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ORCIDNucleic 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
, Alex Bateman, Cath Brooksbank, Mallory Ann Freeberg, Melissa Harrison, Matthew Hartley, Thomas M. Keane, Gerard J. Kleywegt, Andrew Leach, Maria Levchenko, Sarah L. Morgan, Ellen M. McDonagh, Sandra E. Orchard, Irene Papatheodorou, Sameer Velankar, Juan Antonio Vizcaíno, Rick Witham, Barbara Zdrazil, Johanna R. McEntyre:
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, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Catherine M. Farrell, Michael Feldgarden, Anna M. Fine, Kathryn Funk, Eneida Hatcher, Sivakumar Kannan, Christopher Kelly, Sunghwan Kim, William Klimke, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Adriana J. Malheiro, Aron Marchler-Bauer, Terence D. Murphy, Lon Phan, Shashikant Pujar, Sanjida H. Rangwala, Valerie A. Schneider, Tony Tse, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the National Center for Biotechnology Information in 2023. 29-38 - Wen-Kang Shen, Si-Yi Chen, Zi-Quan Gan, Yu-Zhu Zhang, Tao Yue, Miaomiao Chen, Yu Xue, Hui Hu, An-Yuan Guo:
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, Chang Liu, Di Wu, Qiaojuan Huang, Ling-Ling Zheng, Shurong Liu, Keren Zhou, Liang-Hu Qu, Bin Li, Jian-Hua Yang:
ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes. 46-56 - Qiangwei Zhou, Sheng Cheng, Shanshan Zheng, Zhenji Wang, Pengpeng Guan, Zhixian Zhu, Xingyu Huang, Cong Zhou, Guoliang Li:
ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms. 57-69 - Jiankang Wang, Ryuichiro Nakato:
CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells. 70-79 - Takeshi Obayashi, Shun Kodate, Himiko Hibara, Yuki Kagaya, Kengo Kinoshita:
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, Qiuyu Wang, Hong Sun, Qiaoli Fang, Xiaozheng Xu, Enmin Li, Chunquan Li:
CRdb: a comprehensive resource for deciphering chromatin regulators in human. 88-100 - Yasuhiro Tanizawa, Takatomo Fujisawa, Yuichi Kodama, Takehide Kosuge, Jun Mashima, Tomoya Tanjo, Yasukazu Nakamura:
DNA Data Bank of Japan (DDBJ) update report 2022. 101-105 - Yuxin Zhang, Jie Jiang, Jiongming Ma, Zhen Wei, Yue Wang, Bowen Song, Jia Meng, Guifang Jia, João Pedro de Magalhães, Daniel J. Rigden, Daiyun Hang, Kunqi Chen:
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. 106-116 - Mei-Jing Dong, Hao Luo, Feng Gao:
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes. 117-120 - Josephine Burgin, Alisha Ahamed, Carla A. Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan Gupta, Vikas Gupta, Muhammad Haseeb, Maira Ihsan, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Ankur Lathi, Rasko Leinonen, Milena Mansurova, Jasmine McKinnon, Colman O'Cathail, Joana Paupério, Stephane Pesant, Nadim Rahman, Gabriele Rinck, Sandeep Selvakumar, Swati Suman, Senthilnathan Vijayaraja, Zahra Waheed, Peter Woollard, David Yuan, Ahmad Zyoud, Tony Burdett, Guy Cochrane:
The European Nucleotide Archive in 2022. 121-125 - Haopeng Yu, Yiman Qi, Bibo Yang, Xiaofei Yang, Yiliang Ding:
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, Mark Cavanaugh, Karen Clark, Kim D. Pruitt, Stephen T. Sherry, Linda Yankie, Ilene Karsch-Mizrachi:
GenBank 2023 update. 141-144 - Priyanka Raina, Rodrigo Guinea, Kasit Chatsirisupachai, Inês Lopes, Zoya Farooq, Cristina Guinea, Csaba-Attila Solyom, João Pedro de Magalhães:
GeneFriends: gene co-expression databases and tools for humans and model organisms. 145-158 - Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong:
HiChIPdb: a comprehensive database of HiChIP regulatory interactions. 159-166 - Sonia García-Ruíz, Emil K. Gustavsson, David Zhang, Regina H. Reynolds, Zhongbo Chen, Aine Fairbrother-Browne, Ana Luisa Gil-Martínez, Juan A. Botía, Leonardo Collado-Torres, Mina Ryten:
IntroVerse: a comprehensive database of introns across human tissues. 167-178 - Ernesto Aparicio-Puerta, Pascal Hirsch, Georges Pierre Schmartz, Tobias Fehlmann, Verena Keller, Annika Engel, Fabian Kern, Michael Hackenberg, Andreas Keller:
isomiRdb: microRNA expression at isoform resolution. 179-185 - Zhao Li, Lin Liu, Changrui Feng, Yuxin Qin, Jing-Fa Xiao, Zhang Zhang, Lina Ma:
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, Jing Gong:
lncRNASNP v3: an updated database for functional variants in long non-coding RNAs. 192-198 - Hongying Zhao, Xiangzhe Yin, Haotian Xu, Kailai Liu, Wangyang Liu, Lixia Wang, Caiyu Zhang, Lin Bo, Xicheng Lan, Shihua Lin, Ke Feng, Shangwei Ning, Yunpeng Zhang, Li Wang:
LncTarD 2.0: an updated comprehensive database for experimentally-supported functional lncRNA-target regulations in human diseases. 199-207 - Mochen Zhang, Wenting Zong, Dong Zou, Guoliang Wang, Wei Zhao, Fei Yang, Song Wu, Xinran Zhang, Xutong Guo, Yingke Ma, Zhuang Xiong, Zhang Zhang, Yiming Bao, Rujiao Li:
MethBank 4.0: an updated database of DNA methylation across a variety of species. 208-2016 - Anne-Christin Hauschild, Chiara Pastrello, Gitta Kirana Anindya Ekaputeri, Dylan Bethune-Waddell, Mark Abovsky, Zuhaib Ahmed, Max Kotlyar, Richard Lu, Igor Jurisica:
MirDIP 5.2: tissue context annotation and novel microRNA curation. 217-225 - Andrea Cappannini, Kevin Mosca, Sunandan Mukherjee, Seyed Naeim Moafinejad, Richard R. Sinden, Veronique Arluison, Janusz M. Bujnicki, Frank Wien:
NACDDB: Nucleic Acid Circular Dichroism Database. 226-231 - Yu Zheng, Huaxia Luo, XueYi Teng, Xinpei Hao, Xiaoyu Yan, Yiheng Tang, Wanyu Zhang, Yuanxin Wang, Peng Zhang, Yanyan Li, Yi Zhao, Runsheng Chen, Shunmin He:
NPInter v5.0: ncRNA interaction database in a new era. 232-239 - Sébastien Bourdon, Pauline Herviou, Leïla Dumas, Eliana Destefanis, Andrea Zen, Anne Cammas, Stefania Millevoi, Erik Dassi:
QUADRatlas: the RNA G-quadruplex and RG4-binding proteins database. 240-247 - Qi Liu, Xin Peng, Mengyuan Shen, Qian Qian, Junlian Xing, Chen Li, Richard I. Gregory:
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, Yuanyin Huang, Taijiao Jiang, David M. J. Lilley, Zhichao Miao, Lin Huang:
Ribocentre: a database of ribozymes. 262-268 - Xiaoqiong Bao, Yin Zhang, Huiqin Li, Yuyan Teng, Lixia Ma, Zhihang Chen, Xiaotong Luo, Jian Zheng, An Zhao, Jian Ren, Zhixiang Zuo:
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, Étienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Laurence Faucher-Giguère, Philia Bouchard-Bourelle, Sherif Abou Elela, Frédéric Catez, Virginie Marcel, Michelle S. Scott:
snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs. 291-296 - Lingyu Guan, Andrey Grigoriev:
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, Yang Sun, Shi-Qiang Mei, Jian-Hua Yang, Liang-Hu Qu, Ling-Ling Zheng:
tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data. 315-327 - Felix Manske, Lynn Ogoniak, Lara Jürgens, Norbert Grundmann, Wojciech Makalowski, Klaus Wethmar:
The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. 328-336 - Claudio Lo Giudice, Federico Zambelli, Matteo Chiara, Giulio Pavesi, Marco Antonio Tangaro, Ernesto Picardi, Graziano Pesole:
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, Dominik Rafacz, Agnieszka Barbach, Katarzyna Hubicka, Laura Bakala, Anna Lassota, Jakub Stecko, Natalia Szymanska, Jakub Wojciechowski, Dominika Kozakiewicz, Natalia Szulc, Jaroslaw Chilimoniuk, Izabela Jeskowiak, Marlena Gasior-Glogowska, Malgorzata Kotulska:
AmyloGraph: a comprehensive database of amyloid-amyloid interactions. 352-357 - Anita E. Bandrowski, Mason Pairish, Peter Eckmann, Jeffrey S. Grethe, Maryann E. Martone:
The Antibody Registry: ten years of registering antibodies. 358-367 - Jeffrey C. Hoch, Kumaran Baskaran, Harrison Burr, John Chin, Hamid R. Eghbalnia, Toshimichi Fujiwara, Michael R. Gryk, Takeshi Iwata, Chojiro Kojima, Genji Kurisu, Dimitri Maziuk, Yohei Miyanoiri, Jonathan R. Wedell, Colin Wilburn, Hongyang Yao, Masashi Yokochi:
Biological Magnetic Resonance Data Bank. 368-376 - Ulka Gawde, Shuvechha Chakraborty, Faiza Hanif Waghu, Ram Shankar Barai, Ashlesha Khanderkar, Rishikesh Indraguru, Tanmay Shirsat, Susan Idicula-Thomas:
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, Damian Szklarczyk, Jorge Botas, Carlos P. Cantalapiedra, Joaquín Giner-Lamia, Daniel R. Mende, Rebecca Kirsch, Thomas Rattei, Ivica Letunic, Lars Juhl Jensen, Peer Bork, Christian von Mering, Jaime Huerta-Cepas:
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, David E. Gloriam:
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources. 395-402 - Jiho Sim, Sohee Kwon, Chaok Seok:
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, Zhenwei Pan, Xia Li, Juan Xu:
IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions. 409-417 - Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan Bridge, Lucy J. Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman:
InterPro in 2022. 418-427 - Daniel M. Tadros, Simon Eggenschwiler, Julien Racle, David Gfeller:
The MHC Motif Atlas: a database of MHC binding specificities and ligands. 428-437 - Damiano Piovesan, Alessio Del Conte, Damiano Clementel, Alexander Miguel Monzon, Martina Bevilacqua, Maria Cristina Aspromonte, Javier Iserte, Fernando E. Orti, Cristina Marino Buslje, Silvio C. E. Tosatto:
MobiDB: 10 years of intrinsically disordered proteins. 438-444 - Dmitry Kuznetsov, Fredrik Tegenfeldt, Mosè Manni, Mathieu Seppey, Matthew Berkeley, Evgenia V. Kriventseva, Evgeny M. Zdobnov:
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, Zheng Zhang:
PAT: a comprehensive database of prokaryotic antimicrobial toxins. 452-459 - Chao Hou, Xinxin Wang, Haotai Xie, Taoyu Chen, Peiyu Zhu, Xiaofeng Xu, Kaiqiang You, Tingting Li:
PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information. 460-465 - Qifang Xu, Roland L. Dunbrack Jr.:
The protein common assembly database (ProtCAD) - a comprehensive structural resource of protein complexes. 466-478 - Kai Yu, Ye Wang, Yongqiang Zheng, Zekun Liu, Qingfeng Zhang, Siyu Wang, Qi Zhao, Xiaolong Zhang, Xiaoxing Li, Rui-Hua Xu, Zexian Liu:
qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast. 479-487 - Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg V. Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Igor Khokhriakov, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben M. Webb, John D. Westbrook, Shamara Whetstone, Jasmine Young, Arthur O. Zalevsky, Christine Zardecki:
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, Anton S. Petrov, Khanh Dao Duc:
RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures. 509-516 - Laszlo Dobson, Levente I Szekeres, Csongor Gerdán, Tamás Langó, András Zeke, Gábor E. Tusnády:
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, Sarah Lafrance, Yifei Xing, Alberto A Nava, Héctor García Martín, Jay D. Keasling, Tyler W. H. Backman:
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, Barbara Brauner, Gisela Fobo, Goar Frishman, Corinna Montrone, Andreas Ruepp:
CORUM: the comprehensive resource of mammalian protein complexes-2022. 539-545 - Kuerbannisha Amahong, Wei Zhang, Ying Zhou, Song Zhang, Jiayi Yin, Fengcheng Li, Hong-Quan Xu, Tian-Ci Yan, Zi-Xuan Yue, Yu-Hong Liu, Tingjun Hou, Yunqing Qiu, Lin Tao, Lianyi Han, Feng Zhu:
CovInter: interaction data between coronavirus RNAs and host proteins. 546-556 - Jinfang Zheng, Boyang Hu, Xinpeng Zhang, Qiwei Ge, Yuchen Yan, Jerry Akresi, Ved Piyush, Le Huang, Yanbin Yin:
dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes. 557-563 - Daria Marakulina, Ilya E. Vorontsov, Ivan V. Kulakovskiy, Andreas Lennartsson, Finn Drabløs, Yulia A. Medvedeva:
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes. 564-570 - Nan Zhou, Xiaoqing Yuan, Qingsong Du, Zhiyu Zhang, Xiaolei Shi, Jinku Bao, Yuping Ning, Li Peng:
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations. 571-582 - Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen:
GotEnzymes: an extensive database of enzyme parameter predictions. 583-586 - Minoru Kanehisa, Miho Furumichi, Yoko Sato, Masayuki Kawashima, Mari Ishiguro-Watanabe:
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, Kai Blin, Jorge C. Navarro-Muñoz, Nicole E. Avalon, Marc G. Chevrette, Susan Egbert, Sanghoon Lee, David Meijer, Michael J. Recchia, Zachary L. Reitz, Jeffrey A. van Santen, Nelly Selem Mojica, Thomas Tørring, Liana Zaroubi, Mohammad Alanjary, Gajender Aleti, César Aguilar, Suhad A. Al-Salihi, Hannah E. Augustijn, J. Abraham Avelar-Rivas, Luis A. Avitia-Domínguez, Francisco Barona-Gómez, Jordan Bernaldo-Agüero, Vincent A. Bielinski, Friederike Biermann, Thomas J. Booth, J. Carrion Bravo, Raquel Castelo-Branco, Fernanda O. Chagas, Pablo Cruz-Morales, Chao Du, Katherine R. Duncan, Athina Gavriilidou, Damien Gayrard, Karina Gutiérrez-García, Kristina Haslinger, Eric J. N. Helfrich, Justin J. J. van der Hooft, Afif P. Jati, Edward Kalkreuter, Nikolaos Kalyvas, Kyo Bin Kang, Satria A. Kautsar, Wonyong Kim, Aditya M. Kunjapur, Yong-Xin Li, Geng-Min Lin, Catarina Loureiro, Joris J. R. Louwen, Nico l L. Louwen, George Lund, Jonathan Parra, Benjamin Philmus, Bita Pourmohsenin, Lotte U. Pronk, Adriana Rego, Devasahayam Arokia Balaya Rex, Serina L. Robinson, L. Rodrigo Rosas-Becerra, Eve T. Roxborough, Michelle A. Schorn, Darren J. Scobie, Kumar Saurabh Singh, Nika Sokolova, Xiaoyu Tang, Daniel W. Udwary, Aruna Vigneshwari, Kristiina Vind, Sophie P. J. M. Vromans, Valentin Waschulin, Sam E. Williams, Jaclyn M. Winter, Thomas E. Witte, Huali Xie, Dong Yang, Jingwei Yu, Mitja Zdouc, Zheng Zhong, Jérôme Collemare, Roger G. Linington, Tilmann Weber, Marnix H. Medema:
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. 603-610 - David S. Wishart, Eponine Oler, Harrison Peters, Anchi Guo, Sagan Girod, Scott Han, Sukanta Saha, Vicki W. Lui, Marcia Levatte, Vasuk Gautam, Rima Kaddurah-Daouk, Naama Karu:
MiMeDB: the Human Microbial Metabolome Database. 611-620 - Hui Zhao, Yuan Yang, Shuaiqi Wang, Xue Yang, Kaicheng Zhou, Caili Xu, Xuyao Zhang, Jiajun Fan, Dongyue Hou, Xingxiu Li, Hanbo Lin, Ying Tan, Shanshan Wang, Xinyi Chu, Dongzhi Zhuoma, Fengying Zhang, Dianwen Ju, Xian Zeng, Yu Zong Chen:
NPASS database update 2023: quantitative natural product activity and species source database for biomedical research. 621-628 - Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
REBASE: a database for DNA restriction and modification: enzymes, genes and genomes. 629-630 - Prisca Lo Surdo, Marta Iannuccelli, Silvia Contino, Luisa Castagnoli, Luana Licata, Gianni Cesareni, Livia Perfetto:
SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update. 631-637 - Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina C. Nastou, Farrokh Mehryary, Radja Hachilif, Annika L. Gable, Tao Fang, Nadezhda T. Doncheva, Sampo Pyysalo, Peer Bork, Lars Juhl Jensen, Christian von Mering:
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, Erwan Le Corre, Tristan Barbeyron, Gurvan Michel:
SulfAtlas, the sulfatase database: state of the art and new developments. 647-653 - Kathleen Gallo, Emanuel Kemmler, Andrean Goede, Finnja Becker, Mathias Dunkel, Robert Preissner, Priyanka Banerjee:
SuperNatural 3.0 - a database of natural products and natural product-based derivatives. 654-659 - Nozomu Sakurai, Shinichi Yamazaki, Kunihiro Suda, Ai Hosoki, Nayumi Akimoto, Haruya Takahashi, Daisuke Shibata, Yuichi Aoki:
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, Donald M. Dempsey, Allan Dickerman, Emily M. Dietrich, Ronald W. Kenyon, Mehmet Kuscuoglu, Elliot J. Lefkowitz, Jian Lu, Dustin Machi, Catherine Macken, Chunhong Mao, Anna Maria Niewiadomska, Marcus Nguyen, Gary J. Olsen, Jamie C. Overbeek, Bruce D. Parrello, Victoria Parrello, Jacob s Porter, Gordon D. Pusch, Maulik Shukla, Indresh Singh, Lucy Stewart, Gene Tan, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Zachary S. Wallace, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann, Rick L. Stevens:
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. 678-689 - Brian P. Alcock, William Huynh, Romeo Chalil, Keaton W. Smith, Amogelang R. Raphenya, Mateusz A. Wlodarski, Arman Edalatmand, Aaron J. Petkau, Sohaib A. Syed, Kara K. Tsang, Sheridan J. C. Baker, Mugdha Dave, Madeline C. McCarthy, Karyn M. Mukiri, Jalees A. Nasir, Bahar Golbon, Hamna Imtiaz, Xingjian Jiang, Komal Kaur, Megan Kwong, Zi Cheng Liang, Keyu C. Niu, Prabakar Shan, Jasmine Y. J. Yang, Kristen L. Gray, Gemma Hoad, Baofeng Jia, Timsy Bhando, Lindsey A. Carfrae, Maya A. Farha, Shawn French, Rodion Gordzevich, Kenneth Rachwalski, Megan M. Tu, Emily Bordeleau, Damion M. Dooley, Emma J. Griffiths, Haley L. Zubyk, Eric D. Brown, Finlay Maguire, Robert G. Beiko, William W. L. Hsiao, Fiona S. L. Brinkman, Gary H. Van Domselaar, Andrew G. McArthur:
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, Mingjun Zhao, Paul M. Kirk, Guomei Fan, Qinglan Sun, Bo Li, Shuai Wang, Zhengfei Yu, Dong Han, Juncai Ma, Linhuan Wu, Yijian Yao:
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, Tongze Fu, Tianyi Zhao, Liang Cheng, Lei Shi, Xue Zhang:
gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions. 717-722 - I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan Ritter, Cody Webb, Dongying Wu, Neha Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos Kyrpides, Natalia Ivanova:
The IMG/M data management and analysis system v.7: content updates and new features. 723-732 - Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos Kyrpides, Simon Roux:
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. 733-743 - Nathalie Bonin, Enrique Doster, Hannah Worley, Lee J. Pinnell, Jonathan E. Bravo, Peter Ferm, Simone Marini, Mattia Prosperi, Noelle R. Noyes, Paul S. Morley, Christina Boucher:
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, Ben Allen, Germana Baldi, Martin Beracochea, Maxwell L. Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero, Guy Cochrane, Lucy J. Colwell, Tom Curtis, Alejandra Escobar-Zepeda, Tatiana A. Gurbich, Varsha Kale, Anton I. Korobeynikov, Shriya Raj, Alexander b Rogers, Ekaterina A. Sakharova, Santiago Sanchez, Darren J. Wilkinson, Robert D. Finn:
MGnify: the microbiome sequence data analysis resource in 2023. 753-759 - Anthony Fullam, Ivica Letunic, Thomas S. B. Schmidt, Quinten R. Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M. Maistrenko, Lukas Malfertheiner, Alessio Milanese, João F. Matias Rodrigues, Claudia Sanchis-López, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R. Mende:
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, Cameron L. M. Gilchrist, Jongsik Chun, Martin Steinegger:
UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. 777-784 - Miguel Cacho Teixeira, Romeu Viana, Margarida Palma, Jorge Oliveira, Mónica Galocha, Marta Neves Mota, Diogo Couceiro, Maria Galhardas Pereira, Miguel Antunes, Inês V. Costa, Pedro Pais, Carolina Parada, Claudine Chaouiya, Isabel Sá-Correia, Pedro Tiago Monteiro:
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. 785-791 - Xin Gao, Fang Hong, Zhenyu Hu, Zilong Zhang, Le Yang, Xiaoyun Li, Tao Cheng:
ABC portal: a single-cell database and web server for blood cells. 792-804