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Semantic ScholarNucleic Acids Research, Volume 46
Volume 46, Number Database-Issue, January 2018
- Daniel J. Rigden, Xosé M. Fernández-Suárez:
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. D1-D7
- Database resources of the National Center for Biotechnology Information. D8-D13
- Database Resources of the BIG Data Center in 2018. D14-D20
- Charles E. Cook
, Mary Todd Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney:
The European Bioinformatics Institute in 2017: data coordination and integration. D21-D29
- Yuichi Kodama, Jun Mashima, Takehide Kosuge, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi:
DNA Data Bank of Japan: 30th anniversary. D30-D35 - Nicole Silvester, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Laura Clarke, Iain Cleland, Peter W. Harrison, Suran Jayathilaka, Simon Kay, Thomas M. Keane, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Manuela Menchi, Kethi Reddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Dmitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane:
The European Nucleotide Archive in 2017. D36-D40 - Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, James Ostell, Kim D. Pruitt, Eric W. Sayers:
GenBank. D41-D47 - Ilene Karsch-Mizrachi, Toshihisa Takagi, Guy Cochrane:
The international nucleotide sequence database collaboration. D48-D51 - Dongchan Yang, Insu Jang, Jinhyuk Choi, Minseo Kim, Andrew J. Lee, Hyun-Woong Kim, Junghyun Eom, Dongsup Kim, Inkyung Jung, Byungwook Lee:
3DIV: A 3D-genome Interaction Viewer and database. D52-D57 - Daejin Hyung, Jihyun Kim, Sooyoung Cho, Charny Park:
ASpedia: a comprehensive encyclopedia of human alternative splicing. D58-D63 - Xianfeng Li, Leisheng Shi, Kun Zhang, Wenqing Wei, Qi Liu, Fengbiao Mao, Jinchen Li, Wanshi Cai, Huiqian Chen, Huajing Teng, Jiada Li, Zhongsheng Sun:
CirGRDB: a database for the genome-wide deciphering circadian genes and regulators. D64-D70 - Moli Huang, Ye Chen, Manqiu Yang, Anyuan Guo, Ying Xu, Liang Xu, H. Phillip Koeffler:
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. D71-D77 - Guanxiong Zhang, Jian Shi, Shiwei Zhu, Yujia Lan, Liwen Xu, Huating Yuan, Gaoming Liao, Xiaoqin Liu, Yunpeng Zhang, Yun Xiao, Xia Li:
DiseaseEnhancer: a resource of human disease-associated enhancer catalog. D78-D84 - Ling-Ling Zheng, Ke-ren Zhou, Shun Liu, Ding-Yao Zhang, Ze-Lin Wang, Zhi-Rong Chen, Jian-Hua Yang, Liang-Hu Qu:
dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease. D85-D91 - Fengbiao Mao, Qi Liu, Xiaolu Zhao, Haonan Yang, Sen Guo, Luoyuan Xiao, Xianfeng Li, Huajing Teng, Zhongsheng Sun, Yali Dou:
EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases. D92-D99 - Bailing Zhou, Huiying Zhao, Jia-Feng Yu, Chengang Guo, Xianghua Dou, Feng Song, Guodong Hu, Zanxia Cao, Yuanxu Qu, Yuedong Yang, Yaoqi Zhou, Jihua Wang:
EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. D100-D105 - Shengli Li, Yuchen Li, Bing Chen, Jingjing Zhao, Shulin Yu, Yan Tang, Qiupeng Zheng, Yan Li, Peng Wang, Xianghuo He, Shenglin Huang:
exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. D106-D112 - Zhen Wang, Quanwei Zhang, Wen Zhang, Jhih-rong Lin, Ying Cai, Joydeep Mitra, Zhengdong D. Zhang:
HEDD: Human Enhancer Disease Database. D113-D120 - Jian Sang, Zhennan Wang, Man Li, Jiabao Cao, Guangyi Niu, Lin Xia, Dong Zou, Fan Wang, Xingjian Xu, Xiaojiao Han, Jinqi Fan, Ye Yang, Wanzhu Zuo, Yang Zhang, Wenming Zhao, Yiming Bao, Jing-Fa Xiao, Songnian Hu, Lili Hao, Zhang Zhang:
ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. D121-D126 - Monica Santamaria, Bruno Fosso, Flavio Licciulli, Bachir Balech, Ilaria Larini, Giorgio Grillo, Giorgio De Caro, Sabino Liuni, Graziano Pesole:
ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences. D127-D132 - Hui Zhi, Xin Li, Peng Wang, Yue Gao, Baoqing Gao, Dianshuang Zhou, Yan Zhang, Maoni Guo, Ming Yue, Weitao Shen, Shangwei Ning, Lianhong Jin, Xia Li:
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease. D133-D138 - Yueyuan Zheng, Peng Nie, Di Peng, Zhihao He, Mengni Liu, Yubin Xie, Yanyan Miao, Zhixiang Zuo, Jian Ren:
m6AVar: a database of functional variants involved in m6A modification. D139-D145 - Guohua Wang, Ximei Luo, Jianan Wang, Jun Wan, Shuli Xia, Heng Zhu, Jiang Qian, Yadong Wang:
MeDReaders: a database for transcription factors that bind to methylated DNA. D146-D151 - Venetia Pliatsika, Phillipe Loher, Rogan Magee, Aristeidis G. Telonis, Eric Londin, Megumi Shigematsu, Yohei Kirino, Isidore Rigoutsos:
MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. D152-D159 - Christina Backes, Tobias Fehlmann, Fabian Kern, Tim Kehl, Hans-Peter Lenhof, Eckart Meese, Andreas Keller:
miRCarta: a central repository for collecting miRNA candidates. D160-D167 - Xu Hua, Rongjun Tang, Xiuxiu Xu, Zhi Wang, Qi Xu, Luxiao Chen, Edgar Wingender, Jie Li, Chenyu Zhang, Jin Wang:
mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines. D168-D174 - René Dreos, Giovanna Ambrosini, Romain Groux, Rouaïda Cavin Périer, Philipp Bucher:
MGA repository: a curated data resource for ChIP-seq and other genome annotated data. D175-D180 - Ming Yue, Dianshuang Zhou, Hui Zhi, Peng Wang, Yan Zhang, Yue Gao, Maoni Guo, Xin Li, Yanxia Wang, Yunpeng Zhang, Shangwei Ning, Xia Li:
MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases. D181-D185 - Wojciech Rosikiewicz, Yutaka Suzuki, Izabela Makalowska:
OverGeneDB: a database of 5′ end protein coding overlapping genes in human and mouse genomes. D186-D193 - Jing Gong, Di Shao, Kui Xu, Zhipeng Lu, Zhi John Lu, Yu-Cheng T. Yang, Qiangfeng Cliff Zhang:
RISE: a database of RNA interactome from sequencing experiments. D194-D201 - Pietro Boccaletto, Marcin Magnus, Catarina Almeida, Adriana Zyla, Astha Astha, Radoslaw Pluta, Blazej Baginski, Elzbieta Jankowska, Stanislaw Dunin-Horkawicz, Tomasz Wirecki, Michal Boniecki, Filip Stefaniak, Janusz M. Bujnicki:
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information. D202-D205 - Wanting Liu, Lunping Xiang, Tingkai Zheng, Jingjie Jin, Gong Zhang:
TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data. D206-D212 - Jose Manuel Rodriguez, Juan Rodriguez-Rivas, Tomás Di Domenico, Jesús Vázquez, Alfonso Valencia, Michael L. Tress:
APPRIS 2017: principal isoforms for multiple gene sets. D213-D217 - Tala Bakheet, Edward Hitti, Khalid S. A. Khabar:
ARED-Plus: an updated and expanded database of AU-rich element-containing mRNAs and pre-mRNAs. D218-D220 - Shashikant Pujar, Nuala A. O'Leary, Catherine M. Farrell, Jane Loveland, Jonathan M. Mudge, Craig Wallin, Carlos García-Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E. Berry, Eric Cox, Claire Davidson, Tamara Goldfarb, Jose M. Gonzalez, Toby Hunt, John Jackson, Vinita S. Joardar, Mike P. Kay, Vamsi K. Kodali, Fergal J. Martin, Monica McAndrews, Kelly M. McGarvey, Michael R. Murphy, Bhanu Rajput, Sanjida H. Rangwala, Lillian D. Riddick, Ruth L. Seal, Marie-Marthe Suner, David Webb, Sophia Zhu, Bronwen L. Aken, Elspeth A. Bruford, Carol J. Bult, Adam Frankish, Terence D. Murphy, Kim D. Pruitt:
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. D221-D228 - Ayako Suzuki, Shin Kawano, Toutai Mituyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki:
DBTSS/DBKERO for integrated analysis of transcriptional regulation. D229-D238 - Dimitra Karagkouni, Maria D. Paraskevopoulou, Serafeim Chatzopoulos, Ioannis S. Vlachos, Spyros Tastsoglou, Ilias Kanellos, Dimitris Papadimitriou, Ioannis Kavakiotis, Sofia Maniou, Giorgos Skoufos, Thanasis Vergoulis, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. D239-D245 - Irene Papatheodorou, Nuno A. Fonseca, Maria Keays, Y. Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew J. Geniza, Justin Preece, Pankaj Jaiswal, Andrew Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaíno, Alvis Brazma, Robert Petryszak:
Expression Atlas: gene and protein expression across multiple studies and organisms. D246-D251 - Ivan V. Kulakovskiy, Ilya E. Vorontsov, Ivan S. Yevshin, Ruslan N. Sharipov, Alla D. Fedorova, Eugene I. Rumynskiy, Yulia A. Medvedeva, Arturo Magana-Mora, Vladimir B. Bajic, Dmitri A. Papatsenko, Fedor A. Kolpakov, Vsevolod J. Makeev:
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. D252-D259 - Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime Abraham Castro-Mondragón, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R. Kulkarni, Ge Tan, Damir Baranasic, David J. Arenillas, Albin Sandelin, Klaas Vandepoele, Boris Lenhard, Benoît Ballester, Wyeth W. Wasserman, François Parcy, Anthony Mathelier:
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. D260-D266 - Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, Benoît Ballester:
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. D267-D275 - Ya-Ru Miao, Wei Liu, Qiong Zhang, An-Yuan Guo:
lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs. D276-D280 - Hui Liu, Huaizhi Wang, Zhen Wei, Songyao Zhang, Gang Hua, Shao-Wu Zhang, Lin Zhang, Shou-Jiang Gao, Jia Meng, Xing Chen, Yufei Huang:
MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. D281-D287 - Rujiao Li, Fang Liang, Mengwei Li, Dong Zou, Shixiang Sun, Yongbing Zhao, Wenming Zhao, Yiming Bao, Jing-Fa Xiao, Zhang Zhang:
MethBank 3.0: a database of DNA methylomes across a variety of species. D288-D295 - Chih-Hung Chou, Sirjana Shrestha, Chi-Dung Yang, Nai-Wen Chang, Yu-Ling Lin, Kuang-Wen Liao, Wei-Chih Huang, Ting-Hsuan Sun, Siang-Jyun Tu, Wei-Hsiang Lee, Men-Yee Chiew, Chun-San Tai, Ting-Yen Wei, Tzi-Ren Tsai, Hsin-Tzu Huang, Chung-Yu Wang, Hsin-Yi Wu, Shu-Yi Ho, Pin-Rong Chen, Cheng-Hsun Chuang, Pei-Jung Hsieh, Yi-Shin Wu, Wen-Liang Chen, Meng-Ju Li, Yu-chun Wu, Xin-Yi Huang, Fung Ling Ng, Waradee Buddhakosai, Pei-Chun Huang, Kuan-Chun Lan, Chia-Yen Huang, Shun-Long Weng, Yeong-Nan Cheng, Chao Liang, Wen-Lian Hsu, Hsien-Da Huang:
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. D296-D302 - Pietro Boccaletto, Magdalena A. Machnicka, Elzbieta Purta, Pawel Piatkowski, Blazej Baginski, Tomasz Wirecki, Valérie de Crécy-Lagard, Robert Ross, Patrick A. Limbach, Annika Kotter, Mark Helm, Janusz M. Bujnicki:
MODOMICS: a database of RNA modification pathways. 2017 update. D303-D307 - Shuangsang Fang, Lili Zhang, Jincheng Guo, Yiwei Niu, Yang Wu, Hui Li, Lianhe Zhao, Xiyuan Li, XueYi Teng, XianHui Sun, Liang Sun, Michael Q. Zhang, Runsheng Chen, Yi Zhao:
NONCODEV5: a comprehensive annotation database for long non-coding RNAs. D308-D314 - Ruijia Wang, Ram Nambiar, Dinghai Zheng, Bin Tian:
PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes. D315-D319 - Denitsa Eckweiler, Christian-Alexander Dudek, Juliane Hartlich, David Brötje, Dieter Jahn:
PRODORIC2: the bacterial gene regulation database in 2018. D320-D326 - Jia-Jia Xuan, Wen-Ju Sun, Peng-Hui Lin, Ke-ren Zhou, Shun Liu, Ling-Ling Zheng, Liang-Hu Qu, Jian-Hua Yang:
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. D327-D334 - Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P. Nawrocki, Elena Rivas, Sean R. Eddy, Alex Bateman, Robert D. Finn, Anton I. Petrov:
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. D335-D342 - Edgar Wingender, Torsten Schoeps, Martin Haubrock, Mathias Krull, Jürgen Dönitz:
TFClass: expanding the classification of human transcription factors to their mammalian orthologs. D343-D347 - Miguel C. Teixeira, Pedro T. Monteiro, Margarida Palma, Catarina Costa, Cláudia P. Godinho, Pedro Pais, Mafalda Cavalheiro, Miguel Antunes, Alexandre Lemos, Tiago Pedreira, Isabel Sá-Correia:
YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. D348-D353 - Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Laganà, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars Juhl Jensen, Søren Brunak, Marco Pellegrini, Alfredo Ferro:
miRandola 2017: a curated knowledge base of non-invasive biomarkers. D354-D359 - Tomás Tokár, Chiara Pastrello, Andrea E. M. Rossos, Mark Abovsky, Anne-Christin Hauschild, Mike Tsay, Richard Lu, Igor Jurisica:
mirDIP 4.1 - integrative database of human microRNA target predictions. D360-D370 - Tianyu Cui, Lin Zhang, Yan Huang, Ying Yi, Puwen Tan, Yue Zhao, Yongfei Hu, Liyan Xu, Enmin Li, Dong Wang:
MNDR v2.0: an updated resource of ncRNA-disease associations in mammals. D371-D374 - Joseph D. Yesselman, Siqi Tian, Xin Liu, Lei Shi, Jin Billy Li, Rhiju Das:
Updates to the RNA mapping database (RMDB), version 2. D375-D379 - Heonjong Han, Jae-Won Cho, Sang-Young Lee, Ayoung Yun, Hyojin Kim, Dasom Bae, Sunmo Yang, Chan Yeong Kim, Muyoung Lee, Eunbeen Kim, Sungho Lee, Byunghee Kang, Dabin Jeong, Yaeji Kim, Hyeon-Nae Jeon, Haein Jung, Sunhwee Nam, Michael Chung, Jong-Hoon Kim, Insuk Lee:
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. D380-D386
- Mihaly Varadi, Greet De Baets, Wim F. Vranken, Peter Tompa, Rita Pancsa:
AmyPro: a database of proteins with validated amyloidogenic regions. D387-D392 - Chuan Dong, Ge-Fei Hao, Hong-Li Hua, Shuo Liu, Abraham A. Labena, Guoshi Chai, Jian Huang, Nini Rao, Feng-Biao Guo:
Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins. D393-D398 - Lukás Pravda, David Sehnal, Radka Svobodová Vareková, Veronika Navrátilová, Dominik Tousek, Karel Berka, Michal Otyepka, Jaroslav Koca:
ChannelsDB: database of biomacromolecular tunnels and pores. D399-D405 - Jinwoo Leem, Saulo Henrique Pires de Oliveira, Konrad Krawczyk, Charlotte M. Deane:
STCRDab: the structural T-cell receptor database. D406-D412 - Ezequiel J. Sosa, Germán Burguener, Esteban Lanzarotti, Lucas A. Defelipe, Leandro G. Radusky, Agustín M. Pardo, Marcelo A. Marti, Adrian Gustavo Turjanski, Darío Fernández Do Porto:
Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens. D413-D418 - Mikhail Shugay, Dmitriy V. Bagaev, Ivan V. Zvyagin, Renske M. A. Vroomans, Jeremy Chase Crawford, Garry Dolton, Ekaterina Komech, Anastasiya L. Sycheva, Anna E. Koneva, Evgeniy S. Egorov, Alexey V. Eliseev, Ewald van Dyk, Pradyot Dash, Meriem Attaf, Cristina Rius, Kristin Ladell, James E. McLaren, Katherine K. Matthews, E. Bridie Clemens, Daniel C. Douek, Fabio Luciani, Debbie van Baarle, Katherine Kedzierska, Can Kesmir, Paul G. Thomas, David A. Price, Andrew K. Sewell, Dmitry M. Chudakov:
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. D419-D427 - Marc Gouw, Sushama Michael, Hugo Sámano-Sánchez, Manjeet Kumar, András Zeke, Benjamin Lang, Benoit Bely, Lucía B. Chemes, Norman E. Davey, Ziqi Deng, Francesca Diella, Clara-Marie Gürth, Ann-Kathrin Huber, Stefan Kleinsorg, Lara S. Schlegel, Nicolas Palopoli, Kim Van Roey, Brigitte Altenberg, Attila Reményi, Holger Dinkel, Toby J. Gibson:
The eukaryotic linear motif resource - 2018 update. D428-D434 - Tony E. Lewis, Ian Sillitoe, Natalie L. Dawson, Su Datt Lam, Tristan Clarke, David A. Lee, Christine A. Orengo, Jonathan G. Lees:
Gene3D: Extensive prediction of globular domains in proteins. D435-D439 - Gáspár Pándy-Szekeres, Christian Munk, Tsonko M. Tsonkov, Stefan Mordalski, Kasper Harpsøe, Alexander S. Hauser, Andrzej J. Bojarski, David E. Gloriam:
GPCRdb in 2018: adding GPCR structure models and ligands. D440-D446 - Jiaqi Zhou, Yang Xu, Shaofeng Lin, Yaping Guo, Wankun Deng, Ying Zhang, Anyuan Guo, Yu Xue:
iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. D447-D453 - Guillaume Postic, Jérôme Gracy, Charlotte Périn, Laurent Chiche, Jean-Christophe Gelly:
KNOTTIN: the database of inhibitor cystine knot scaffold after 10 years, toward a systematic structure modeling. D454-D458 - Valeria Putignano, Antonio Rosato, Lucia Banci, Claudia Andreini:
MetalPDB in 2018: a database of metal sites in biological macromolecular structures. D459-D464 - Kenneth F. Lyon, Xingyu Cai, Richard J. Young, Abdullah-Al Mamun, Sanguthevar Rajasekaran, Martin R. Schiller:
Minimotif Miner 4: a million peptide minimotifs and counting. D465-D470 - Damiano Piovesan, Francesco Tabaro, Lisanna Paladin, Marco Necci, Ivan Micetic, Carlo Camilloni, Norman E. Davey, Zsuzsanna Dosztányi, Bálint Mészáros, Alexander Miguel Monzon, Gustavo D. Parisi, Eva Schad, Pietro Sormanni, Peter Tompa, Michele Vendruscolo, Wim F. Vranken, Silvio C. E. Tosatto:
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. D471-D476 - Adrian M. Altenhoff, Natasha Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy, David Dylus, Tarcisio M. Farias, Karina Zile, Charles Stevenson, Jiao Long, Henning Redestig, Gaston H. Gonnet, Christophe Dessimoz:
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. D477-D485 - Saqib Mir, Younes Alhroub, Stephen Anyango, David R. Armstrong, John M. Berrisford, Alice R. Clark, Matthew J. Conroy, Jose M. Dana, Mandar S. Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam, Lora Mak, Abhik Mukhopadhyay, Nurul Nadzirin, Typhaine Paysan-Lafosse, David Sehnal, Sanchayita Sen, Oliver S. Smart, Mihaly Varadi, Gerard J. Kleywegt, Sameer Velankar:
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. D486-D492 - Ivica Letunic, Peer Bork:
20 years of the SMART protein domain annotation resource. D493-D496 - Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert:
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. D497-D502 - Michael Bernhofer, Tatyana Goldberg, Silvana Wolf, Mohamed Ahmed, Julian Zaugg, Mikael Bodén, Burkhard Rost:
NLSdb - major update for database of nuclear localization signals and nuclear export signals. D503-D508
- Clara H. Eng, Tyler W. H. Backman, Constance B. Bailey, Christophe N. Magnan, Héctor García Martín, Leonard Katz, Pierre Baldi, Jay D. Keasling:
ClusterCAD: a computational platform for type I modular polyketide synthase design. D509-D515 - Le Huang, Han Zhang, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu Yang, Yanbin Yin:
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. D516-D521 - Omer Basha, Rotem Shpringer, Chanan M. Argov, Esti Yeger Lotem:
The DifferentialNet database of differential protein-protein interactions in human tissues. D522-D526 - Prisca Lo Surdo, Alberto Calderone, Marta Iannuccelli, Luana Licata, Daniele Peluso, Luisa Castagnoli, Gianni Cesareni, Livia Perfetto:
DISNOR: a disease network open resource. D527-D534 - Chengsheng Zhu, Yannick Mahlich, Maximilian Miller, Yana Bromberg:
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks. D535-D541 - Hongzhan Huang, Cecilia N. Arighi, Karen E. Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K. Vijay-Shanker, Cathy H. Wu:
iPTMnet: an integrated resource for protein post-translational modification network discovery. D542-D550 - Shu Tadaka, Daisuke Saigusa, Ikuko N. Motoike, Jin Inoue, Yuichi Aoki, Matsuyuki Shirota, Seizo Koshiba, Masayuki Yamamoto, Kengo Kinoshita:
jMorp: Japanese Multi Omics Reference Panel. D551-D557 - Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J. Cooper, John Paul Turner, Dusica Vidovic, Michele Forlin, Tanya T. Kelley, Alessandro D'Urso, Bryce K. Allen, Denis Torre, Kathleen M. Jagodnik, Lily Wang, Sherry L. Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Al Mahi, Marcin Pilarczyk, Nicholas Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C. Schürer:
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. D558-D566 - Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie E. Mohr, Norbert Perrimon:
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. D567-D574 - Weiliang Huang, Luke K. Brewer, Jace W. Jones, Angela T. Nguyen, Ana Marcu, David S. Wishart, Amanda G. Oglesby-Sherrouse, Maureen A. Kane, Angela Wilks:
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. D575-D580 - Surya Gupta, Demet Turan, Jan Tavernier, Lennart Martens:
The online Tabloid Proteome: an annotated database of protein associations. D581-D585 - Karel Miettinen, Sabrina Iñigo, Lukasz Kreft, Jacob Pollier, Christof De Bo, Alexander Botzki, Frederik Coppens, Søren Bak, Alain Goossens:
The TriForC database: a comprehensive up-to-date resource of plant triterpene biosynthesis. D586-D594 - Sunjae Lee, Cheng Zhang, Muhammad Arif, Zhengtao Liu, Rui Benfeitas, Gholamreza Bidkhori, Sumit Deshmukh, Mohamed Al Shobky, Alen Lovric, Jan Boren, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu:
TCSBN: a database of tissue and cancer specific biological networks. D595-D600 - Christoph Ogris, Dimitri Guala, Mateusz Kaduk, Erik L. L. Sonnhammer:
FunCoup 4: new species, data, and visualization. D601-D607 - David S. Wishart, Yannick Djoumbou Feunang, Ana Marcu, An Chi Guo, Kevin Liang, Rosa Vázquez-Fresno, Tanvir Sajed, Daniel Johnson, Carin Li, Naama Karu, Zinat Sayeeda, Elvis J. Lo, Nazanin Assempour, Mark V. Berjanskii, Sandeep Singhal, David Arndt, Yongjie Liang, Hasan Badran, Jason R. Grant, Arnau Serra-Cayuela, Yifeng Liu, Rupa Mandal, Vanessa Neveu, Allison Pon, Craig Knox, Michael Wilson, Claudine Manach, Augustin Scalbert:
HMDB 4.0: the human metabolome database for 2018. D608-D617 - António J. M. Ribeiro, Gemma L. Holliday, Nicholas Furnham, Jonathan D. Tyzack, Katherine Ferris, Janet M. Thornton:
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. D618-D623 - Neil D. Rawlings, Alan J. Barrett, Paul D. Thomas, Xiaosong Huang, Alex Bateman, Robert D. Finn:
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. D624-D632 - Ron Caspi, Richard Billington, Carol A. Fulcher, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E. Midford, Quang Ong, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti, Peter D. Karp:
The MetaCyc database of metabolic pathways and enzymes. D633-D639 - Chang Chen, Shadi Zabad, Haipeng Liu, Wangfei Wang, Constance J. Jeffery:
MoonProt 2.0: an expansion and update of the moonlighting proteins database. D640-D644 - Luís Franco-Serrano, Sergio Hernández, Alejandra Calvo, María A. Severi, Gabriela Ferragut, JosepAntoni Perez-Pons, Jaume Piñol, Òscar Pich, Angel Mozo-Villarias, Isaac Amela, Enrique Querol, Juan Cedano:
MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins. D645-D648 - Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The Reactome Pathway Knowledgebase. D649-D655 - Ulrike Wittig, Maja Rey, Andreas Weidemann, Renate Kania, Wolfgang Müller:
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. D656-D660 - Denise Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L. Coort, Daniela Digles, Friederike Ehrhart, Pieter Giesbertz, Marianthi Kalafati, Marvin Martens, Ryan Miller, Kozo Nishida, Linda Rieswijk, Andra Waagmeester, Lars M. T. Eijssen, Chris T. A. Evelo, Alexander R. Pico, Egon L. Willighagen:
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. D661-D667 - Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y. Chen:
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. D668-D676