bank of Japan (DDBJ) update report 2021. 102-105 - Carla A. Cummins
The European Nucleotide Archive in 2021. 106-110 - Chun-Jie Liu
EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles. 111-117 - Hongyan Lai, Yuchen Li
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids. 118-128 - Pablo A. Moreno
Expression Atlas update: gene and protein expression in multiple species. 129-140 - Henry E. Pratt, Gregory R. Andrews, Nishigandha Phalke, Jack D. Huey, Michael J. Purcaro, Arjan van der Velde, Jill Moore, Zhiping Weng
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. 141-149 - Yu-Huan Wang, Qian-Fan Yang
G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands. 150-160 - Eric W. Sayers
GenBank. 161-164 - Jaime Abraham Castro-Mondragón
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. 165-173 - Lihua Jia, Yang Li, Fangfang Huang, Yingru Jiang, Haoran Li, Zhizhan Wang, Tiantian Chen, Jiaming Li, Zhang Zhang
LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes. 174-182 - Peng Wang
LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine. 183-189 - Lin Liu
LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. 190-195 - Jiongming Ma, Bowen Song, Zhen Wei, Daiyun Huang
m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. 196-203 - Bastian Fromm
MirGeneDB 2.1: toward a complete sampling of all major animal phyla. 204-210 - Andreas Keller
miRNATissueAtlas2: an update to the human miRNA tissue atlas. 211-221 - Hsi-Yuan Huang, Yang-Chi-Dung Lin, Shi-Dong Cui, Yixian Huang, Yun Tang, Jia-Tong Xu, Jiayang Bao, Yulin Li, Jia Wen, Hua-Li Zuo
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. 222-230 - Pietro Boccaletto
MODOMICS: a database of RNA modification pathways. 2021 update. 2231-235 - Xingyu Liao
msRepDB: a comprehensive repetitive sequence database of over 80 000 species. 236-245 - Erik Poppleton, Aatmik Mallya, Swarup Dey
Nanobase.org: a repository for DNA and RNA nanostructures. 246-252 - Tomasz Zok
ONQUADRO: a database of experimentally determined quadruplex structures. 253-258 - David Rosenkranz, Hans Zischler
piRNAclusterDB 2.0: update and expansion of the piRNA cluster database. 259-264 - Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang
piRBase: integrating piRNA annotation in all aspects. 265-272 - Georges Pierre Schmartz
PLSDB: advancing a comprehensive database of bacterial plasmids. 273-278 - Li Cai, Jia-Jia Xuan
Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. 279-286 - Weihao Zhao
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. 287-294 - Christian-Alexander Dudek
PRODORIC: state-of-the-art database of prokaryotic gene regulation. 295-302 - Ruoyao Lin, Xiaoming Zhong, Yongli Zhou, Huichao Geng, Qingxi Hu, Zhihao Huang, Jun Hu, Xiang-Dong Fu, Liang Chen
R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. 303-315 - Fayrouz Hammal
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. 316-325 - Juanjuan Kang
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. 326-332 - Tianyu Cui, Yiying Dou, Puwen Tan, Zhen Ni, Tianyuan Liu, Duolin Wang, Yan Huang, Kaican Cai, Xiaoyang Zhao, Dong Xu
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. 333-339 - Haibo Zhu, Hao Fu, Tianyu Cui, Lin Ning, Huaguo Shao
RNAPhaSep: a resource of RNAs undergoing phase separation. 340-346 - Mengni Liu, Huiqin Li, Xiaotong Luo, Jieyi Cai, Tianjian Chen, Yubin Xie
RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation. 347-355 - Xiaoxiao Yang, Yang Tong, Gerui Liu, Jiapei Yuan, Yang Yang:
scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse. 356-364 - Sheng Zhu, Qiwei Lian, Wenbin Ye
scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution. 365-370 - Tianshun Gao
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. 371-379 - Wenting Zong
scMethBank: a database for single-cell whole genome DNA methylation maps. 380-386 - Kenneth S. Katz
The Sequence Read Archive: a decade more of explosive growth. 387-390 - Yuexin Zhang, Chao Song, Yimeng Zhang, Yuezhu Wang, Chenchen Feng, Jiaxin Chen, Ling Wei, Qi Pan, Desi Shang
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. 391-412 - Dezhong Lv, Zhenghong Chang, Yangyang Cai, Junyi Li, Liping Wang, Qiushuang Jiang, Kang Xu
TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome. 413-420 - Jun-Hao Wang, Wen-Xin Chen, Shi-Qiang Mei, Yue-Dong Yang
tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. 421-431 - Benjamin D. Lee
ViroidDB: a database of viroids and viroid-like circular RNAs. 432-438 - Mihaly Varadi
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. 439-444 - Mingjie Gao, Aurélien F. A. Moumbock
CovPDB: a high-resolution coverage of the covalent protein-ligand interactome. 445-450 - Weizhi Zhang, Xiaodan Tan, Shaofeng Lin
CPLM 4.0: an updated database with rich annotations for protein lysine modifications. 451-459 - Jhih-Hua Jhong
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. 460-470 - Zhongyan Li, Shangfu Li, Mengqi Luo
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. 471-479 - Federica Quaglia
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. 480-487 - Guobang Shi
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides. 488-496 - Manjeet Kumar
The Eukaryotic Linear Motif resource: 2022 release. 497-508 - András Hatos
FuzDB: a new phase in understanding fuzzy interactions. 509-517 - Gáspár Pándy-Szekeres, Mauricio Esguerra
The G protein database, GproteinDb. 518-525 - Michael A. R. Hollas
The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms. 526-533 - Mihaly Varadi
PDBe-KB: collaboratively defining the biological context of structural data. 534-542 - Yasset Pérez-Riverol
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. 543-552 - John-Marc Chandonia
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. 553-559 - Xiaona Wang
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. 560-570 - Elodie Drula, Marie-Line Garron, Suzan Dogan, Vincent Lombard
The carbohydrate-active enzyme database: functions and literature. 571-577 - Birgit H. M. Meldal
Complex Portal 2022: new curation frontiers. 578-586 - Atanas Kamburov
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. 587-595 - Mengwei Li
DISCO: a database of Deeply Integrated human Single-Cell Omics data. 596-602 - Moritz E. Beber
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. 603-609 - Marouen Ben Guebila
GRAND: a database of gene regulatory network models across human conditions. 610-621 - David S. Wishart
HMDB 5.0: the Human Metabolome Database for 2022. 622-631 - Chan Yeong Kim
HumanNet v3: an improved database of human gene networks for disease research. 632-639 - Max Kotlyar
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. 640-647 - Noemi del-Toro
The IntAct database: efficient access to fine-grained molecular interaction data. 648-653 - Vivek Modi, Roland L. Dunbrack Jr.
Kincore: a web resource for structural classification of protein kinases and their inhibitors. 654-664 - David S. Wishart
NP-MRD: the Natural Products Magnetic Resonance Database. 665-677 - Anju Sharma, Bishal Kumar Saha, Rajnish Kumar
OlfactionBase: a repository to explore odors, odorants, olfactory receptors and odorant-receptor interactions. 678-686 - Marc Gillespie
The reactome pathway knowledgebase 2022. 687-692 - Parit Bansal
Rhea, the reaction knowledgebase in 2022. 693-700 - Luca Csabai, Dávid Fazekas, Tamás Kadlecsik, Máté Szalay-Beko, Balázs Bohár, Matthew Madgwick, Dezsö Módos, Marton Olbei
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. 701-709 - Cui-Xiang Lin
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. 710-718 - Xun Wang
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. 719-728 - Junwon Yang
AMDB: a database of animal gut microbial communities with manually curated metadata. 729-735 - Mehmet Direnç Mungan
ARTS-DB: a database for antibiotic resistant targets. 736-740 - Lorenz Christian Reimer
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. 741-746 - Wenliang Zhang
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale. 747-757 - Peng Zhou, Li Wang, Hai Liu, Chunyan Li, Zhimin Li, Jinxiang Wang, Xiaoming Tan
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. 758-764 - Nishadi De Silva
The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. 765-770 - Mercy Rophina
ESC: a comprehensive resource for SARS-CoV-2 immune escape variants. 771-776 - Die Dai, Jiaying Zhu
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. 777-784 - Donovan H. Parks
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. 785-794 - Liang Cheng
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites. 795-800 - Jan P. Meier-Kolthoff
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. 801-807 - Hanbo Jin, Guoru Hu, Chuqing Sun
mBodyMap: a curated database for microbes across human body and their associations with health and diseases. 808-816 - Zhidong Tang, Weiliang Fan, Qiming Li, Dehe Wang
MVIP: multi-omics portal of viral infection. 817-836 - Martin Urban
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. 837-847 - Wei Dai, Jiahui Li
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. 848-857 - Mariona Torrens-Fontanals
SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. 858-866 - Changlu Qi, Chao Wang, Lingling Zhao
SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues. 867-874 - Tiago Pedreira, Christoph Elfmann
The current state of SubtiWiki, the database for the model organism Bacillus subtilis. 875-882 - Stepan A. Nersisyan
T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations. 883-887 - Qinglan Sun, Chang Shu, Wenyu Shi, Yingfeng Luo, Guomei Fan, Jingyi Nie, Yuhai Bi, Qihui Wang, Jianxun Qi, Jian Lu
VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes. 888-897 - Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. 898-911 - Bo Liu
VFDB 2022: a general classification scheme for bacterial virulence factors. 912-917 - Ying Wang
ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects. 918-927 - Jun Cheng, Yunqing Lin, Linfu Xu, Kechen Chen
ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation. 928-933 - Dongsheng Chen
VThunter: a database for single-cell screening of virus target cells in the animal kingdom. 934-942 - Siyu Zhou, Bo Liu
ZOVER: the database of zoonotic and vector-borne viruses. 943-949 - Cheng Quan, Jie Ping
3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database. 950-955 - Zhi-Liang Hu
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. 956-961 - Shuai Jiang
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. 962-969 - Bradley I. Arshinoff, Gregory A. Cary
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms. 970-979 - Mallory Ann Freeberg
The European Genome-phenome Archive in 2021. 980-987 - Fiona Cunningham
Ensembl 2022. 988-995 - Andrew D. Yates
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. 996-1003 - Zhuang Xiong
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. 1004-1009 - Sue A. Krause
FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas. 1010-1015 - Yuansheng Zhang, Dong Zou, Tongtong Zhu, Tianyi Xu
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. 1016-1024 - Nga Thi Thuy Nguyen, Pierre Vincens
Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors. 1025-1031 - Amy T. Walsh, Deborah A. Triant, Justin J. Le Tourneau, Md. Shamimuzzaman, Christine G. Elsik
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. 1032-1039 - Yang Mei
InsectBase 2.0: a comprehensive gene resource for insects. 1040-1045 - Jinding Liu, Fei Yin, Kun Lang, Wencai Jie, Suxu Tan, Rongjing Duan, Shuiqing Huang, Wen Huang
MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species. 1046-1054 - Ioannis Kavakiotis, Athanasios Alexiou, Spyros Tastsoglou
DIANA-miTED: a microRNA tissue expression database. 1055-1061 - Diego Fuentes
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. 1062-1068 - Aina Colomer-Vilaplana
PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans. 1069-1076 - Katherine Decker
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. 1077-1090 - Weiwei Fu, Rui Wang, Hojjat Asadollahpour Nanaei, Jinxin Wang, Dexiang Hu, Yu Jiang
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. 1091-1099 - Shixiang Sun
SomaMutDB: a database of somatic mutations in normal human tissues. 1100-1108 - Massimo Andreatta
SPICA: Swiss portal for immune cell analysis. 1109-1114 - Brian T. Lee
The UCSC Genome Browser database: 2022 update. 1115-1122 - Chen Cao
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. 1123-1130 - Lin Liu
BrainBase: a curated knowledgebase for brain diseases. 1131-1138 - Ruidong Li
CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer. 1139-1146 - Jingyao Zeng
CancerSCEM: a database of single-cell expression map across various human cancers. 1147-1155 - Cari Martini, Ying Frances Liu, Hui Gong, Nicole Sayers, German Segura, Jennifer Fostel
CEBS update: curated toxicology database with enhanced tools for data integration. 1156-1163 - Yin-Ying Wang, Hongen Kang
CeDR Atlas: a knowledgebase of cellular drug response. 1164-1171 - Mustafa S. Pir
ConVarT: a search engine for matching human genetic variants with variants from non-human species. 1172-1178 - Jing Feng, Wenbo Chen
CSCD2: an integrated interactional database of cancer-specific circular RNAs. 1179-1183 - Zhongyang Liu, Jiale Liu, Xinyue Liu
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. 1184-1199 - Guo-Li Xiong
DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety. 1200-1207 - Jie Xing, Ruiyang Zhai, Cong Wang, Honghao Liu, Jiaqi Zeng, Dianshuang Zhou, Mengyan Zhang, Liru Wang, Qiong Wu, Yue Gu, Yan Zhang
DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database. 1208-1215 - Timothee Cezard
The European Variation Archive: a FAIR resource of genomic variation for all species. 1216-1220 - Pora Kim
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. 1221-1230 - Hang Ruan, Qiang Li, Yuan Liu
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers. 1231-1237 - Deyu Yan
HIT 2.0: an enhanced platform for Herbal Ingredients' Targets. 1238-1243 - Lize Wu
huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level. 1244-1254 - Lynn M. Schriml
The Human Disease Ontology 2022 update. 1255-1261 - Taciana Manso, Géraldine Folch, Véronique Giudicelli
IMGT® databases, related tools and web resources through three main axes of research and development. 1262-1272 - Piotr Deszynski, Jakub Mlokosiewicz, Adam Volanakis, Igor Jaszczyszyn, Natalie Castellana, Stefano Bonissone, Rajkumar Ganesan, Konrad Krawczyk
INDI - integrated nanobody database for immunoinformatics. 1273-1281 - Simon D. Harding
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. 1282-1294 - Mengyuan Yang
lncRNAfunc: a knowledgebase of lncRNA function in human cancer. 1295-1306 - Vishal B. Siramshetty
NCATS Inxight Drugs: a comprehensive and curated portal for translational research. 1307-1316 - Jeffrey A. van Santen
The Natural Products Atlas 2.0: a database of microbially-derived natural products. 1317-1323 - Xueni Sun, Yintao Zhang
NPCDR: natural product-based drug combination and its disease-specific molecular regulation. 1324-1333 - Gongyu Tang
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer. 1334-1339 - Yangjun Zhang
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. 1340-1347 - Nikta Feizi, Sisira Kadambat Nair
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. 1348-1357 - Hai Fang
Priority index: database of genetic targets in immune-mediated disease. 1358-1367 - Constantin Schneider
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker. 1368-1372 - Xiaotong Luo, Yuantai Huang, Huiqin Li, Yihai Luo
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients. 1373-1381 - Alessandro Cuozzo, Antoine Daina
SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface. 1382-1390 - Zexian Zeng
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. 1391-1397 - Ying Zhou, Yintao Zhang
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents. 1398-1407 - Dandan Huang, Yao Zhou
VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. 1408-1416 - Tingting Fu, Fengcheng Li
VARIDT 2.0: structural variability of drug transporter. 1417-1431 - Haixu Chen, Tianpeng Wang
BRAD V3.0: an upgraded Brassicaceae database. 1432-1441 - Marco Di Marsico, Andreu Paytuví Gallart, Walter Sanseverino
GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. 1442-1447 - Jingjing Jin
PCMDB: a curated and comprehensive resource of plant cell markers. 1448-1455 - Xuelian Ma
PlantGSAD: a comprehensive gene set annotation database for plant species. 1456-1467 - Michiel Van Bel
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants. 1468-1474 - Zhonglong Guo
PmiREN2.0: from data annotation to functional exploration of plant microRNAs. 1475-1482 - Joan Calle García
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process. 1483-1490 - Han Xue
qPTMplants: an integrative database of quantitative post-translational modifications in plants. 1491-1499 - Mélanie Courtot
BioSamples database: FAIRer samples metadata to accelerate research data management. 1500-1507 - Rita Pancsa
dNTPpoolDB: a manually curated database of experimentally determined dNTP pools and pool changes in biological samples. 1508-1514 - Suvarna Nadendla, Rebecca C. Jackson
ECO: the Evidence and Conclusion Ontology, an update for 2022. 1515-1521 - Tao Chen, Jie Ma
iProX in 2021: connecting proteomics data sharing with big data. 1522-1527 - Kannan Harini
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. 1528-1534 - Lukasz Pawel Kozlowski
Proteome-pI 2.0: proteome isoelectric point database update. 1535-1540 - Ludwig Lautenbacher
ProteomicsDB: toward a FAIR open-source resource for life-science research. 1541-
Volume 50, Number W1, July 2022
- Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022. 1-3
- Polina Belokopytova
3DGenBench: a web-server to benchmark computational models for 3D Genomics. 4-12 - Jake E. McGreig
3DLigandSite: structure-based prediction of protein-ligand binding sites. 13-20 - Chih-Chieh Chen
5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey. 21-28 - René Staritzbichler
AlignMe: an update of the web server for alignment of membrane protein sequences. 29-35 - Minh N. Nguyen
AllerCatPro 2.0: a web server for predicting protein allergenicity potential. 36-43 - Wanda Niemyska
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. 44-50 - Alexandr Boytsov
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. 51-56 - Zhu Liu, Tremayne Mushayahama, Bryan Queme
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. 57-65 - Qifan Zeng, Baojun Zhao
Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture. 66-74 - Yi Yang, Yufeng Mao, Ruoyu Wang, Haoran Li, Ye Liu, Haijiao Cheng, Zhenkun Shi
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms. 75-82 - Robin Steinhaus
AutozygosityMapper: Identification of disease-mutations in consanguineous families. 83-89 - András Micsonai, Éva Moussong
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy. 90-98 - Genis Bayarri
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. 99-107 - Bilal Shaikh
BioSimulators: a central registry of simulation engines and services for recommending specific tools. 108-114 - David S. Wishart
BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. 115-123 - Fedor A. Kolpakov
BioUML - towards a universal research platform. 124-131 - Georges Pierre Schmartz
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning. 132-137 - Michael Hartung
Cancer driver drug interaction explorer. 138-144 - Antonin Kunka, David Lacko, Jan Stourac
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. 145-151 - David Kuták
CATANA: an online modelling environment for proteins and nucleic acid nanostructures. 152-158 - Yang Liu
CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting. 159-164 - Fei Wang, Dana Allen, Siyang Tian, Eponine Oler, Vasuk Gautam, Russell Greiner, Thomas O. Metz, David S. Wishart
CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. 165-174 - Zhaonan Zou
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. 175-182 - Muntaha Samad, Forest Agostinelli, Tomoki Sato
CircadiOmics: circadian omic web portal. 183-190 - Vasileios Konstantakos
CRISPRedict: a CRISPR-Cas9 web tool for interpretable efficiency predictions. 191-198 - Thach Nguyen
Identification of genome edited cells using CRISPRnano. 199-203 - Carlos H. M. Rodrigues, David B. Ascher
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. 204-209 - Liisa Holm
Dali server: structural unification of protein families. 210-215 - Brad T. Sherman, Ming Hao
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). 216-221 - Ludovica Montanucci, Emidio Capriotti
DDGun: an untrained predictor of protein stability changes upon amino acid variants. 222-227 - Vineet Thumuluri, José Juan Almagro Armenteros
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. 228-234 - Xiaogen Zhou
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. 235-245 - Fei Ji, Gracia Bonilla, Rustem Krykbaev, Gary Ruvkun, Yuval Tabach, Ruslan I. Sadreyev
DEPCOD: a tool to detect and visualize co-evolution of protein domains. 246-253 - Suyeon Wy
DLEB: a web application for building deep learning models in biological research. 254-260 - Razieh Mohammadi-Arani
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes. 261-265 - Christopher P. Jurich, Amir Brivanlou, Silvi Rouskin, Joseph D. Yesselman
Web-based platform for analysis of RNA folding from high throughput chemical probing data. 266-271 - Aleksandr Ianevski
DrugVirus.info 2.0: an integrative data portal for broad-spectrum antivirals (BSA) and BSA-containing drug combinations (BCCs). 272-275 - Fábio Madeira
Search and sequence analysis tools services from EMBL-EBI in 2022. 276-279 - Michael Soutschek
enrichMiR predicts functionally relevant microRNAs based on target collections. 280-289 - Li Tang, Zhizhou Zhong
EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions. 290-297 - Zhitao Mao
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. 298-304 - Marc-André Legault
ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans. 305-311 - Xian Liu
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data. 312-321 - Robin Steinhaus
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding. 322-329 - Anne de Jong
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. 330-336 - András Hatos
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. 337-344 - Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. 345-351 - Jorge Botas
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. 352-357 - Christopher A. Mancuso, Patrick S. Bills
GenePlexus: a web-server for gene discovery using network-based machine learning. 358-366 - Guy P. Hunt
GEOexplorer: a webserver for gene expression analysis and visualisation. 367-374 - Nur Syatila Abdul Ghani
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA. 375-383 - Erich R. Kuechler
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents. 384-391 - Charles Abreu Santana, Sandro C. Izidoro
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. 392-397 - Deniz Seçilmis
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods. 398-404 - Wanshan Ning
HemI 2.0: an online service for heatmap illustration. 405-411 - Francesco Oteri
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families. 412-419 - Yubin Xie
IBS 2.0: an upgraded illustrator for the visualization of biological sequences. 420-426 - Andrew Jiang
ICARUS, an interactive web server for single cell RNA-seq analysis. 427-433 - Zhen Chen, Xuhan Liu
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. 434-447 - Dmitri S. Pavlichin, Hojoon Lee
KmerKeys: a web resource for searching indexed genome assemblies and variants. 448-453 - Wei Zheng
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. 454-464 - Joan Planas-Iglesias
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. 465-473 - Aleksandra E. Badaczewska-Dawid
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes. 474-482 - Michelle Kampfrath
MDsrv: visual sharing and analysis of molecular dynamics simulations. 483-489 - Fabio Marchiano
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context. 490-499 - Shu-Cheng Liu, Yan-Ru Ju, Chin Lung Lu
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes. 500-509 - Magnus Haraldson Høie
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning. 510-515 - Caroline Vernette
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. 516-526 - Guangyan Zhou, Zhiqiang Pang, Yao Lu, Jessica Ewald
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics. 527-533 - Ivan S. Ilnitskiy
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins. 534-540 - Leighton J. Payne
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. 541-550 - Tianyuan Liu
PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. 551-559 - Mirko Schmitz
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures. 560-567 - Chao Xue
PCGA: a comprehensive web server for phenotype-cell-gene association analysis. 568-576 - Ziqi Deng
PhyloCloud: an online platform for making sense of phylogenomic data. 577-582 - Hai Fang
PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions. 583-592 - David Jakubec, Petr Skoda
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. 593-597 - Marin Matic, Gurdeep Singh, Francesco Carli, Natalia De Oliveira Rosa, Pasquale Miglionico, Lorenzo Magni, J. Silvio Gutkind
PRECOGx: exploring GPCR signaling mechanisms with deep protein representations. 598-610 - Katrin Schöning-Stierand
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. 611-615 - Peng-Hsuan Li
pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature. 616-622 - Yannis Nevers, Tamsin E. M. Jones
The Quest for Orthologs orthology benchmark service in 2022. 623-632 - Lei Zheng
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets. 633-638 - Zoe Weiss
REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments. 639-650 - Damiano Clementel
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles. 651-656 - Marcin Magnus
rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow. 657-662 - Kamil Luwanski, Vladyslav Hlushchenko, Mariusz Popenda, Tomasz Zok
RNAspider: a webserver to analyze entanglements in RNA 3D structures. 663-669 - Walter Santana-Garcia
RSAT 2022: regulatory sequence analysis tools. 670-676 - Robin Steinhaus
Deep phenotyping: symptom annotation made simple with SAMS. 677-681 - Mehmet Direnç Mungan
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. 682-689 - Mariia Emelianova, Anastasiia N. Gainullina, Nikolay Poperechnyi, Alexander A. Loboda, Maxim N. Artyomov, Alexey A. Sergushichev
Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks. 690-696 - John Erol Evangelista
SigCom LINCS: data and metadata search engine for a million gene expression signatures. 697-709 - Ernesto Aparicio-Puerta
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. 710-717 - Joanne Watson, Michael Smith
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment. 718-725 - Kathleen Gallo, Andrean Goede
SuperPred 3.0: drug classification and target prediction - a machine learning approach. 726-731 - Gabriel Cretin
SWORD2: hierarchical analysis of protein 3D structures. 732-738 - Aleksandr Ianevski
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. 739-743 - Barbara Poszewiecka
TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure. 744-752 - Dominique Sydow
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. 753-760 - Li Chen, Tianjian Chen, Ya Zhang, Haichen Lin, Ruihan Wang, Yihang Wang, Hongyu Li, Zhixiang Zuo
TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response. 761-767 - Meng Wang
VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens. 768-773 - Daofeng Li
WashU Epigenome Browser update 2022. 774-781 - Yulin Dai
WebCSEA: web-based cell-type-specific enrichment analysis of genes. 782-
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