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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 J. 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 - Kexin Huang, Hoaran Gong, Jingjing Guan, Lingxiao Zhang, Changbao Hu, Weiling Zhao, Liyu Huang, Wei Zhang, Pora Kim, Xiaobo Zhou:
AgeAnno: a knowledgebase of single-cell annotation of aging in human. 805-815 - Yingjie Gao, Guanghui Jiang, Wenqian Yang, Weiwei Jin, Jing Gong, Xuewen Xu, Xiaohui Niu:
Animal-SNPAtlas: a comprehensive SNP database for multiple animals. 816-826 - Yi-Min Zheng, Yitian Chen, Xianting Ding, Koon Ho Wong, Edwin Cheung:
Aquila: a spatial omics database and analysis platform. 827-834 - Siyu Pan, Hongen Kang, Xinxuan Liu, Shiqi Lin, Na Yuan, Zhang Zhang, Yiming Bao, Peilin Jia:
Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits. 835-844 - Zeynep Kosaloglu-Yalçin, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters:
The Cancer Epitope Database and Analysis Resource (CEDAR). 845-852 - Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Yunfei Shang, Tong Jin, Yuansheng Zhang, Ming Chen, Zishan Wu, Yuan Chu, Rongqin Zhang, Sicheng Luo, Wei Jing, Dong Zou, Yiming Bao, Jing-Fa Xiao, Zhang Zhang:
Cell Taxonomy: a curated repository of cell types with multifaceted characterization. 853-860 - Qiuyan Guo, Peng Wang, Qian Liu, Yangyang Hao, Yue Gao, Yue Qi, Rongji Xu, Hongyan Chen, Mengyu Xin, Xiaoting Wu, Rui Sun, Hui Zhi, Yunpeng Zhang, Shangwei Ning, Xia Li:
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, Peng Wang, Yunpeng Zhang:
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, Miren Bravo, Fei Chen, María L. Martínez-Chantar, Antonio del Sol:
ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells. 877-889 - Zhichao Li, Xiaosen Jiang, Mingyan Fang, Yong Bai, Siyang Liu, Shujia Huang, Xin Jin:
CMDB: the comprehensive population genome variation database of China. 890-895 - Dapeng Wang, Vinod Kumar, Katie L. Burnham, Alexander J. Mentzer, Brian D. Marsden, Julian C. Knight:
COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas. 896-905 - Jianguo Lu, Peilin Huang, Jialiang Sun, Jian Liu:
DupScan: predicting and visualizing vertebrate genome duplication database. 906-912 - Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong:
EDomics: a comprehensive and comparative multi-omics database for animal evo-devo. 913-923 - Lei Zheng, Pengfei Liang, Chunshen Long, Haicheng Li, Hanshuang Li, Yuchao Liang, Xiang He, Qilemuge Xi, Yongqiang Xing, Yongchun Zuo:
EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis. 924-932 - Fergal J. Martin, M. Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew E. Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R. B. Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Sarah M. Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García-Girón, Thiago Augusto Lopes Genez, Gurpreet S. Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike P. Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N. Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, José G. Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Elizabeth Wass, Natalie L. Willhoft, Jamie Allen, Jorge Álvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E. Loveland, Benjamin Moore, Jonathan M. Mudge, John G. Tate, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E. Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D. Finn, Kevin L. Howe, Peter W. Harrison, Andrew D. Yates, Paul Flicek:
Ensembl 2023. 933-941 - Adam Frankish, Silvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew E. Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet Riera, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah M. Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos García-Girón, Jose M. Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike P. Kay, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew D. Yates, Zahoor Zafrulla, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek:
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, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A. Nicolopoulos, Alessandro Favognano, I-Min A. Chen, Nikos Kyrpides, T. B. K. Reddy:
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9. 957-963 - Shipeng Guo, Zhougeng Xu, Xiangjun Dong, Dongjie Hu, Yanshuang Jiang, Qunxian Wang, Jie Zhang, Qian Zhou, Shengchun Liu, Weihong Song:
GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets. 964-968 - Xiaonan Liu, Dongmei Tian, Cuiping Li, Bixia Tang, Zhonghuang Wang, Rongqin Zhang, Yitong Pan, Yi Wang, Dong Zou, Zhang Zhang, Shuhui Song:
GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals. 969-976 - Elliot Sollis, Abayomi Mosaku, Ala Abid, Annalisa Buniello, Maria Cerezo, Laurent Gil, Tudor Groza, Osman Nuri Günes, Peggy Hall, James D. Hayhurst, Arwa Ibrahim, Yue Ji, Sajo John, Elizabeth Lewis, Jacqueline A. L. MacArthur, Aoife McMahon, David Osumi-Sutherland, Kalliope Panoutsopoulou, Zoë May Pendlington, Santhi Ramachandran, Raymund Stefancsik, Jonathan Stewart, Patricia L. Whetzel, Robert J. Wilson, Lucia Hindorff, Fiona Cunningham, Samuel A. Lambert, Michael Inouye, Helen E. Parkinson, Laura W. Harris:
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. 977-985 - Tim Beck, Thomas Rowlands, Tom Shorter, Anthony J. Brookes:
GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies. 986-993 - Guangya Duan, Gangao Wu, Xiaoning Chen, Dongmei Tian, Zhaohua Li, Yanling Sun, Zhenglin Du, Lili Hao, Shuhui Song, Yuan Gao, Jing-Fa Xiao, Zhang Zhang, Yiming Bao, Bixia Tang, Wenming Zhao:
HGD: an integrated homologous gene database across multiple species. 994-1002 - Ruth L. Seal, Bryony Braschi, Kristian A. Gray, Tamsin E. M. Jones, Susan Tweedie, Liora Haim-Vilmovsky, Elspeth A. Bruford:
Genenames.org: the HGNC resources in 2023. 1003-1009 - Youngseok Choi, Sojin Ahn, Myeongkyu Park, Saetbyeol Lee, Seoae Cho, Heebal Kim:
HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method. 1010-1018 - Lu Pan, Shaobo Shan, Roman Tremmel, Weiyuan Li, Zehuan Liao, Hangyu Shi, Qishuang Chen, Xiaolu Zhang, Xuexin Li:
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, Federico López-Gómez, Hamed Haseli Mashhadi, Violeta Muñoz-Fuentes, Osman Nuri Günes, Robert J. Wilson, Pilar Cacheiro, Anthony Frost, Piia Keskivali-Bond, Bora Vardal, Aaron McCoy, Tsz Kwan Cheng, Luis A. Santos, Sara Wells, Damian Smedley, Ann-Marie Mallon, Helen E. Parkinson:
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. 1038-1045 - Xuelian Ma, Shumin Cheng, Ruofan Ding, Zhaozhao Zhao, Xudong Zou, Shouhong Guang, Qixuan Wang, Huan Jing, Chen Yu, Ting Ni, Lei Li:
ipaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues. 1046-1052 - Dominic J. Barker, Giuseppe Maccari, Xenia Georgiou, Michael A. Cooper, Paul Flicek, James Robinson, Steven G. E. Marsh:
The IPD-IMGT/HLA Database. 1053-1060 - Haoteng Yan, Ronghao Wang, Shuai Ma, Daoran Huang, Si Wang, Jie Ren, Changfa Lu, Xin Chen, Xiaoyong Lu, Zikai Zheng, Weiqi Zhang, Jing Qu, Yuanchun Zhou, Guang-Hui Liu:
Lineage Landscape: a comprehensive database that records lineage commitment across species. 1061-1066 - Molly A. Bogue, Robyn L. Ball, Vivek M. Philip, David O. Walton, Matthew H. Dunn, Georgi Kolishovski, Anna Lamoureux, Matthew Gerring, Hongping Liang, Jake Emerson, Tim Stearns, Hao He, Gaurab Mukherjee, John Bluis, Sejal Desai, Beth A. Sundberg, Beena Kadakkuzha, Kunde Ramamoorthy Govindarajan, Elissa J. Chesler:
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, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather Huot Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn a Garden, Michelle G. Giglio, Brian R. Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P. Receveur, Mike Schor, Shreyash Sonthalia, Timothy L. Tickle, Jessica Way, Ronna Hertzano, Anup A. Mahurkar, Owen R. White:
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, Qiang Li, Zhaoyu Zhai, Xuelu Zhang, Zhewei Lin, Ni Kuang, Jianbo Pan:
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, Jieya Gao, Shiyong Ma, Jianbo Pan:
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, Shaohua Fan, Guoqing Zhang, Shuhua Xu:
PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. 1109-1116 - Lance C. Novak, Juihsuan Chou, Medina Colic, Christopher A. Bristow, G. Traver Hart:
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, Daniel Montemayor, Janet Li, Simon A. Levy, Roshan Pawar, Stella Hartono, Kumar Sharma, Bess Frost, Frédéric Chedin, Alexander J. R. Bishop:
Exploration and analysis of R-loop mapping data with RLBase. 1129-1137 - Zhiwei Fan, Yangyang Luo, Huifen Lu, Tiangang Wang, Yuzhou Feng, Weiling Zhao, Pora Kim, Xiaobo Zhou:
SPASCER: spatial transcriptomics annotation at single-cell resolution. 1138-1149 - Yangfeng Chen, Xingliang Zhang, Xi Peng, Yicheng Jin, Peiwen Ding, Jiedan Xiao, Changxiao Li, Fei Wang, Ashley Chang, Qizhen Yue, Mingyi Pu, Peixin Chen, Jiayi Shen, Mengrou Li, Tengfei Jia, Haoyu Wang, Li Huang, Guoji Guo, Wensheng Zhang, Hebin Liu, Xiangdong Wang, Dongsheng 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, Mulong Du, Meilin Wang:
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, Xiaosen Jiang, Ziyuan Ke, Xiaoyan Chen, Ye Cao, Yvonne K. Kwok, Matthew I. Bellgard, Tak Yeung Leung, Kwong wai Choy, Zirui Dong:
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, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qain, Jie Liu, Meiye Jiang, Hao Zhang, Congfan Bu, Jinyue Wang, Zhewen Zhang, Zaichao Zhang, Jingyao Zeng, Jiao Li, Jing-Fa Xiao:
TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. 1179-1187 - Luis R. Nassar, Galt P. Barber, Anna Benet-Pagès, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clayton M. Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Brian T. Lee, Christopher M. Lee, Pranav Muthuraman, Beagan Nguy, Tiana Pereira, Parisa Nejad, Gerardo Perez, Brian J. Raney, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent:
The UCSC Genome Browser database: 2023 update. 1188-1195 - Song Wu, Yue Huang, Mochen Zhang, Zheng Gong, Guoliang Wang, Xinchang Zheng, Wenting Zong, Wei Zhao, Peiqi Xing, Rujiao Li, Zhaoqi Liu, Yiming Bao:
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, Hsueh-Fen Juan:
BIC: a database for the transcriptional landscape of bacteria in cancer. 1205-1211 - Patrizio Di Micco, Albert A. Antolin, Costas Mitsopoulos, Eloy D. Villasclaras-Fernández, Domenico Sanfelice, Daniela Dolciami, Pradeep Ramagiri, Ioan L. Mica, Joseph E. Tym, Philip w Gingrich, Huabin Hu, Paul Workman, Bissan Al-Lazikani:
canSAR: update to the cancer translational research and drug discovery knowledgebase. 1212-1219 - David S. Wishart, Sagan Girod, Harrison Peters, Eponine Oler, Juan Jovel, Zachary Budinski, Ralph Milford, Vicki W. Lui, Zinat Sayeeda, Robert Mah, William Wei, Hasan Badran, Elvis J. Lo, Mai Yamamoto, Yannick Djoumbou Feunang, Naama Karu, Vasuk Gautam:
ChemFOnt: the chemical functional ontology resource. 1220-1229 - Kilannin Krysiak, Arpad M. Danos, Jason Saliba, Joshua F. McMichael, Adam C. Coffman, Susanna Kiwala, Erica K. Barnell, Lana Sheta, Cameron J. Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Sarah Ridd, Nicholas C. Spies, Veronica Andric, Andreea Chiorean, Damian Tobias Rieke, Kaitlin A. Clark, Caralyn Reisle, Ajay C. Venigalla, Mark Evans, Payal Jani, Hideaki Takahashi, Avila Suda, Peter Horák, Deborah i Ritter, Xin Zhou, Benjamin J. Ainscough, Sean Delong, Chimene Kesserwan, Mario Lamping, Haolin Shen, Alex Marr, My Hoang, Kartik Singhal, Mariam Khanfar, Brian V. Li, Wan-Hsin Lin, Panieh Terraf, Laura B. Corson, Yasser Salama, Katie M. Campbell, Kirsten M. Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Ian King, Kelsy C. Cotto, Zachary L. Skidmore, Jason R. Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y. Patel, Rachel H. Giles, Raymond H. Kim, Lynn M. Schriml, Elaine R. Mardis, Steven J. M. Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H. Wagner, Malachi Griffith, Obi L. Griffith:
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. 1230-1241 - Hatairat Yingtaweesittikul, Jiaxi Wu, Aanchal Mongia, Rafael Peres, Karrie Ko, Niranjan Nagarajan, Chayaporn Suphavilai:
CREAMMIST: an integrative probabilistic database for cancer drug response prediction. 1242-1248 - Jibiao Fan, Leisheng Shi, Qi Liu, Zhipeng Zhu, Fan Wang, Runxian Song, Jimeng Su, Degui Zhou, Xiao Chen, Kailong Li, Lixiang Xue, Lichao Sun, Fengbiao Mao:
Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase. 1249-1256 - Allan Peter Davis, Thomas C. Wiegers, Robin J. Johnson, Daniela Sciaky, Jolene Wiegers, Carolyn J. Mattingly:
Comparative Toxicogenomics Database (CTD): update 2023. 1257-1262 - Xiuna Sun, Yintao Zhang, Hanyang Li, Ying Zhou, Shuiyang Shi, Zhen Chen, Xin He, Hanyu Zhang, Fengcheng Li, Jiayi Yin, Minjie Mou, Yunzhu Wang, Yunqing Qiu, Feng Zhu:
DRESIS: the first comprehensive landscape of drug resistance information. 1263-1275 - Sorin I. Avram, Thomas B. Wilson, Ramona Curpan, Liliana Halip, Ana Borota, Alina Bora, Cristian Bologa, Jayme Holmes, Jeffrey Knockel, Jeremy J. Yang, Tudor I. Oprea:
DrugCentral 2023 extends human clinical data and integrates veterinary drugs. 1276-1287 - Fengcheng Li, Jiayi Yin, Mingkun Lu, Minjie Mou, Zhaorong Li, Zhenyu Zeng, Ying Tan, Shanshan Wang, Xinyi Chu, Haibin Dai, Tingjun Hou, Su Zeng, Yuzong Chen, Feng Zhu:
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, Xuewen Xu, Haohao Zhang, Lilin Yin, Mengjin Zhu, Mei Yu, Xinyun Li, Xiaolei Liu, Shuhong Zhao:
IAnimal: a cross-species omics knowledgebase for animals. 1312-1324 - Tiantongfei Jiang, Weiwei Zhou, Qi Sheng, Jiaxin Yu, Yunjin Xie, Na Ding, Yunpeng Zhang, Juan Xu, Yongsheng Li:
ImmCluster: an ensemble resource for immunology cell type clustering and annotations in normal and cancerous tissues. 1325-1332 - Shuiping Liu, Lu Chen, Yintao Zhang, Ying Zhou, Ying He, Zhen Chen, Shasha Qi, Jinyu Zhu, Xudong Chen, Hao Zhang, Yongchao Luo, Yunqing Qiu, Lin Tao, Feng Zhu:
M6AREG: m6A-centered regulation of disease development and drug response. 1333-1344 - Ping Wang, Sainan Zhang, Guoyou He, Meiyu Du, Changlu Qi, Ruyue Liu, Siyuan Zhang, Liang Cheng, Lei Shi, Xue Zhang:
microbioTA: an atlas of the microbiome in multiple disease tissues of Homo sapiens and Mus musculus. 1345-1352 - David Ochoa, Andrew Hercules, Miguel Carmona, Daniel Suveges, Jarrod Baker, Cinzia Malangone, Irene Lopez, Alfredo Miranda, Carlos Cruz-Castillo, Luca Fumis, Manuel Bernal Llinares, Kirill Tsukanov, Helena Cornu, Konstantinos Tsirigos, Olesya Razuvayevskaya, Annalisa Buniello, Jeremy Schwartzentruber, Mohd Anisul Karim, Bruno Ariano, Ricardo Esteban Martinez Osorio, Javier Ferrer, Xiangyu Ge, Sandra Machlitt-Northen, Asier Gonzalez-Uriarte, Shyamasree Saha, Santosh Tirunagari, Chintan Mehta, Juan María Roldán-Romero, Stuart Horswell, Sarah Young, Maya Ghoussaini, David G. Hulcoop, Ian Dunham, Ellen M. McDonagh:
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt. 1353-1359 - Zinaida Perova, Mauricio Martínez, Tushar Mandloi, Federico López-Gómez, Csaba Halmagyi, Alex Follette, Jeremy C. Mason, Steven Newhauser, Dale A. Begley, Debra M. Krupke, Carol J. Bult, Helen E. Parkinson, Tudor Groza:
PDCM Finder: an open global research platform for patient-derived cancer models. 1360-1366 - Gaoqi Weng, Xuanyan Cai, Dong-Sheng Cao, Hongyan Du, Chao Shen, Yafeng Deng, Qiaojun He, Bo Yang, Dan Li, Tingjun Hou:
PROTAC-DB 2.0: an updated database of PROTACs. 1367-1372 - Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A. Shoemaker, Paul A. Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E. Bolton:
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, Mingming Zhang:
RABC: Rheumatoid Arthritis Bioinformatics Center. 1381-1387 - Bowen Song, Xuan Wang, Zhanmin Liang, Jiongming Ma, Daiyun Huang, Yue Wang, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng, Gang Liu, Kunqi Chen, Zhen Wei:
RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. 1388-1396 - Jia Chen, Jiahao Lin, Yongfei Hu, Meijun Ye, Linhui Yao, Le Wu, Wenhai Zhang, Meiyi Wang, Tingting Deng, Feng Guo, Yan Huang, Bofeng Zhu, Dong Wang:
RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. 1397-1404 - Keith J. Kelleher, Timothy Sheils, Stephen L. Mathias, Jeremy J. Yang, Vincent T. Metzger, Vishal B. Siramshetty, Dac-Trung Nguyen, Lars Juhl Jensen, Dusica Vidovic, Stephan C. Schürer, Jayme Holmes, Karlie R. Sharma, Ajay Pillai, Cristian Bologa, Jeremy S. Edwards, Ewy A Mathé, Tudor I. Oprea:
Pharos 2023: an integrated resource for the understudied human proteome. 1405-1416 - Xueying Wang, Lingxi Chen, Wei Liu, Yuanzheng Zhang, Dawei Liu, Chenxin Zhou, Shuai Shi, Jiajie Dong, Zhengtao Lai, Bingran Zhao, Wenjingyu Zhang, Haoyue Cheng, Shuaicheng Li:
TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization. 1417-1424 - Ya Han, Yuting Wang, Xin Dong, Dongqing Sun, Zhaoyang Liu, Jiali Yue, Haiyun Wang, Taiwen Li, Chenfei Wang:
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment. 1425-1431 - Lianlian Wu, Bowei Yan, Junshan Han, Ruijiang Li, Jian Xiao, Song He, Xiaochen Bo:
TOXRIC: a comprehensive database of toxicological data and benchmarks. 1432-1445 - Zhiquan Yang, Jing Wang, Yiming Huang, Shengbo Wang, Lulu Wei, Dongxu Liu, Yonglin Weng, Jinhai Xiang, Qiang Zhu, Zhaoen Yang, Xinhui Nie, Yu Yu, Zuoren Yang, Qing-Yong 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, Sanwen Huang, Yong Xu, Yiqun Weng, Michael Mazourek, Cecilia McGregor, Susanne S. Renner, Sandra Branham, Chandrasekar Kousik, W. Patrick Wechter, Amnon Levi, Rebecca Grumet, Yi Zheng, Zhangjun Fei:
CuGenDBv2: an updated database for cucurbit genomics. 1457-1464 - Pragna Kotni, Theo J. L. van Hintum, Lorenzo Maggioni, Markus Oppermann, Stephan Weise:
EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material. 1465-1469 - Eliza C. Martin, Catalin F. Ion, Florin Ifrimescu, Laurentiu Spiridon, Jaap Bakker, Aska Goverse, Andrei-J. Petrescu:
NLRscape: an atlas of plant NLR proteins. 1470-1482 - Jinding Liu, Yaru Zhang, Yiqing Zheng, Yali Zhu, Yapin Shi, Zhuoran Guan, Kun Lang, Danyu Shen, Wen Huang, Daolong Dou:
PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples. 1483-1491 - Albert A. Antolin, Domenico Sanfelice, Alisa Crisp, Eloy Villasclaras fernandez, Ioan L. Mica, Yi Chen, Ian Collins, Aled Edwards, Susanne Müller, Bissan Al-Lazikani, Paul Workman:
The Chemical Probes Portal: an expert review-based public resource to empower chemical probe assessment, selection and use. 1492-1502 - Andrii Iudin, Paul K. Korir, Sriram Somasundharam, Simone Weyand, Cesare Cattavitello, Neli Fonseca, Osman Salih, Gerard J. Kleywegt, Ardan Patwardhan:
EMPIAR: the Electron Microscopy Public Image Archive. 1503-1511 - Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu:
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, Philipp Halama, Stefan Spring, Vera Thiel, Christiane Baschien, Richard L. Hahnke, Michael Pester, Jörg Overmann, Lorenz Christian Reimer:
MediaDive: the expert-curated cultivation media database. 1531-1538 - Eric W. Deutsch, Nuno Bandeira, Yasset Pérez-Riverol, Vagisha Sharma, Jeremy Carver, Luis Mendoza, Deepti Jaiswal Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaíno:
The ProteomeXchange consortium at 10 years: 2023 update. 1539-1548 - Louis Philip Benoit Bouvrette, Xiaofeng Wang, Jonathan Boulais, Jian Kong, Easin Uddin Syed, Steven M. Blue, Lijun Zhan, Sara Olson, Rebecca Stanton, Xintao Wei, Brian Yee, Eric L. Van nostrand, Xiang-Dong Fu, Christopher B. Burge, Brenton R. Graveley, Gene W. Yeo, Eric Lécuyer:
RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins. 1549-1557 - Esteban Martínez-García, Sofía Fraile, Elena Algar, Tomás Aparicio, Elena Velázquez, Belén Calles, Huseyin Tas, Blas Blázquez, Bruno Martín, Clara Prieto, Lucas Sánchez-Sampedro, Morten h H. Nørholm, Daniel c Volke, Nicolas T. Wirth, Pavel Dvorák, Lorea Alejaldre, Lewis Grozinger, Matthew Crowther, Ángel Goñi Moreno, Pablo I. Nikel, Juan Nogales, Víctor de Lorenzo:
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, Michal Kadlof, Kaustav Sengupta, Dariusz Plewczynski:
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, Karel Berka, Alessio Cantara, Ales Krenek, Dominik Tichý, Tomás Racek, Radka Svobodová Vareková:
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, Fan Wang, Ge-Fei Hao, Guangfu Yang:
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, Kun Song, Liang Zhang, Xuefeng Lu, Shaoyong Lu, Jian Zhang:
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, Simon Shaw, Hannah E. Augustijn, Zachary L. Reitz, Friederike Biermann, Mohammad Alanjary, Artem Fetter, Barbara R. Terlouw, William W. Metcalf, Eric J. N. Helfrich, Gilles P. van Wezel, Marnix H. Medema, Tilmann Weber:
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. 46-50 - Joshua S. Martin Beem, Sravani Venkatayogi, Barton F. Haynes, Kevin Wiehe:
ARMADiLLO: a web server for analyzing antibody mutation probabilities. 51-56 - Potdar Swapnil, Filipp Ianevski, Aleksandr Ianevski, ZiaurRehman Tanoli, Krister Wennerberg, Brinton Seashore-Ludlow, Olli-P. Kallioniemi, Päivi Östling, Tero Aittokallio, Saarela Jani:
Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. 57-61 - Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan:
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. 62-69 - Zhitao Mao, Qianqian Yuan, Haoran Li, Yue Zhang, Yuanyuan Huang, Chunhe Yang, Ruoyu Wang, Yongfu Yang, Yalun Wu, Shihui Yang, Xiaoping Liao, Hongwu Ma:
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. 70-77 - Alexandre Borrel, Mike Conway, Sue Nolte, Aswani Unnikrishnan, Charles Schmitt, Nicole C. Kleinstreuer:
ChemMaps.com v2.0: exploring the environmental chemical universe. 78-82 - Ottavio Croci, Stefano Campaner:
ChroKit: a Shiny-based framework for interactive analysis, visualization and integration of genomic data. 83-92 - Fengxia Zhou, Xiaorong Yu, Rui Gan, Kuan Ren, Chuangeng Chen, Chunyan Ren, Meng Cui, Yuchen Liu, Yiyang Gao, Shouyu Wang, Mingyu Yin, Tengjin Huang, Zhiwei Huang, Fan Zhang:
CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing. 93-107 - Kristian Barrett, Cameron J. Hunt, Lene Lange, Igor V. Grigoriev, Anne S. Meyer:
Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes. 108-114 - Jinfang Zheng, Qiwei Ge, Yuchen Yan, Xinpeng Zhang, Le Huang, Yanbin Yin:
dbCAN3: automated carbohydrate-active enzyme and substrate annotation. 115-121 - Yunzhuo Zhou, Qisheng Pan, Douglas E. V. Pires, Carlos H. M. Rodrigues, David B. Ascher:
DDMut: predicting effects of mutations on protein stability using deep learning. 122-128 - Qianqian Song, Mingyu Li, Qian Li, Xun Lu, Kun Song, Ziliang Zhang, Jiale Wei, Liang Zhang, Jiacheng Wei, Youqiong Ye, Jinyin Zha, Qiufen Zhang, Qiang Gao, Jiang Long, Xinyi Liu, Xuefeng Lu, Jian Zhang:
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, Jörg Gsponer, Lukasz A. Kurgan:
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, Egor Semenchenko, Irmtraud M. Meyer:
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, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan:
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, Yijie Wang, Yu Zhang, Sha Cao, Chi Zhang:
FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data. 180-190 - Turgut Mesut Yilmaz, Mehmet Direnç Mungan, Aileen Berasategui, Nadine Ziemert:
FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi. 191-197 - András Hatos, João M. C. Teixeira, Susana Barrera-Vilarmau, Attila Horvath, Silvio C. E. Tosatto, Michele Vendruscolo, Mónika Fuxreiter:
FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins. 198-206 - Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson:
g:Profiler - interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update). 207-212 - Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan:
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. 213-224 - Alan M. Cleary, Andrew D. Farmer:
Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes. 225-231 - Edo Dotan, Michael Alburquerque, Elya Wygoda, Dorothée Huchon, Tal Pupko:
GenomeFLTR: filtering reads made easy. 232-236 - Erik Faessler, Udo Hahn, Sascha Schäuble:
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, Di Peng, Yu Xue:
GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins. 243-250 - Urszula Orzel, Pawel Pasznik, Przemyslaw Miszta, Marcin Lorkowski, Szymon Niewieczerzal, Jakub Jakowiecki, Slawomir Filipek:
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, Florian Kronenberg, Lukas Forer:
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, Nicholas S. Edmunds, Ahmet G. Genc, Shuaa M. A Alharbi, Bajuna R. Salehe, Recep Adiyaman:
Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers. 274-280 - Guillaume Postic, Christophe Tav, Ludovic Platon, Farida Zehraoui, Fariza Tahi:
IRSOM2: a web server for predicting bifunctional RNAs. 281-288 - João Victor da Silva Guerra, Helder Veras Ribeiro filho, José Geraldo de Carvalho Pereira, Paulo Sérgio Lopes-de-Oliveira:
KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities. 289-297 - Brian Jiménez-García, Jorge Roel-Touris, Didier Barradas-Bautista:
The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions. 298-304 - Javier López-Ibáñez, Florencio Pazos, Monica Chagoyen:
MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. 305-309 - Yao Lu, Guangyan Zhou, Jessica Ewald, Zhiqiang Pang, Tanisha Shiri, Jianguo Xia:
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data. 310-318 - Ernesto Aparicio-Puerta, Pascal Hirsch, Georges Pierre Schmartz, Fabian Kern, Tobias Fehlmann, Andreas Keller:
miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations. 319-325 - Aliaksei Chareshneu, Adam Midlik, Crina-Maria Ionescu, Alexander S. Rose, Vladimír Horský, Alessio Cantara, Radka Svobodová Vareková, Karel Berka, David Sehnal:
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. 326-330 - Ferdous Nasri, Kunaphas Kongkitimanon, Alice Wittig, Jorge Sánchez Cortés, Annika Brinkmann, Andreas Nitsche, Anna-Juliane Schmachtenberg, Bernhard Y. Renard, Stephan Fuchs:
MpoxRadar: a worldwide MPXV genomic surveillance dashboard. 331-337 - Arthur Declercq, Robbin Bouwmeester, Cristina Chiva, Eduard Sabidó, Aurélie Hirschler, Christine Carapito, Lennart Martens, Sven Degroeve, Ralf Gabriels:
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, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodrigo Rodolpho, Ginger Tsueng, Casey S. Greene, Chunlei Wu:
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes. 350-356 - Qi Xu, Jeanne Kowalski:
NBBC: a non-B DNA burden explorer in cancer. 357-364 - Kai Liu, Xufeng Lu, Hang Shi, Xiaojun Xu, Ren Kong, Shan Chang:
nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands. 365-371 - Chantal Scheepbouwer, Michael Hackenberg, Monique A J. van Eijndhoven, Alan Gerber, Michiel Pegtel, Cristina Gómez-Martín:
NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods. 372-378 - Oriol Fornes, Tamar Vered Av-Shalom, Andrea J. Korecki, Rachelle A. Farkas, David J. Arenillas, Anthony Mathelier, Elizabeth M. Simpson, Wyeth W. Wasserman:
OnTarget: in silico design of MiniPromoters for targeted delivery of expression. 379-386 - Chaohui Bao, Shan Wang, Lulu Jiang, Zhongcheng Fang, Kexin Zou, James Lin, Saijuan Chen, Hai Fang:
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, Jörg Stülke:
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, Elena Piñeiro-Yáñez, Hugo López-Fernández, Santiago García-Martín, Paula Gómez-Plana, Miguel Reboiro-Jato, Gonzalo Gómez-López, Daniel Glez-Peña, Fátima Al-Shahrour:
PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data. 411-418 - Yanhui Hu, Aram Comjean, Helen Attrill, Giulia Antonazzo, Jim Thurmond, Weihang Chen, Fangge Li, Tiffany Chao, Stephanie E. Mohr, Nicholas H. Brown, Norbert Perrimon:
PANGEA: a new gene set enrichment tool for Drosophila and common research organisms. 419-426 - Hao Tian, Sian Xiao, Xi Jiang, Peng Tao:
PASSer: fast and accurate prediction of protein allosteric sites. 427-431 - Julien Rey, Samuel Murail, Sjoerd Jacob de Vries, Philippe Derreumaux, Pierre Tufféry:
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution. 432-437 - Anastasija Zaiko, Maximilian Scheel, Jessica Schattschneider, Ulla von Ammon, Michelle Scriver, Xavier Pochon, John K. Pearman:
Pest Alert Tool - a web-based application for flagging species of concern in metabarcoding datasets. 438-442 - David S. Wishart, Scott Han, Sukanta Saha, Eponine Oler, Harrison Peters, Jason R. Grant, Paul Stothard, Vasuk Gautam:
PHASTEST: faster than PHASTER, better than PHAST. 443-450 - Emidio Capriotti, Piero Fariselli:
PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants. 451-458 - David S. Wishart, Leah Ren, Jacques Leong-Sit, Sukanta Saha, Jason R. Grant, Paul Stothard, Upasana Singh, Abby Kropielnicki, Eponine Oler, Harrison Peters, Vasuk Gautam:
PlasMapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps. 459-467 - Yiran Xu, Jianghui Zhu, Wenze Huang, Kui Xu, Rui Yang, Qiangfeng Cliff Zhang, Lei Sun:
PrismNet: predicting protein-RNA interaction using in vivo RNA structural information. 468-477 - Moran Sharon, Gil Gruber, Chanan M. Argov, Miri Volozhinsky, Esti Yeger Lotem:
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, Morag Graham, Gary H. Van Domselaar, Paul Stothard:
Proksee: in-depth characterization and visualization of bacterial genomes. 484-492 - Rémi Gschwind, Svetlana Ugarcina perovic, Maja Weiss, Marie Petitjean, Julie Lao, Luís Pedro Coelho, Etienne Ruppé:
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. 493-500 - Philip Z. Johnson, Anne E. Simon:
RNAcanvas: interactive drawing and exploration of nucleic acid structures. 501-508 - Yunxia Wang, Zhen Chen, Ziqi Pan, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu:
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, Lu Zhang, Zikun Chen, Yuan Wang, Tiantian Mao, Caicui Wang, Yewei Cun, Genhui Zheng, Deyu Yan, Mengdi Zhou, Kailin Tang, Zhiwei Cao:
SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs. 528-534 - Simon Mendelsohn, David Froelicher, Denis Loginov, David Bernick, Bonnie Berger, Hyunghoon Cho:
sfkit: a web-based toolkit for secure and federated genomic analysis. 535-541 - Dávid Bajusz, Gáspár Pándy-Szekeres, Ágnes Takács, Elvin D. de araujo, György M. Keserü:
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, Chunfu Xiao, Juntian Qi, Weizhen Xue, Xinwei Xu, Zelin Mu, Jie Zhang, Chuan-Yun Li, Wanqiu Ding:
STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data. 560-568 - Rui Yin, Helder Veras Ribeiro filho, Valerie Lin, Ragul Gowthaman, Melyssa Cheung, Brian G. Pierce:
TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning. 569-576 - Tomasz Wozniak, Weronika Sura, Marta Kazimierska, Marta elzbieta Kasprzyk, Marta Podralska, Agnieszka Dzikiewicz-Krawczyk:
TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs. 577-586 - Jianmin Xie, Yuerong Chen, Guanjing Cai, Runlin Cai, Zhong Hu, Hui Wang:
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees. 587-592 - Ahmed Mohamed, Dharmesh D. Bhuva, Sam Lee, Ning Liu, Chin Wee Tan, Melissa J. Davis:
vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis. 593-600 - Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey A. Gurevich:
WebQUAST: online evaluation of genome assemblies. 601-606 - Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok:
WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. 607-612
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