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ORCIDNucleic 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, Keren 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 K. Wirecki, Michal J. 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 E. 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, Yunxia 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 L. Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew J. Geniza, Justin Preece, Pankaj Jaiswal, Andrew F. 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 K. 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, Keren 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, Éva Schád, 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 M. 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 A. 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 Y. H. 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 V. 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 N. 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 A. 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 - Nicolas Terrapon, Vincent Lombard, Elodie Drula, Pascal Lapébie, Saad Al-Masaudi, Harry J. Gilbert, Bernard Henrissat:
PULDB: the expanded database of Polysaccharide Utilization Loci. D677-D683
- Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting:
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. D684-D691 - Terje Klemetsen, Inge Alexander Raknes, Juan Fu, Alexander Agafonov, Sudhagar V. Balasundaram, Giacomo Tartari, Espen Mikal Robertsen, Nils Peder Willassen:
The MAR databases: development and implementation of databases specific for marine metagenomics. D692-D699 - Na L. Gao, Chengwei Zhang, Zhanbing Zhang, Songnian Hu, Martin J. Lercher, Xing-Ming Zhao, Peer Bork, Zhi Liu, Wei-Hua Chen:
MVP: a microbe-phage interaction database. D700-D707 - Elliot J. Lefkowitz, Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton, Stuart G. Siddell, Donald B. Smith:
Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). D708-D717 - Matija Brozovic, Christelle Dantec, Justine Dardaillon, Delphine Dauga, Emmanuel Faure, Mathieu Gineste, Alexandra Louis, Magali Naville, Kazuhiro R. Nitta, Jacques Piette, Wendy Reeves, Céline Scornavacca, Paul Simion, Renaud Vincentelli, Maelle Bellec, Sameh Ben Aicha, Marie Fagotto, Marion Guéroult-Bellone, Maximilian Haeussler, Edwin Jacox, Elijah K. Lowe, Mickaël Mendez, Alexis Roberge, Alberto Stolfi, Rui Yokomori, C. Titus Brown, Christian Cambillau, Lionel A. Christiaen, Frédéric Delsuc, Emmanuel J. P. Douzery, Rémi Dumollard, Takehiro Kusakabe, Kenta Nakai, Hiroki Nishida, Yutaka Satou, Billie J. Swalla, Michael Veeman, Jean-Nicolas Volff, Patrick Lemaire:
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. D718-D725 - Alex L. Mitchell, Maxim Scheremetjew, Hubert Denise, Simon C. Potter, Aleksandra Tarkowska, Matloob Qureshi, Gustavo A. Salazar, Sebastien Pesseat, Miguel A. Boland, Fiona M. I. Hunter, Petra ten Hoopen, Blaise T. F. Alako, Clara Amid, Darren J. Wilkinson, Thomas P. Curtis, Guy Cochrane, Robert D. Finn:
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. D726-D735 - Marek S. Skrzypek, Robert S. Nash, Edith D. Wong, Kevin A. MacPherson, Sage T. Hellerstedt, Stacia R. Engel, Kalpana Karra, Shuai Weng, Travis K. Sheppard, Gail Binkley, Matt Simison, Stuart R. Miyasato, J. Michael Cherry:
Saccharomyces genome database informs human biology. D736-D742 - Bingyao Zhu, Jörg Stülke:
SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. D743-D748 - Yingzhou Xie, Yiqing Wei, Yue Shen, Xiaobin Li, Hao Zhou, Cui Tai, Zixin Deng, Hong-Yu Ou:
TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci. D749-D753
- Daniel R. Zerbino, Premanand Achuthan, Wasiu A. Akanni, M. Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla A. Cummins, Astrid Gall, Carlos García-Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, Thomas Maurel, William M. McLaren, Benjamin Moore, Jonathan M. Mudge, Daniel N. Murphy, Victoria Newman, Michael Nuhn, Denye N. Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Daniel Sheppard, Helen Sparrow, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Fiona Cunningham, Andrew D. Yates, Paul Flicek:
Ensembl 2018. D754-D761 - Jonathan Casper, Ann S. Zweig, Chris Villarreal, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, Donna Karolchik, Angie S. Hinrichs, Maximilian Haeussler, Luvina Guruvadoo, Jairo Navarro Gonzalez, David Gibson, Ian T. Fiddes, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Galt P. Barber, Joel Armstrong, David Haussler, Robert M. Kuhn, W. James Kent:
The UCSC Genome Browser database: 2018 update. D762-D769 - Valeria Palmieri, Christina Backes, Nicole Ludwig, Tobias Fehlmann, Fabian Kern, Eckart Meese, Andreas Keller:
IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA-target interactions. D770-D775 - Walter F. Lenoir, Tassica L. Lim, G. Traver Hart:
PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens. D776-D780 - Imad Abugessaisa, Shuhei Noguchi, Michael Böttcher, Akira Hasegawa, Tsukasa Kouno, Sachi Kato, Yuhki Tada, Hiroki Ura, Kuniya Abe, Jay W. Shin, Charles Plessy, Piero Carninci, Takeya Kasukawa:
SCPortalen: human and mouse single-cell centric database. D781-D787 - José P. Pinto, Rui S. R. Machado, Ramiro Magno, Daniel V. Oliveira, Susana Machado, Raquel P. Andrade, José Bragança, Isabel Duarte, Matthias E. Futschik:
StemMapper: a curated gene expression database for stem cell lineage analysis. D788-D793 - Carrie A. Davis, Benjamin C. Hitz, Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Idan Gabdank, Jason A. Hilton, Kriti Jain, Ulugbek K. Baymuradov, Aditi K. Narayanan, Kathrina C. Onate, Keenan Graham, Stuart R. Miyasato, Timothy R. Dreszer, J. Seth Strattan, Otto Jolanki, Forrest Tanaka, J. Michael Cherry:
The Encyclopedia of DNA elements (ENCODE): data portal update. D794-D801 - Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu, Thomas Maurel, Benjamin Moore, Mark D. McDowall, Uma Maheswari, Guy Naamati, Victoria Newman, Chuang Kee Ong, Michael Paulini, Helder Pedro, Emily Perry, Matthew Russell, Helen Sparrow, Electra Tapanari, Kieron R. Taylor, Alessandro Vullo, Gareth Williams, Amonida Zadissa, Andrew Olson, Joshua C. Stein, Sharon Wei, Marcela K. Tello-Ruiz, Doreen Ware, Aurelien Luciani, Simon C. Potter, Robert D. Finn, Martin Urban, Kim E. Hammond-Kosack, Dan M. Bolser, Nishadi De Silva, Kevin L. Howe, Nicholas Langridge, Gareth Maslen, Daniel Michael Staines, Andrew D. Yates:
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. D802-D808 - David P. Leader, Sue A. Krause, Aniruddha Pandit, Shireen A. Davies, Julian A. T. Dow:
FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data. D809-D815 - Nga Thi Thuy Nguyen, Pierre Vincens, Hugues Roest Crollius, Alexandra Louis:
Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing. D816-D822 - Audrey M. Michel, Stephen J. Kiniry, Patrick B. F. O'Connor, James P. A. Mullan, Pavel V. Baranov:
GWIPS-viz: 2018 update. D823-D830 - Jürgen Dönitz, Lizzy Gerischer, Stefan Hahnke, Stefan Pfeiffer, Gregor Bucher:
Expanded and updated data and a query pipeline for iBeetle-Base. D831-D835 - Cynthia L. Smith, Judith A. Blake, James A. Kadin, Joel E. Richardson, Carol J. Bult, The Mouse Genome Database Group:
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. D836-D842 - Molly A. Bogue, Stephen C. Grubb, David O. Walton, Vivek M. Philip, Georgi Kolishovski, Tim Stearns, Matthew H. Dunn, Daniel A. Skelly, Beena Kadakkuzha, Gregg TeHennepe, Kunde Ramamoorthy Govindarajan, Elissa J. Chesler:
Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice. D843-D850 - Daniel H. Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K. Derbyshire, Noreen R. Gonzales, Marc Gwadz, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Françoise Thibaud-Nissen, Lewis Y. Geer, Aron Marchler-Bauer, Kim D. Pruitt:
RefSeq: an update on prokaryotic genome annotation and curation. D851-D860 - Kamran Karimi, Joshua D. Fortriede, Vaneet Lotay, Kevin A. Burns, Dong Zhou Wang, Malcolm E. Fisher, Troy J. Pells, Christina James-Zorn, Ying Wang, Virgilio G. Ponferrada, Stanley Chu, Praneet Chaturvedi, Aaron M. Zorn, Peter D. Vize:
Xenbase: a genomic, epigenomic and transcriptomic model organism database. D861-D868 - Raymond Y. N. Lee, Kevin L. Howe, Todd W. Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, Sibyl Gao, Christian A. Grove, Ranjana Kishore, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini, Daniela Raciti, Faye Rodgers, Matthew Russell, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Qinghua Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman, Paul J. Kersey, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
WormBase 2017: molting into a new stage. D869-D874 - Atul Kakrana, Andrian Yang, Deepti Anand, Djordje Djordjevic, S. Deepthi Ramachandruni, Abhyudai Singh, Hongzhan Huang, Joshua Wing Kei Ho, Salil A. Lachke:
iSyTE 2.0: a database for expression-based gene discovery in the eye. D875-D885
- Jianbo Pan, Sheng Liu, Heng Zhu, Jiang Qian:
AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases. D886-D893 - Akanksha Rajput, Anamika Thakur, Shivangi Sharma, Manoj Kumar:
aBiofilm: a resource of anti-biofilm agents and their potential implications in targeting antibiotic drug resistance. D894-D900 - Michal Krassowski, Marta Paczkowska, Kim Cullion, Tina Huang, Irakli Dzneladze, B. F. Francis Ouellette, Joseph Tadashi Yamada, Amelie Fradet-Turcotte, Jüri Reimand:
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. D901-D910 - Li-Hong Huang, Qiu-Shun He, Ke Liu, Jiao Cheng, Mindong Zhong, Lin-Shan Chen, Li-Xia Yao, Zhi-Liang Ji:
ADReCS-Target: target profiles for aiding drug safety research and application. D911-D917 - Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang:
CR2Cancer: a database for chromatin regulators in human cancer. D918-D924 - Siyu Xia, Jing Feng, Ke Chen, Yanbing Ma, Jing Gong, Fangfang Cai, Yuxuan Jin, Yang Gao, Linjian Xia, Hong Chang, Lei Wei, Leng Han, Chunjiang He:
CSCD: a database for cancer-specific circular RNAs. D925-D929 - Bas Verbruggen, Lina Gunnarsson, Erik Kristiansson, Tobias Österlund, Stewart F. Owen, Jason R. Snape, Charles R. Tyler:
ECOdrug: a database connecting drugs and conservation of their targets across species. D930-D936 - Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Yunxiang Liang, Dongming Guo, Xin Li, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi:
eRAM: encyclopedia of rare disease annotations for precision medicine. D937-D943 - Shuhui Song, Dongmei Tian, Cuiping Li, Bixia Tang, Lili Dong, Jing-Fa Xiao, Yiming Bao, Wenming Zhao, Hang He, Zhang Zhang:
Genome Variation Map: a data repository of genome variations in BIG Data Center. D944-D949 - Guantao Zheng, Yijie Ma, Yang Zou, An Yin, Wushuang Li, Dong Dong:
HCMDB: the human cancer metastasis database. D950-D955 - Suhas V. Vasaikar, Peter Straub, Jing Wang, Bing Zhang:
LinkedOmics: analyzing multi-omics data within and across 32 cancer types. D956-D963 - Po-Jung Huang, Ling-Ya Chiu, Chi-Ching Lee, Yuan-Ming Yeh, Kuo-Yang Huang, Cheng-Hsun Chiu, Petrus Tang:
mSignatureDB: a database for deciphering mutational signatures in human cancers. D964-D970 - Jing Gong, Shufang Mei, Chun-Jie Liu, Yu Xiang, Youqiong Ye, Zhao Zhang, Jing Feng, Renyan Liu, Lixia Diao, An-Yuan Guo, Xiaoping Miao, Leng Han:
PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types. D971-D976 - Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Xin Li, Yunxiang Liang, Dongming Guo, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi:
PedAM: a database for Pediatric Disease Annotation and Medicine. D977-D983 - Chao Zhang, Yang Gao, Jiaojiao Liu, Zhe Xue, Yan Lu, Lian Deng, Lei Tian, Qidi Feng, Shuhua Xu:
PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations. D984-D993 - Petr Smirnov, Victor Kofia, Alexander Maru, Mark Freeman, Chantal Ho, Nehme El-Hachem, George-Alexandru Adam, Wail Ba-alawi, Zhaleh Safikhani, Benjamin Haibe-Kains:
PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. D994-D1002 - Sònia Casillas, Roger Mulet, Pablo Villegas-Mirón, Sergi Hervas, Esteve Sanz, Daniel Velasco, Jaume Bertranpetit, Hafid Laayouni, Antonio Barbadilla:
PopHuman: the human population genomics browser. D1003-D1010 - Justin Newberg, Karen M. Mann, Michael B. Mann, Nancy A. Jenkins, Neal G. Copeland:
SBCDDB: Sleeping Beauty Cancer Driver Database for gene discovery in mouse models of human cancers. D1011-D1017 - Hongyi Zhang, Shangyi Luo, Xinxin Zhang, Jianlong Liao, Fei Quan, Erjie Zhao, Chenfen Zhou, Fulong Yu, Wenkang Yin, Yunpeng Zhang, Yun Xiao, Xia Li:
SEECancer: a resource for somatic events in evolution of cancer genome. D1018-D1026 - Xin Feng, Lei Li, Eric J. Wagner, Wei Li:
TC3A: The Cancer 3′ UTR Atlas. D1027-D1030 - Pora Kim, Aekyung Park, Guangchun Han, Hua Sun, Peilin Jia, Zhongming Zhao:
TissGDB: tissue-specific gene database in cancer. D1031-D1038 - Jinchen Li, Leisheng Shi, Kun Zhang, Yi Zhang, Shanshan Hu, Tingting Zhao, Huajing Teng, Xianfeng Li, Yi Jiang, Liying Ji, Zhongsheng Sun:
VarCards: an integrated genetic and clinical database for coding variants in the human genome. D1039-D1048 - Wayne Pereanu, Eric C. Larsen, Ishita Das, Marcel A. Estévez, Anjali A. Sarkar, Senanu Spring-Pearson, Ravi Kollu, Saumyendra N. Basu, Sharmila Banerjee-Basu:
AutDB: a platform to decode the genetic architecture of autism. D1049-D1054 - Emanuela Gadaleta, Stefano Pirrò, Abu Z. Dayem Ullah, Jacek Marzec, Claude Chelala:
BCNTB bioinformatics: the next evolutionary step in the bioinformatics of breast cancer tissue banking. D1055-D1061 - Melissa J. Landrum, Jennifer M. Lee, Mark Benson, Garth R. Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang, Karen Karapetyan, Kenneth S. Katz, Chunlei Liu, Zenith Maddipatla, Adriana J. Malheiro, Kurt McDaniel, Michael Ovetsky, George R. Riley, George Zhou, J. Bradley Holmes, Brandi L. Kattman, Donna R. Maglott:
ClinVar: improving access to variant interpretations and supporting evidence. D1062-D1067 - David S. Wishart, Yannick D. Feunang, An Chi Guo, Elvis J. Lo, Ana Marcu, Jason R. Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda, Nazanin Assempour, Ithayavani Iynkkaran, Yifeng Liu, Adam Maciejewski, Nicola Gale, Alex Wilson, Lucy Chin, Ryan Cummings, Diana Le, Allison Pon, Craig Knox, Michael Wilson:
DrugBank 5.0: a major update to the DrugBank database for 2018. D1074-D1082 - Robi Tacutu, Daniel Thornton, Emily Johnson, Arie Budovsky, Diogo Barardo, Thomas Craig, Eugene Diana, Gilad Lehmann, Dmitri Toren, Jingwei Wang, Vadim E. Fraifeld, João Pedro de Magalhães:
Human Ageing Genomic Resources: new and updated databases. D1083-D1090 - Simon D. Harding, Joanna L. Sharman, Elena Faccenda, Christopher Southan, Adam J. Pawson, Sam M. Ireland, Alasdair J. G. Gray, Liam Bruce, Stephen P. H. Alexander, Stephen Anderton, Clare Bryant, Anthony P. Davenport, Christian Doerig, Doriano Fabbro, Francesca Levi-Schaffer, Michael Spedding, Jamie A. Davies, NC-IUPHAR:
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. D1091-D1106 - Jacek Marzec, Abu Z. Dayem Ullah, Stefano Pirrò, Emanuela Gadaleta, Tatjana Crnogorac-Jurcevic, Nicholas R. Lemoine, Hemant M. Kocher, Claude Chelala:
The Pancreatic Expression Database: 2018 update. D1107-D1110 - Liyuan Guo, Jing Wang:
rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks. D1111-D1116 - Lin Huang, Duoli Xie, Yiran Yu, Huanlong Liu, Yan Shi, Tieliu Shi, Chengping Wen:
TCMID 2.0: a comprehensive resource for TCM. D1117-D1120 - Ying Hong Li, Chun Yan Yu, Xiao Xu Li, Peng Zhang, Jing Tang, Qingxia Yang, Tingting Fu, Xiaoyu Zhang, Xuejiao Cui, Gao Tu, Yang Zhang, Shuang Li, Fengyuan Yang, Qiu Sun, Chu Qin, Xian Zeng, Zhe Chen, Yuzong Chen, Feng Zhu:
Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. D1121-D1127 - Hayley Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Y. Kahsay:
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. D1128-D1136 - Vishal B. Siramshetty, Andreas Eckert, Björn-Oliver Gohlke, Andrean Goede, Qiaofeng Chen, Prashanth Devarakonda, Saskia Preissner, Robert Preissner:
SuperDRUG2: a one stop resource for approved/marketed drugs. D1137-D1143 - Xin Hu, Qianghu Wang, Ming Tang, Floris P. Barthel, Samirkumar B. Amin, Kosuke Yoshihara, Frederick M. Lang, Emmanuel Martínez-Ledesma, Soo Hyun Lee, Siyuan Zheng, Roel G. W. Verhaak:
TumorFusions: an integrative resource for cancer-associated transcript fusions. D1144-D1149
- Matteo Togninalli, Ümit Seren, Dazhe Meng, Joffrey Fitz, Magnus Nordborg, Detlef Weigel, Karsten M. Borgwardt, Arthur Korte, Dominik G. Grimm:
The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. D1150-D1156 - Yue Liu, Tian Tian, Kang Zhang, Qi You, Hengyu Yan, Nannan Zhao, Xin Yi, Wenying Xu, Zhen Su:
PCSD: a plant chromatin state database. D1157-D1167 - Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios V. Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud, Pankaj Jaiswal:
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. D1168-D1180 - Marcela K. Tello-Ruiz, Sushma Naithani, Joshua C. Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J. Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M. Bolser, Guy Naamati, Electra Tapanari, Nuno A. Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Muñoz-Pomer Fuentes, Y. Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D. Stein, Robert Petryszak, Irene Papatheodorou, Paul J. Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware:
Gramene 2018: unifying comparative genomics and pathway resources for plant research. D1181-D1189 - Michiel Van Bel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, Klaas Vandepoele:
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. D1190-D1196 - Cristina M. Osuna-Cruz, Andreu Paytuví Gallart, Antimo Di Donato, Vicky Sundesha, Giuseppe Andolfo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria Raffaella Ercolano:
PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. D1197-D1201
- Alejandro Brenes, Vackar Afzal, Robert Kent, Angus I. Lamond:
The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics. D1202-D1209 - Neelansh Garg, Apuroop Sethupathy, Rudraksh Tuwani, Rakhi NK, Shubham Dokania, Arvind Iyer, Ayushi Gupta, Shubhra Agrawal, Navjot Singh, Shubham Shukla, Kriti Kathuria, Rahul Badhwar, Rakesh Kanji, Anupam Jain, Avneet Kaur, Rashmi Nagpal, Ganesh Bagler:
FlavorDB: a database of flavor molecules. D1210-D1216 - Xian Zeng, Peng Zhang, Weidong He, Chu Qin, Shangying Chen, Lin Tao, Yali Wang, Ying Tan, Dan Gao, Bo-hua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yuzong Chen:
NPASS: natural product activity and species source database for natural product research, discovery and tool development. D1217-D1222 - Shyamasree Saha, Eleni A. Chatzimichali, David A. Matthews, Conrad Bessant:
PITDB: a database of translated genomic elements. D1223-D1228 - Kun Lu, Tian Li, Jian He, Wei Chang, Rui Zhang, Miao Liu, Mengna Yu, Yonghai Fan, Jinqi Ma, Wei Sun, Cunmin Qu, Liezhao Liu, Nannan Li, Ying Liang, Rui Wang, Wei Qian, Zhanglin Tang, Xinfu Xu, Bo Lei, Kai Zhang, Jiana Li:
qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. D1229-D1236 - Wenguang Shao, Patrick G. A. Pedrioli, Witold Wolski, Christian Scurtescu, Emanuel Schmid, Juan Antonio Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S. Lindestam Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H. M. Ottenhoff, Krista E. Meijgaarden, Natalie Nieuwenhuizen, Stefan H. E. Kaufmann, Ralph Schlapbach, John C. Castle, Alexey I. Nesvizhskii, Morten Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. van Veelen, Cécile A. C. M. van Els, Albert J. R. Heck, Gustavo A. de Souza, Ludvig Magne Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron:
The SysteMHC Atlas project. D1237-D1247 - Mihai Glont, Tung V. N. Nguyen, Martin Graesslin, Robert Hälke, Raza Ali, Jochen Schramm, Sarala M. Wimalaratne, Varun B. Kothamachu, Nicolas Rodriguez, Maciej J. Swat, Jurgen Eils, Roland Eils, Camille Laibe, Rahuman S. Malik-Sheriff, Vijayalakshmi Chelliah, Nicolas Le Novère, Henning Hermjakob:
BioModels: expanding horizons to include more modelling approaches and formats. D1248-D1253 - Maria Levchenko, Yuci Gou, Florian Graef, Audrey Hamelers, Zhan Huang, Michele Ide-Smith, Anusha Iyer, Oliver Kilian, Jyothi Katuri, Jee-Hyub Kim, Nikos Marinos, Rakesh Nambiar, Michael Parkin, Xingjun Pi, Frances Rogers, Francesco Talo', Vid Vartak, Aravind Venkatesan, Johanna R. McEntyre:
Europe PMC in 2017. D1254-D1260 - Marie Chantal Lemfack, Björn-Oliver Gohlke, Serge M. T. Toguem, Saskia Preissner, Birgit Piechulla, Robert Preissner:
mVOC 2.0: a database of microbial volatiles. D1261-D1265 - Ugis Sarkans, Mikhail Gostev, Awais Athar, Ehsan Behrangi, Olga Melnichuk, Ahmed Ali, Jasmine Minguet, Juan Camillo Rada, Catherine Snow, Andrew Tikhonov, Alvis Brazma, Johanna R. McEntyre:
The BioStudies database - one stop shop for all data supporting a life sciences study. D1266-D1270 - Tobias Schmidt, Patroklos Samaras, Martin Frejno, Siegfried Gessulat, Maximilian Barnert, Harald Kienegger, Helmut Krcmar, Judith Schlegl, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Küster, Mathias Wilhelm:
ProteomicsDB. D1271-D1281
- 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. D1282 - Chengsheng Zhu, Yannick Mahlich, Maximilian Miller, Yana Bromberg:
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks. D1283
- 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. D1284
Volume 46, Number Webserver-Issue, July 2018
- Editorial: The 16th annual Nucleic Acids Research web server issue 2018. W1-W4
- Lennart De Bruin, John H. Maddocks:
cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA. W5-W10 - Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A. Grüning:
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. W11-W16 - Joanna I. Sulkowska, Szymon Niewieczerzal, Aleksandra I. Jarmolinska, Jonathan T. Siebert, Peter Virnau, Wanda Niemyska:
KnotGenome: a server to analyze entanglements of chromosomes. W17-W24 - Martin Raden, Syed M. Ali, Omer S. Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A. Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen Lott, Mostafa M. Mohamed, Alexander Mattheis, Milad Miladi, Andreas S. Richter, Sebastian Will, Joachim Wolff, Patrick R. Wright, Rolf Backofen:
Freiburg RNA tools: a central online resource for RNA-focused research and teaching. W25-W29 - Tomasz Zok, Maciej Antczak, Michal Zurkowski, Mariusz Popenda, Jacek Blazewicz, Ryszard W. Adamiak, Marta Szachniuk:
RNApdbee 2.0: multifunctional tool for RNA structure annotation. W30-W35 - Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung:
SPAR: small RNA-seq portal for analysis of sequencing experiments. W36-W42 - Wei-Sheng Wu, Wei-Che Huang, Jordan S. Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, Heng-Chi Lee:
pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. W43-W48 - Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao:
psRNATarget: a plant small RNA target analysis server (2017 release). W49-W54 - Kun-Tze Chen, Chin Lung Lu:
CSAR-web: a web server of contig scaffolding using algebraic rearrangements. W55-W59 - Max Franz, Harold Rodriguez, Christian Tannus Lopes, Khalid Zuberi, Jason Montojo, Gary D. Bader, Quaid Morris:
GeneMANIA update 2018. W60-W64 - Aaron K. Wong, Arjun Krishnan, Olga G. Troyanskaya:
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. W65-W70 - Jia Ye, Yong Zhang, Huihai Cui, Jiawei Liu, Yuqing Wu, Yun Cheng, Huixing Xu, Xingxin Huang, Shengting Li, An Zhou, Xiuqing Zhang, Lars Bolund, Qiang Chen, Jian Wang, Huanming Yang, Lin Fang, Chunmei Shi:
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. W71-W75 - Camilla Ferrari, Sebastian Proost, Colin Ruprecht, Marek Mutwil:
PhytoNet: comparative co-expression network analyses across phytoplankton and land plants. W76-W83 - Petri Törönen, Alan Medlar, Liisa Holm:
PANNZER2: a rapid functional annotation web server. W84-W88 - Daehong Kwon, Daehwan Lee, Juyeon Kim, Jongin Lee, Mikang Sim, Jaebum Kim:
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. W89-W94 - Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter Kamp Busk, Ying Xu, Yanbin Yin:
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. W95-W101 - Jongkeun Lee, Andy Jinseok Lee, June-Koo Lee, Jong-Keun Park, Youngoh Kwon, Seongyeol Park, Hyonho Chun, Young Seok Ju, Dongwan Hong:
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures. W102-W108 - Abu Z. Dayem Ullah, Jorge Oscanoa, Jun Wang, Ai Nagano, Nicholas R. Lemoine, Claude Chelala:
SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine. W109-W113 - Dandan Huang, Xianfu Yi, Shijie Zhang, Zhanye Zheng, Panwen Wang, Chenghao Xuan, Pak Chung Sham, Junwen Wang, Mulin Jun Li:
GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits. W114-W120 - Aroon T. Chande, Lu Wang, Lavanya Rishishwar, Andrew B. Conley, Emily T. Norris, Augusto Valderrama-Aguirre, I. King Jordan:
GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide. W121-W126 - Carlos H. M. Rodrigues, David B. Ascher, Douglas E. V. Pires:
Kinact: a computational approach for predicting activating missense mutations in protein kinases. W127-W132 - Sebastian Proost, Marek Mutwil:
CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses. W133-W140 - Divyanshu Srivastava, Arvind Iyer, Vibhor Kumar, Debarka Sengupta:
CellAtlasSearch: a scalable search engine for single cells. W141-W147 - Jimmy Caroli, Giovanni Sorrentino, Mattia Forcato, Giannino Del Sal, Silvio Bicciato:
GDA, a web-based tool for Genomics and Drugs integrated analysis. W148-W156 - Nicholas Ceglia, Yu Liu, Siwei Chen, Forest Agostinelli, Kristin Eckel-Mahan, Paolo Sassone-Corsi, Pierre Baldi:
CircadiOmics: circadian omic web portal. W157-W162 - Ashwini Jeggari, Zhanna Alekseenko, Iurii Petrov, José M. Dias, Johan Ericson, Andrey Alexeyenko:
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets. W163-W170 - Daniel J. B. Clarke, Maxim V. Kuleshov, Brian M. Schilder, Denis Torre, Mary E. Duffy, Alexandra B. Keenan, Alexander Lachmann, Axel S. Feldmann, Gregory W. Gundersen, Moshe C. Silverstein, Zichen Wang, Avi Ma'ayan:
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. W171-W179 - Jianwei Li, Xiaofen Han, Yanping Wan, Shan Zhang, Yingshu Zhao, Rui Fan, Qinghua Cui, Yuan Zhou:
TAM 2.0: tool for MicroRNA set analysis. W180-W185 - Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander V. Favorov, Ryan M. Layer, Andrey A. Mironov, Aaron R. Quinlan, Nathan C. Sheffield, Gosia Trynka, Geir Kjetil Sandve:
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. W186-W193 - V. P. Nagraj, Neal E. Magee, Nathan C. Sheffield:
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. W194-W199 - Simon C. Potter, Aurelien Luciani, Sean R. Eddy, Young Mi Park, Rodrigo Lopez, Robert D. Finn:
HMMER web server: 2018 update. W200-W204 - Kai Blin, Wolfgang Wohlleben, Tilmann Weber:
Patscanui: an intuitive web interface for searching patterns in DNA and protein data. W205-W208 - Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime Abraham Castro-Mondragón, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera, Morgane Thomas-Chollier:
RSAT 2018: regulatory sequence analysis tools 20th anniversary. W209-W214 - Anja Kiesel, Christian Roth, Wanwan Ge, Maximilian Weß, Markus Meier, Johannes Söding:
The BaMM web server for de-novo motif discovery and regulatory sequence analysis. W215-W220 - Maya Polishchuk, Inbal Paz, Zohar Yakhini, Yael Mandel-Gutfreund:
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. W221-W228 - Xiaobin Li, Yingzhou Xie, Meng Liu, Cui Tai, Jingyong Sun, Zixin Deng, Hong-Yu Ou:
oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. W229-W234 - Izabella Krystkowiak, Jean Manguy, Norman E. Davey:
PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants. W235-W241 - Jean-Paul Concordet, Maximilian Haeussler:
CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. W242-W245 - David Couvin, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P. C. Rocha, Gilles Vergnaud, Daniel Gautheret, Christine Pourcel:
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. W246-W251 - Michaela Hendling, Stephan Pabinger, Konrad Peters, Noa Wolff, Rick Conzemius, Ivan Barisic:
Oli2go: an automated multiplex oligonucleotide design tool. W252-W256 - Priyanka Banerjee, Andreas Eckert, Anna K. Schrey, Robert Preissner:
ProTox-II: a webserver for the prediction of toxicity of chemicals. W257-W263 - Christian Margreitter, Hui-Chun Lu, Catherine Townsend, Alexander Stewart, Deborah K. Dunn-Walters, Franca Fraternali:
BRepertoire: a user-friendly web server for analysing antibody repertoire data. W264-W270 - Matthias Döring, Joachim Büch, Georg Friedrich, Alejandro Pironti, Prabhav Kalaghatgi, Elena Knops, Eva Heger, Martin Obermeier, Martin Däumer, Alexander Thielen, Rolf Kaiser, Thomas Lengauer, Nico Pfeifer:
geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data. W271-W277 - Auke J. van Heel, Anne de Jong, Chunxu Song, Jakob H. Viel, Jan Kok, Oscar P. Kuipers:
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. W278-W281 - Luis Miguel Rodriguez-Rojas, Santosh Gunturu, William T. Harvey, Ramon Rosselló-Mora, James M. Tiedje, James R. Cole, Konstantinos T. Konstantinidis:
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. W282-W288 - Emilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Miguelangel Cuenca, Aurélien Alexandre, Paul Bachelerie, Thomas Rosnet, Eric Pelletier, Shinichi Sunagawa, Pascal Hingamp:
The Ocean Gene Atlas: exploring the biogeography of plankton genes online. W289-W295 - Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T. Heer, Tjaart A. P. de Beer, Christine Rempfer, Lorenza Bordoli, Rosalba Lepore, Torsten Schwede:
SWISS-MODEL: homology modelling of protein structures and complexes. W296-W303 - Cezary Czaplewski, Agnieszka S. Karczynska, Adam K. Sieradzan, Adam Liwo:
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. W304-W309 - Johanna K. S. Tiemann, Alexander S. Rose, Jochen Ismer, Mitra D. Darvish, Tarek Hilal, Christian M. T. Spahn, Peter W. Hildebrand:
FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps. W310-W314 - András Micsonai, Frank Wien, Éva Bulyáki, Judit Kun, Éva Moussong, Young-Ho Lee, Yuji Goto, Matthieu Réfrégiers, József Kardos:
BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. W315-W322 - Eloy A. Colell, Javier Iserte, Franco L. Simonetti, Cristina Marino Buslje:
MISTIC2: comprehensive server to study coevolution in protein families. W323-W328 - Bálint Mészáros, Gábor Erdös, Zsuzsanna Dosztányi:
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. W329-W337 - Aleksander Kuriata, Aleksandra Maria Gierut, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik:
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. W338-W343 - Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljkovic, David Bednar, Zbynek Prokop, Jirí Damborský:
CalFitter: a web server for analysis of protein thermal denaturation data. W344-W349 - Carlos H. M. Rodrigues, Douglas E. V. Pires, David B. Ascher:
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. W350-W355 - Lenka Sumbalova, Jan Stourac, Tomás Martínek, David Bednar, Jirí Damborský:
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. W356-W362 - Wei Tian, Chang Chen, Xue Lei, Jieling Zhao, Jie Liang:
CASTp 3.0: computed atlas of surface topography of proteins. W363-W367 - Lukás Pravda, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka:
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). W368-W373 - Youjun Xu, Shiwei Wang, Qiwan Hu, Shuaishi Gao, Xiaomin Ma, Weilin Zhang, Yihang Shen, Fangjin Chen, Luhua Lai, Jianfeng Pei:
CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction. W374-W379 - Runze Dong, Shuo Pan, Zhenling Peng, Yang Zhang, Jianyi Yang:
mTM-align: a server for fast protein structure database search and multiple protein structure alignment. W380-W386 - Przemyslaw Miszta, Pawel Pasznik, Jakub Jakowiecki, Agnieszka Sztyler, Dorota Latek, Slawomir Filipek:
GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models. W387-W395 - Ragul Gowthaman, Brian G. Pierce:
TCRmodel: high resolution modeling of T cell receptors from sequence. W396-W401 - Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto:
RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins. W402-W407 - Chloé Quignot, Julien Rey, Jinchao Yu, Pierre Tufféry, Raphaël Guérois, Jessica Andreani:
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs. W408-W416 - Sébastien Reille, Mélanie Garnier, Xavier Robert, Patrice Gouet, Juliette Martin, Guillaume Launay:
Identification and visualization of protein binding regions with the ArDock server. W417-W422 - Yumeng Yan, Huanyu Tao, Sheng-You Huang:
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. W423-W431 - Hong Zeng, Sheng Wang, Tianming Zhou, Feifeng Zhao, Xiufeng Li, Qing Wu, Jinbo Xu:
ComplexContact: a web server for inter-protein contact prediction using deep learning. W432-W437 - Qi Wu, Zhenling Peng, Yang Zhang, Jianyi Yang:
COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. W438-W442 - Pei Zhou, Bowen Jin, Hao Li, Sheng-You Huang:
HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. W443-W450 - Min Huang, Kun Song, Xinyi Liu, Shaoyong Lu, Qiancheng Shen, Renxiao Wang, Jingze Gao, Yuanyuan Hong, Qian Li, Duan Ni, Jianrong Xu, Guoqiang Chen, Jian Zhang:
AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. W451-W458 - Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Rita Casadio:
BUSCA: an integrative web server to predict subcellular localization of proteins. W459-W466 - Grigorios Koulouras, Andreas Panagopoulos, Maria Anna Rapsomaniki, Nickolaos-Nikiforos Giakoumakis, Stavros L. Taraviras, Zoi Lygerou:
EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data. W467-W472 - Lars Kolbowski, Colin W. Combe, Juri Rappsilber:
xiSPEC: web-based visualization, analysis and sharing of proteomics data. W473-W478 - Alan Medlar, Petri Törönen, Liisa Holm:
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. W479-W485 - Jasmine Chong, Othman Soufan, Carin Li, Iurie Caraus, Shuzhao Li, Guillaume Bourque, David S. Wishart, Jianguo Xia:
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. W486-W494 - Ludovic Cottret, Clément Frainay, Maxime Chazalviel, Floréal Cabanettes, Yoann Gloaguen, Etienne Camenen, Benjamin Merlet, Stéphanie Heux, Jean-Charles Portais, Nathalie Poupin, Florence Vinson, Fabien Jourdan:
MetExplore: collaborative edition and exploration of metabolic networks. W495-W502 - Rafael Hernández-de-Diego, Sonia Tarazona, Carlos Martínez-Mira, Leandro Balzano-Nogueira, Pedro Furió-Tarí, Georgios Joannis Pappas Jr., Ana Conesa:
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data. W503-W509 - Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada:
iPath3.0: interactive pathways explorer v3. W510-W513 - Guangyan Zhou, Jianguo Xia:
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space. W514-W522 - Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
ezTag: tagging biomedical concepts via interactive learning. W523-W529 - Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu:
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. W530-W536 - Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia D. Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel J. Blankenberg:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. W537-W544
- Jean-Pierre Desvignes, Marc Bartoli, Valérie Delague, Martin Krahn, Morgane Miltgen, Christophe Béroud, David Salgado:
VarAFT: a variant annotation and filtration system for human next generation sequencing data. W545-W553 - Onur Serçinoglu, Pemra Ozbek:
gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations. W554-W562
- Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Bo Yu, Evan Bolton:
An update on PUG-REST: RESTful interface for programmatic access to PubChem. W563-W570
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