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ORCIDNucleic Acids Research, Volume 48
Volume 48, Number Database-Issue, January 2020
- Daniel J. Rigden
, Xosé M. Fernández:
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. D1-D8
- Eric W. Sayers, Jeffrey Beck, J. Rodney Brister, Evan Bolton, Kathi Canese, Donald C. Comeau, Kathryn Funk, Anne Ketter, Sunghwan Kim, Avi Kimchi, Paul A. Kitts, Anatoliy Kuznetsov, Stacy Lathrop, Zhiyong Lu, Kelly M. McGarvey, Thomas L. Madden, Terence D. Murphy, Nuala A. O'Leary, Lon Phan, Valerie A. Schneider, Françoise Thibaud-Nissen, Barton W. Trawick, Kim D. Pruitt, James Ostell:
Database resources of the National Center for Biotechnology Information. D9-D16 - Charles E. Cook, Oana Stroe, Guy Cochrane, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. D17-D23 - Database Resources of the National Genomics Data Center in 2020. D24-D33
- Wei Hong, Hang Ruan, Zhao Zhang, Youqiong Ye, Yaoming Liu, Shengli Li, Ying Jing, Huiwen Zhang, Lixia Diao, Han Liang, Leng Han:
APAatlas: decoding alternative polyadenylation across human tissues. D34-D39 - Fulong Yu, Kai Li, Shuangquan Li, Jiaqi Liu, Yan Zhang, Meng Zhou, Hengqiang Zhao, Hongyan Chen, Nan Wu, Zhihua Liu, Jianzhong Su:
CFEA: a cell-free epigenome atlas in human diseases. D40-D44 - Osamu Ogasawara, Yuichi Kodama, Jun Mashima, Takehide Kosuge, Takatomo Fujisawa:
DDBJ Database updates and computational infrastructure enhancement. D45-D50 - Xuefeng Bai, Shanshan Shi, Bo Ai, Yong Jiang, Yuejuan Liu, Xiaole Han, Mingcong Xu, Qi Pan, Fan Wang, Qiuyu Wang, Jian Zhang, Xuecang Li, Chenchen Feng, Yanyu Li, Yuezhu Wang, Yiwei Song, Ke Feng, Chunquan Li:
ENdb: a manually curated database of experimentally supported enhancers for human and mouse. D51-D57 - Tianshun Gao, Jiang Qian:
EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. D58-D64 - Patrick Meylan, René Dreos, Giovanna Ambrosini, Romain Groux, Philipp Bucher:
EPD in 2020: enhanced data visualization and extension to ncRNA promoters. D65-D69 - Clara Amid, Blaise T. F. Alako, Vishnukumar Balavenkataraman Kadhirvelu, Tony Burdett, Josephine Burgin, Jun Fan, Peter W. Harrison, Sam Holt, Abdulrahman Hussein, Eugene Ivanov, Suran Jayathilaka, Simon Kay, Thomas M. Keane, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Annalisa Milano, Amir Pakseresht, Nadim Rahman, Jeena Rajan, Kethi Reddy, Edward Richards, Dmitriy Smirnov, Alexey Sokolov, Senthilnathan Vijayaraja, Guy Cochrane:
The European Nucleotide Archive in 2019. D70-D76 - Irene Papatheodorou, Pablo A. Moreno, Jonathan R. Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A. Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F. Jarnuczak, Simon Jupp, John C. Marioni, Kerstin B. Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma:
Expression Atlas update: from tissues to single cells. D77-D83 - Eric W. Sayers, Mark Cavanaugh, Karen Clark, James Ostell, Kim D. Pruitt, Ilene Karsch-Mizrachi:
GenBank. D84-D86 - Oriol Fornes, Jaime Abraham Castro-Mondragón, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip Andrew Richmond, Bhavi P. Modi, Solenne Correard, Marius Gheorghe, Damir Baranasic, Walter Santana-Garcia, Ge Tan, Jeanne Chèneby, Benoît Ballester, François Parcy, Albin Sandelin, Boris Lenhard, Wyeth W. Wasserman, Anthony Mathelier:
JASPAR 2020: update of the open-access database of transcription factor binding profiles. D87-D92 - Chenchen Feng, Chao Song, Yuejuan Liu, Fengcui Qian, Yu Gao, Ziyu Ning, Qiuyu Wang, Yong Jiang, Yanyu Li, Meng Li, Jiaxin Chen, Jian Zhang, Chunquan Li:
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. D93-D100 - Dimitra Karagkouni, Maria D. Paraskevopoulou, Spyros Tastsoglou, Giorgos Skoufos, Anna Karavangeli, Vasileios Pierros, Elissavet Zacharopoulou, Artemis G. Hatzigeorgiou:
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. D101-D110 - Peng Wang, Xin Li, Yue Gao, Qiuyan Guo, Shangwei Ning, Yunpeng Zhang, Shipeng Shang, Junwei Wang, Yanxia Wang, Hui Zhi, Ying Fang, Weitao Shen, Guangmei Zhang, Steven Xi Chen, Xia Li:
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation. D111-D117 - Hongying Zhao, Jian Shi, Yunpeng Zhang, Aimin Xie, Lei Yu, Caiyu Zhang, Junjie Lei, Haotian Xu, Zhijun Leng, Tengyue Li, Waidong Huang, Shihua Lin, Li Wang, Yun Xiao, Xia Li:
LncTarD: a manually-curated database of experimentally-supported functional lncRNA?target regulations in human diseases. D118-D126 - Yuhao Chen, Xiaowei Wang:
miRDB: an online database for prediction of functional microRNA targets. D127-D131 - Bastian Fromm, Diana Domanska, Eirik Høye, Vladimir Ovchinnikov, Wenjing Kang, Ernesto Aparicio-Puerta, Morten Johansen, Kjersti Flatmark, Anthony Mathelier, Eivind Hovig, Michael Hackenberg, Marc R. Friedländer, Kevin J. Peterson:
MirGeneDB 2.0: the metazoan microRNA complement. D132-D141 - Tim Kehl, Fabian Kern, Christina Backes, Tobias Fehlmann, Daniel Stöckel, Eckart Meese, Hans-Peter Lenhof, Andreas Keller:
miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. D142-D147 - Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yi-Gang Chen, Chen-Nan Jin, Yuan Yu, Jia-Tong Xu, Yue-Ming Li, Xiao-Xuan Cai, Zhen-Yu Zhou, Xiao-Hang Chen, Yuan-Yuan Pei, Liang Hu, Jin-Jiang Su, Shi-Dong Cui, Fei Wang, Yue-Yang Xie, Si-Yuan Ding, Meng-Fan Luo, Chih-Hung Chou, Nai-Wen Chang, Kai-Wen Chen, Yu-Hsiang Cheng, Xin-Hong Wan, Wen-Lian Hsu, Tzong-Yi Lee, Feng-Xiang Wei, Hsien-Da Huang:
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database. D148-D154 - Akshay Kumar Avvaru, Deepak Sharma, Archana Verma, Rakesh K. Mishra, Divya Tej Sowpati:
MSDB: a comprehensive, annotated database of microsatellites. D155-D159 - XueYi Teng, Xiaomin Chen, Hua Xue, Yiheng Tang, Peng Zhang, Quan Kang, Yajing Hao, Runsheng Chen, Yi Zhao, Shunmin He:
NPInter v4.0: an integrated database of ncRNA interactions. D160-D165 - Louis Philip Benoit Bouvrette, Samantha Bovaird, Mathieu Blanchette, Eric Lécuyer:
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species. D166-D173 - Christina J. Herrmann, Ralf Schmidt, Alexander Kanitz, Panu Artimo, Andreas J. Gruber, Mihaela Zavolan:
PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3? end sequencing. D174-D179 - Jeanne Chèneby, Zacharie Ménétrier, Martin Mestdagh, Thomas Rosnet, Allyssa Douida, Wassim Rhalloussi, Aurélie Bergon, Fabrice Lopez, Benoît Ballester:
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. D180-D188 - Yunqing Lin, Tianyuan Liu, Tianyu Cui, Zhao Wang, Yuncong Zhang, Puwen Tan, Yan Huang, Jia Yu, Dong Wang:
RNAInter in 2020: RNA interactome repository with increased coverage and annotation. D189-D197 - Chuangeng Chen, Dianshuang Zhou, Yue Gu, Cong Wang, Mengyan Zhang, Xiangyu Lin, Jie Xing, Hongli Wang, Yan Zhang:
SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive. D198-D203 - Raza-Ur Rahman, Anna-Maria Liebhoff, Vikas Bansal, Maksims Fiosins, Ashish Rajput, Abdul Sattar, Daniel Sumner Magruder, Sumit Madan, Ting Sun, Abhivyakti Gautam, Sven Heins, Timur Liwinski, Jörn Bethune, Claudia Trenkwalder, Juliane Fluck, Brit Mollenhauer, Stefan Bonn:
SEAweb: the small RNA Expression Atlas web application. D204-D219 - Philia Bouchard-Bourelle, Clément Desjardins-Henri, Darren Mathurin-St-Pierre, Gabrielle Deschamps-Francoeur, Étienne Fafard-Couture, Jean-Michel Garant, Sherif Abou Elela, Michelle S. Scott:
snoDB: an interactive database of human snoRNA sequences, abundance and interactions. D220-D225 - Yanbo Yang, Qiong Zhang, Ya-Ru Miao, Jiajun Yang, Wenqian Yang, Fangda Yu, Dongyang Wang, An-Yuan Guo, Jing Gong:
SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers. D226-D232 - Zhen Fan, Runsheng Chen, Xiaowei Chen:
SpatialDB: a database for spatially resolved transcriptomes. D233-D237 - Oleksii Bryzghalov, Michal Wojciech Szczesniak, Izabela Makalowska:
SyntDB: defining orthologues of human long noncoding RNAs across primates. D238-D245 - Tsu-Pei Chiu, Beibei Xin, Nicholas Markarian, Yingfei Wang, Remo Rohs:
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. D246-D255 - Marcin Piotr Sajek, Tomasz Wozniak, Mathias Sprinzl, Jadwiga Jaruzelska, Jan Barciszewski:
T-psi-C: user friendly database of tRNA sequences and structures. D256-D260
- Wanessa C. Lima, Elisabeth Gasteiger, Paolo Marcatili, Paula Duek Roggli, Amos Bairoch, Pierre Cosson:
The ABCD database: a repository for chemically defined antibodies. D261-D264 - Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Gabriele H. Marchler, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Mingzhang Yang, Dachuan Zhang, Chanjuan Zheng, Christopher J. Lanczycki, Aron Marchler-Bauer:
CDD/SPARCLE: the conserved domain database in 2020. D265-D268 - András Hatos, Borbála Hajdu-Soltész, Alexander Miguel Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykaç Fas, Claudio Bassot, Guillermo I. Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucía B. Chemes, Norman E. Davey, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan:
DisProt: intrinsic protein disorder annotation in 2020. D269-D276 - Jared M. Sagendorf, Nicholas Markarian, Helen M. Berman, Remo Rohs:
DNAproDB: an expanded database and web-based tool for structural analysis of DNA?protein complexes. D277-D287 - Wanshan Ning, Yaping Guo, Shaofeng Lin, Bin Mei, Yu Wu, Peiran Jiang, Xiaodan Tan, Weizhi Zhang, Guowei Chen, Di Peng, Liang Chu:
DrLLPS: a data resource of liquid?liquid phase separation in eukaryotes. D288-D295 - Manjeet Kumar, Marc Gouw, Sushama Michael, Hugo Sámano-Sánchez, Rita Pancsa, Juliana Glavina, Athina Diakogianni, Jesús Alvarado Valverde, Dayana Bukirova, Jelena Calyseva, Nicolas Palopoli, Norman E. Davey, Lucía B. Chemes:
ELM - the eukaryotic linear motif resource in 2020. D296-D306 - Jian-You Liao, Bing Yang, Yu-Chan Zhang, Xiao-Juan Wang, Yushan Ye, Jing-Wen Peng, Zhi-Zhi Yang, Jie-Hua He, Yin Zhang, Kaishun Hu, De-Chen Lin, Dong Yin:
EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs). D307-D313 - Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Robert D. Finn, Julian Gough, David T. Jones, Lawrence A. Kelley, Typhaine Paysan-Lafosse, Su Datt Lam, Alexey G. Murzin, Arun Prasad Pandurangan, Gustavo A. Salazar, Marcin J. Skwark, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo:
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. D314-D319 - Qian Li, Xiaojun Peng, Yuanqing Li, Wenqin Tang, Jia'an Zhu, Jing Huang, Yifei Qi, Zhuqing Zhang:
LLPSDB: a database of proteins undergoing liquid-liquid phase separation in vitro. D320-D327 - Monique Zahn-Zabal, Pierre-André Michel, Alain Gateau, Frédéric Nikitin, Mathieu Schaeffer, Estelle Audot, Pascale Gaudet, Paula Duek Roggli, Daniel Dinis Teixeira, Valentine Rech de Laval, Kasun Samarasinghe, Amos Bairoch, Lydie Lane:
The neXtProt knowledgebase in 2020: data, tools and usability improvements. D328-D334 - David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Aleksandras Gutmanas, Stephen Anyango, Preeti Choudhary, Alice R. Clark, Jose M. Dana, Mandar S. Deshpande, Roisin Dunlop, Paul J. Gane, Romana Gáborová, Deepti Gupta, Pauline Haslam, Jaroslav Koca, Lora Mak, Saqib Mir, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair, Typhaine Paysan-Lafosse, Lukás Pravda, David Sehnal, Osman Salih, Oliver S. Smart, James Tolchard, Mihaly Varadi, Radka Svobodová Vareková, Hossam Zaki, Gerard J. Kleywegt, Sameer Velankar:
PDBe: improved findability of macromolecular structure data in the PDB. D335-D343 - Mihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath Nair, Aleksandras Gutmanas, David R. Armstrong, Lukás Pravda, Bissan Al-Lazikani, Stephen Anyango, Geoffrey J. Barton, Karel Berka, Tom L. Blundell, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar:
PDBe-KB: a community-driven resource for structural and functional annotations. D344-D353 - Kaiqiang You, Qi Huang, Chunyu Yu, Boyan Shen, Cristoffer Sevilla, Minglei Shi, Henning Hermjakob, Yang Chen, Tingting Li:
PhaSepDB: a database of liquid-liquid phase separation related proteins. D354-D359 - Bálint Mészáros, Gábor Erdös, Beáta Szabó, Éva Schád, Ágnes Tantos, Rawan Abukhairan, Tamás Horváth, Nikoletta Murvai, Orsolya P. Kovács, Márton Kovács, Silvio C. E. Tosatto, Peter Tompa, Zsuzsanna Dosztányi, Rita Pancsa:
PhaSePro: the database of proteins driving liquid?liquid phase separation. D360-D367 - Liviu Copoiu, Pedro H. M. Torres, David B. Ascher, Tom L. Blundell, Sony Malhotra:
ProCarbDB: a database of carbohydrate-binding proteins. D368-D375 - Antonina Andreeva, Eugene Kulesha, Julian Gough, Alexey G. Murzin:
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. D376-D382 - Matthew I. J. Raybould, Claire Marks, Alan P. Lewis, Jiye Shi, Alexander Bujotzek, Bruck Taddese, Charlotte M. Deane:
Thera-SAbDab: the Therapeutic Structural Antibody Database. D383-D388 - Nikolaos N. Louros, Katerina Konstantoulea, Matthias De vleeschouwer, Meine Ramakers, Joost Schymkowitz, Frederic Rousseau:
WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides. D389-D393
- Xinyi Liu, Shaoyong Lu, Kun Song, Qiancheng Shen, Duan Ni, Qian Li, Xinheng He, Hao Zhang, Qi Wang, Yingyi Chen, Xinyi Li, Jing Wu, Chunquan Sheng, Guoqiang Chen, Yaqin Liu, Xuefeng Lu, Jian Zhang:
Unraveling allosteric landscapes of allosterome with ASD. D394-D401 - Charles J. Norsigian, Neha Pusarla, John Luke McConn, James T. Yurkovich, Andreas Dräger, Bernhard O. Palsson, Zachary A. King:
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. D402-D406 - Rahuman S. Malik-Sheriff, Mihai Glont, Tung V. N. Nguyen, Krishan K. Tiwari, Matthew G. Roberts, Ashley Xavier, Manh T. Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L. Fairbanks, Johannes P. Meyer, Chinmay Arankalle, Thawfeek M. Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M. Keating, Young Mi Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, Henning Hermjakob:
BioModels - 15 years of sharing computational models in life science. D407-D415 - Marta Iannuccelli, Elisa Micarelli, Prisca Lo Surdo, Alessandro Palma, Livia Perfetto, Ilaria Rozzo, Luisa Castagnoli, Luana Licata, Gianni Cesareni:
CancerGeneNet: linking driver genes to cancer hallmarks. D416-D421 - Krishnaveni Palaniappan, I-Min A. Chen, Ken Chu, Anna Ratner, Rekha Seshadri, Nikos Kyrpides, Natalia N. Ivanova, Nigel J. Mouncey:
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. D422-D430 - Vasileios Stathias, John Paul Turner, Amar Koleti, Dusica Vidovic, Daniel J. Cooper, Mehdi Fazel-Najafabadi, Marcin Pilarczyk, Raymond Terryn, Caty Chung, Afoma Umeano, Daniel J. B. Clarke, Alexander Lachmann, John Erol Evangelista, Avi Ma'ayan, Mario Medvedovic, Stephan C. Schürer:
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. D431-D439 - Kenneth Haug, Keeva Cochrane, Venkata Chandrasekhar Nainala, Mark Williams, Jiakang Chang, Kalai Vanii Jayaseelan, Claire O'Donovan:
MetaboLights: a resource evolving in response to the needs of its scientific community. D440-D444 - Ron Caspi, Richard Billington, Ingrid M. Keseler, Anamika Kothari, Markus Krummenacker, Peter E. Midford, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti, Peter D. Karp:
The MetaCyc database of metabolic pathways and enzymes - a 2019 update. D445-D453 - Satria A. Kautsar, Kai Blin, Simon Shaw, Jorge C. Navarro-Muñoz, Barbara R. Terlouw, Justin J. J. van der Hooft, Jeffrey A. van Santen, Vittorio Tracanna, Hernando G. Suarez Duran, Victòria Pascal Andreu, Nelly Selem Mojica, Mohammad Alanjary, Serina L. Robinson, George Lund, Samuel C. Epstein, Ashley C. Sisto, Louise K. Charkoudian, Jérôme Collemare, Roger G. Linington, Tilmann Weber, Marnix H. Medema:
MIBiG 2.0: a repository for biosynthetic gene clusters of known function. D454-D458 - Vadim M. Gumerov, Davi R. Ortega, Ogun Adebali, Luke E. Ulrich, Igor B. Zhulin:
MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems. D459-D464 - Areski Flissi, Emma Ricart, Clémentine Campart, Mickael Chevalier, Yoann Dufresne, Juraj Michalik, Philippe Jacques, Christophe Flahaut, Frédérique Lisacek, Valérie Leclère, Maude Pupin:
Norine: update of the nonribosomal peptide resource. D465-D469 - David S. Wishart, Carin Li, Ana Marcu, Hasan Badran, Allison Pon, Zachary Budinski, Jonas Patron, Debra Lipton, Xuan Cao, Eponine Oler, Krissa Li, Maïlys Paccoud, Chelsea Hong, An Chi Guo, Christopher Chan, William Wei, Miguel Ramirez-Gaona:
PathBank: a comprehensive pathway database for model organisms. D470-D478 - Sara Rahmati, Mark Abovsky, Chiara Pastrello, Max Kotlyar, Richard Lu, Christian A. Cumbaa, Proton Rahman, Vinod Chandran, Igor Jurisica:
pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. D479-D488 - Igor V. Rodchenkov, Ozgun Babur, Augustin Luna, Bülent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander:
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. D489-D497 - Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw, Fred Loney, Bruce May, Marija Milacic, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The reactome pathway knowledgebase. D498-D503 - Luana Licata, Prisca Lo Surdo, Marta Iannuccelli, Alessandro Palma, Elisa Micarelli, Livia Perfetto, Daniele Peluso, Alberto Calderone, Luisa Castagnoli, Gianni Cesareni:
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. D504-D510
Structure Databases
- Javier Macho Rendón, Benjamin Lang, Gian Gaetano Tartaglia, Marc Torrent Burgas:
BacFITBase: a database to assess the relevance of bacterial genes during host infection. D511-D516 - Brian P. Alcock, Amogelang R. Raphenya, Tammy T. Y. Lau, Kara K. Tsang, Mégane Bouchard, Arman Edalatmand, William Huynh, Anna-Lisa V. Nguyen, Annie A. Cheng, Sihan Liu, Sally Y. Min, Anatoly Miroshnichenko, Hiu-Ki Tran, Rafik E. Werfalli, Jalees A. Nasir, Martins Oloni, David J. Speicher, Alexandra Florescu, Bhavya Singh, Mateusz Faltyn, Anastasia Hernández-Koutoucheva, Arjun N. Sharma, Emily Bordeleau, Andrew C. Pawlowski, Haley L. Zubyk, Damion M. Dooley, Emma J. Griffiths, Finlay Maguire, Geoffrey L. Winsor, Robert G. Beiko, Fiona S. L. Brinkman, William W. L. Hsiao, Gary H. Van Domselaar, Andrew G. McArthur:
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. D517-D525 - Trestan Pillonel, Florian Tagini, Claire Bertelli, Gilbert Greub:
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. D526-D534 - Christine Pourcel, Marie Touchon, Nicolas Villeriot, Jean-Philippe Vernadet, David Couvin, Claire Toffano-Nioche, Gilles Vergnaud:
CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. D535-D544 - Sicheng Wu, Chuqing Sun, Yanze Li, Teng Wang, Long-Hao Jia, Senying Lai, Yaling Yang, Pengyu Luo, Die Dai, Yong-Qing Yang, Qibin Luo, Na L. Gao, Ning Kang, Lijie He, Xing-Ming Zhao, Wei-Hua Chen:
GMrepo: a database of curated and consistently annotated human gut metagenomes. D545-D553 - Liang Cheng, Changlu Qi, He Zhuang, Tongze Fu, Xue Zhang:
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. D554-D560 - Enrique Doster, Steven M. Lakin, Christopher J. Dean, Cory Wolfe, Jared G. Young, Christina Boucher, Keith E. Belk, Noelle R. Noyes, Paul S. Morley:
MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. D561-D569 - Alex L. Mitchell, Alexandre Almeida, Martin Beracochea, Miguel A. Boland, Josephine Burgin, Guy Cochrane, Michael R. Crusoe, Varsha Kale, Simon C. Potter, Lorna J. Richardson, Ekaterina A. Sakharova, Maxim Scheremetjew, Anton I. Korobeynikov, Alexander Shlemov, Olga Kunyavskaya, Alla L. Lapidus, Robert D. Finn:
MGnify: the microbiome analysis resource in 2020. D570-D578 - David Vallenet, Alexandra Calteau, Mathieu Dubois, Paul Amours, Adelme Bazin, Mylène Beuvin, Laura Burlot, Xavier Bussell, Stéphanie Fouteau, Guillaume Gautreau, Aurélie Lajus, Jordan Langlois, Rémi Planel, David Roche, Johan Rollin, Zoé Rouy, Valentin Sabatet, Claudine Médigue:
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. D579-D589 - Yadong Zhang, Zhewen Zhang, Hao Zhang, Yongbing Zhao, Zaichao Zhang, Jing-Fa Xiao:
PADS Arsenal: a database of prokaryotic defense systems related genes. D590-D598 - Olivier Arnaiz, Eric Meyer, Linda Sperling:
ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology. D599-D605 - James J. Davis, Alice R. Wattam, Ramy K. Aziz, Thomas S. Brettin, Ralph Butler, Rory Butler, Philippe Chlenski, Neal Conrad, Allan Dickerman, Emily M. Dietrich, Joseph L. Gabbard, Svetlana Gerdes, Andrew Guard, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Marcus Nguyen, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Jamie C. Overbeek, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Dawen Xie, Hyun Seung Yoo, Rick Stevens:
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. D606-D612 - Martin Urban, Alayne Cuzick, James Seager, Valerie Wood, Kim Rutherford, Shilpa Yagwakote Venkatesh, Nishadi De Silva, Manuel Carbajo Martinez, Helder Pedro, Andrew D. Yates, Keywan Hassani-Pak, Kim E. Hammond-Kosack:
PHI-base: the pathogen?host interactions database. D613-D620 - Daniel R. Mende, Ivica Letunic, Oleksandr M. Maistrenko, Thomas S. B. Schmidt, Alessio Milanese, Lucas Paoli, Ana Hernández-Plaza, Askarbek N. Orakov, Sofia K. Forslund, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Luís Pedro Coelho, Peer Bork:
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. D621-D625 - Felipe Borim Corrêa, João Pedro Saraiva, Peter F. Stadler, Ulisses Nunes da Rocha:
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. D626-D632 - Deyou Tang, Bingrui Li, Tianyi Xu, Ruifeng Hu, Daqiang Tan, Xiaofeng Song, Peilin Jia, Zhongming Zhao:
VISDB: a manually curated database of viral integration sites in the human genome. D633-D641 - Pedro T. Monteiro, Jorge Oliveira, Pedro Pais, Miguel Antunes, Margarida Palma, Mafalda Cavalheiro, Mónica Galocha, Cláudia P. Godinho, Luís C. Martins, Nuno Bourbon, Marta Neves Mota, Ricardo A. Ribeiro, Romeu Viana, Isabel Sá-Correia, Miguel C. Teixeira:
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. D642-D649
Genomic Databases (Non-Vertebrate)
- Julie Agapite, Laurent-Philippe Albou, Suzi A. Aleksander, Joanna Argasinska, Valerio Arnaboldi, Helen Attrill, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jae-Hyoung Cho, Karen R. Christie, Madeline A. Crosby, Jeff de Pons, Mary E. Dolan, Gilberto dos Santos, Barbara Dunn, Nathan A. Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Ken Frazer, Sibyl Gao, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Todd W. Harris, Marie-Claire Harrison, Douglas G. Howe, Kevin L. Howe, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Stanley J. F. Laulederkind, Raymond Y. N. Lee, Kevin A. MacPherson, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Stuart R. Miyasato, Sierra A. T. Moxon, Hans-Michael Müller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S. Nash, Patrick Ng, Michael Paulini, Norbert Perrimon, Christian Pich, Daniela Raciti, Joel E. Richardson, Matthew Russell, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Mary Shimoyama, Matt Simison, Cynthia L. Smith, David R. Shaw, Ajay Shrivatsav, Marek S. Skrzypek, Jennifer R. Smith, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Shur-Jen Wang, Shuai Weng, Monte Westerfield, Gary Williams, Edith D. Wong, Adam Wright, Karen Yook:
Alliance of Genome Resources Portal: unified model organism research platform. D650-D658 - Wenqian Yang, Yanbo Yang,